From pgoodin at swin.edu.au Thu May 1 07:30:41 2014 From: pgoodin at swin.edu.au (Peter Goodin) Date: Thu, 1 May 2014 05:30:41 +0000 Subject: [FieldTrip] Multiple source inversion problems for group MNE analysis Message-ID: Hi Fieldtrip list, I'm trying to do group source analysis using MNE but have run into a bit of a snag. After running ft_sourceanalysis (data is 1600ms / 901 data points, source model has been made via SPM (8196 verticies), head model through segmentation of the individual's MRI - all looks to be aligned, similar to the output of SPM (see and plots sensibly using ft_sourcemovie) I've tried running ft_sourceinterpolation using the data on an individual's MRI (freshly read in using ft_read_mri) or the SPM T1 template (also using ft_read_mri). If using the individual's MRI (dimensions = 256 256 176), with or without downsampling, after an hour or so I get an out of memory error and that's that. Running it with the template works fine and is finished ~90 seconds. The results using ft_sourceplot (ortho method) however don't look right (see interp.jpg). Additionally there's no field in the interpolated's cfg about anatomy afterward. So taking another route and just trying to use ft_sourcegrandaverage on the output of ft_sourcelocalisation I'm met with "??? Error using ==> ft_sourcegrandaverage at 111 different grid locations in source reconstructions" I have absolutely no idea what I'm doing wrong and would appreciate any help. An abridged version of the script I'm using for mass conversion to source space is below: sourcemodel = ft_read_headshape(gii_list(i,:)); <-- this is the ...2cortex_8196.surf.gii mesh from spm mri = ft_read_mri([structdir mri_list(i,1:end-2)]); <--- individual participant's raw MRI in nii form. cfg = []; cfg.coordsys = 'spm'; cfg.output = {'brain'}; seg = ft_volumesegment(cfg, mri); cfg = []; cfg.method = 'singleshell'; conductionmodel = ft_prepare_headmodel(cfg, seg); conductionmodel = ft_convert_units(conductionmodel,'cm'); conductionmodel = ft_convert_units(conductionmodel,'mm'); %%Check everything's aligned correctly: figure;hold on; subplot(1,2,1), ft_plot_vol(conductionmodel, 'facecolor', [0 0 1]);alpha 0.5; ft_plot_mesh(sourcemodel, 'edgecolor', [0 1 0]); camlight ft_plot_sens(sens, 'style', 'r*'); subplot(1,2,2), ft_plot_vol(conductionmodel, 'facecolor', [0 0 1]);alpha 0.5; ft_plot_mesh(sourcemodel, 'edgecolor', [0 1 0]); camlight ft_plot_sens(sens, 'style', 'r*'); view([90 0]); view([90 0]) gcf; suptitle([gii_list(i,2:5) ' source model']); saveas(gcf, [gii_list(i,2:6) 'source model.tiff']); close(gcf); assignin('base', [gii_list(i,2:6) 'sourcemodel'], sourcemodel); <--- rename hold variable to participant number assignin('base', [gii_list(i,2:6) 'conductionmodel'], conductionmodel); <--- ditto save([gii_list(i,2:6) 'model'], [gii_list(i,2:6) 'sourcemodel'], [gii_list(i,2:6) 'conductionmodel'], '-v6'); %% CREATE LEADFIELD & LOCALISED DATA load(sens_data_list(i,:)); <--- Load sensor space condition data conds_list = (who('*nback*av')) <--- Create participant specific list datcm = eval(conds_list{1,1}); dat = datcm; dat.grad = ft_convert_units(datcm.grad, 'mm'); %Leadfield goes here <--- Mostly taken from the tutorial cfg = []; cfg.grad = dat.grad; % sensor positions cfg.channel = 'MEG'; % the used channels cfg.grid.pos = sourcemodel.pnt; % source points <---Does this have something to do with the problem? cfg.grid.inside = 1:size(sourcemodel.pnt,1); % all source points are inside of the brain <--- Or this? cfg.vol = conductionmodel; % volume conduction model leadfield = ft_prepare_leadfield(cfg); assignin('base', [conds_list{1,1} '_leadfield'], leadfield); save([gii_list(i,2:6) 'model'], [conds_list{1,1} '_leadfield'], '-v6', '-append'); clear dat; for k = 1:size(conds_list,1); disp('---'); disp(['Creating source data for ' conds_list{k,1}]); disp('---'); datcm = eval(conds_list{k,1}); dat = datcm; dat.grad = ft_convert_units(datcm.grad, 'mm'); %Inversion goes here <--- Mostly taken from the tutorial cfg = []; cfg.method = 'mne'; cfg.grid = leadfield; cfg.vol = conductionmodel; cfg.mne.prewhiten = 'yes'; cfg.mne.lambda = 3; cfg.mne.scalesourcecov = 'yes'; sourcedat = ft_sourceanalysis(cfg,dat); assignin('base', [conds_list{k,1} '_source'], sourcedat); k = k + 1; end %%General saving stuff a = who('*C_av_source'); b = a(1:2:end,1); save([sourcedatadir gii_list(i,2:6) 'condep_conds'], char(b(1,1)), '-v6'); for l = 2:size(b,1); save([sourcedatadir gii_list(i,2:6) 'condep_conds'], char(b(l,1)), '-append', '-v6'); l = l + 1; end save([sourcedatadir gii_list(i,2:6) 'source'], '*_source', '-v6'); Thanks again, Peter __________________________ Peter Goodin, BSc (Hons), Ph.D Candidate. Brain and Psychological Sciences Research Centre (BPsych) Swinburne University, Hawthorn, Vic, 3122 http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149 Monash Alfred Psychiatry Research Centre (MAPrc) Level 4, 607 St Kilda Road, Melbourne 3004 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: interp.jpg Type: image/jpeg Size: 17514 bytes Desc: interp.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: c112_source model.tiff Type: image/tiff Size: 233110 bytes Desc: c112_source model.tiff URL: From pierpaolo12croce at gmail.com Thu May 1 14:56:59 2014 From: pierpaolo12croce at gmail.com (Pierpaolo Croce) Date: Thu, 1 May 2014 14:56:59 +0200 Subject: [FieldTrip] Undefined function 'mtimes' for input arguments of type 'cell'. Message-ID: Undefined function 'mtimes' for input arguments of type 'cell'. I have this error in using "ft_databrowser" like im the tutorial web page. can someone help me? -- PC -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu May 1 15:01:58 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 1 May 2014 15:01:58 +0200 Subject: [FieldTrip] Undefined function 'mtimes' for input arguments of type 'cell'. In-Reply-To: References: Message-ID: Hi Pierpaolo, Could you show us what input data and cfg you are providing for ft_databrowser? Best, Eelke On 1 May 2014 14:56, Pierpaolo Croce wrote: > Undefined function 'mtimes' for input arguments of type 'cell'. > > I have this error in using "ft_databrowser" like im the tutorial web page. > > can someone help me? > > > -- > PC > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From eliasc at live.it Thu May 1 23:54:32 2014 From: eliasc at live.it (Elias P. Casula) Date: Thu, 1 May 2014 23:54:32 +0200 Subject: [FieldTrip] ft_preproc_dftfilter function In-Reply-To: References: Message-ID: Dear all,I found some problems with the ft_preproc_dftfilter function. This function should remove the 50hz noise from the signal. But when I call the function with [filt] = ft_preproc_dftfilter(mymatrixdata, 1024, 50) the 50hz noise is still in the filtered signal. Does anyone else had the same problem?Thanks a lot, Elias -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Fri May 2 08:51:11 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 02 May 2014 08:51:11 +0200 Subject: [FieldTrip] ft_preproc_dftfilter function In-Reply-To: References: Message-ID: <5363405F.3010802@donders.ru.nl> Hi Elias, please see http://fieldtrip.fcdonders.nl/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter that should enlighten you :) Best, Jörn On 5/1/2014 11:54 PM, Elias P. Casula wrote: > > Dear all, > I found some problems with the ft_preproc_dftfilter function. This > function should remove the 50hz noise from the signal. But when I call > the function with > > [filt] = ft_preproc_dftfilter(mymatrixdata, 1024, 50) > > the 50hz noise is still in the filtered signal. Does anyone else had > the same problem? > Thanks a lot, > > Elias > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From eliasc at live.it Fri May 2 09:36:35 2014 From: eliasc at live.it (Elias P. Casula) Date: Fri, 2 May 2014 09:36:35 +0200 Subject: [FieldTrip] ft_preproc_dftfilter function In-Reply-To: <5363405F.3010802@donders.ru.nl> References: , , <5363405F.3010802@donders.ru.nl> Message-ID: Thanks Jorn, Unfortunately in my case the signal remains exactly the same after the dft filter. Maybe there is something that I'm missing in the procedure? When I call the function I just insert my data matrix, the sampling frequency (1024) and the frequency band that I want to filter (50). The function generates a new file but apparently nothing changes. > Date: Fri, 2 May 2014 08:51:11 +0200 > From: jm.horschig at donders.ru.nl > To: fieldtrip at science.ru.nl > Subject: Re: [FieldTrip] ft_preproc_dftfilter function > > Hi Elias, > > please see > http://fieldtrip.fcdonders.nl/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter > that should enlighten you :) > > Best, > Jörn > > On 5/1/2014 11:54 PM, Elias P. Casula wrote: > > > > Dear all, > > I found some problems with the ft_preproc_dftfilter function. This > > function should remove the 50hz noise from the signal. But when I call > > the function with > > > > [filt] = ft_preproc_dftfilter(mymatrixdata, 1024, 50) > > > > the 50hz noise is still in the filtered signal. Does anyone else had > > the same problem? > > Thanks a lot, > > > > Elias > > > > > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Fri May 2 10:27:35 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Fri, 2 May 2014 08:27:35 +0000 Subject: [FieldTrip] clustering of bipolar referenced data Message-ID: Hi all, I would just like to confirm that I am not missing something. I am using cluster-based permutation stats for an intracranial dataset consisting of three bipolar channels. These are derived from four neighbouring contacts on the same electrode (i.e., channel 1 = contact 1 vs. contact 2, channel 2 = contact 2 vs. contact 3, etc.). For clustering in space, I've defined 2 to be a neighbour of 1 (and 3), and vice versa (etc. for the other channels). Since bipolar referencing means looking at differences between contacts, the fact that channels 1 and 2, for example, are partially derived from the same contact (contact 2), should not prevent me from clustering across these two channels when running stats - is that correct? Thanks! Best Max From martine.vanschouwenburg at ucsf.edu Fri May 2 20:16:29 2014 From: martine.vanschouwenburg at ucsf.edu (Martine van Schouwenburg) Date: Fri, 2 May 2014 11:16:29 -0700 Subject: [FieldTrip] ft_databrowser crashes Matlab Message-ID: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> Hi Fieldtrip experts, I am experiencing a problem with the ft_databrowser routine. Matlab crashes when I'm trying to run it, forcing me to end the Matlab session. ('Matlab has encountered an internal problem and needs to close.'). It seems more like a Matlab/Windows related issue when looking at the crash report (see below), but I am posting it here because it also seems to depend on the data that I use as input. When I run the routine on the 'raw' data (after defining the trials) it is working fine, but after I ran ICA and try to use the databrowser to look at the components, it crashes at line 676. This is the part where it calls the subfunction redraw_cb. Does anyone might have a clue what in the component data might cause this problem? Maybe some of you have experienced this before? I also send a request for Tech Support to Matlab. Best, Martine Here is the Matlab crash report if that is of any help: ------------------------------------------------------------------------ Segmentation violation detected at Thu May 01 22:28:30 2014 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Default Encoding: windows-1252 MATLAB Root : C:\Program Files\MATLAB\R2012b MATLAB Version : 8.0.0.783 (R2012b) Operating System: Microsoft Windows 7 Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode Window System : Version 6.1 (Build 7601: Service Pack 1) Fault Count: 1 Abnormal termination: Segmentation violation Register State (from fault): RAX = 00000000000001a4 RBX = 000000007a8425c0 RCX = 00000000000262de RDX = 00000000000001b2 RSP = 0000000004110a50 RBP = 000000000000007e RSI = 000000007a75cab0 RDI = 000000013942b996 R8 = 00000000000262de R9 = 0000000000000230 R10 = 0000000000000000 R11 = 0000000004110b28 R12 = 0000000000f206cd R13 = 0000000077ce4060 R14 = 000000000002635c R15 = 00000000000006c8 RIP = 000000006000d341 EFL = 00010216 CS = 0033 FS = 0053 GS = 002b Stack Trace (from fault): [ 0] 0x000000006000d341 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( RenderEngineBase::~RenderEngineBase+171553 ) [ 1] 0x000000005ff83130 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) [ 2] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) [ 3] 0x000000005fede587 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( renderAnimatedKids+000519 ) [ 4] 0x000000005fee3788 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) [ 5] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) [ 6] 0x000000005ff04729 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( FigureSetVisualAutoMode+001561 ) [ 7] 0x000000005ff0abbd C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( UIJ_CreatePeerWindow+001597 ) [ 8] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) [ 9] 0x0000000060013548 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( RenderEngineBase::~RenderEngineBase+196648 ) [ 10] 0x000000005ff06b87 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( FigureSetVisualAutoMode+010871 ) [ 11] 0x000000005ff06c0d C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( FigureSetVisualAutoMode+011005 ) [ 12] 0x0000000063425006 C:\Program Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( wm_ExposeFcn_Pre_Optional+000374 ) [ 13] 0x0000000064c8c694 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) [ 14] 0x0000000064c8e456 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( UIJ_IsWindowShowing+000438 ) [ 15] 0x0000000064c8f943 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( UIJ_clearWaitForResize+002067 ) [ 16] 0x0000000064c8fa61 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) [ 17] 0x0000000064c707ae C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( UIJ_MarkEventFinished+005838 ) [ 18] 0x0000000064c70800 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( UIJ_MarkEventFinished+005920 ) [ 19] 0x0000000064c892ac C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( uij::JavaDraw2D::paintQuadStrip+001324 ) [ 20] 0x0000000064d4e808 C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( uddSetListenerRecursionWarning+000680 ) [ 21] 0x0000000064d4ee6c C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( UDListenerManagerHost::notifyEvent+000076 ) [ 22] 0x0000000064d4697d C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( UDEventInfo::send+000093 ) [ 23] 0x000000005fb9cedb C:\Program Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( MErrorException::operator=+047675 ) [ 24] 0x00000000055ce0b6 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( UIW_IsUserMessage+000086 ) [ 25] 0x00000000055ce7b9 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( UIW_SetGLIMUserMsg+000153 ) [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( GetMenuBarInfo+000638 ) [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( SystemParametersInfoW+000235 ) [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( IsProcessDPIAware+000465 ) [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( KiUserCallbackDispatcher+000031 ) [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( PeekMessageW+000186 ) [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( GetKeyState+000238 ) [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( PeekMessageA+000087 ) [ 33] 0x00000000055a8f4b C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( UIW_SetCurrentDialog+000731 ) [ 34] 0x00000000055cfbe2 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( ws_FreeSystemFont+000546 ) [ 35] 0x000000000485e6a3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( sysq::removeCommitDatabaseUpdatesHook+002131 ) [ 36] 0x000000000485fe18 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( sysq::removeCommitDatabaseUpdatesHook+008136 ) [ 37] 0x0000000004861a20 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( sysq::addProcessPendingEventsUnitTestHook+000240 ) [ 38] 0x0000000004861ae8 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( sysq::addProcessPendingEventsUnitTestHook+000440 ) [ 39] 0x0000000004861ca3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( sysq::addProcessPendingEventsUnitTestHook+000883 ) [ 40] 0x0000000004861d76 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( sysq::addProcessPendingEventsUnitTestHook+001094 ) [ 41] 0x000000005ff0c4fe C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) [ 42] 0x0000000074e8d17f C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( Mfunction_handle::dispatch+001023 ) [ 43] 0x0000000074e8cf82 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( Mfunction_handle::dispatch+000514 ) [ 44] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) [ 45] 0x000007feef3a5ca4 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( inFunctionHandleInterface::DestroyWorkspace+295012 ) [ 46] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) [ 47] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) [ 48] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) [ 49] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) [ 50] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) [ 51] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) [ 52] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) [ 53] 0x000007feef38210b C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( inFunctionHandleInterface::DestroyWorkspace+148683 ) [ 54] 0x000007feef393edf C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( inFunctionHandleInterface::DestroyWorkspace+221855 ) [ 55] 0x000007feef3b0ae8 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( inFunctionHandleInterface::DestroyWorkspace+339624 ) [ 56] 0x000007feef398d94 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( inFunctionHandleInterface::DestroyWorkspace+242004 ) [ 57] 0x000007feef3a2978 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( inFunctionHandleInterface::DestroyWorkspace+281912 ) [ 58] 0x000007feef3a5a8b C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( inFunctionHandleInterface::DestroyWorkspace+294475 ) [ 59] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) [ 60] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) [ 61] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) [ 62] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) [ 63] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) [ 64] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) [ 65] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) [ 66] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) [ 67] 0x000007feef43318f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( inEachVisibleName+014415 ) [ 68] 0x000007feef3a74ca C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( inFunctionHandleInterface::DestroyWorkspace+301194 ) [ 69] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) [ 70] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) [ 71] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) [ 72] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) [ 73] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) [ 74] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) [ 75] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) [ 76] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) [ 77] 0x000007feef43318f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( inEachVisibleName+014415 ) [ 78] 0x000007feef3a74ca C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( inFunctionHandleInterface::DestroyWorkspace+301194 ) [ 79] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) [ 80] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) [ 81] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) [ 82] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) [ 83] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) [ 84] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) [ 85] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) [ 86] 0x000007feef4451e5 C:\Program 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URL: From mcantor at umich.edu Fri May 2 20:58:06 2014 From: mcantor at umich.edu (Max Cantor) Date: Fri, 2 May 2014 14:58:06 -0400 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: <5363e841.061d2a0a.2297.ffffb0e2SMTPIN_ADDED_BROKEN@mx.google.com> References: <5363e841.061d2a0a.2297.ffffb0e2SMTPIN_ADDED_BROKEN@mx.google.com> Message-ID: Hi Martine, I can't say for sure, but I believe it's because ft_databrowser is only designed to take channel data, not component data. To view component data, you should use ft_componentbrowser. Hope that helps, Max Cantor Research Assistant Computational Neurolinguistics Lab University of Michigan On Fri, May 2, 2014 at 2:16 PM, Martine van Schouwenburg < martine.vanschouwenburg at ucsf.edu> wrote: > Hi Fieldtrip experts, > > > > I am experiencing a problem with the ft_databrowser routine. Matlab > crashes when I’m trying to run it, forcing me to end the Matlab session. > (‘Matlab has encountered an internal problem and needs to close.’). It > seems more like a Matlab/Windows related issue when looking at the crash > report (see below), but I am posting it here because it also seems to > depend on the data that I use as input. When I run the routine on the ‘raw’ > data (after defining the trials) it is working fine, but after I ran ICA > and try to use the databrowser to look at the components, it crashes at > line 676. > > This is the part where it calls the subfunction redraw_cb. Does anyone > might have a clue what in the component data might cause this problem? > Maybe some of you have experienced this before? I also send a request for > Tech Support to Matlab. > > > > Best, Martine > > > > Here is the Matlab crash report if that is of any help: > > > > > > > > ------------------------------------------------------------------------ > > Segmentation violation detected at Thu May 01 22:28:30 2014 > > ------------------------------------------------------------------------ > > > > Configuration: > > Crash Decoding : Disabled > > Default Encoding: windows-1252 > > MATLAB Root : C:\Program Files\MATLAB\R2012b > > MATLAB Version : 8.0.0.783 (R2012b) > > Operating System: Microsoft Windows 7 > > Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD > > Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java > HotSpot(TM) 64-Bit Server VM mixed mode > > Window System : Version 6.1 (Build 7601: Service Pack 1) > > > > Fault Count: 1 > > > > > > Abnormal termination: > > Segmentation violation > > > > Register State (from fault): > > RAX = 00000000000001a4 RBX = 000000007a8425c0 > > RCX = 00000000000262de RDX = 00000000000001b2 > > RSP = 0000000004110a50 RBP = 000000000000007e > > RSI = 000000007a75cab0 RDI = 000000013942b996 > > > > R8 = 00000000000262de R9 = 0000000000000230 > > R10 = 0000000000000000 R11 = 0000000004110b28 > > R12 = 0000000000f206cd R13 = 0000000077ce4060 > > R14 = 000000000002635c R15 = 00000000000006c8 > > > > RIP = 000000006000d341 EFL = 00010216 > > > > CS = 0033 FS = 0053 GS = 002b > > > > Stack Trace (from fault): > > [ 0] 0x000000006000d341 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( > RenderEngineBase::~RenderEngineBase+171553 ) > > [ 1] 0x000000005ff83130 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) > > [ 2] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 3] 0x000000005fede587 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( renderAnimatedKids+000519 ) > > [ 4] 0x000000005fee3788 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) > > [ 5] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 6] 0x000000005ff04729 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( > FigureSetVisualAutoMode+001561 ) > > [ 7] 0x000000005ff0abbd C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( UIJ_CreatePeerWindow+001597 > ) > > [ 8] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 9] 0x0000000060013548 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( > RenderEngineBase::~RenderEngineBase+196648 ) > > [ 10] 0x000000005ff06b87 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( > FigureSetVisualAutoMode+010871 ) > > [ 11] 0x000000005ff06c0d C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( > FigureSetVisualAutoMode+011005 ) > > [ 12] 0x0000000063425006 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( > wm_ExposeFcn_Pre_Optional+000374 ) > > [ 13] 0x0000000064c8c694 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) > > [ 14] 0x0000000064c8e456 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( > UIJ_IsWindowShowing+000438 ) > > [ 15] 0x0000000064c8f943 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( > UIJ_clearWaitForResize+002067 ) > > [ 16] 0x0000000064c8fa61 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) > > [ 17] 0x0000000064c707ae C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( > UIJ_MarkEventFinished+005838 ) > > [ 18] 0x0000000064c70800 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( > UIJ_MarkEventFinished+005920 ) > > [ 19] 0x0000000064c892ac C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( > uij::JavaDraw2D::paintQuadStrip+001324 ) > > [ 20] 0x0000000064d4e808 C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( > uddSetListenerRecursionWarning+000680 ) > > [ 21] 0x0000000064d4ee6c C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( > UDListenerManagerHost::notifyEvent+000076 ) > > [ 22] 0x0000000064d4697d C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( UDEventInfo::send+000093 ) > > [ 23] 0x000000005fb9cedb C:\Program > Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( > MErrorException::operator=+047675 ) > > [ 24] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( UIW_IsUserMessage+000086 ) > > [ 25] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( UIW_SetGLIMUserMsg+000153 ) > > [ 26] 0x00000000774a87fe > C:\Windows\system32\USER32.dll+00165886 ( GetMenuBarInfo+000638 ) > > [ 27] 0x000000007748f5fb > C:\Windows\system32\USER32.dll+00062971 ( SystemParametersInfoW+000235 ) > > [ 28] 0x0000000077494895 > C:\Windows\system32\USER32.dll+00084117 ( IsProcessDPIAware+000465 ) > > [ 29] 0x00000000775d11f5 > C:\Windows\SYSTEM32\ntdll.dll+00332277 ( KiUserCallbackDispatcher+000031 ) > > [ 30] 0x000000007749908a > C:\Windows\system32\USER32.dll+00102538 ( PeekMessageW+000186 ) > > [ 31] 0x00000000774950fe > C:\Windows\system32\USER32.dll+00086270 ( GetKeyState+000238 ) > > [ 32] 0x0000000077493a6f > C:\Windows\system32\USER32.dll+00080495 ( PeekMessageA+000087 ) > > [ 33] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [ 34] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( ws_FreeSystemFont+000546 ) > > [ 35] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [ 36] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [ 37] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [ 38] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [ 39] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [ 40] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [ 41] 0x000000005ff0c4fe C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) > > [ 42] 0x0000000074e8d17f C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( > Mfunction_handle::dispatch+001023 ) > > [ 43] 0x0000000074e8cf82 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( > Mfunction_handle::dispatch+000514 ) > > [ 44] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 45] 0x000007feef3a5ca4 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( > inFunctionHandleInterface::DestroyWorkspace+295012 ) > > [ 46] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 47] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 48] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 49] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 50] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 51] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 52] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 53] 0x000007feef38210b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( > inFunctionHandleInterface::DestroyWorkspace+148683 ) > > [ 54] 0x000007feef393edf C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( > inFunctionHandleInterface::DestroyWorkspace+221855 ) > > [ 55] 0x000007feef3b0ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( > inFunctionHandleInterface::DestroyWorkspace+339624 ) > > [ 56] 0x000007feef398d94 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( > inFunctionHandleInterface::DestroyWorkspace+242004 ) > > [ 57] 0x000007feef3a2978 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( > inFunctionHandleInterface::DestroyWorkspace+281912 ) > > [ 58] 0x000007feef3a5a8b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( > inFunctionHandleInterface::DestroyWorkspace+294475 ) > > [ 59] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 60] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 61] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 62] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 63] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 64] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 65] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 66] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 67] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 68] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 69] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 70] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 71] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 72] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 73] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 74] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 75] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 76] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 77] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 78] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 79] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 80] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 81] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 82] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 83] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 84] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 85] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 86] 0x000007feef4451e5 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( > inValidateLoadedObject+001893 ) > > [ 87] 0x000007feef454595 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( > init_cleaner+015541 ) > > [ 88] 0x000007feef457b75 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( > inSetMaxFrameCount+002261 ) > > [ 89] 0x000007feef457b48 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( > inSetMaxFrameCount+002216 ) > > [ 90] 0x000007feef457b07 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( > inSetMaxFrameCount+002151 ) > > [ 91] 0x000007feef340213 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( > inPathNotification::function_clear_notification+004019 ) > > [ 92] 0x000007feef44aed0 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( > inEvalCmdWithLocalReturn+000416 ) > > [ 93] 0x000007feef44ae2c C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( > inEvalCmdWithLocalReturn+000252 ) > > [ 94] 0x000007feef44ad71 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( > inEvalCmdWithLocalReturn+000065 ) > > [ 95] 0x0000000079fbf90d C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( > mnDebugPrompt+000109 ) > > [ 96] 0x0000000079fc0471 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( mnParser+000593 ) > > [ 97] 0x00000000749a64a4 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( > mcrInstance::mnParser_on_interpreter_thread+000036 ) > > [ 98] 0x000000007498681f C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( > mcr::setInterpreterThreadToCurrent+029887 ) > > [ 99] 0x0000000074986881 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( > mcr::setInterpreterThreadToCurrent+029985 ) > > [100] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( UIW_IsUserMessage+000086 ) > > [101] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( UIW_SetGLIMUserMsg+000153 ) > > [102] 0x00000000774a87fe > C:\Windows\system32\USER32.dll+00165886 ( GetMenuBarInfo+000638 ) > > [103] 0x000000007748f5fb > C:\Windows\system32\USER32.dll+00062971 ( SystemParametersInfoW+000235 ) > > [104] 0x0000000077494895 > C:\Windows\system32\USER32.dll+00084117 ( IsProcessDPIAware+000465 ) > > [105] 0x00000000775d11f5 > C:\Windows\SYSTEM32\ntdll.dll+00332277 ( KiUserCallbackDispatcher+000031 ) > > [106] 0x000000007749908a > C:\Windows\system32\USER32.dll+00102538 ( PeekMessageW+000186 ) > > [107] 0x00000000774950fe > C:\Windows\system32\USER32.dll+00086270 ( GetKeyState+000238 ) > > [108] 0x0000000077493a6f > C:\Windows\system32\USER32.dll+00080495 ( PeekMessageA+000087 ) > > [109] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [110] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( ws_FreeSystemFont+000546 ) > > [111] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [112] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [113] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [114] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [115] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [116] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [117] 0x000000007498837e C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( > mcr::setInterpreterThreadToCurrent+036894 ) > > [118] 0x0000000074988665 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( > mcr::setInterpreterThreadToCurrent+037637 ) > > [119] 0x000000007497b166 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( > DepfunRules::postWarning+003430 ) > > [120] 0x000000013fc78a33 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) > > [121] 0x000000013fc78c97 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) > > [122] 0x000000013fc79163 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) > > [123] 0x00000000773759ed > C:\Windows\system32\kernel32.dll+00088557 ( BaseThreadInitThunk+000013 ) > > [124] 0x00000000775ac541 > C:\Windows\SYSTEM32\ntdll.dll+00181569 ( > RtlUserThreadStart+000033 ) > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri May 2 21:15:00 2014 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 2 May 2014 21:15:00 +0200 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: References: <5363e841.061d2a0a.2297.ffffb0e2SMTPIN_ADDED_BROKEN@mx.google.com> Message-ID: <1B783442-BFEC-4625-AB21-F59A3ABF1011@donders.ru.nl> Dear Martine, Although I don't have a solution right now, the error message indeed suggest a very low level crash of MATLAB. Therefore, I don't think it is likely that it is related to the fact that you are trying to visualize 'component'-data (which in principle should be possible with ft_databrowser). It's more likely that it's a platform dependent issue, likely related to (compiled) mex-files, or a graphics issue. I remember that occasionally in the past people reported crashes specifically with ft_databrowser, but I don't remember the technical details about this. Could I suggest you to create an account on our bugzilla.fcdonders.nl site, and file this as a new bug, with as much information about it as possible? It would even be better to browse around a bit (use the search functionality, and search for ft_databrowser), you may be able to add this issue as a comment to an already existing bug with the same content. Best, JM On May 2, 2014, at 8:58 PM, Max Cantor wrote: > Hi Martine, > > I can't say for sure, but I believe it's because ft_databrowser is only designed to take channel data, not component data. To view component data, you should use ft_componentbrowser. > > Hope that helps, > > Max Cantor > Research Assistant > Computational Neurolinguistics Lab > University of Michigan > > > > On Fri, May 2, 2014 at 2:16 PM, Martine van Schouwenburg wrote: > Hi Fieldtrip experts, > > > > I am experiencing a problem with the ft_databrowser routine. Matlab crashes when I’m trying to run it, forcing me to end the Matlab session. (‘Matlab has encountered an internal problem and needs to close.’). It seems more like a Matlab/Windows related issue when looking at the crash report (see below), but I am posting it here because it also seems to depend on the data that I use as input. When I run the routine on the ‘raw’ data (after defining the trials) it is working fine, but after I ran ICA and try to use the databrowser to look at the components, it crashes at line 676. > > This is the part where it calls the subfunction redraw_cb. Does anyone might have a clue what in the component data might cause this problem? Maybe some of you have experienced this before? I also send a request for Tech Support to Matlab. > > > > Best, Martine > > > > Here is the Matlab crash report if that is of any help: > > > > > > > > ------------------------------------------------------------------------ > > Segmentation violation detected at Thu May 01 22:28:30 2014 > > ------------------------------------------------------------------------ > > > > Configuration: > > Crash Decoding : Disabled > > Default Encoding: windows-1252 > > MATLAB Root : C:\Program Files\MATLAB\R2012b > > MATLAB Version : 8.0.0.783 (R2012b) > > Operating System: Microsoft Windows 7 > > Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD > > Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode > > Window System : Version 6.1 (Build 7601: Service Pack 1) > > > > Fault Count: 1 > > > > > > Abnormal termination: > > Segmentation violation > > > > Register State (from fault): > > RAX = 00000000000001a4 RBX = 000000007a8425c0 > > RCX = 00000000000262de RDX = 00000000000001b2 > > RSP = 0000000004110a50 RBP = 000000000000007e > > RSI = 000000007a75cab0 RDI = 000000013942b996 > > > > R8 = 00000000000262de R9 = 0000000000000230 > > R10 = 0000000000000000 R11 = 0000000004110b28 > > R12 = 0000000000f206cd R13 = 0000000077ce4060 > > R14 = 000000000002635c R15 = 00000000000006c8 > > > > RIP = 000000006000d341 EFL = 00010216 > > > > CS = 0033 FS = 0053 GS = 002b > > > > Stack Trace (from fault): > > [ 0] 0x000000006000d341 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( RenderEngineBase::~RenderEngineBase+171553 ) > > [ 1] 0x000000005ff83130 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) > > [ 2] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 3] 0x000000005fede587 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( renderAnimatedKids+000519 ) > > [ 4] 0x000000005fee3788 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) > > [ 5] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 6] 0x000000005ff04729 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( FigureSetVisualAutoMode+001561 ) > > [ 7] 0x000000005ff0abbd C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( UIJ_CreatePeerWindow+001597 ) > > [ 8] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 9] 0x0000000060013548 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( RenderEngineBase::~RenderEngineBase+196648 ) > > [ 10] 0x000000005ff06b87 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( FigureSetVisualAutoMode+010871 ) > > [ 11] 0x000000005ff06c0d C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( FigureSetVisualAutoMode+011005 ) > > [ 12] 0x0000000063425006 C:\Program Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( wm_ExposeFcn_Pre_Optional+000374 ) > > [ 13] 0x0000000064c8c694 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) > > [ 14] 0x0000000064c8e456 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( UIJ_IsWindowShowing+000438 ) > > [ 15] 0x0000000064c8f943 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( UIJ_clearWaitForResize+002067 ) > > [ 16] 0x0000000064c8fa61 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) > > [ 17] 0x0000000064c707ae C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( UIJ_MarkEventFinished+005838 ) > > [ 18] 0x0000000064c70800 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( UIJ_MarkEventFinished+005920 ) > > [ 19] 0x0000000064c892ac C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( uij::JavaDraw2D::paintQuadStrip+001324 ) > > [ 20] 0x0000000064d4e808 C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( uddSetListenerRecursionWarning+000680 ) > > [ 21] 0x0000000064d4ee6c C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( UDListenerManagerHost::notifyEvent+000076 ) > > [ 22] 0x0000000064d4697d C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( UDEventInfo::send+000093 ) > > [ 23] 0x000000005fb9cedb C:\Program Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( MErrorException::operator=+047675 ) > > [ 24] 0x00000000055ce0b6 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( UIW_IsUserMessage+000086 ) > > [ 25] 0x00000000055ce7b9 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( UIW_SetGLIMUserMsg+000153 ) > > [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( GetMenuBarInfo+000638 ) > > [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( SystemParametersInfoW+000235 ) > > [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( IsProcessDPIAware+000465 ) > > [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( KiUserCallbackDispatcher+000031 ) > > [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( PeekMessageW+000186 ) > > [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( GetKeyState+000238 ) > > [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( PeekMessageA+000087 ) > > [ 33] 0x00000000055a8f4b C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( UIW_SetCurrentDialog+000731 ) > > [ 34] 0x00000000055cfbe2 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( ws_FreeSystemFont+000546 ) > > [ 35] 0x000000000485e6a3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [ 36] 0x000000000485fe18 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [ 37] 0x0000000004861a20 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [ 38] 0x0000000004861ae8 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [ 39] 0x0000000004861ca3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [ 40] 0x0000000004861d76 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [ 41] 0x000000005ff0c4fe C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) > > [ 42] 0x0000000074e8d17f C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( Mfunction_handle::dispatch+001023 ) > > [ 43] 0x0000000074e8cf82 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( Mfunction_handle::dispatch+000514 ) > > [ 44] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 45] 0x000007feef3a5ca4 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( inFunctionHandleInterface::DestroyWorkspace+295012 ) > > [ 46] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 47] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 48] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 49] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 50] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 51] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) > > [ 52] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) > > [ 53] 0x000007feef38210b C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( inFunctionHandleInterface::DestroyWorkspace+148683 ) > > [ 54] 0x000007feef393edf C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( inFunctionHandleInterface::DestroyWorkspace+221855 ) > > [ 55] 0x000007feef3b0ae8 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( inFunctionHandleInterface::DestroyWorkspace+339624 ) > > [ 56] 0x000007feef398d94 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( inFunctionHandleInterface::DestroyWorkspace+242004 ) > > [ 57] 0x000007feef3a2978 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( inFunctionHandleInterface::DestroyWorkspace+281912 ) > > [ 58] 0x000007feef3a5a8b C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( inFunctionHandleInterface::DestroyWorkspace+294475 ) > > [ 59] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 60] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 61] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 62] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 63] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 64] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) > > [ 65] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) > > [ 66] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 67] 0x000007feef43318f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( inEachVisibleName+014415 ) > > [ 68] 0x000007feef3a74ca C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 69] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 70] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 71] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 72] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 73] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 74] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) > > [ 75] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) > > [ 76] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 77] 0x000007feef43318f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( inEachVisibleName+014415 ) > > [ 78] 0x000007feef3a74ca C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 79] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 80] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 81] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 82] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 83] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 84] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) > > [ 85] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) > > [ 86] 0x000007feef4451e5 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( inValidateLoadedObject+001893 ) > > [ 87] 0x000007feef454595 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( init_cleaner+015541 ) > > [ 88] 0x000007feef457b75 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( inSetMaxFrameCount+002261 ) > > [ 89] 0x000007feef457b48 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( inSetMaxFrameCount+002216 ) > > [ 90] 0x000007feef457b07 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( inSetMaxFrameCount+002151 ) > > [ 91] 0x000007feef340213 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( inPathNotification::function_clear_notification+004019 ) > > [ 92] 0x000007feef44aed0 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( inEvalCmdWithLocalReturn+000416 ) > > [ 93] 0x000007feef44ae2c C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( inEvalCmdWithLocalReturn+000252 ) > > [ 94] 0x000007feef44ad71 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( inEvalCmdWithLocalReturn+000065 ) > > [ 95] 0x0000000079fbf90d C:\Program Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( mnDebugPrompt+000109 ) > > [ 96] 0x0000000079fc0471 C:\Program Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( mnParser+000593 ) > > [ 97] 0x00000000749a64a4 C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( mcrInstance::mnParser_on_interpreter_thread+000036 ) > > [ 98] 0x000000007498681f C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( mcr::setInterpreterThreadToCurrent+029887 ) > > [ 99] 0x0000000074986881 C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( mcr::setInterpreterThreadToCurrent+029985 ) > > [100] 0x00000000055ce0b6 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( UIW_IsUserMessage+000086 ) > > [101] 0x00000000055ce7b9 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( UIW_SetGLIMUserMsg+000153 ) > > [102] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( GetMenuBarInfo+000638 ) > > [103] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( SystemParametersInfoW+000235 ) > > [104] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( IsProcessDPIAware+000465 ) > > [105] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( KiUserCallbackDispatcher+000031 ) > > [106] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( PeekMessageW+000186 ) > > [107] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( GetKeyState+000238 ) > > [108] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( PeekMessageA+000087 ) > > [109] 0x00000000055a8f4b C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( UIW_SetCurrentDialog+000731 ) > > [110] 0x00000000055cfbe2 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( ws_FreeSystemFont+000546 ) > > [111] 0x000000000485e6a3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [112] 0x000000000485fe18 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [113] 0x0000000004861a20 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [114] 0x0000000004861ae8 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [115] 0x0000000004861ca3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [116] 0x0000000004861d76 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [117] 0x000000007498837e C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( mcr::setInterpreterThreadToCurrent+036894 ) > > [118] 0x0000000074988665 C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( mcr::setInterpreterThreadToCurrent+037637 ) > > [119] 0x000000007497b166 C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( DepfunRules::postWarning+003430 ) > > [120] 0x000000013fc78a33 C:\Program Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) > > [121] 0x000000013fc78c97 C:\Program Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) > > [122] 0x000000013fc79163 C:\Program Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) > > [123] 0x00000000773759ed C:\Windows\system32\kernel32.dll+00088557 ( BaseThreadInitThunk+000013 ) > > [124] 0x00000000775ac541 C:\Windows\SYSTEM32\ntdll.dll+00181569 ( RtlUserThreadStart+000033 ) > > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl 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URL: From kkb268 at nyu.edu Fri May 2 22:41:24 2014 From: kkb268 at nyu.edu (Kristen Berry) Date: Fri, 2 May 2014 16:41:24 -0400 Subject: [FieldTrip] ft_timelockstatistics cluster correction using ECoG data Message-ID: Dear all, I am using an intracranial EEG dataset to compare average high gamma power waveforms between conditions. I want to correct for multiple comparisons across time, but not across number of electrodes. Here is my input code: cfg=[]; cfg.latency = [0.05 .5]; cfg.parameter = 'trial'; cfg.method = 'montecarlo'; cfg.correctm = 'cluster'; cfg.neighbours = []; cfg.numrandomization = 1000; cfg.statistic = 'indepsamplesT'; cfg.channel = ‘all’; cfg.alpha = 0.05; cfg.clusteralpha = 0.05; cfg.tail = 0; stats = ft_timelockstatistics(cfg, data,control); Fieldtrip’s montecarlo reference page ( http://fieldtrip.fcdonders.nl/reference/ft_statistics_montecarlo) says, “If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels.” However, my input code corrects for the number of channels as well. As an example, when cfg.channel = ‘all’ for ft_timelockstatistics, then Elec11 is not significant. However, if the analysis is limited to Elec11 (cfg.channel = 11), then Elec11 has a significant cluster. Is there a mistake in my code that is causing this? Or is there an older version of fieldtrip that doesn’t correct for # of channels, when cfg.neighbours is empty? Thank you for your input! Best regards, Kristen Kristen Berry Research Assistant NYU School of Medicine -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Sat May 3 11:04:42 2014 From: jm.horschig at donders.ru.nl (=?windows-1252?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Sat, 03 May 2014 11:04:42 +0200 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> References: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> Message-ID: <5364B12A.80807@donders.ru.nl> Hi Martine, great to hear that you are using FieldTrip ;) hope you like it. As JM said, it is indeed some low-level problem with Windows 7, Matlab and the databrowser. The only way to escape this is to use another OS... in the past we have not been successful in tracing this down, because it is such a low-level error on only happens on some PCs with Win7, but not on all. There is already a bug on bugzilla for this. Maybe we need to ask Mathworks for support on this ;) @Max: The databrowser is specifically designed to also show components if you set cfg.viewmode = 'components'. The error also has nothing to do with showing components, as it also happens for plotting channel-level data. Best, Jörn On 5/2/2014 8:16 PM, Martine van Schouwenburg wrote: > > Hi Fieldtrip experts, > > I am experiencing a problem with the ft_databrowser routine. Matlab > crashes when I’m trying to run it, forcing me to end the Matlab > session. (‘Matlab has encountered an internal problem and needs to > close.’). It seems more like a Matlab/Windows related issue when > looking at the crash report (see below), but I am posting it here > because it also seems to depend on the data that I use as input. When > I run the routine on the ‘raw’ data (after defining the trials) it is > working fine, but after I ran ICA and try to use the databrowser to > look at the components, it crashes at line 676. > > This is the part where it calls the subfunction redraw_cb. Does anyone > might have a clue what in the component data might cause this problem? > Maybe some of you have experienced this before? I also send a request > for Tech Support to Matlab. > > Best, Martine > > Here is the Matlab crash report if that is of any help: > > ------------------------------------------------------------------------ > > Segmentation violation detected at Thu May 01 22:28:30 2014 > > ------------------------------------------------------------------------ > > Configuration: > > Crash Decoding : Disabled > > Default Encoding: windows-1252 > > MATLAB Root : C:\Program Files\MATLAB\R2012b > > MATLAB Version : 8.0.0.783 (R2012b) > > Operating System: Microsoft Windows 7 > > Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD > > Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java > HotSpot(TM) 64-Bit Server VM mixed mode > > Window System : Version 6.1 (Build 7601: Service Pack 1) > > Fault Count: 1 > > Abnormal termination: > > Segmentation violation > > Register State (from fault): > > RAX = 00000000000001a4 RBX = 000000007a8425c0 > > RCX = 00000000000262de RDX = 00000000000001b2 > > RSP = 0000000004110a50 RBP = 000000000000007e > > RSI = 000000007a75cab0 RDI = 000000013942b996 > > R8 = 00000000000262de R9 = 0000000000000230 > > R10 = 0000000000000000 R11 = 0000000004110b28 > > R12 = 0000000000f206cd R13 = 0000000077ce4060 > > R14 = 000000000002635c R15 = 00000000000006c8 > > RIP = 000000006000d341 EFL = 00010216 > > CS = 0033 FS = 0053 GS = 002b > > Stack Trace (from fault): > > [ 0] 0x000000006000d341 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( > RenderEngineBase::~RenderEngineBase+171553 ) > > [ 1] 0x000000005ff83130 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) > > [ 2] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 3] 0x000000005fede587 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( > renderAnimatedKids+000519 ) > > [ 4] 0x000000005fee3788 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) > > [ 5] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 6] 0x000000005ff04729 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( > FigureSetVisualAutoMode+001561 ) > > [ 7] 0x000000005ff0abbd C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( > UIJ_CreatePeerWindow+001597 ) > > [ 8] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 9] 0x0000000060013548 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( > RenderEngineBase::~RenderEngineBase+196648 ) > > [ 10] 0x000000005ff06b87 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( > FigureSetVisualAutoMode+010871 ) > > [ 11] 0x000000005ff06c0d C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( > FigureSetVisualAutoMode+011005 ) > > [ 12] 0x0000000063425006 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( > wm_ExposeFcn_Pre_Optional+000374 ) > > [ 13] 0x0000000064c8c694 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) > > [ 14] 0x0000000064c8e456 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( > UIJ_IsWindowShowing+000438 ) > > [ 15] 0x0000000064c8f943 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( > UIJ_clearWaitForResize+002067 ) > > [ 16] 0x0000000064c8fa61 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) > > [ 17] 0x0000000064c707ae C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( > UIJ_MarkEventFinished+005838 ) > > [ 18] 0x0000000064c70800 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( > UIJ_MarkEventFinished+005920 ) > > [ 19] 0x0000000064c892ac C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( > uij::JavaDraw2D::paintQuadStrip+001324 ) > > [ 20] 0x0000000064d4e808 C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( > uddSetListenerRecursionWarning+000680 ) > > [ 21] 0x0000000064d4ee6c C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( > UDListenerManagerHost::notifyEvent+000076 ) > > [ 22] 0x0000000064d4697d C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( > UDEventInfo::send+000093 ) > > [ 23] 0x000000005fb9cedb C:\Program > Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( > MErrorException::operator=+047675 ) > > [ 24] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( > UIW_IsUserMessage+000086 ) > > [ 25] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( > UIW_SetGLIMUserMsg+000153 ) > > [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( > GetMenuBarInfo+000638 ) > > [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( > SystemParametersInfoW+000235 ) > > [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( > IsProcessDPIAware+000465 ) > > [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( > KiUserCallbackDispatcher+000031 ) > > [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( > PeekMessageW+000186 ) > > [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( > GetKeyState+000238 ) > > [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( > PeekMessageA+000087 ) > > [ 33] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [ 34] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( > ws_FreeSystemFont+000546 ) > > [ 35] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [ 36] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [ 37] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [ 38] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [ 39] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [ 40] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [ 41] 0x000000005ff0c4fe C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) > > [ 42] 0x0000000074e8d17f C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( > Mfunction_handle::dispatch+001023 ) > > [ 43] 0x0000000074e8cf82 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( > Mfunction_handle::dispatch+000514 ) > > [ 44] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 45] 0x000007feef3a5ca4 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( > inFunctionHandleInterface::DestroyWorkspace+295012 ) > > [ 46] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 47] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 48] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 49] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 50] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 51] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 52] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 53] 0x000007feef38210b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( > inFunctionHandleInterface::DestroyWorkspace+148683 ) > > [ 54] 0x000007feef393edf C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( > inFunctionHandleInterface::DestroyWorkspace+221855 ) > > [ 55] 0x000007feef3b0ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( > inFunctionHandleInterface::DestroyWorkspace+339624 ) > > [ 56] 0x000007feef398d94 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( > inFunctionHandleInterface::DestroyWorkspace+242004 ) > > [ 57] 0x000007feef3a2978 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( > inFunctionHandleInterface::DestroyWorkspace+281912 ) > > [ 58] 0x000007feef3a5a8b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( > inFunctionHandleInterface::DestroyWorkspace+294475 ) > > [ 59] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 60] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 61] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 62] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 63] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 64] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 65] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 66] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 67] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 68] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 69] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 70] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 71] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 72] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 73] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 74] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 75] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 76] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 77] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 78] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 79] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 80] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 81] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 82] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 83] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 84] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 85] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 86] 0x000007feef4451e5 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( > inValidateLoadedObject+001893 ) > > [ 87] 0x000007feef454595 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( > init_cleaner+015541 ) > > [ 88] 0x000007feef457b75 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( > inSetMaxFrameCount+002261 ) > > [ 89] 0x000007feef457b48 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( > inSetMaxFrameCount+002216 ) > > [ 90] 0x000007feef457b07 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( > inSetMaxFrameCount+002151 ) > > [ 91] 0x000007feef340213 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( > inPathNotification::function_clear_notification+004019 ) > > [ 92] 0x000007feef44aed0 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( > inEvalCmdWithLocalReturn+000416 ) > > [ 93] 0x000007feef44ae2c C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( > inEvalCmdWithLocalReturn+000252 ) > > [ 94] 0x000007feef44ad71 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( > inEvalCmdWithLocalReturn+000065 ) > > [ 95] 0x0000000079fbf90d C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( > mnDebugPrompt+000109 ) > > [ 96] 0x0000000079fc0471 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( mnParser+000593 ) > > [ 97] 0x00000000749a64a4 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( > mcrInstance::mnParser_on_interpreter_thread+000036 ) > > [ 98] 0x000000007498681f C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( > mcr::setInterpreterThreadToCurrent+029887 ) > > [ 99] 0x0000000074986881 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( > mcr::setInterpreterThreadToCurrent+029985 ) > > [100] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( > UIW_IsUserMessage+000086 ) > > [101] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( > UIW_SetGLIMUserMsg+000153 ) > > [102] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( > GetMenuBarInfo+000638 ) > > [103] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( > SystemParametersInfoW+000235 ) > > [104] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( > IsProcessDPIAware+000465 ) > > [105] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( > KiUserCallbackDispatcher+000031 ) > > [106] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( > PeekMessageW+000186 ) > > [107] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( > GetKeyState+000238 ) > > [108] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( > PeekMessageA+000087 ) > > [109] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [110] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( > ws_FreeSystemFont+000546 ) > > [111] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [112] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [113] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [114] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [115] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [116] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [117] 0x000000007498837e C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( > mcr::setInterpreterThreadToCurrent+036894 ) > > [118] 0x0000000074988665 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( > mcr::setInterpreterThreadToCurrent+037637 ) > > [119] 0x000000007497b166 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( > DepfunRules::postWarning+003430 ) > > [120] 0x000000013fc78a33 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) > > [121] 0x000000013fc78c97 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) > > [122] 0x000000013fc79163 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) > > [123] 0x00000000773759ed C:\Windows\system32\kernel32.dll+00088557 ( > BaseThreadInitThunk+000013 ) > > [124] 0x00000000775ac541 C:\Windows\SYSTEM32\ntdll.dll+00181569 ( > RtlUserThreadStart+000033 ) > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From martine.vanschouwenburg at ucsf.edu Sat May 3 23:16:43 2014 From: martine.vanschouwenburg at ucsf.edu (Martine van Schouwenburg) Date: Sat, 3 May 2014 14:16:43 -0700 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: <5364B12A.80807@donders.ru.nl> References: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> <5364B12A.80807@donders.ru.nl> Message-ID: <009501cf6714$fbc5e110$f351a330$@vanschouwenburg@ucsf.edu> Hi all, Thank you for all of your quick replies! I have traced the problem down to the ft_plot_topo script, specifically when it calls the 'surf' function. I have been in touch with someone from Mathworks, and I have send him the script and all the variables he needs to run it, and he is looking into the issue. I'll let you know once he gets back to me. Hopefully, with a solution. :) Best, Martine -----Original Message----- From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" Sent: Saturday, May 03, 2014 2:05 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] ft_databrowser crashes Matlab Hi Martine, great to hear that you are using FieldTrip ;) hope you like it. As JM said, it is indeed some low-level problem with Windows 7, Matlab and the databrowser. The only way to escape this is to use another OS... in the past we have not been successful in tracing this down, because it is such a low-level error on only happens on some PCs with Win7, but not on all. There is already a bug on bugzilla for this. Maybe we need to ask Mathworks for support on this ;) @Max: The databrowser is specifically designed to also show components if you set cfg.viewmode = 'components'. The error also has nothing to do with showing components, as it also happens for plotting channel-level data. Best, Jörn On 5/2/2014 8:16 PM, Martine van Schouwenburg wrote: > > Hi Fieldtrip experts, > > I am experiencing a problem with the ft_databrowser routine. Matlab > crashes when I’m trying to run it, forcing me to end the Matlab > session. (‘Matlab has encountered an internal problem and needs to > close.’). It seems more like a Matlab/Windows related issue when > looking at the crash report (see below), but I am posting it here > because it also seems to depend on the data that I use as input. When > I run the routine on the ‘raw’ data (after defining the trials) it is > working fine, but after I ran ICA and try to use the databrowser to > look at the components, it crashes at line 676. > > This is the part where it calls the subfunction redraw_cb. Does anyone > might have a clue what in the component data might cause this problem? > Maybe some of you have experienced this before? I also send a request > for Tech Support to Matlab. > > Best, Martine > > Here is the Matlab crash report if that is of any help: > > ---------------------------------------------------------------------- > -- > > Segmentation violation detected at Thu May 01 22:28:30 2014 > > ---------------------------------------------------------------------- > -- > > Configuration: > > Crash Decoding : Disabled > > Default Encoding: windows-1252 > > MATLAB Root : C:\Program Files\MATLAB\R2012b > > MATLAB Version : 8.0.0.783 (R2012b) > > Operating System: Microsoft Windows 7 > > Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD > > Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java > HotSpot(TM) 64-Bit Server VM mixed mode > > Window System : Version 6.1 (Build 7601: Service Pack 1) > > Fault Count: 1 > > Abnormal termination: > > Segmentation violation > > Register State (from fault): > > RAX = 00000000000001a4 RBX = 000000007a8425c0 > > RCX = 00000000000262de RDX = 00000000000001b2 > > RSP = 0000000004110a50 RBP = 000000000000007e > > RSI = 000000007a75cab0 RDI = 000000013942b996 > > R8 = 00000000000262de R9 = 0000000000000230 > > R10 = 0000000000000000 R11 = 0000000004110b28 > > R12 = 0000000000f206cd R13 = 0000000077ce4060 > > R14 = 000000000002635c R15 = 00000000000006c8 > > RIP = 000000006000d341 EFL = 00010216 > > CS = 0033 FS = 0053 GS = 002b > > Stack Trace (from fault): > > [ 0] 0x000000006000d341 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( > RenderEngineBase::~RenderEngineBase+171553 ) > > [ 1] 0x000000005ff83130 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) > > [ 2] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 3] 0x000000005fede587 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( > renderAnimatedKids+000519 ) > > [ 4] 0x000000005fee3788 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) > > [ 5] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 6] 0x000000005ff04729 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( > FigureSetVisualAutoMode+001561 ) > > [ 7] 0x000000005ff0abbd C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( > UIJ_CreatePeerWindow+001597 ) > > [ 8] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 9] 0x0000000060013548 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( > RenderEngineBase::~RenderEngineBase+196648 ) > > [ 10] 0x000000005ff06b87 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( > FigureSetVisualAutoMode+010871 ) > > [ 11] 0x000000005ff06c0d C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( > FigureSetVisualAutoMode+011005 ) > > [ 12] 0x0000000063425006 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( > wm_ExposeFcn_Pre_Optional+000374 ) > > [ 13] 0x0000000064c8c694 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) > > [ 14] 0x0000000064c8e456 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( > UIJ_IsWindowShowing+000438 ) > > [ 15] 0x0000000064c8f943 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( > UIJ_clearWaitForResize+002067 ) > > [ 16] 0x0000000064c8fa61 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) > > [ 17] 0x0000000064c707ae C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( > UIJ_MarkEventFinished+005838 ) > > [ 18] 0x0000000064c70800 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( > UIJ_MarkEventFinished+005920 ) > > [ 19] 0x0000000064c892ac C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( > uij::JavaDraw2D::paintQuadStrip+001324 ) > > [ 20] 0x0000000064d4e808 C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( > uddSetListenerRecursionWarning+000680 ) > > [ 21] 0x0000000064d4ee6c C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( > UDListenerManagerHost::notifyEvent+000076 ) > > [ 22] 0x0000000064d4697d C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( > UDEventInfo::send+000093 ) > > [ 23] 0x000000005fb9cedb C:\Program > Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( > MErrorException::operator=+047675 ) > > [ 24] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( > UIW_IsUserMessage+000086 ) > > [ 25] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( > UIW_SetGLIMUserMsg+000153 ) > > [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( > GetMenuBarInfo+000638 ) > > [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( > SystemParametersInfoW+000235 ) > > [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( > IsProcessDPIAware+000465 ) > > [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( > KiUserCallbackDispatcher+000031 ) > > [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( > PeekMessageW+000186 ) > > [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( > GetKeyState+000238 ) > > [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( > PeekMessageA+000087 ) > > [ 33] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [ 34] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( > ws_FreeSystemFont+000546 ) > > [ 35] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [ 36] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [ 37] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [ 38] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [ 39] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [ 40] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [ 41] 0x000000005ff0c4fe C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) > > [ 42] 0x0000000074e8d17f C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( > Mfunction_handle::dispatch+001023 ) > > [ 43] 0x0000000074e8cf82 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( > Mfunction_handle::dispatch+000514 ) > > [ 44] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 45] 0x000007feef3a5ca4 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( > inFunctionHandleInterface::DestroyWorkspace+295012 ) > > [ 46] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 47] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 48] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 49] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 50] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 51] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 52] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 53] 0x000007feef38210b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( > inFunctionHandleInterface::DestroyWorkspace+148683 ) > > [ 54] 0x000007feef393edf C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( > inFunctionHandleInterface::DestroyWorkspace+221855 ) > > [ 55] 0x000007feef3b0ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( > inFunctionHandleInterface::DestroyWorkspace+339624 ) > > [ 56] 0x000007feef398d94 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( > inFunctionHandleInterface::DestroyWorkspace+242004 ) > > [ 57] 0x000007feef3a2978 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( > inFunctionHandleInterface::DestroyWorkspace+281912 ) > > [ 58] 0x000007feef3a5a8b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( > inFunctionHandleInterface::DestroyWorkspace+294475 ) > > [ 59] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 60] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 61] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 62] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 63] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 64] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 65] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 66] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 67] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 68] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 69] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 70] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 71] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 72] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 73] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 74] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 75] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 76] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 77] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 78] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 79] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 80] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 81] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 82] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 83] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 84] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 85] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 86] 0x000007feef4451e5 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( > inValidateLoadedObject+001893 ) > > [ 87] 0x000007feef454595 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( > init_cleaner+015541 ) > > [ 88] 0x000007feef457b75 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( > inSetMaxFrameCount+002261 ) > > [ 89] 0x000007feef457b48 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( > inSetMaxFrameCount+002216 ) > > [ 90] 0x000007feef457b07 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( > inSetMaxFrameCount+002151 ) > > [ 91] 0x000007feef340213 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( > inPathNotification::function_clear_notification+004019 ) > > [ 92] 0x000007feef44aed0 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( > inEvalCmdWithLocalReturn+000416 ) > > [ 93] 0x000007feef44ae2c C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( > inEvalCmdWithLocalReturn+000252 ) > > [ 94] 0x000007feef44ad71 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( > inEvalCmdWithLocalReturn+000065 ) > > [ 95] 0x0000000079fbf90d C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( > mnDebugPrompt+000109 ) > > [ 96] 0x0000000079fc0471 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( mnParser+000593 ) > > [ 97] 0x00000000749a64a4 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( > mcrInstance::mnParser_on_interpreter_thread+000036 ) > > [ 98] 0x000000007498681f C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( > mcr::setInterpreterThreadToCurrent+029887 ) > > [ 99] 0x0000000074986881 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( > mcr::setInterpreterThreadToCurrent+029985 ) > > [100] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( > UIW_IsUserMessage+000086 ) > > [101] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( > UIW_SetGLIMUserMsg+000153 ) > > [102] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( > GetMenuBarInfo+000638 ) > > [103] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( > SystemParametersInfoW+000235 ) > > [104] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( > IsProcessDPIAware+000465 ) > > [105] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( > KiUserCallbackDispatcher+000031 ) > > [106] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( > PeekMessageW+000186 ) > > [107] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( > GetKeyState+000238 ) > > [108] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( > PeekMessageA+000087 ) > > [109] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [110] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( > ws_FreeSystemFont+000546 ) > > [111] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [112] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [113] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [114] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [115] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [116] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [117] 0x000000007498837e C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( > mcr::setInterpreterThreadToCurrent+036894 ) > > [118] 0x0000000074988665 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( > mcr::setInterpreterThreadToCurrent+037637 ) > > [119] 0x000000007497b166 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( > DepfunRules::postWarning+003430 ) > > [120] 0x000000013fc78a33 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) > > [121] 0x000000013fc78c97 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) > > [122] 0x000000013fc79163 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) > > [123] 0x00000000773759ed C:\Windows\system32\kernel32.dll+00088557 ( > BaseThreadInitThunk+000013 ) > > [124] 0x00000000775ac541 C:\Windows\SYSTEM32\ntdll.dll+00181569 ( > RtlUserThreadStart+000033 ) > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From e.maris at psych.ru.nl Sun May 4 12:33:35 2014 From: e.maris at psych.ru.nl (Eric Maris) Date: Sun, 4 May 2014 12:33:35 +0200 (CEST) Subject: [FieldTrip] ft_timelockstatistics cluster correction using ECoG data In-Reply-To: References: Message-ID: <036d01cf6784$4b2602c0$e1720840$@maris@psych.ru.nl> Hi Kristen, If you supply ft_timelockstatistics with data containing multiple channels it will always “correct” (this is not the best word to denote what the method does, but let’s use it anyhow) for the number of channels. By requesting not to do clustering in space you just achieve that a clusters are computed in a different way (ie, assuming that the channels measure functionally independent signals). If you do not want correction for multiple channels, then you must analyze the data per channel, as you did for Elec11. If you have a low number of channels, then you could combine the permutation-based p-value with regular Bonferroni correction (dividing the critical alpha-level by the number of channels). Good luck, Eric Maris From: Kristen Berry [mailto:kkb268 at nyu.edu] Sent: vrijdag 2 mei 2014 22:41 To: fieldtrip at science.ru.nl Subject: [FieldTrip] ft_timelockstatistics cluster correction using ECoG data Dear all, I am using an intracranial EEG dataset to compare average high gamma power waveforms between conditions. I want to correct for multiple comparisons across time, but not across number of electrodes. Here is my input code: cfg=[]; cfg.latency = [0.05 .5]; cfg.parameter = 'trial'; cfg.method = 'montecarlo'; cfg.correctm = 'cluster'; cfg.neighbours = []; cfg.numrandomization = 1000; cfg.statistic = 'indepsamplesT'; cfg.channel = ‘all’; cfg.alpha = 0.05; cfg.clusteralpha = 0.05; cfg.tail = 0; stats = ft_timelockstatistics(cfg, data,control); Fieldtrip’s montecarlo reference page ( http://fieldtrip.fcdonders.nl/reference/ft_statistics_montecarlo) says, “If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels.” However, my input code corrects for the number of channels as well. As an example, when cfg.channel = ‘all’ for ft_timelockstatistics, then Elec11 is not significant. However, if the analysis is limited to Elec11 (cfg.channel = 11), then Elec11 has a significant cluster. Is there a mistake in my code that is causing this? Or is there an older version of fieldtrip that doesn’t correct for # of channels, when cfg.neighbours is empty? Thank you for your input! Best regards, Kristen Kristen Berry Research Assistant NYU School of Medicine -------------- next part -------------- An HTML attachment was scrubbed... URL: From lmelloni at gmail.com Mon May 5 01:10:07 2014 From: lmelloni at gmail.com (Lucia Melloni) Date: Sun, 4 May 2014 19:10:07 -0400 Subject: [FieldTrip] deadline extended for the Neurobiology of Cognition GRC/GRS! Message-ID: Dear colleagues, The deadline for application and abstract submission for the Gordon Research Seminar has been extended to the *15th of May*. Please submit your application and abstract soon!. We are very much looking forward to receiving your contributions and to a vibrant seminar. We have also added a mentorship component which promises to provide us with important tips for a successful transition from postdoc to PI. Looking forward to seeing you at the GRS/GRC! Lucia Melloni. Ayelet A. Landau [image: Gordon Research Conferences] Join us at the 2014 *Gordon Conference* and *Seminar* On *Neurobiology of Cognition* Circuits, Dynamics, Action and Perception We are meeting *July 20-25, 2014 -*New GRC site: *Sunday River Resort* Newry, Maine Click *here*to see the *GRC* program. There is also an associated *GRS* *July 19-20 *for students and postdocs Click *here*to see the *GRS* website. *GRS* application & abstract deadline to be considered for oral presentation- *May 15* *Please use attached **flyer **to help spread the word! * The Neurobiology of Cognition is a recently-inaugurated GRC designed to foster convergence of traditional neuroscience investigations with more recent developments in systems, cellular and molecular neurobiology, in engineering and imaging and in computational sciences. Cognition is construed broadly to embrace empirical findings in a range of species including humans, and there is a strong focus on integration of findings and principles across species and levels of analysis. In the opening Keynote Session, two leading neuroscientists with provide an experimental and computational perspective on the recent initiative, termed Brain Research through Advancing Innovative Neurotechnologies (BRAIN). This initiative, spearheaded by the President and NIH, is aimed at developing innovative methodologies to study how complex systems of neurons interact in time and in space during complex behaviors. Along with recent findings in a few traditional "core" areas, formal sessions will then explore several new themes, including: 1) the neuroanatomy and 2) coordination of cognitive circuits in the brain, 3) motor cognition and brain-computer interfaces, 4) music and language, and 5) learning and plasticity. The program juxtaposes human psychophysical, neuroimaging and electrophysiological studies with parallel investigations in rodents and non-human primates, and with computational approaches that explicate empirical findings and construct robust, detailed models to represent the developing picture and guide future experimentation. The program also underscores novel experimental and theoretical approaches that promise to define fundamental principles that guide and integrate the understanding of cognition at a fundamental level, and to extend these to improved treatment of brain dysfunction. The format of the meeting promotes intensive interactions among investigators and trainees from different perspectives and analytic levels, and in particular, between experimentalists and theorists. There is a linked Gordon Research Seminar for trainees, most of whom also attend the GRC. All that is missing now is your *application* to attend. Click *here*for the *GRC*. Click* here*for the *GRS*. (You must apply to both to attend both.) Best regards, GRC Chair: *Charles E. Schroeder* GRC V. Chair:*Tatiana Pasternak* GRS Chair: *Lucia Melloni* GRS Assoc. Chair: *Ayelet N. Landau* *Apply* now and see why our attendees consistently rate GRCs "the best conference I've attended this year"! [image: Like us on Facebook] [image: Follow us on Twitter] [image: View our profile on LinkedIn] *Forward this email * This email was sent to htobin at grc.org by announcements at grc.org | Instant removal with SafeUnsubscribe™ | Privacy Policy . Gordon Research Conferences | 512 Liberty Lane | West Kingston | RI | 02892 Follow GRC: Facebook | Twitter Call Send SMS Add to Skype You'll need Skype CreditFree via Skype -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue May 6 08:26:21 2014 From: jm.horschig at donders.ru.nl (=?windows-1252?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 06 May 2014 08:26:21 +0200 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: <009501cf6714$fbc5e110$f351a330$@vanschouwenburg@ucsf.edu> References: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> <5364B12A.80807@donders.ru.nl> <009501cf6714$fbc5e110$f351a330$@vanschouwenburg@ucsf.edu> Message-ID: <5368808D.4000803@donders.ru.nl> Hi Martine, that's great, thanks. Looking forward to hearing what they say. @Max: then it seems like Martine's problem really is specific to viewing components, sorry :) Best, Jörn On 5/3/2014 11:16 PM, Martine van Schouwenburg wrote: > Hi all, > > Thank you for all of your quick replies! I have traced the problem down to > the ft_plot_topo script, specifically when it calls the 'surf' function. I > have been in touch with someone from Mathworks, and I have send him the > script and all the variables he needs to run it, and he is looking into the > issue. I'll let you know once he gets back to me. Hopefully, with a > solution. :) > > Best, Martine > > > > > -----Original Message----- > From: fieldtrip-bounces at science.ru.nl > [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" > Sent: Saturday, May 03, 2014 2:05 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] ft_databrowser crashes Matlab > > Hi Martine, > > great to hear that you are using FieldTrip ;) hope you like it. > As JM said, it is indeed some low-level problem with Windows 7, Matlab and > the databrowser. The only way to escape this is to use another OS... > in the past we have not been successful in tracing this down, because it is > such a low-level error on only happens on some PCs with Win7, but not on > all. There is already a bug on bugzilla for this. Maybe we need to ask > Mathworks for support on this ;) > > @Max: The databrowser is specifically designed to also show components if > you set cfg.viewmode = 'components'. The error also has nothing to do with > showing components, as it also happens for plotting channel-level data. > > Best, > Jörn > > On 5/2/2014 8:16 PM, Martine van Schouwenburg wrote: >> Hi Fieldtrip experts, >> >> I am experiencing a problem with the ft_databrowser routine. Matlab >> crashes when I’m trying to run it, forcing me to end the Matlab >> session. (‘Matlab has encountered an internal problem and needs to >> close.’). It seems more like a Matlab/Windows related issue when >> looking at the crash report (see below), but I am posting it here >> because it also seems to depend on the data that I use as input. When >> I run the routine on the ‘raw’ data (after defining the trials) it is >> working fine, but after I ran ICA and try to use the databrowser to >> look at the components, it crashes at line 676. >> >> This is the part where it calls the subfunction redraw_cb. Does anyone >> might have a clue what in the component data might cause this problem? >> Maybe some of you have experienced this before? I also send a request >> for Tech Support to Matlab. >> >> Best, Martine >> >> Here is the Matlab crash report if that is of any help: >> >> ---------------------------------------------------------------------- >> -- >> >> Segmentation violation detected at Thu May 01 22:28:30 2014 >> >> ---------------------------------------------------------------------- >> -- >> >> Configuration: >> >> Crash Decoding : Disabled >> >> Default Encoding: windows-1252 >> >> MATLAB Root : C:\Program Files\MATLAB\R2012b >> >> MATLAB Version : 8.0.0.783 (R2012b) >> >> Operating System: Microsoft Windows 7 >> >> Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD >> >> Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java >> HotSpot(TM) 64-Bit Server VM mixed mode >> >> Window System : Version 6.1 (Build 7601: Service Pack 1) >> >> Fault Count: 1 >> >> Abnormal termination: >> >> Segmentation violation >> >> Register State (from fault): >> >> RAX = 00000000000001a4 RBX = 000000007a8425c0 >> >> RCX = 00000000000262de RDX = 00000000000001b2 >> >> RSP = 0000000004110a50 RBP = 000000000000007e >> >> RSI = 000000007a75cab0 RDI = 000000013942b996 >> >> R8 = 00000000000262de R9 = 0000000000000230 >> >> R10 = 0000000000000000 R11 = 0000000004110b28 >> >> R12 = 0000000000f206cd R13 = 0000000077ce4060 >> >> R14 = 000000000002635c R15 = 00000000000006c8 >> >> RIP = 000000006000d341 EFL = 00010216 >> >> CS = 0033 FS = 0053 GS = 002b >> >> Stack Trace (from fault): >> >> [ 0] 0x000000006000d341 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( >> RenderEngineBase::~RenderEngineBase+171553 ) >> >> [ 1] 0x000000005ff83130 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) >> >> [ 2] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 3] 0x000000005fede587 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( >> renderAnimatedKids+000519 ) >> >> [ 4] 0x000000005fee3788 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) >> >> [ 5] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 6] 0x000000005ff04729 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( >> FigureSetVisualAutoMode+001561 ) >> >> [ 7] 0x000000005ff0abbd C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( >> UIJ_CreatePeerWindow+001597 ) >> >> [ 8] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 9] 0x0000000060013548 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( >> RenderEngineBase::~RenderEngineBase+196648 ) >> >> [ 10] 0x000000005ff06b87 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( >> FigureSetVisualAutoMode+010871 ) >> >> [ 11] 0x000000005ff06c0d C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( >> FigureSetVisualAutoMode+011005 ) >> >> [ 12] 0x0000000063425006 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( >> wm_ExposeFcn_Pre_Optional+000374 ) >> >> [ 13] 0x0000000064c8c694 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) >> >> [ 14] 0x0000000064c8e456 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( >> UIJ_IsWindowShowing+000438 ) >> >> [ 15] 0x0000000064c8f943 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( >> UIJ_clearWaitForResize+002067 ) >> >> [ 16] 0x0000000064c8fa61 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) >> >> [ 17] 0x0000000064c707ae C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( >> UIJ_MarkEventFinished+005838 ) >> >> [ 18] 0x0000000064c70800 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( >> UIJ_MarkEventFinished+005920 ) >> >> [ 19] 0x0000000064c892ac C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( >> uij::JavaDraw2D::paintQuadStrip+001324 ) >> >> [ 20] 0x0000000064d4e808 C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( >> uddSetListenerRecursionWarning+000680 ) >> >> [ 21] 0x0000000064d4ee6c C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( >> UDListenerManagerHost::notifyEvent+000076 ) >> >> [ 22] 0x0000000064d4697d C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( >> UDEventInfo::send+000093 ) >> >> [ 23] 0x000000005fb9cedb C:\Program >> Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( >> MErrorException::operator=+047675 ) >> >> [ 24] 0x00000000055ce0b6 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( >> UIW_IsUserMessage+000086 ) >> >> [ 25] 0x00000000055ce7b9 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( >> UIW_SetGLIMUserMsg+000153 ) >> >> [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( >> GetMenuBarInfo+000638 ) >> >> [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( >> SystemParametersInfoW+000235 ) >> >> [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( >> IsProcessDPIAware+000465 ) >> >> [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( >> KiUserCallbackDispatcher+000031 ) >> >> [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( >> PeekMessageW+000186 ) >> >> [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( >> GetKeyState+000238 ) >> >> [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( >> PeekMessageA+000087 ) >> >> [ 33] 0x00000000055a8f4b C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( >> UIW_SetCurrentDialog+000731 ) >> >> [ 34] 0x00000000055cfbe2 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( >> ws_FreeSystemFont+000546 ) >> >> [ 35] 0x000000000485e6a3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( >> sysq::removeCommitDatabaseUpdatesHook+002131 ) >> >> [ 36] 0x000000000485fe18 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( >> sysq::removeCommitDatabaseUpdatesHook+008136 ) >> >> [ 37] 0x0000000004861a20 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( >> sysq::addProcessPendingEventsUnitTestHook+000240 ) >> >> [ 38] 0x0000000004861ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( >> sysq::addProcessPendingEventsUnitTestHook+000440 ) >> >> [ 39] 0x0000000004861ca3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( >> sysq::addProcessPendingEventsUnitTestHook+000883 ) >> >> [ 40] 0x0000000004861d76 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( >> sysq::addProcessPendingEventsUnitTestHook+001094 ) >> >> [ 41] 0x000000005ff0c4fe C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) >> >> [ 42] 0x0000000074e8d17f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( >> Mfunction_handle::dispatch+001023 ) >> >> [ 43] 0x0000000074e8cf82 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( >> Mfunction_handle::dispatch+000514 ) >> >> [ 44] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 45] 0x000007feef3a5ca4 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( >> inFunctionHandleInterface::DestroyWorkspace+295012 ) >> >> [ 46] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 47] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 48] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 49] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 50] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 51] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 52] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 53] 0x000007feef38210b C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( >> inFunctionHandleInterface::DestroyWorkspace+148683 ) >> >> [ 54] 0x000007feef393edf C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( >> inFunctionHandleInterface::DestroyWorkspace+221855 ) >> >> [ 55] 0x000007feef3b0ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( >> inFunctionHandleInterface::DestroyWorkspace+339624 ) >> >> [ 56] 0x000007feef398d94 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( >> inFunctionHandleInterface::DestroyWorkspace+242004 ) >> >> [ 57] 0x000007feef3a2978 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( >> inFunctionHandleInterface::DestroyWorkspace+281912 ) >> >> [ 58] 0x000007feef3a5a8b C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( >> inFunctionHandleInterface::DestroyWorkspace+294475 ) >> >> [ 59] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 60] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 61] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 62] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 63] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 64] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 65] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 66] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 67] 0x000007feef43318f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( >> inEachVisibleName+014415 ) >> >> [ 68] 0x000007feef3a74ca C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( >> inFunctionHandleInterface::DestroyWorkspace+301194 ) >> >> [ 69] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 70] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 71] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 72] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 73] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 74] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 75] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 76] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 77] 0x000007feef43318f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( >> inEachVisibleName+014415 ) >> >> [ 78] 0x000007feef3a74ca C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( >> inFunctionHandleInterface::DestroyWorkspace+301194 ) >> >> [ 79] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 80] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 81] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 82] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 83] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 84] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 85] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 86] 0x000007feef4451e5 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( >> inValidateLoadedObject+001893 ) >> >> [ 87] 0x000007feef454595 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( >> init_cleaner+015541 ) >> >> [ 88] 0x000007feef457b75 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( >> inSetMaxFrameCount+002261 ) >> >> [ 89] 0x000007feef457b48 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( >> inSetMaxFrameCount+002216 ) >> >> [ 90] 0x000007feef457b07 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( >> inSetMaxFrameCount+002151 ) >> >> [ 91] 0x000007feef340213 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( >> inPathNotification::function_clear_notification+004019 ) >> >> [ 92] 0x000007feef44aed0 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( >> inEvalCmdWithLocalReturn+000416 ) >> >> [ 93] 0x000007feef44ae2c C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( >> inEvalCmdWithLocalReturn+000252 ) >> >> [ 94] 0x000007feef44ad71 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( >> inEvalCmdWithLocalReturn+000065 ) >> >> [ 95] 0x0000000079fbf90d C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( >> mnDebugPrompt+000109 ) >> >> [ 96] 0x0000000079fc0471 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( mnParser+000593 ) >> >> [ 97] 0x00000000749a64a4 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( >> mcrInstance::mnParser_on_interpreter_thread+000036 ) >> >> [ 98] 0x000000007498681f C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( >> mcr::setInterpreterThreadToCurrent+029887 ) >> >> [ 99] 0x0000000074986881 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( >> mcr::setInterpreterThreadToCurrent+029985 ) >> >> [100] 0x00000000055ce0b6 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( >> UIW_IsUserMessage+000086 ) >> >> [101] 0x00000000055ce7b9 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( >> UIW_SetGLIMUserMsg+000153 ) >> >> [102] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( >> GetMenuBarInfo+000638 ) >> >> [103] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( >> SystemParametersInfoW+000235 ) >> >> [104] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( >> IsProcessDPIAware+000465 ) >> >> [105] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( >> KiUserCallbackDispatcher+000031 ) >> >> [106] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( >> PeekMessageW+000186 ) >> >> [107] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( >> GetKeyState+000238 ) >> >> [108] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( >> PeekMessageA+000087 ) >> >> [109] 0x00000000055a8f4b C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( >> UIW_SetCurrentDialog+000731 ) >> >> [110] 0x00000000055cfbe2 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( >> ws_FreeSystemFont+000546 ) >> >> [111] 0x000000000485e6a3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( >> sysq::removeCommitDatabaseUpdatesHook+002131 ) >> >> [112] 0x000000000485fe18 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( >> sysq::removeCommitDatabaseUpdatesHook+008136 ) >> >> [113] 0x0000000004861a20 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( >> sysq::addProcessPendingEventsUnitTestHook+000240 ) >> >> [114] 0x0000000004861ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( >> sysq::addProcessPendingEventsUnitTestHook+000440 ) >> >> [115] 0x0000000004861ca3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( >> sysq::addProcessPendingEventsUnitTestHook+000883 ) >> >> [116] 0x0000000004861d76 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( >> sysq::addProcessPendingEventsUnitTestHook+001094 ) >> >> [117] 0x000000007498837e C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( >> mcr::setInterpreterThreadToCurrent+036894 ) >> >> [118] 0x0000000074988665 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( >> mcr::setInterpreterThreadToCurrent+037637 ) >> >> [119] 0x000000007497b166 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( >> DepfunRules::postWarning+003430 ) >> >> [120] 0x000000013fc78a33 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) >> >> [121] 0x000000013fc78c97 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) >> >> [122] 0x000000013fc79163 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) >> >> [123] 0x00000000773759ed C:\Windows\system32\kernel32.dll+00088557 ( >> BaseThreadInitThunk+000013 ) >> >> [124] 0x00000000775ac541 C:\Windows\SYSTEM32\ntdll.dll+00181569 ( >> RtlUserThreadStart+000033 ) >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From Gregor.Volberg at psychologie.uni-regensburg.de Tue May 6 11:03:52 2014 From: Gregor.Volberg at psychologie.uni-regensburg.de (Gregor Volberg) Date: Tue, 06 May 2014 11:03:52 +0200 Subject: [FieldTrip] PhD Job offer in Visual Neuroscience, University of Regensburg (Germany) Message-ID: <5368C198020000570001653B@gwsmtp1.uni-regensburg.de> Dear colleagues, please find below a job offer for a PhD position at the University of Regensburg, Germany. You might send it to interested students if you like. Best regards, Gregor **** The University of Regensburg (Germany), Institute for Psychology, Workgroup Experimental Psychology offers a 65 % position for a three-year PhD project starting in October 2014 (Chair: Prof. Dr. Mark Greenlee; Principal Investigator: PD Dr. G. Volberg). The salary will be according to German TV-L E 13 (65 % position) payment plan. The DFG-funded research project is on the neural basis of grapheme-color synesthesia, a perceptual phenomenon where achromatic letters or numbers produce a simultaneous sensation of color. Methods include electroencephalography (EEG) and functional magnetic resonance imaging (fMRI). Eligible job applicants must hold a masters degree (or comparable) in psychology or neighboring disciplines. They should have an academic background in visual neuroscience, especially in the acquisition and analysis of EEG and/or fMRI data. Programming experience in MatLab is advantageous. Job holders will need to recruit and test synesthetic participants from the local student population. Good skills in German are therefore necessary. We can offer an active research environment, an interesting topic for your PhD thesis, a friendly team and a UNESCO-heritage city located on the Danube River. We are looking forward to receiving your application! The University of Regensburg supports the reconcilability between family and career (see http://www.uni-regensburg.de/chancengleichheit). Physically challenged applicants will be preferred in cases of equivalent qualification. If applicable, please convey extend and type of disability in your résumé. Please note that the university does not refund costs ensuing from job interviews. Please send your application by June 1st, 2014 to PD Dr. Volberg, gregor.volberg at ur.de. The application should hold pertinent information about your academic career. Please send in the application in an electronic form (pdf) and use the subject matter „Application Synesthesia“ in the e-mail. The contact person is PD Dr. Gregor Volberg (office hours, Wednesday 10-12, Tel. +49 941 943 3862; http://www.uni-regensburg.de/psychologie-paedagogik-sport/psychologie-greenlee/team/volberg/index.html). -- PD Dr. rer. nat. Gregor Volberg gregor.volberg at ur.deUniversity of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From martine.vanschouwenburg at ucsf.edu Tue May 6 18:59:06 2014 From: martine.vanschouwenburg at ucsf.edu (Martine van Schouwenburg) Date: Tue, 6 May 2014 09:59:06 -0700 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: <5368808D.4000803@donders.ru.nl> References: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> <5364B12A.80807@donders.ru.nl> <009501cf6714$fbc5e110$f351a330$@vanschouwenburg@ucsf.edu> <5368808D.4000803@donders.ru.nl> Message-ID: <00ff01cf694c$7d847f20$788d7d60$@vanschouwenburg@ucsf.edu> Hi all, Problem is solved! I have had great help from the Mathworks support team and it turns out it was a rendering issue (see below part of the email that I got from Mathworks). Setting the renderer to 'Paintings' did the trick for me, so I have now added this line [set(gcf,'renderer','painters');] to the script, just before it calls the 'surf' function (line 242 of ft_plot_topo). This issue seems to depend strongly on OS, graphics card, software version etc, but if anyone runs into a similar problem you could try to see if changing the renderer works for you too. Best, Martine EMAIL SUPPORT TEAM MATHWORKS: "I have a feeling that the crash might be because of the renderer being chosen by MATLAB to plot the surface plot. MATLAB has three renderers- OpenGL, Painters and Z-Buffer. Each of these renderers has its own merits and limitations. MATLAB chooses the correct renderer based on the type of figure that you are plotting. Here is a documentation page that talks more about the three renderers in MATLAB: http://www.mathworks.com/help/matlab/creating_plots/changing-a-figures-setti ngs.html#f3-102410 Of the three renderers OpenGL has the ability to use the graphics hardware on your system to help render the graphics. This can occasionally cause incompatibilities due to the many different graphics cards out there and also the many different driver versions that exist for each of these cards. So, you can try and switch to the software implementation of OpenGL by executing the following command in the command window: >>opengl software This setting is retained for the current session of MATLAB. If you want MATLAB to remember this setting across settings, then I would suggest that you add this command to your "startup.m". Please use the above command and then run your code to see if the crash still occurs. IF THE ABOVE PROCEDURE DOES NOT WORK: We can try and change the renderer to one of the other two and see if this helps. You can change the renderer by using the "set" command: >> set(gcf,'renderer','painters'); OR >>set(gcf,'renderer','zbuffer'); OR >>set(gcf,'renderer','opengl'); Here "gcf" refers to the currently active figure window. I would suggest that you try changing the renderer just before the "surf" command is executed and see if the crash stops happening when using a particular renderer." -----Original Message----- From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" Sent: Monday, May 05, 2014 11:26 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] ft_databrowser crashes Matlab Hi Martine, that's great, thanks. Looking forward to hearing what they say. @Max: then it seems like Martine's problem really is specific to viewing components, sorry :) Best, Jörn On 5/3/2014 11:16 PM, Martine van Schouwenburg wrote: > Hi all, > > Thank you for all of your quick replies! I have traced the problem > down to the ft_plot_topo script, specifically when it calls the 'surf' > function. I have been in touch with someone from Mathworks, and I have > send him the script and all the variables he needs to run it, and he > is looking into the issue. I'll let you know once he gets back to me. > Hopefully, with a solution. :) > > Best, Martine > > > > > -----Original Message----- > From: fieldtrip-bounces at science.ru.nl > [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" > Sent: Saturday, May 03, 2014 2:05 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] ft_databrowser crashes Matlab > > Hi Martine, > > great to hear that you are using FieldTrip ;) hope you like it. > As JM said, it is indeed some low-level problem with Windows 7, Matlab > and the databrowser. The only way to escape this is to use another OS... > in the past we have not been successful in tracing this down, because > it is such a low-level error on only happens on some PCs with Win7, > but not on all. There is already a bug on bugzilla for this. Maybe we > need to ask Mathworks for support on this ;) > > @Max: The databrowser is specifically designed to also show components > if you set cfg.viewmode = 'components'. The error also has nothing to > do with showing components, as it also happens for plotting channel-level data. > > Best, > Jörn > > On 5/2/2014 8:16 PM, Martine van Schouwenburg wrote: >> Hi Fieldtrip experts, >> >> I am experiencing a problem with the ft_databrowser routine. Matlab >> crashes when I’m trying to run it, forcing me to end the Matlab >> session. (‘Matlab has encountered an internal problem and needs to >> close.’). It seems more like a Matlab/Windows related issue when >> looking at the crash report (see below), but I am posting it here >> because it also seems to depend on the data that I use as input. When >> I run the routine on the ‘raw’ data (after defining the trials) it is >> working fine, but after I ran ICA and try to use the databrowser to >> look at the components, it crashes at line 676. >> >> This is the part where it calls the subfunction redraw_cb. Does >> anyone might have a clue what in the component data might cause this problem? >> Maybe some of you have experienced this before? I also send a request >> for Tech Support to Matlab. >> >> Best, Martine >> >> Here is the Matlab crash report if that is of any help: >> >> --------------------------------------------------------------------- >> - >> -- >> >> Segmentation violation detected at Thu May 01 22:28:30 2014 >> >> --------------------------------------------------------------------- >> - >> -- >> >> Configuration: >> >> Crash Decoding : Disabled >> >> Default Encoding: windows-1252 >> >> MATLAB Root : C:\Program Files\MATLAB\R2012b >> >> MATLAB Version : 8.0.0.783 (R2012b) >> >> Operating System: Microsoft Windows 7 >> >> Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD >> >> Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java >> HotSpot(TM) 64-Bit Server VM mixed mode >> >> Window System : Version 6.1 (Build 7601: Service Pack 1) >> >> Fault Count: 1 >> >> Abnormal termination: >> >> Segmentation violation >> >> Register State (from fault): >> >> RAX = 00000000000001a4 RBX = 000000007a8425c0 >> >> RCX = 00000000000262de RDX = 00000000000001b2 >> >> RSP = 0000000004110a50 RBP = 000000000000007e >> >> RSI = 000000007a75cab0 RDI = 000000013942b996 >> >> R8 = 00000000000262de R9 = 0000000000000230 >> >> R10 = 0000000000000000 R11 = 0000000004110b28 >> >> R12 = 0000000000f206cd R13 = 0000000077ce4060 >> >> R14 = 000000000002635c R15 = 00000000000006c8 >> >> RIP = 000000006000d341 EFL = 00010216 >> >> CS = 0033 FS = 0053 GS = 002b >> >> Stack Trace (from fault): >> >> [ 0] 0x000000006000d341 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( >> RenderEngineBase::~RenderEngineBase+171553 ) >> >> [ 1] 0x000000005ff83130 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 >> ) >> >> [ 2] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 3] 0x000000005fede587 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( >> renderAnimatedKids+000519 ) >> >> [ 4] 0x000000005fee3788 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) >> >> [ 5] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 6] 0x000000005ff04729 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( >> FigureSetVisualAutoMode+001561 ) >> >> [ 7] 0x000000005ff0abbd C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( >> UIJ_CreatePeerWindow+001597 ) >> >> [ 8] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 9] 0x0000000060013548 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( >> RenderEngineBase::~RenderEngineBase+196648 ) >> >> [ 10] 0x000000005ff06b87 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( >> FigureSetVisualAutoMode+010871 ) >> >> [ 11] 0x000000005ff06c0d C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( >> FigureSetVisualAutoMode+011005 ) >> >> [ 12] 0x0000000063425006 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( >> wm_ExposeFcn_Pre_Optional+000374 ) >> >> [ 13] 0x0000000064c8c694 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( >> GetframeJava+001332 ) >> >> [ 14] 0x0000000064c8e456 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( >> UIJ_IsWindowShowing+000438 ) >> >> [ 15] 0x0000000064c8f943 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( >> UIJ_clearWaitForResize+002067 ) >> >> [ 16] 0x0000000064c8fa61 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( >> UIJ_ExposeFcn+000145 ) >> >> [ 17] 0x0000000064c707ae C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( >> UIJ_MarkEventFinished+005838 ) >> >> [ 18] 0x0000000064c70800 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( >> UIJ_MarkEventFinished+005920 ) >> >> [ 19] 0x0000000064c892ac C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( >> uij::JavaDraw2D::paintQuadStrip+001324 ) >> >> [ 20] 0x0000000064d4e808 C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( >> uddSetListenerRecursionWarning+000680 ) >> >> [ 21] 0x0000000064d4ee6c C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( >> UDListenerManagerHost::notifyEvent+000076 ) >> >> [ 22] 0x0000000064d4697d C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( >> UDEventInfo::send+000093 ) >> >> [ 23] 0x000000005fb9cedb C:\Program >> Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( >> MErrorException::operator=+047675 ) >> >> [ 24] 0x00000000055ce0b6 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( >> UIW_IsUserMessage+000086 ) >> >> [ 25] 0x00000000055ce7b9 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( >> UIW_SetGLIMUserMsg+000153 ) >> >> [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( >> GetMenuBarInfo+000638 ) >> >> [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( >> SystemParametersInfoW+000235 ) >> >> [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( >> IsProcessDPIAware+000465 ) >> >> [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( >> KiUserCallbackDispatcher+000031 ) >> >> [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( >> PeekMessageW+000186 ) >> >> [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( >> GetKeyState+000238 ) >> >> [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( >> PeekMessageA+000087 ) >> >> [ 33] 0x00000000055a8f4b C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( >> UIW_SetCurrentDialog+000731 ) >> >> [ 34] 0x00000000055cfbe2 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( >> ws_FreeSystemFont+000546 ) >> >> [ 35] 0x000000000485e6a3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( >> sysq::removeCommitDatabaseUpdatesHook+002131 ) >> >> [ 36] 0x000000000485fe18 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( >> sysq::removeCommitDatabaseUpdatesHook+008136 ) >> >> [ 37] 0x0000000004861a20 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( >> sysq::addProcessPendingEventsUnitTestHook+000240 ) >> >> [ 38] 0x0000000004861ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( >> sysq::addProcessPendingEventsUnitTestHook+000440 ) >> >> [ 39] 0x0000000004861ca3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( >> sysq::addProcessPendingEventsUnitTestHook+000883 ) >> >> [ 40] 0x0000000004861d76 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( >> sysq::addProcessPendingEventsUnitTestHook+001094 ) >> >> [ 41] 0x000000005ff0c4fe C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) >> >> [ 42] 0x0000000074e8d17f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( >> Mfunction_handle::dispatch+001023 ) >> >> [ 43] 0x0000000074e8cf82 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( >> Mfunction_handle::dispatch+000514 ) >> >> [ 44] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 45] 0x000007feef3a5ca4 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( >> inFunctionHandleInterface::DestroyWorkspace+295012 ) >> >> [ 46] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 47] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 48] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 49] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 50] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 51] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 52] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 53] 0x000007feef38210b C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( >> inFunctionHandleInterface::DestroyWorkspace+148683 ) >> >> [ 54] 0x000007feef393edf C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( >> inFunctionHandleInterface::DestroyWorkspace+221855 ) >> >> [ 55] 0x000007feef3b0ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( >> inFunctionHandleInterface::DestroyWorkspace+339624 ) >> >> [ 56] 0x000007feef398d94 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( >> inFunctionHandleInterface::DestroyWorkspace+242004 ) >> >> [ 57] 0x000007feef3a2978 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( >> inFunctionHandleInterface::DestroyWorkspace+281912 ) >> >> [ 58] 0x000007feef3a5a8b C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( >> inFunctionHandleInterface::DestroyWorkspace+294475 ) >> >> [ 59] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 60] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 61] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 62] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 63] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 64] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 65] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 66] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 67] 0x000007feef43318f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( >> inEachVisibleName+014415 ) >> >> [ 68] 0x000007feef3a74ca C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( >> inFunctionHandleInterface::DestroyWorkspace+301194 ) >> >> [ 69] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 70] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 71] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 72] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 73] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 74] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 75] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 76] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 77] 0x000007feef43318f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( >> inEachVisibleName+014415 ) >> >> [ 78] 0x000007feef3a74ca C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( >> inFunctionHandleInterface::DestroyWorkspace+301194 ) >> >> [ 79] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 80] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 81] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 82] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 83] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 84] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 85] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 86] 0x000007feef4451e5 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( >> inValidateLoadedObject+001893 ) >> >> [ 87] 0x000007feef454595 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( >> init_cleaner+015541 ) >> >> [ 88] 0x000007feef457b75 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( >> inSetMaxFrameCount+002261 ) >> >> [ 89] 0x000007feef457b48 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( >> inSetMaxFrameCount+002216 ) >> >> [ 90] 0x000007feef457b07 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( >> inSetMaxFrameCount+002151 ) >> >> [ 91] 0x000007feef340213 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( >> inPathNotification::function_clear_notification+004019 ) >> >> [ 92] 0x000007feef44aed0 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( >> inEvalCmdWithLocalReturn+000416 ) >> >> [ 93] 0x000007feef44ae2c C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( >> inEvalCmdWithLocalReturn+000252 ) >> >> [ 94] 0x000007feef44ad71 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( >> inEvalCmdWithLocalReturn+000065 ) >> >> [ 95] 0x0000000079fbf90d C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( >> mnDebugPrompt+000109 ) >> >> [ 96] 0x0000000079fc0471 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( >> mnParser+000593 ) >> >> [ 97] 0x00000000749a64a4 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( >> mcrInstance::mnParser_on_interpreter_thread+000036 ) >> >> [ 98] 0x000000007498681f C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( >> mcr::setInterpreterThreadToCurrent+029887 ) >> >> [ 99] 0x0000000074986881 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( >> mcr::setInterpreterThreadToCurrent+029985 ) >> >> [100] 0x00000000055ce0b6 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( >> UIW_IsUserMessage+000086 ) >> >> [101] 0x00000000055ce7b9 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( >> UIW_SetGLIMUserMsg+000153 ) >> >> [102] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( >> GetMenuBarInfo+000638 ) >> >> [103] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( >> SystemParametersInfoW+000235 ) >> >> [104] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( >> IsProcessDPIAware+000465 ) >> >> [105] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( >> KiUserCallbackDispatcher+000031 ) >> >> [106] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( >> PeekMessageW+000186 ) >> >> [107] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( >> GetKeyState+000238 ) >> >> [108] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( >> PeekMessageA+000087 ) >> >> [109] 0x00000000055a8f4b C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( >> UIW_SetCurrentDialog+000731 ) >> >> [110] 0x00000000055cfbe2 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( >> ws_FreeSystemFont+000546 ) >> >> [111] 0x000000000485e6a3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( >> sysq::removeCommitDatabaseUpdatesHook+002131 ) >> >> [112] 0x000000000485fe18 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( >> sysq::removeCommitDatabaseUpdatesHook+008136 ) >> >> [113] 0x0000000004861a20 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( >> sysq::addProcessPendingEventsUnitTestHook+000240 ) >> >> [114] 0x0000000004861ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( >> sysq::addProcessPendingEventsUnitTestHook+000440 ) >> >> [115] 0x0000000004861ca3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( >> sysq::addProcessPendingEventsUnitTestHook+000883 ) >> >> [116] 0x0000000004861d76 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( >> sysq::addProcessPendingEventsUnitTestHook+001094 ) >> >> [117] 0x000000007498837e C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( >> mcr::setInterpreterThreadToCurrent+036894 ) >> >> [118] 0x0000000074988665 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( >> mcr::setInterpreterThreadToCurrent+037637 ) >> >> [119] 0x000000007497b166 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( >> DepfunRules::postWarning+003430 ) >> >> [120] 0x000000013fc78a33 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) >> >> [121] 0x000000013fc78c97 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) >> >> [122] 0x000000013fc79163 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) >> >> [123] 0x00000000773759ed C:\Windows\system32\kernel32.dll+00088557 ( >> BaseThreadInitThunk+000013 ) >> >> [124] 0x00000000775ac541 C:\Windows\SYSTEM32\ntdll.dll+00181569 ( >> RtlUserThreadStart+000033 ) >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From ahmeedzeki at yahoo.com Tue May 6 22:41:13 2014 From: ahmeedzeki at yahoo.com (ahmeedzeki at yahoo.com) Date: Tue, 6 May 2014 20:41:13 +0000 Subject: [FieldTrip] =?utf-8?q?Leadfield_Matrix?= Message-ID: <687035.72317.bm@smtp110.mail.bf1.yahoo.com> Dear leadfield Developers and Users: My name is Ahmed Al Hilli, I am a PhD student at Rutgers University. I am working on EEG source localization. I have difficulties in generating the leadfield matrix. I want to generate the leadfield matrix using just a cortex of the brain and I want to use a realistic head model. I’ve generated the cortex sheet using ft_volume_segment function, and also I have the scalp binary mask. My question is what to do next to apply BEM method? Thank you very much Sent from Windows Mail -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.rombetto at cib.na.cnr.it Wed May 7 13:00:50 2014 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Wed, 7 May 2014 13:00:50 +0200 Subject: [FieldTrip] problem occurs when using ft_timelockanalysis Message-ID: <20140507130050.cctyuq8m1w80o4g4@arco.cib.na.cnr.it> Dear fieldtrippers I'm encountering a problem when running ft_timelockanalysis in Matlab. I receive the following message: "A Undefined function 'mxSerialize_cpp' for input arguments of type 'struct' Error in mxSerialize (line 35) argout = mxSerialize_cpp(argin); Error in ft_preamble_provenance (line 67) cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); Error in ft_preamble (line 54) evalin('caller', ['ft_preamble_' cmd]); Error in ft_timelockanalysis (line 95) ft_preamble provenance data" I am using \fieldtrip-20140506 and matlab R2014a - 64 bit Any suggestion is highly appreciated. ------------------------- Dott.ssa Sara Rombetto Istituto di Cibernetica "E. Caianiello" Via Campi Flegrei, 34 80078 Pozzuoli (NA) Italy mob +39 3401689815 tel +39 0818675361 fax +39 0818675128 Lab MEG 0817483511 -------------------------- "I disapprove of what you say, but I will defend to the death your right to say it." [Evelyn Beatrice Hall, The Friends Of Voltaire] ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From yingli.ucla at gmail.com Wed May 7 23:14:22 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Wed, 7 May 2014 14:14:22 -0700 Subject: [FieldTrip] Failed to download the sample data - the links no longer exist Message-ID: Dear all, I am learning to use fieldtrip to do source localization. When I tried to download some sample data, such as 1) The MEG data: ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip 2) The MRI data: ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip . It shows that the links don't exist any more. Are there any other ways for me to download these sample data? Thanks a lot! Ying -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Thu May 8 11:00:29 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 8 May 2014 09:00:29 +0000 Subject: [FieldTrip] (no subject) Message-ID: Dear all, has anyone come across (or used) cluster-based permutation statistics for (human) LFP data obtained from DBS-electrodes? I am looking for a reference and, after a quick search, didn't find any, thanks! Best wishes Max From jm.horschig at donders.ru.nl Thu May 8 13:02:59 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 08 May 2014 13:02:59 +0200 Subject: [FieldTrip] (no subject) In-Reply-To: References: Message-ID: <536B6463.3080504@donders.ru.nl> Hi Max-Philipp, what is it that you want to do specifically? Basically, there is nothing different from doing scalp EEG statistics. Regarding a reference, if you wait for a few more months, then you can cite my paper... once I've written it down ;) Best, Jörn On 5/8/2014 11:00 AM, Stenner, Max-Philipp wrote: > Dear all, > has anyone come across (or used) cluster-based permutation statistics for (human) LFP data obtained from DBS-electrodes? I am looking for a reference and, after a quick search, didn't find any, > thanks! > Best wishes > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From max-philipp.stenner at med.ovgu.de Thu May 8 13:24:47 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 8 May 2014 11:24:47 +0000 Subject: [FieldTrip] (no subject) In-Reply-To: <536B6463.3080504@donders.ru.nl> References: , <536B6463.3080504@donders.ru.nl> Message-ID: Hi Jörn, thanks, you are right, there is no difference to any other montage with a common reference. And thanks for the prospective citation, I'll look out for it, best Max ________________________________________ Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" im Auftrag von ""Jörn M. Horschig" [jm.horschig at donders.ru.nl] Gesendet: Donnerstag, 8. Mai 2014 13:02 An: FieldTrip discussion list Betreff: Re: [FieldTrip] (no subject) Hi Max-Philipp, what is it that you want to do specifically? Basically, there is nothing different from doing scalp EEG statistics. Regarding a reference, if you wait for a few more months, then you can cite my paper... once I've written it down ;) Best, Jörn On 5/8/2014 11:00 AM, Stenner, Max-Philipp wrote: > Dear all, > has anyone come across (or used) cluster-based permutation statistics for (human) LFP data obtained from DBS-electrodes? I am looking for a reference and, after a quick search, didn't find any, > thanks! > Best wishes > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From greg at think-now.com Thu May 8 19:52:17 2014 From: greg at think-now.com (Greg Simpson) Date: Thu, 8 May 2014 10:52:17 -0700 Subject: [FieldTrip] Research Associate Position Available Message-ID: Dear Colleagues - please note our job opening below and spread the word to those that might be interested. Thank you! Greg EEG Research Associate (Data Analysis) Think Now Inc. has a Research Associate opening for an EEG data analyst for 2 NIH-funded studies being conducted with UCLA on the neurophysiological bases of sustained attention, its deficits in ADHD and the effects of computerized brain training. We are seeking candidates with direct hands-on experience in EEG data analysis. MatLab programming skills are required. We prefer strongly self-directed individuals to take on this work. The successful candidate will report directly to Gregory V. Simpson, Ph.D., Chief Scientific Officer of Think Now and will collaborate with Mark Cohen, Ph.D., Agatha Lenartowicz, Ph.D. and the team at UCLA. Think Now is located in San Francisco, so the successful candidate can be located in either San Francisco or Los Angeles. Think Now is creating EEG and mobile-app based solutions for the diagnosis and amelioration of neurological disorders with a focus on attention and its control. Please send your CV and a description of your prior experience with EEG data analysis and MatLab to *jobs at think-now.com *. Gregory V. Simpson, Ph.D. Founder & CSO Think Now, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mossa.luca86 at gmail.com Fri May 9 12:38:05 2014 From: mossa.luca86 at gmail.com (Luca Mossa) Date: Fri, 9 May 2014 12:38:05 +0200 Subject: [FieldTrip] Combine Fieldtrip with BCI2000 Message-ID: Dear community, My name is Luca Mossa and I'm working in a company in Turin (Italy) on BCI experiments. Currently I'm trying to develop some Matlab code to improve the signal processing process. I'm currently trying to use FieldTripBuffer (in matlab) as the Signal Processing module for a mu rhythm application. I have no problems to read the raw signal and states but I have trouble to find a way to sent the processing result back to Bci for the classification. Thanks to Mr. Oostenveld now I know that I must use the ft_write_event function but when I tried to use my code (with ft_write_event function) appears an error: Error using buffer events must be given as struct. Error in ft_write_event buffer('put_evt', event, host, port) Now I think that I must define some parameters, like: event.type=.... event.sample=.... event.offset=.... event.duration=.... event.value=.... but I don't understand which kind of value to insert in these field. Have you some hint? Did you make me some example? Thank you very much. Luca -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Fri May 9 15:20:04 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Fri, 9 May 2014 15:20:04 +0200 Subject: [FieldTrip] Failed to download the sample data - the links no longer exist In-Reply-To: References: Message-ID: Dear Ying, I can download the files with no problems (to an off-campus computer). Are you still having trouble? Best, Eelke On 7 May 2014 23:14, Ying Li wrote: > Dear all, > > I am learning to use fieldtrip to do source localization. When I tried to > download some sample data, such as > 1) The MEG data: ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip > 2) The MRI data: > ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip. > It shows that the links don't exist any more. > > Are there any other ways for me to download these sample data? > > Thanks a lot! > > Ying > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From t.grent-tjong at donders.ru.nl Sun May 11 11:22:14 2014 From: t.grent-tjong at donders.ru.nl (Tineke Grent-'t-Jong) Date: Sun, 11 May 2014 11:22:14 +0200 Subject: [FieldTrip] cfg.parameter definition problem in ft_sourcegrandaverage Message-ID: <30DB2C9C4EC049A4A1128699BF86E778@socrates> Dear all, I tried to grandaverage beamformer source-reconstructions of beta-coherent sources (coherent with a seed-region) this morning and received the following error message: ??? Reference to a non-existent field 'avg.coh' (refering to my specification of cfg.parameter = 'avg.coh', which is where the data truly is) This is strange given the fact that the same procedure worked just fine on comparable data (same analysis, different settings) a few weeks ago. Running the function again with cfg.parameter = 'coh' did initially seem to work, but in hindsight gave the wrong output, likely related to the fact that the field 'coh' was simply ignored (warning during running read: "skipping unknown field 'coh'). Has anyone any idea what the problem is and how to resolve it? Best, Tineke Grent-'t-Jong -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon May 12 09:14:17 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 12 May 2014 09:14:17 +0200 Subject: [FieldTrip] Combine Fieldtrip with BCI2000 In-Reply-To: References: Message-ID: <537074C9.4090303@donders.ru.nl> Hi Luca, nice to hear that you are using the FieldTrip buffer. I guess you saw the relevant pages on our wiki? Like http://fieldtrip.fcdonders.nl/faq/what_is_the_relation_between_events_such_as_triggers_and_trials http://fieldtrip.fcdonders.nl/development/realtime/buffer_protocol?s[]=event http://fieldtrip.fcdonders.nl/example/measuring_the_timing_delay_and_jitter_for_a_real-time_application?s[]=event In general for sending events, you can set all relevant fields to anything you want, so if you want to define: > event.type=.... > event.sample=.... > event.offset=.... > event.duration=.... > event.value=.... The type is a string, and you can set it to whatever you want to distinguish in your code between different types. Sample will be automatically set by the buffer. Offset and duration are, for usual purposes, not necessary in a real-time application (though you could set them to meaningful values). The event.value field is the probably most important field. This is your trigger value, in your case for example the classification outcome. Check out the pages above, especially the last one, I guess it will become clearer then. Also check out the example scripts in the realtime folder. If you have any more questions that don't become obvious from above pages, feel free to ask again here ;) Best, Jörn On 5/9/2014 12:38 PM, Luca Mossa wrote: > Dear community, > > My name is Luca Mossa and I'm working in a company in Turin (Italy) on > BCI experiments. > Currently I'm trying to develop some Matlab code to improve the signal > processing process. > > I'm currently trying to use FieldTripBuffer (in matlab) as the Signal > Processing module for a mu rhythm application. I have no problems to > read the raw signal and states but I have trouble to find a way to > sent the processing result back to Bci for the classification. > > Thanks to Mr. Oostenveld now I know that I must use the ft_write_event > function but when I tried to use my code (with ft_write_event > function) appears an error: > > Error using buffer > events must be given as struct. > > Error in ft_write_event > buffer('put_evt', event, host, port) > > Now I think that I must define some parameters, like: > > event.type=.... > event.sample=.... > event.offset=.... > event.duration=.... > event.value=.... > > but I don't understand which kind of value to insert in these field. > Have you some hint? Did you make me some example? > > Thank you very much. > > Luca > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From j.herring at fcdonders.ru.nl Mon May 12 16:02:01 2014 From: j.herring at fcdonders.ru.nl (Herring, J.D. (Jim)) Date: Mon, 12 May 2014 16:02:01 +0200 (CEST) Subject: [FieldTrip] Brain Stimulation (TMS-tCS-EEG) toolkit course at Donders, Nijmegen - registration is now open Message-ID: <003601cf6dea$bf8df480$3ea9dd80$@herring@fcdonders.ru.nl> On June 24-27, 2014, we will host the “Toolkit of Cognitive Neuroscience: Transcranial Brain Stimulation” at the Donders Institute in Nijmegen. This intensive four-day toolkit course will provide in-depth knowledge on transcranial magnetic stimulation (TMS) and transcranial current stimulation (tDCS/tACS). The course will cover both basic and advanced topics, discussing online and offline approaches of quantification, interference, and modulation of neural activity. We will specifically address multimodal applications of non-invasive brain stimulation, with a special emphasis on concurrent electroencephalography (EEG). The course involves a series of lectures and hands-on training of stimulation application, data acquisition and data analysis. These address fundamental paradigms, such as single-pulse TMS, repetitive TMS, tDCS and tACS, and advanced topics, such as paired-pulse TMS and concurrent TMS-tDCS-EEG, and MEG. Keynote lectures will be announced in the coming months. Please see the attached preliminary program for more details. The participation fee is €200 for (PhD) students and €400 for more senior researchers. This includes coffee/tea, Dutch sandwich lunches, and social events. Because of space limitations the number of participants in the hands-on sessions is limited to 30. Location: Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Kapittelweg 29, 6525 EN Nijmegen Organizers: Ian Cameron (ian.cameron at donders.ru.nl) Dilene van Campen ( a.vancampen at donders.ru.nl) Registration: http://www.ru.nl/donders/toolkit2014 ------------------------------------------------------------------------------------------------------------------------------ Jim Herring, MSc. Neuronal Oscillations Group Centre for Cognitive Neuroimaging Donders Institute for Brain, Cognition and Behaviour Radboud University Nijmegen -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: toolkittms_program2014 (2).pdf Type: application/pdf Size: 336353 bytes Desc: not available URL: From s.rombetto at cib.na.cnr.it Tue May 13 16:15:34 2014 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Tue, 13 May 2014 16:15:34 +0200 Subject: [FieldTrip] problem occurs when using ft_timelockanalysis Message-ID: <20140513161534.pe4l2mabwo8wk40k@arco.cib.na.cnr.it> Any suggestion concerning this problem? it works finewith Matlab 2013 ----- Messaggio inoltrato da s.rombetto at cib.na.cnr.it ----- Data: Wed, 7 May 2014 13:00:50 +0200 Da: s.rombetto at cib.na.cnr.it Rispondi-A:s.rombetto at cib.na.cnr.it Oggetto: problem occurs when using ft_timelockanalysis A: fieldtrip at science.ru.nl Dear fieldtrippers I'm encountering a problem when running ft_timelockanalysis in Matlab. I receive the following message: "A Undefined function 'mxSerialize_cpp' for input arguments of type 'struct' Error in mxSerialize (line 35) argout = mxSerialize_cpp(argin); Error in ft_preamble_provenance (line 67) cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); Error in ft_preamble (line 54) evalin('caller', ['ft_preamble_' cmd]); Error in ft_timelockanalysis (line 95) ft_preamble provenance data" I am using \fieldtrip-20140506 and matlab R2014a - 64 bit Any suggestion is highly appreciated. ------------------------- Dott.ssa Sara Rombetto Istituto di Cibernetica "E. Caianiello" Via Campi Flegrei, 34 80078 Pozzuoli (NA) Italy mob +39 3401689815 tel +39 0818675361 fax +39 0818675128 Lab MEG 0817483511 -------------------------- "I disapprove of what you say, but I will defend to the death your right to say it." [Evelyn Beatrice Hall, The Friends Of Voltaire] ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ----- Fine del messaggio inoltrato ----- ------------------------- Dott.ssa Sara Rombetto Istituto di Cibernetica "E. Caianiello" Via Campi Flegrei, 34 80078 Pozzuoli (NA) Italy mob +39 3401689815 tel +39 0818675361 fax +39 0818675128 Lab MEG 0817483511 -------------------------- "I disapprove of what you say, but I will defend to the death your right to say it." [Evelyn Beatrice Hall, The Friends Of Voltaire] ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From gamaliel.ghu at gmail.com Tue May 13 18:20:03 2014 From: gamaliel.ghu at gmail.com (gamaliel huerta urrea) Date: Tue, 13 May 2014 12:20:03 -0400 Subject: [FieldTrip] questions about ft_prepare_headmodel, error: the compartment nesting cannot be determined Message-ID: hi all fieldtrip my experience is limited, and attempt a head model. I analyze the documents for the user's site, and could reach the head model is presented in the official website successfully. But when trying to do the same from imr own size: 512x512x22, throws me the following errors when trying to run the function ft_headmodel. What could be the problem? because with the Subject01.mri file, the code itself works fine, but with the mri.mat (attached) file not working properly the error is as follows Warning: please specify cfg.method='projectmesh', 'iso2mesh' or 'isosurface' > In ft_prepare_mesh at 116 In ft_prepare_headmodel at 251 In fm_0 at 41 Warning: using 'projectmesh' as default > In ft_prepare_mesh at 117 In ft_prepare_headmodel at 251 In fm_0 at 41 making mesh for scalp tissue making mesh for brain tissue making mesh for skull tissue converting seg creating probabilistic representation for scalp creating probabilistic representation for brain creating probabilistic representation for skull triangulating the outer boundary of compartment 1 (scalp) with 3000 vertices triangulating the outer boundary of compartment 2 (brain) with 3000 vertices triangulating the outer boundary of compartment 3 (skull) with 3000 vertices the call to "ft_prepare_mesh" took 6 seconds Error using surface_nesting (line 26) the compartment nesting cannot be determined Error in ft_headmodel_bemcp (line 66) order = surface_nesting(vol.bnd, 'insidefirst'); Error in ft_prepare_headmodel (line 257) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in fm_0 (line 41) vol = ft_prepare_headmodel(cfg, segmentedmri); the used code is: %% load MRI data mri = ft_read_mri('IM-0001-0001.dcm'); disp(mri)%muestra informacion de mri data cfg = []; cfg.output = {'brain','skull','scalp'};%escoge las superficies segmentedmri = ft_volumesegment(cfg, mri);%Realiza la segmentacion save segmentedmri segmentedmri disp(segmentedmri) %% Mesh cfg=[]; cfg.tissue={'brain','skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); save bnd bnd disp(bnd(1)) %% Head Model cfg = []; cfg.method ='bemcp';% el tipo de modelo se puede cambiar vol = ft_prepare_headmodel(cfg, segmentedmri); save vol vol disp(vol) -- regards -- *Gamaliel Huerta* *Ingeniería Civil Biomédica* *Universidad de Valparaíso* -------------- next part -------------- An HTML attachment was scrubbed... URL: From gamaliel.ghu at gmail.com Wed May 14 08:24:32 2014 From: gamaliel.ghu at gmail.com (gamaliel huerta urrea) Date: Wed, 14 May 2014 02:24:32 -0400 Subject: [FieldTrip] questions about ft_prepare_headmodel, error: the compartment nesting cannot be determined Message-ID: hi all fieldtrip my experience is limited, and attempt a head model. I analyze the documents for the user's site, and could reach the head model is presented in the official website successfully. But when trying to do the same from imr own size: 512x512x22, throws me the following errors when trying to run the function ft_headmodel. What could be the problem? because with the Subject01.mri file, the code itself works fine, but with the mri.mat (attached) file not working properly the error is as follows Warning: please specify cfg.method='projectmesh', 'iso2mesh' or 'isosurface' > In ft_prepare_mesh at 116 In ft_prepare_headmodel at 251 In fm_0 at 41 Warning: using 'projectmesh' as default > In ft_prepare_mesh at 117 In ft_prepare_headmodel at 251 In fm_0 at 41 making mesh for scalp tissue making mesh for brain tissue making mesh for skull tissue converting seg creating probabilistic representation for scalp creating probabilistic representation for brain creating probabilistic representation for skull triangulating the outer boundary of compartment 1 (scalp) with 3000 vertices triangulating the outer boundary of compartment 2 (brain) with 3000 vertices triangulating the outer boundary of compartment 3 (skull) with 3000 vertices the call to "ft_prepare_mesh" took 6 seconds Error using surface_nesting (line 26) the compartment nesting cannot be determined Error in ft_headmodel_bemcp (line 66) order = surface_nesting(vol.bnd, 'insidefirst'); Error in ft_prepare_headmodel (line 257) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in fm_0 (line 41) vol = ft_prepare_headmodel(cfg, segmentedmri); the used code is: %% load MRI data mri = ft_read_mri('IM-0001-0001.dcm'); disp(mri)%muestra informacion de mri data cfg = []; cfg.output = {'brain','skull','scalp'};%escoge las superficies segmentedmri = ft_volumesegment(cfg, mri);%Realiza la segmentacion save segmentedmri segmentedmri disp(segmentedmri) %% Mesh cfg=[]; cfg.tissue={'brain','skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); save bnd bnd disp(bnd(1)) %% Head Model cfg = []; cfg.method ='bemcp';% el tipo de modelo se puede cambiar vol = ft_prepare_headmodel(cfg, segmentedmri); save vol vol disp(vol) -- *Gamaliel Huerta* *Ingeniería Civil Biomédica* *Universidad de Valparaíso* -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Wed May 14 10:35:03 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 14 May 2014 10:35:03 +0200 Subject: [FieldTrip] problem occurs when using ft_timelockanalysis In-Reply-To: <20140513161534.pe4l2mabwo8wk40k@arco.cib.na.cnr.it> References: <20140513161534.pe4l2mabwo8wk40k@arco.cib.na.cnr.it> Message-ID: <53732AB7.6020203@donders.ru.nl> Hi Sara, I guess you are not using a mac. What you describe concerns bug 2452 on our Bugzilla page: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2452 which pertains to some undocumented change in Matlab. Therefore it is necessary to use a different mxserialize function that from matlab 2014a onwards than before. This is a c++ function, which requires to be compiled for each platform independently. In FieldTrip, this file exists e.g. in fileio/private but only for MacOS 64-bit platforms. Apparently, we still need to compile it for MacOS 32bit, Windows and Linux platforms. I guess we should do that quite soon ;) I'll bring it up in today's FT meeting so that hopefully from tomorrow onwards it should work. btw, for you it will help to go to the FieldTrip/src directory in Matlab and type >> mex mxSerialize_cpp.cpp Then Matlab will mex (~compile) the file for you. You can then copy that file to your matlab code directory and everything should work out fine for you. I'll keep you updated on this. Best, Jörn On 5/13/2014 4:15 PM, s.rombetto at cib.na.cnr.it wrote: > Any suggestion concerning this problem? > > it works finewith Matlab 2013 > > > > ----- Messaggio inoltrato da s.rombetto at cib.na.cnr.it ----- > Data: Wed, 7 May 2014 13:00:50 +0200 > Da: s.rombetto at cib.na.cnr.it > Rispondi-A:s.rombetto at cib.na.cnr.it > Oggetto: problem occurs when using ft_timelockanalysis > A: fieldtrip at science.ru.nl > > Dear fieldtrippers > > I'm encountering a problem when running ft_timelockanalysis in Matlab. > I receive the following message: > > "A Undefined function 'mxSerialize_cpp' for input arguments of type > 'struct' > > Error in mxSerialize (line 35) > argout = mxSerialize_cpp(argin); > > Error in ft_preamble_provenance (line 67) > cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); > > Error in ft_preamble (line 54) > evalin('caller', ['ft_preamble_' cmd]); > > Error in ft_timelockanalysis (line 95) > ft_preamble provenance data" > > > I am using \fieldtrip-20140506 and matlab R2014a - 64 bit > > Any suggestion is highly appreciated. > ------------------------- > Dott.ssa Sara Rombetto > Istituto di Cibernetica > "E. Caianiello" > Via Campi Flegrei, 34 > 80078 Pozzuoli (NA) > Italy > mob +39 3401689815 > tel +39 0818675361 > fax +39 0818675128 > Lab MEG 0817483511 > -------------------------- > "I disapprove of what you say, but I will defend to the death your > right to say > it." [Evelyn Beatrice Hall, The Friends Of Voltaire] > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > ----- Fine del messaggio inoltrato ----- > > > ------------------------- > Dott.ssa Sara Rombetto > Istituto di Cibernetica > "E. Caianiello" > Via Campi Flegrei, 34 > 80078 Pozzuoli (NA) > Italy > mob +39 3401689815 > tel +39 0818675361 > fax +39 0818675128 > Lab MEG 0817483511 > -------------------------- > "I disapprove of what you say, but I will defend to the death your > right to say > it." [Evelyn Beatrice Hall, The Friends Of Voltaire] > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From max-philipp.stenner at med.ovgu.de Wed May 14 16:25:44 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Wed, 14 May 2014 14:25:44 +0000 Subject: [FieldTrip] (no subject) Message-ID: Dear fieldtrippers, I was planning to use cluster-based permutation statistics for group-level inference on the difference between two conditions (depsamplesT) for a fairly small number of subjects (as few as 5). However, this would mean a total of only 2^5=32 possible permutations (=discrete values for the non-parametric null distribution), and therefore a maximum "p-value-resolution" of only 1/32=.0313. Does this mean that group-level permutation statistics are not appropriate for small sample sizes? How do people correct for MC in these cases (using fieldtrip)? (I am specifically interested in group-level analyses, not primarily in within-subject/across-trials testing). Thanks in advance, best Max From r.oostenveld at donders.ru.nl Wed May 14 18:10:09 2014 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 14 May 2014 18:10:09 +0200 Subject: [FieldTrip] postdoc position at NatMEG, Karolinska Institute, Stockholm, Sweden Message-ID: <4B9B1EED-6A34-4E46-95B8-F8F30B155399@donders.ru.nl> Post doc, Stockholm, Sweden The Department of Clinical Neuroscience at Karolinska Institutet offers a 2 year post doc position giving the researcher an unique mix of inspiring interactions with researchers from a wide range of research areas and a freedom to pursuit one's own qualified research questions. NatMEG – the national facility for magnetoencephalography (MEG) As of September 2013 Karolinska Institutet hosts a superbly equipped MEG lab. The NatMEG lab is a national facility open for researchers from all across Sweden. Due to it being a national facility, a wide array of projects is currently ongoing or under initiation at NatMEG. We are covering areas such as next generation SQUIDS, computational modelling, epilepsy work-ups and cognitive neuroscience in the areas of memory, language, attention, perception, pain, music, decision making, emotion, autism, schizophrenia, Parkinson's and Alzheimer's disease and more. We currently have 1 post doc and 3 guest professors that supports and initiates research at NatMEG and we are now recruiting another postdoc researcher to the lab. Please visit http://www.natmeg.se for more information. Duties Your duties as a postdoc will consist of: • The postdocs own qualified research with MEG and/or simultaneous MEG & EEG. • Research at the national infrastructure for magnetoencephalography (NatMEG), including some general operation. • Scientific support to users at NatMEG, regarding methods, experimental design and analysis. • Development of routines, experimental design and analysis with MEG and EEG. Entry requirements An ideal candidate has extensive MEG experience and is experienced in psychophysiology measurements. The person has strong skills in FieldTrip, MNE or other MEG analysis tools as well as in MatLab and/or Python. We are looking for candidates with a research interest within the cognitive neuroscience domain, that master academic English, is independent and service minded. A person is eligible for a position as postdoctoral research fellow if he or she has obtained a PhD no more than seven years before the last date of employment as postdoc. Application process Read more about the application process at https://ki.mynetworkglobal.com/en/what:job/jobID:35553/. Applications are to be submitted in the recruitment system NetRecruiter. Application deadline 2014-06-15 Contact information Daniel Lundqvist, Project manager daniel.lundqvist at ki.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.rombetto at cib.na.cnr.it Thu May 15 10:29:35 2014 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Thu, 15 May 2014 10:29:35 +0200 Subject: [FieldTrip] problem occurs when using ft_timelockanalysis In-Reply-To: <53732AB7.6020203@donders.ru.nl> References: <20140513161534.pe4l2mabwo8wk40k@arco.cib.na.cnr.it> <53732AB7.6020203@donders.ru.nl> Message-ID: <20140515102935.krkki9plw4gw40k0@arco.cib.na.cnr.it> dear Jörn thanks for your answer. You were right, I am using a win 64 pc. With your trick it works now :) Sara > Hi Sara, > > I guess you are not using a mac. What you describe concerns bug 2452 on > our Bugzilla page: > http://bugzilla.fcdonders.nl/show_bug.cgi?id=2452 > which pertains to some undocumented change in Matlab. Therefore it is > necessary to use a different mxserialize function that from matlab > 2014a onwards than before. This is a c++ function, which requires to > be compiled for each platform independently. In FieldTrip, this file > exists e.g. in fileio/private but only for MacOS 64-bit platforms. > Apparently, we still need to compile it for MacOS 32bit, Windows and > Linux platforms. I guess we should do that quite soon ;) I'll bring it > up in today's FT meeting so that hopefully from tomorrow onwards it > should work. > > btw, for you it will help to go to the FieldTrip/src directory in > Matlab and type >>> mex mxSerialize_cpp.cpp > > Then Matlab will mex (~compile) the file for you. You can then copy > that file to your matlab code directory and everything should work out > fine for you. I'll keep you updated on this. > > Best, > Jörn > > On 5/13/2014 4:15 PM, s.rombetto at cib.na.cnr.it wrote: >> Any suggestion concerning this problem? >> >> it works finewith Matlab 2013 >> >> >> >> ----- Messaggio inoltrato da s.rombetto at cib.na.cnr.it ----- >> Data: Wed, 7 May 2014 13:00:50 +0200 >> Da: s.rombetto at cib.na.cnr.it >> Rispondi-A:s.rombetto at cib.na.cnr.it >> Oggetto: problem occurs when using ft_timelockanalysis >> A: fieldtrip at science.ru.nl >> >> Dear fieldtrippers >> >> I'm encountering a problem when running ft_timelockanalysis in Matlab. >> I receive the following message: >> >> "A Undefined function 'mxSerialize_cpp' for input arguments of type 'struct' >> >> Error in mxSerialize (line 35) >> argout = mxSerialize_cpp(argin); >> >> Error in ft_preamble_provenance (line 67) >> cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); >> >> Error in ft_preamble (line 54) >> evalin('caller', ['ft_preamble_' cmd]); >> >> Error in ft_timelockanalysis (line 95) >> ft_preamble provenance data" >> >> >> I am using \fieldtrip-20140506 and matlab R2014a - 64 bit >> >> Any suggestion is highly appreciated. >> ------------------------- >> Dott.ssa Sara Rombetto >> Istituto di Cibernetica >> "E. Caianiello" >> Via Campi Flegrei, 34 >> 80078 Pozzuoli (NA) >> Italy >> mob +39 3401689815 >> tel +39 0818675361 >> fax +39 0818675128 >> Lab MEG 0817483511 >> -------------------------- >> "I disapprove of what you say, but I will defend to the death your >> right to say >> it." [Evelyn Beatrice Hall, The Friends Of Voltaire] >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> >> ----- Fine del messaggio inoltrato ----- >> >> >> ------------------------- >> Dott.ssa Sara Rombetto >> Istituto di Cibernetica >> "E. Caianiello" >> Via Campi Flegrei, 34 >> 80078 Pozzuoli (NA) >> Italy >> mob +39 3401689815 >> tel +39 0818675361 >> fax +39 0818675128 >> Lab MEG 0817483511 >> -------------------------- >> "I disapprove of what you say, but I will defend to the death your >> right to say >> it." [Evelyn Beatrice Hall, The Friends Of Voltaire] >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ------------------------- Dott.ssa Sara Rombetto Istituto di Cibernetica "E. Caianiello" Via Campi Flegrei, 34 80078 Pozzuoli (NA) Italy mob +39 3401689815 tel +39 0818675361 fax +39 0818675128 Lab MEG 0817483511 -------------------------- "I disapprove of what you say, but I will defend to the death your right to say it." [Evelyn Beatrice Hall, The Friends Of Voltaire] ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From max-philipp.stenner at med.ovgu.de Thu May 15 17:09:18 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 15 May 2014 15:09:18 +0000 Subject: [FieldTrip] within-subject partition for between-subject stats Message-ID: Dear fieldtrippers, I have a question regarding permutation statistics in a mixed design with only very few subjects (5 subjects, 2 conditions/subject; this follows up on my email yesterday). Since the number of unique permutations of *trial-averaged* data is limited (2^5=32), would it make sense (is it statistically sound) to re-compute trial-averages for each subject after randomly partitioning trials *within* each of the five subjects for a large number of iterations first (since there are >>5 trials/subject the number of unique permutations is much larger than for trial-averaged data) and then re-compute cluster-statistics (e.g. maxsum) for each of these sets of re-computed trial-averages to obtain a null-distribution? Thanks very much in advance, best Max ________________________________________ Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" im Auftrag von "Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de] Gesendet: Mittwoch, 14. Mai 2014 16:25 An: FieldTrip discussion list Betreff: [FieldTrip] (no subject) Dear fieldtrippers, I was planning to use cluster-based permutation statistics for group-level inference on the difference between two conditions (depsamplesT) for a fairly small number of subjects (as few as 5). However, this would mean a total of only 2^5=32 possible permutations (=discrete values for the non-parametric null distribution), and therefore a maximum "p-value-resolution" of only 1/32=.0313. Does this mean that group-level permutation statistics are not appropriate for small sample sizes? How do people correct for MC in these cases (using fieldtrip)? (I am specifically interested in group-level analyses, not primarily in within-subject/across-trials testing). Thanks in advance, best Max _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From laura.marzetti at gmail.com Thu May 15 18:44:26 2014 From: laura.marzetti at gmail.com (Laura Marzetti) Date: Thu, 15 May 2014 18:44:26 +0200 Subject: [FieldTrip] regularized depth weighting for MNE Message-ID: Dear all, I was wondering if the leadfield depth weighting option implemented by the configuration setting cfg.normalize = 'column' or cfg.normalize = 'yes' in input to ft_prepareleadfield, also supports a way to regularize such depth weighting in order to not artificially boost low-gain locations such as the head center in MEG. Thanks, Laura -- Laura Marzetti, PhD Istituto di Tecnologie Avanzate Biomediche Università di Chieti "G. D'Annunzio" Via dei Vestini - Campus Universitario 66013 Chieti - ITALY phone: 0039-0871-3556944 fax: 0039-0871-3556930 From yingli.ucla at gmail.com Sun May 18 00:23:29 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Sat, 17 May 2014 15:23:29 -0700 Subject: [FieldTrip] EEG source reconstruction using fieldtrip (MRI not available) Message-ID: Dear all, Fieldtrip provides a great tool of using MRI to do MEG source reconstruction (http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate). Now I want to do EEG source reconstruction. The EEG cap we used is the standard 10-10 system, but the MRI of the subject is not available. I'm thinking to use another person's MRI instead (i.e. the MNI template). Does fieldtrip provide some tools to match the electrode location and the head model from another person? In addition, since MEG sensor positions are always defined relative to the fiducial coils, so we don't need to transform it into CTF coordinate system any more. When doing EEG source reconstruction, is there any extra steps needed? (i.e. transform the EEG sensor to some certain coordinate system, etc.) Thanks a lot! Best, Ying -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at gmail.com Sun May 18 10:35:34 2014 From: johanna.zumer at gmail.com (Johanna Zumer) Date: Sun, 18 May 2014 09:35:34 +0100 Subject: [FieldTrip] EEG source reconstruction using fieldtrip (MRI not available) In-Reply-To: References: Message-ID: Dear Ying, Yes, that is possible (although in an ideal world, one does have the subject's real MRI). You might gain some help from http://fieldtrip.fcdonders.nl/example/align_eeg_electrode_positions_to_bem_headmodel or http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg (which also then links you to http://fieldtrip.fcdonders.nl/template/headmodel) for the case of using the MNI brain). Best, Johanna 2014-05-17 23:23 GMT+01:00 Ying Li : > Dear all, > > Fieldtrip provides a great tool of using MRI to do MEG source > reconstruction (http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate). > Now I want to do EEG source reconstruction. The EEG cap we used is the > standard 10-10 system, but the MRI of the subject is not available. I'm > thinking to use another person's MRI instead (i.e. the MNI template). Does > fieldtrip provide some tools to match the electrode location and the head > model from another person? > > In addition, since MEG sensor positions are always defined relative to the > fiducial coils, so we don't need to transform it into CTF coordinate system > any more. When doing EEG source reconstruction, is there any extra steps > needed? (i.e. transform the EEG sensor to some certain coordinate system, > etc.) Thanks a lot! > > Best, > > Ying > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From anne.urai at gmail.com Sun May 18 19:41:05 2014 From: anne.urai at gmail.com (anne.urai at gmail.com) Date: Sun, 18 May 2014 19:41:05 +0200 Subject: [FieldTrip] efficiently handling multiple events within a trial Message-ID: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> Hi Fieldtrippers, I have a design in which every trial has several events of interest (two stimuli with a maintenance period in between, response and feedback) - all of which I’d like to analyse at some point. I started by drafting my pipeline separately for stimulus-, response- and feedback-locked trial definitions, but this leads me to do the artefact rejection and ICA multiple times for each subject. I would prefer to reject whole trials and not use any of the events in there, rather than eg. use the response for some and the stimulus for others. I was wondering if you have any advice on how to best store multiple events in one trial (which would be, say, 12 seconds long, and have 4 different evens in it, at times that would also need to be stored). Would it work better to (1) make one big trialfun and store the onset and offset of each of those events in the trl matrix, or (2) have several trl matrices for each event and redefine the trials based on this trl matrix after I applied some other analyses? For example, it would be nice to run ft_freqanalysis once on the whole trial, and then redefine which part of the trial I’m interested in for plotting. Thanks for your thoughts on this! Best, --- Anne E. Urai, MSc PhD student | Institut für Neurophysiologie und Pathophysiologie Universitätsklinikum Hamburg-Eppendorf Martinistrasse 52, 20246 Hamburg, Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From yingli.ucla at gmail.com Mon May 19 08:16:43 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Sun, 18 May 2014 23:16:43 -0700 Subject: [FieldTrip] EEG source reconstruction using fieldtrip (MRI not available) In-Reply-To: References: Message-ID: Hi Johanna, That is exactly what I want! Appreciate your help so much! : ) Best, Ying On Sun, May 18, 2014 at 1:35 AM, Johanna Zumer wrote: > Dear Ying, > > Yes, that is possible (although in an ideal world, one does have the > subject's real MRI). > > You might gain some help from > http://fieldtrip.fcdonders.nl/example/align_eeg_electrode_positions_to_bem_headmodel > or http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg (which also > then links you to http://fieldtrip.fcdonders.nl/template/headmodel) for > the case of using the MNI brain). > > Best, > Johanna > > > > 2014-05-17 23:23 GMT+01:00 Ying Li : > >> Dear all, >> >> Fieldtrip provides a great tool of using MRI to do MEG source >> reconstruction ( >> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate). Now I want >> to do EEG source reconstruction. The EEG cap we used is the standard 10-10 >> system, but the MRI of the subject is not available. I'm thinking to use >> another person's MRI instead (i.e. the MNI template). Does fieldtrip >> provide some tools to match the electrode location and the head model from >> another person? >> >> In addition, since MEG sensor positions are always defined relative to >> the fiducial coils, so we don't need to transform it into CTF coordinate >> system any more. When doing EEG source reconstruction, is there any extra >> steps needed? (i.e. transform the EEG sensor to some certain coordinate >> system, etc.) Thanks a lot! >> >> Best, >> >> Ying >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Mon May 19 09:20:26 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 19 May 2014 09:20:26 +0200 Subject: [FieldTrip] efficiently handling multiple events within a trial In-Reply-To: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> References: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> Message-ID: Hi Anne, What I usually do is segment my data initially such that a "trial" in the data structure really corresponds to a logical trial in the experiment. So, in your case, it would contain the data for both stimuli and the maintenance period. I assume you are writing your own trialfun for this (if not, see http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition). In your trialfun, you can specify arbitrary metadata for every trial by adding extra columns to the output trl-matrix. The 4th and higher columns in the trl matrix will end up in data.trialinfo in the output data. This trialinfo field is kept throughout your analysis pipeline, as long as the data still contains trials. You could, for instance, store the time index of the response as the 4th column of your trl, the time index of the feedback onset as the 5th, etc. I always make sure that at least a condition identifier and a reaction time (if applicable) appear the trialinfo field. Once this information is present in data.trialinfo, you can use ft_selectdata and ft_redefinetrial to select the appropriate trials and (if necessary) shift the time axis, respectively. Hope that helps, Best, Eelke On 18 May 2014 19:41, wrote: > Hi Fieldtrippers, > > I have a design in which every trial has several events of interest (two > stimuli with a maintenance period in between, response and feedback) - all > of which I’d like to analyse at some point. I started by drafting my > pipeline separately for stimulus-, response- and feedback-locked trial > definitions, but this leads me to do the artefact rejection and ICA multiple > times for each subject. I would prefer to reject whole trials and not use > any of the events in there, rather than eg. use the response for some and > the stimulus for others. > > I was wondering if you have any advice on how to best store multiple events > in one trial (which would be, say, 12 seconds long, and have 4 different > evens in it, at times that would also need to be stored). Would it work > better to (1) make one big trialfun and store the onset and offset of each > of those events in the trl matrix, or (2) have several trl matrices for each > event and redefine the trials based on this trl matrix after I applied some > other analyses? For example, it would be nice to run ft_freqanalysis once on > the whole trial, and then redefine which part of the trial I’m interested in > for plotting. > > Thanks for your thoughts on this! > > Best, > > --- > Anne E. Urai, MSc > PhD student | Institut für Neurophysiologie und Pathophysiologie > Universitätsklinikum Hamburg-Eppendorf > Martinistrasse 52, 20246 Hamburg, Germany > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From anne.urai at gmail.com Mon May 19 10:24:08 2014 From: anne.urai at gmail.com (Anne Urai) Date: Mon, 19 May 2014 10:24:08 +0200 Subject: [FieldTrip] efficiently handling multiple events within a trial In-Reply-To: References: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> Message-ID: I've been writing my own trialfun but so far I've gotten by with a separate one for eg. stimulus- and response locked, which seems rather inefficient indeed. Thanks for the suggestion of using ft_selectdata, didn't know that one yet! Anne Anne Urai On 19 May 2014 09:20, Eelke Spaak wrote: > Hi Anne, > > What I usually do is segment my data initially such that a "trial" in > the data structure really corresponds to a logical trial in the > experiment. So, in your case, it would contain the data for both > stimuli and the maintenance period. > > I assume you are writing your own trialfun for this (if not, see > > http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition > ). > In your trialfun, you can specify arbitrary metadata for every trial > by adding extra columns to the output trl-matrix. The 4th and higher > columns in the trl matrix will end up in data.trialinfo in the output > data. This trialinfo field is kept throughout your analysis pipeline, > as long as the data still contains trials. You could, for instance, > store the time index of the response as the 4th column of your trl, > the time index of the feedback onset as the 5th, etc. I always make > sure that at least a condition identifier and a reaction time (if > applicable) appear the trialinfo field. > > Once this information is present in data.trialinfo, you can use > ft_selectdata and ft_redefinetrial to select the appropriate trials > and (if necessary) shift the time axis, respectively. > > Hope that helps, > Best, > Eelke > > On 18 May 2014 19:41, wrote: > > Hi Fieldtrippers, > > > > I have a design in which every trial has several events of interest (two > > stimuli with a maintenance period in between, response and feedback) - > all > > of which I’d like to analyse at some point. I started by drafting my > > pipeline separately for stimulus-, response- and feedback-locked trial > > definitions, but this leads me to do the artefact rejection and ICA > multiple > > times for each subject. I would prefer to reject whole trials and not use > > any of the events in there, rather than eg. use the response for some and > > the stimulus for others. > > > > I was wondering if you have any advice on how to best store multiple > events > > in one trial (which would be, say, 12 seconds long, and have 4 different > > evens in it, at times that would also need to be stored). Would it work > > better to (1) make one big trialfun and store the onset and offset of > each > > of those events in the trl matrix, or (2) have several trl matrices for > each > > event and redefine the trials based on this trl matrix after I applied > some > > other analyses? For example, it would be nice to run ft_freqanalysis > once on > > the whole trial, and then redefine which part of the trial I’m > interested in > > for plotting. > > > > Thanks for your thoughts on this! > > > > Best, > > > > --- > > Anne E. Urai, MSc > > PhD student | Institut für Neurophysiologie und Pathophysiologie > > Universitätsklinikum Hamburg-Eppendorf > > Martinistrasse 52, 20246 Hamburg, Germany > > > > > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.piai.research at gmail.com Mon May 19 23:14:30 2014 From: v.piai.research at gmail.com (Vitoria Piai) Date: Mon, 19 May 2014 14:14:30 -0700 Subject: [FieldTrip] Error: Undefined function 'mxSerialize_cpp' In-Reply-To: References: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> Message-ID: <537A7436.3080307@gmail.com> Hello everyone, I'm getting a low-level error (below) when running ft_singleplotER to plot FFTs. I recently changed to Matlab2014a so I'm guessing that's why I'm getting the error (different FT versions give same error for as far back in time as I could come). Does anyone know a way around this issue? Thanks a lot, Vitoria Undefined function 'mxSerialize_cpp' for input arguments of type 'struct'. Error in mxSerialize (line 35) argout = mxSerialize_cpp(argin); Error in ft_preamble_provenance (line 67) cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); Error in ft_preamble (line 54) evalin('caller', ['ft_preamble_' cmd]); Error in ft_singleplotER (line 109) ft_preamble provenance varargin From jan.schoffelen at donders.ru.nl Tue May 20 11:57:59 2014 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 20 May 2014 11:57:59 +0200 Subject: [FieldTrip] Error: Undefined function 'mxSerialize_cpp' In-Reply-To: <537A7436.3080307@gmail.com> References: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> <537A7436.3080307@gmail.com> Message-ID: Hi Vitoria, Sara Rombetto asked the same question last week (or the week before) ;-), and Jörn provided an adequate answer. See below, with credits to Jörn... +++++++++++++++++++++++++++++++++++++++++++++++++++++++ Hi Sara, I guess you are not using a mac. What you describe concerns bug 2452 on our Bugzilla page: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2452 which pertains to some undocumented change in Matlab. Therefore it is necessary to use a different mxserialize function that from matlab 2014a onwards than before. This is a c++ function, which requires to be compiled for each platform independently. In FieldTrip, this file exists e.g. in fileio/private but only for MacOS 64-bit platforms. Apparently, we still need to compile it for MacOS 32bit, Windows and Linux platforms. I guess we should do that quite soon ;) I'll bring it up in today's FT meeting so that hopefully from tomorrow onwards it should work. btw, for you it will help to go to the FieldTrip/src directory in Matlab and type >> mex mxSerialize_cpp.cpp Then Matlab will mex (~compile) the file for you. You can then copy that file to your matlab code directory and everything should work out fine for you. I'll keep you updated on this. Best, Jörn +++++++++++++++++++++++++++++++++++++++++++++++++++++++ Best, JM On May 19, 2014, at 11:14 PM, Vitoria Piai wrote: > Hello everyone, > > I'm getting a low-level error (below) when running ft_singleplotER to plot FFTs. > I recently changed to Matlab2014a so I'm guessing that's why I'm getting the error (different FT versions give same error for as far back in time as I could come). Does anyone know a way around this issue? > Thanks a lot, Vitoria > > Undefined function 'mxSerialize_cpp' for input arguments of type 'struct'. > > Error in mxSerialize (line 35) > argout = mxSerialize_cpp(argin); > > Error in ft_preamble_provenance (line 67) > cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); > > Error in ft_preamble (line 54) > evalin('caller', ['ft_preamble_' cmd]); > > Error in ft_singleplotER (line 109) > ft_preamble provenance varargin > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue May 20 11:58:11 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 20 May 2014 11:58:11 +0200 Subject: [FieldTrip] Error: Undefined function 'mxSerialize_cpp' In-Reply-To: <537A7436.3080307@gmail.com> References: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> <537A7436.3080307@gmail.com> Message-ID: <537B2733.20802@donders.ru.nl> Hi Vitoria, hope you're enjoying Berkeley ;) I assume the same error will occur for more people in a bit. We'll discuss it in the next FT meeting tomorrow. In the meanwhile, check this out (I responded to Sara last week, who got the same error): > I guess you are not using a mac. What you describe concerns bug 2452 > on our Bugzilla page: > http://bugzilla.fcdonders.nl/show_bug.cgi?id=2452 > which pertains to some undocumented change in Matlab. Therefore it is > necessary to use a different mxserialize function that from matlab > 2014a onwards than before. This is a c++ function, which requires to > be compiled for each platform independently. In FieldTrip, this file > exists e.g. in fileio/private but only for MacOS 64-bit platforms. > Apparently, we still need to compile it for MacOS 32bit, Windows and > Linux platforms. I guess we should do that quite soon I'll bring it up > in today's FT meeting so that hopefully from tomorrow onwards it > should work. > > btw, for you it will help to go to the FieldTrip/src directory in > Matlab and type > >> mex mxSerialize_cpp.cpp > > Then Matlab will mex (~compile) the file for you. You can then copy > that file to your matlab code directory and everything should work out > fine for you. I'll keep you updated on this. > Best, Jörn On 5/19/2014 11:14 PM, Vitoria Piai wrote: > Hello everyone, > > I'm getting a low-level error (below) when running ft_singleplotER to > plot FFTs. > I recently changed to Matlab2014a so I'm guessing that's why I'm > getting the error (different FT versions give same error for as far > back in time as I could come). Does anyone know a way around this issue? > Thanks a lot, Vitoria > > Undefined function 'mxSerialize_cpp' for input arguments of type > 'struct'. > > Error in mxSerialize (line 35) > argout = mxSerialize_cpp(argin); > > Error in ft_preamble_provenance (line 67) > cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); > > Error in ft_preamble (line 54) > evalin('caller', ['ft_preamble_' cmd]); > > Error in ft_singleplotER (line 109) > ft_preamble provenance varargin > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From yingli.ucla at gmail.com Thu May 22 10:26:45 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Thu, 22 May 2014 01:26:45 -0700 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface Message-ID: Dear all, I tried to use fieldtrip to generate a source space and calculate lead field matrix. I found that the dipoles in the source space has x, y, z orientations. Is it possible to generate a source model where the dipole is perpendicular to the cortex surface? Actually this can be very helpful, since it will reduce the unknown variables and make the inverse problem easier to solve. Also, there are some inverse algorithms which require the dipole to be perpendicular to the cortex surface. Thanks a lot!!! Best, Ying -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu May 22 10:56:24 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 22 May 2014 10:56:24 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: References: Message-ID: <537DBBB8.600@donders.ru.nl> Hi Ying, when computing the leadfields you can set the option cfg.reducerank, which 'nulls' the dimension(s) which explain(s) the least variance (this is not quite true, but figuratively speaking). I think this is what comes closest to what you are looking for. There is no way to explicitly set desired orientations to zero apart from modifying the leadfield structure yourself. But that should be easily achievable, right? Best, Jörn On 5/22/2014 10:26 AM, Ying Li wrote: > Dear all, > > I tried to use fieldtrip to generate a source space and calculate lead > field matrix. I found that the dipoles in the source space has x, y, z > orientations. Is it possible to generate a source model where the > dipole is perpendicular to the cortex surface? > > Actually this can be very helpful, since it will reduce the unknown > variables and make the inverse problem easier to solve. Also, there > are some inverse algorithms which require the dipole to be > perpendicular to the cortex surface. > > Thanks a lot!!! > > Best, > > Ying > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From eelke.spaak at donders.ru.nl Thu May 22 11:04:04 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 22 May 2014 11:04:04 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: <537DBBB8.600@donders.ru.nl> References: <537DBBB8.600@donders.ru.nl> Message-ID: Hi Ying, In addition to this, of course first you would need a model of the cortical surface for your subjects. See http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to obtain such a model (using FreeSurfer) and getting it into FieldTrip. Best, Eelke On 22 May 2014 10:56, "Jörn M. Horschig" wrote: > Hi Ying, > > when computing the leadfields you can set the option cfg.reducerank, which > 'nulls' the dimension(s) which explain(s) the least variance (this is not > quite true, but figuratively speaking). I think this is what comes closest > to what you are looking for. There is no way to explicitly set desired > orientations to zero apart from modifying the leadfield structure yourself. > But that should be easily achievable, right? > > Best, > Jörn > > > On 5/22/2014 10:26 AM, Ying Li wrote: >> >> Dear all, >> >> I tried to use fieldtrip to generate a source space and calculate lead >> field matrix. I found that the dipoles in the source space has x, y, z >> orientations. Is it possible to generate a source model where the dipole is >> perpendicular to the cortex surface? >> >> Actually this can be very helpful, since it will reduce the unknown >> variables and make the inverse problem easier to solve. Also, there are some >> inverse algorithms which require the dipole to be perpendicular to the >> cortex surface. >> >> Thanks a lot!!! >> >> Best, >> >> Ying >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Thu May 22 11:47:03 2014 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 22 May 2014 11:47:03 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: References: <537DBBB8.600@donders.ru.nl> Message-ID: <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> Hi Ying, Yes, it's possible to constrain the dipole orientation. If you have a cortical sheet based source model that contains a triangulation that describes the topology, it's in principle possible to compute the orientation perpendicular to the sheet (this can e.g. be done by the 'normals' function which I believe should be in ~/fieldtrip/private). Subsequently, for each vertex in the cortical sheet you can multiply the leadfield matrix with this vector to get a single column leadfield vector per vertex that describes the sensor topography of a dipolar source with orientation perpendicular to the cortex. Best, Jan-Mathijs On May 22, 2014, at 11:04 AM, Eelke Spaak wrote: > Hi Ying, > > In addition to this, of course first you would need a model of the > cortical surface for your subjects. See > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to > obtain such a model (using FreeSurfer) and getting it into FieldTrip. > > Best, > Eelke > > On 22 May 2014 10:56, "Jörn M. Horschig" wrote: >> Hi Ying, >> >> when computing the leadfields you can set the option cfg.reducerank, which >> 'nulls' the dimension(s) which explain(s) the least variance (this is not >> quite true, but figuratively speaking). I think this is what comes closest >> to what you are looking for. There is no way to explicitly set desired >> orientations to zero apart from modifying the leadfield structure yourself. >> But that should be easily achievable, right? >> >> Best, >> Jörn >> >> >> On 5/22/2014 10:26 AM, Ying Li wrote: >>> >>> Dear all, >>> >>> I tried to use fieldtrip to generate a source space and calculate lead >>> field matrix. I found that the dipoles in the source space has x, y, z >>> orientations. Is it possible to generate a source model where the dipole is >>> perpendicular to the cortex surface? >>> >>> Actually this can be very helpful, since it will reduce the unknown >>> variables and make the inverse problem easier to solve. Also, there are some >>> inverse algorithms which require the dipole to be perpendicular to the >>> cortex surface. >>> >>> Thanks a lot!!! >>> >>> Best, >>> >>> Ying >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Jörn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> FieldTrip Development Team >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu May 22 13:25:58 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 22 May 2014 13:25:58 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> References: <537DBBB8.600@donders.ru.nl> <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> Message-ID: Hi Ying & JM & the rest of the list, I've never worked with cortex-constrained source reconstructions before, but one question came to mind: doesn't it make more sense to constrain the dipole orientations to *orthogonal* to the cortex, rather than perpendicular? Given that currents along the aligned dendrites of L5 pyramidal cells are (afaik) likely the most important origin of the MEG signal, and those dendrites are oriented approximately orthogonal to the cortical surface, isn't that what you would expect? Best, Eelke On 22 May 2014 11:47, jan-mathijs schoffelen wrote: > Hi Ying, > > Yes, it's possible to constrain the dipole orientation. If you have a > cortical sheet based source model that contains a triangulation that > describes the topology, it's in principle possible to compute the > orientation perpendicular to the sheet (this can e.g. be done by the > 'normals' function which I believe should be in ~/fieldtrip/private). > Subsequently, for each vertex in the cortical sheet you can multiply the > leadfield matrix with this vector to get a single column leadfield vector > per vertex that describes the sensor topography of a dipolar source with > orientation perpendicular to the cortex. > > Best, > Jan-Mathijs > > On May 22, 2014, at 11:04 AM, Eelke Spaak wrote: > > Hi Ying, > > In addition to this, of course first you would need a model of the > cortical surface for your subjects. See > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to > obtain such a model (using FreeSurfer) and getting it into FieldTrip. > > Best, > Eelke > > On 22 May 2014 10:56, "Jörn M. Horschig" wrote: > > Hi Ying, > > > when computing the leadfields you can set the option cfg.reducerank, which > > 'nulls' the dimension(s) which explain(s) the least variance (this is not > > quite true, but figuratively speaking). I think this is what comes closest > > to what you are looking for. There is no way to explicitly set desired > > orientations to zero apart from modifying the leadfield structure yourself. > > But that should be easily achievable, right? > > > Best, > > Jörn > > > > On 5/22/2014 10:26 AM, Ying Li wrote: > > > Dear all, > > > I tried to use fieldtrip to generate a source space and calculate lead > > field matrix. I found that the dipoles in the source space has x, y, z > > orientations. Is it possible to generate a source model where the dipole is > > perpendicular to the cortex surface? > > > Actually this can be very helpful, since it will reduce the unknown > > variables and make the inverse problem easier to solve. Also, there are some > > inverse algorithms which require the dipole to be perpendicular to the > > cortex surface. > > > Thanks a lot!!! > > > Best, > > > Ying > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > > Jörn M. Horschig > > PhD Student > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Neuronal Oscillations Group > > FieldTrip Development Team > > > P.O. Box 9101 > > NL-6500 HB Nijmegen > > The Netherlands > > > Contact: > > E-Mail: jm.horschig at donders.ru.nl > > Tel: +31-(0)24-36-68493 > > Web: http://www.ru.nl/donders > > > Visiting address: > > Trigon, room 2.30 > > Kapittelweg 29 > > NL-6525 EN Nijmegen > > The Netherlands > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > http://www.hettaligebrein.nl > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Thu May 22 13:42:11 2014 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 22 May 2014 13:42:11 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: References: <537DBBB8.600@donders.ru.nl> <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> Message-ID: <09B16AC6-4417-448C-8B82-1399CEFC062F@donders.ru.nl> Eelke, You're absolutely right one should take the orientation that is othogonal! In my dictionary this is exactly what the word perpendicular means ;-)... JM On May 22, 2014, at 1:25 PM, Eelke Spaak wrote: > Hi Ying & JM & the rest of the list, > > I've never worked with cortex-constrained source reconstructions > before, but one question came to mind: doesn't it make more sense to > constrain the dipole orientations to *orthogonal* to the cortex, > rather than perpendicular? Given that currents along the aligned > dendrites of L5 pyramidal cells are (afaik) likely the most important > origin of the MEG signal, and those dendrites are oriented > approximately orthogonal to the cortical surface, isn't that what you > would expect? > > Best, > Eelke > > On 22 May 2014 11:47, jan-mathijs schoffelen > wrote: >> Hi Ying, >> >> Yes, it's possible to constrain the dipole orientation. If you have a >> cortical sheet based source model that contains a triangulation that >> describes the topology, it's in principle possible to compute the >> orientation perpendicular to the sheet (this can e.g. be done by the >> 'normals' function which I believe should be in ~/fieldtrip/private). >> Subsequently, for each vertex in the cortical sheet you can multiply the >> leadfield matrix with this vector to get a single column leadfield vector >> per vertex that describes the sensor topography of a dipolar source with >> orientation perpendicular to the cortex. >> >> Best, >> Jan-Mathijs >> >> On May 22, 2014, at 11:04 AM, Eelke Spaak wrote: >> >> Hi Ying, >> >> In addition to this, of course first you would need a model of the >> cortical surface for your subjects. See >> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to >> obtain such a model (using FreeSurfer) and getting it into FieldTrip. >> >> Best, >> Eelke >> >> On 22 May 2014 10:56, "Jörn M. Horschig" wrote: >> >> Hi Ying, >> >> >> when computing the leadfields you can set the option cfg.reducerank, which >> >> 'nulls' the dimension(s) which explain(s) the least variance (this is not >> >> quite true, but figuratively speaking). I think this is what comes closest >> >> to what you are looking for. There is no way to explicitly set desired >> >> orientations to zero apart from modifying the leadfield structure yourself. >> >> But that should be easily achievable, right? >> >> >> Best, >> >> Jörn >> >> >> >> On 5/22/2014 10:26 AM, Ying Li wrote: >> >> >> Dear all, >> >> >> I tried to use fieldtrip to generate a source space and calculate lead >> >> field matrix. I found that the dipoles in the source space has x, y, z >> >> orientations. Is it possible to generate a source model where the dipole is >> >> perpendicular to the cortex surface? >> >> >> Actually this can be very helpful, since it will reduce the unknown >> >> variables and make the inverse problem easier to solve. Also, there are some >> >> inverse algorithms which require the dipole to be perpendicular to the >> >> cortex surface. >> >> >> Thanks a lot!!! >> >> >> Best, >> >> >> Ying >> >> >> >> _______________________________________________ >> >> fieldtrip mailing list >> >> fieldtrip at donders.ru.nl >> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -- >> >> Jörn M. Horschig >> >> PhD Student >> >> Donders Institute for Brain, Cognition and Behaviour >> >> Centre for Cognitive Neuroimaging >> >> Radboud University Nijmegen >> >> Neuronal Oscillations Group >> >> FieldTrip Development Team >> >> >> P.O. Box 9101 >> >> NL-6500 HB Nijmegen >> >> The Netherlands >> >> >> Contact: >> >> E-Mail: jm.horschig at donders.ru.nl >> >> Tel: +31-(0)24-36-68493 >> >> Web: http://www.ru.nl/donders >> >> >> Visiting address: >> >> Trigon, room 2.30 >> >> Kapittelweg 29 >> >> NL-6525 EN Nijmegen >> >> The Netherlands >> >> >> _______________________________________________ >> >> fieldtrip mailing list >> >> fieldtrip at donders.ru.nl >> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> http://www.hettaligebrein.nl >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu May 22 13:47:14 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 22 May 2014 13:47:14 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: <09B16AC6-4417-448C-8B82-1399CEFC062F@donders.ru.nl> References: <537DBBB8.600@donders.ru.nl> <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> <09B16AC6-4417-448C-8B82-1399CEFC062F@donders.ru.nl> Message-ID: Haha never mind, I was totally confused. "Perpendicular" and "parallel" both start with a p... On 22 May 2014 13:42, jan-mathijs schoffelen wrote: > Eelke, > > You're absolutely right one should take the orientation that is othogonal! > In my dictionary this is exactly what the word perpendicular means ;-)... > > JM > > On May 22, 2014, at 1:25 PM, Eelke Spaak wrote: > > Hi Ying & JM & the rest of the list, > > I've never worked with cortex-constrained source reconstructions > before, but one question came to mind: doesn't it make more sense to > constrain the dipole orientations to *orthogonal* to the cortex, > rather than perpendicular? Given that currents along the aligned > dendrites of L5 pyramidal cells are (afaik) likely the most important > origin of the MEG signal, and those dendrites are oriented > approximately orthogonal to the cortical surface, isn't that what you > would expect? > > Best, > Eelke > > On 22 May 2014 11:47, jan-mathijs schoffelen > wrote: > > Hi Ying, > > > Yes, it's possible to constrain the dipole orientation. If you have a > > cortical sheet based source model that contains a triangulation that > > describes the topology, it's in principle possible to compute the > > orientation perpendicular to the sheet (this can e.g. be done by the > > 'normals' function which I believe should be in ~/fieldtrip/private). > > Subsequently, for each vertex in the cortical sheet you can multiply the > > leadfield matrix with this vector to get a single column leadfield vector > > per vertex that describes the sensor topography of a dipolar source with > > orientation perpendicular to the cortex. > > > Best, > > Jan-Mathijs > > > On May 22, 2014, at 11:04 AM, Eelke Spaak wrote: > > > Hi Ying, > > > In addition to this, of course first you would need a model of the > > cortical surface for your subjects. See > > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to > > obtain such a model (using FreeSurfer) and getting it into FieldTrip. > > > Best, > > Eelke > > > On 22 May 2014 10:56, "Jörn M. Horschig" wrote: > > > Hi Ying, > > > > when computing the leadfields you can set the option cfg.reducerank, which > > > 'nulls' the dimension(s) which explain(s) the least variance (this is not > > > quite true, but figuratively speaking). I think this is what comes closest > > > to what you are looking for. There is no way to explicitly set desired > > > orientations to zero apart from modifying the leadfield structure yourself. > > > But that should be easily achievable, right? > > > > Best, > > > Jörn > > > > > On 5/22/2014 10:26 AM, Ying Li wrote: > > > > Dear all, > > > > I tried to use fieldtrip to generate a source space and calculate lead > > > field matrix. I found that the dipoles in the source space has x, y, z > > > orientations. Is it possible to generate a source model where the dipole is > > > perpendicular to the cortex surface? > > > > Actually this can be very helpful, since it will reduce the unknown > > > variables and make the inverse problem easier to solve. Also, there are some > > > inverse algorithms which require the dipole to be perpendicular to the > > > cortex surface. > > > > Thanks a lot!!! > > > > Best, > > > > Ying > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > > > Jörn M. Horschig > > > PhD Student > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Neuronal Oscillations Group > > > FieldTrip Development Team > > > > P.O. Box 9101 > > > NL-6500 HB Nijmegen > > > The Netherlands > > > > Contact: > > > E-Mail: jm.horschig at donders.ru.nl > > > Tel: +31-(0)24-36-68493 > > > Web: http://www.ru.nl/donders > > > > Visiting address: > > > Trigon, room 2.30 > > > Kapittelweg 29 > > > NL-6525 EN Nijmegen > > > The Netherlands > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > Jan-Mathijs Schoffelen, MD PhD > > > Donders Institute for Brain, Cognition and Behaviour, > > Centre for Cognitive Neuroimaging, > > Radboud University Nijmegen, The Netherlands > > > Max Planck Institute for Psycholinguistics, > > Nijmegen, The Netherlands > > > J.Schoffelen at donders.ru.nl > > Telephone: +31-24-3614793 > > > http://www.hettaligebrein.nl > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > http://www.hettaligebrein.nl > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From tyler.grummett at flinders.edu.au Fri May 23 04:10:10 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Fri, 23 May 2014 02:10:10 +0000 Subject: [FieldTrip] layout file from beamformer Message-ID: <1400811002490.44354@flinders.edu.au> Hello fieldtrippers, I am trying to create a layout file that has the positions of the beamformer sources. The output of my beamformer analysis was 1400 channels and I am trying to create a layout file with certain position which correspond to certain sources. For example, if I wanted to plot 30 sources and all I had were the x y z position. I am hoping that this made sense, I cant quite work out what I should be asking for. I have worked out how to plot the power of the sources, but ft_topoplotIC is asking for a layout file (after I ran an ICA over it), which I cant work out how to make. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From yingli.ucla at gmail.com Fri May 23 04:18:48 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Thu, 22 May 2014 19:18:48 -0700 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: References: <537DBBB8.600@donders.ru.nl> <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> <09B16AC6-4417-448C-8B82-1399CEFC062F@donders.ru.nl> Message-ID: Dear all, Thanks so much for all of your enthusiastic replies. I'll give a try to your suggestions. Best wishes, Ying On Thu, May 22, 2014 at 4:47 AM, Eelke Spaak wrote: > Haha never mind, I was totally confused. "Perpendicular" and > "parallel" both start with a p... > > On 22 May 2014 13:42, jan-mathijs schoffelen > wrote: > > Eelke, > > > > You're absolutely right one should take the orientation that is > othogonal! > > In my dictionary this is exactly what the word perpendicular means ;-)... > > > > JM > > > > On May 22, 2014, at 1:25 PM, Eelke Spaak wrote: > > > > Hi Ying & JM & the rest of the list, > > > > I've never worked with cortex-constrained source reconstructions > > before, but one question came to mind: doesn't it make more sense to > > constrain the dipole orientations to *orthogonal* to the cortex, > > rather than perpendicular? Given that currents along the aligned > > dendrites of L5 pyramidal cells are (afaik) likely the most important > > origin of the MEG signal, and those dendrites are oriented > > approximately orthogonal to the cortical surface, isn't that what you > > would expect? > > > > Best, > > Eelke > > > > On 22 May 2014 11:47, jan-mathijs schoffelen > > wrote: > > > > Hi Ying, > > > > > > Yes, it's possible to constrain the dipole orientation. If you have a > > > > cortical sheet based source model that contains a triangulation that > > > > describes the topology, it's in principle possible to compute the > > > > orientation perpendicular to the sheet (this can e.g. be done by the > > > > 'normals' function which I believe should be in ~/fieldtrip/private). > > > > Subsequently, for each vertex in the cortical sheet you can multiply the > > > > leadfield matrix with this vector to get a single column leadfield vector > > > > per vertex that describes the sensor topography of a dipolar source with > > > > orientation perpendicular to the cortex. > > > > > > Best, > > > > Jan-Mathijs > > > > > > On May 22, 2014, at 11:04 AM, Eelke Spaak wrote: > > > > > > Hi Ying, > > > > > > In addition to this, of course first you would need a model of the > > > > cortical surface for your subjects. See > > > > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to > > > > obtain such a model (using FreeSurfer) and getting it into FieldTrip. > > > > > > Best, > > > > Eelke > > > > > > On 22 May 2014 10:56, "Jörn M. Horschig" > wrote: > > > > > > Hi Ying, > > > > > > > > when computing the leadfields you can set the option cfg.reducerank, > which > > > > > > 'nulls' the dimension(s) which explain(s) the least variance (this is not > > > > > > quite true, but figuratively speaking). I think this is what comes > closest > > > > > > to what you are looking for. There is no way to explicitly set desired > > > > > > orientations to zero apart from modifying the leadfield structure > yourself. > > > > > > But that should be easily achievable, right? > > > > > > > > Best, > > > > > > Jörn > > > > > > > > > > On 5/22/2014 10:26 AM, Ying Li wrote: > > > > > > > > Dear all, > > > > > > > > I tried to use fieldtrip to generate a source space and calculate lead > > > > > > field matrix. I found that the dipoles in the source space has x, y, z > > > > > > orientations. Is it possible to generate a source model where the dipole > is > > > > > > perpendicular to the cortex surface? > > > > > > > > Actually this can be very helpful, since it will reduce the unknown > > > > > > variables and make the inverse problem easier to solve. Also, there are > some > > > > > > inverse algorithms which require the dipole to be perpendicular to the > > > > > > cortex surface. > > > > > > > > Thanks a lot!!! > > > > > > > > Best, > > > > > > > > Ying > > > > > > > > > > _______________________________________________ > > > > > > fieldtrip mailing list > > > > > > fieldtrip at donders.ru.nl > > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > -- > > > > > > Jörn M. Horschig > > > > > > PhD Student > > > > > > Donders Institute for Brain, Cognition and Behaviour > > > > > > Centre for Cognitive Neuroimaging > > > > > > Radboud University Nijmegen > > > > > > Neuronal Oscillations Group > > > > > > FieldTrip Development Team > > > > > > > > P.O. Box 9101 > > > > > > NL-6500 HB Nijmegen > > > > > > The Netherlands > > > > > > > > Contact: > > > > > > E-Mail: jm.horschig at donders.ru.nl > > > > > > Tel: +31-(0)24-36-68493 > > > > > > Web: http://www.ru.nl/donders > > > > > > > > Visiting address: > > > > > > Trigon, room 2.30 > > > > > > Kapittelweg 29 > > > > > > NL-6525 EN Nijmegen > > > > > > The Netherlands > > > > > > > > _______________________________________________ > > > > > > fieldtrip mailing list > > > > > > fieldtrip at donders.ru.nl > > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > Jan-Mathijs Schoffelen, MD PhD > > > > > > Donders Institute for Brain, Cognition and Behaviour, > > > > Centre for Cognitive Neuroimaging, > > > > Radboud University Nijmegen, The Netherlands > > > > > > Max Planck Institute for Psycholinguistics, > > > > Nijmegen, The Netherlands > > > > > > J.Schoffelen at donders.ru.nl > > > > Telephone: +31-24-3614793 > > > > > > http://www.hettaligebrein.nl > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > Jan-Mathijs Schoffelen, MD PhD > > > > Donders Institute for Brain, Cognition and Behaviour, > > Centre for Cognitive Neuroimaging, > > Radboud University Nijmegen, The Netherlands > > > > Max Planck Institute for Psycholinguistics, > > Nijmegen, The Netherlands > > > > J.Schoffelen at donders.ru.nl > > Telephone: +31-24-3614793 > > > > http://www.hettaligebrein.nl > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Fri May 23 09:01:45 2014 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 23 May 2014 09:01:45 +0200 Subject: [FieldTrip] layout file from beamformer In-Reply-To: <1400811002490.44354@flinders.edu.au> References: <1400811002490.44354@flinders.edu.au> Message-ID: <53A25C84-5000-471D-A96B-A1EEF293ACAD@gmail.com> Dear Tyler, I recently had a similar problem. I solved this by plotting the x,y,z-coordinates of all dipoles within the BEM-Model and assign a color value depending on the power value to the dipole markers. In short: use ft_triplot to plot the mesh of the BEM. Then select the .pos-field of the dipoles inside your volume and plot them with plot3. In the plot3-step, you can assign each dipole a 'Color'-property based on your power or stats value. Alternatively, you can use ft_prepare_layout to get a planar projection of your sources, but at least in my case it did not look too good. Hope that helps, if you want to, I can send you an example of what the plots look like. Best, Julian Am 23.05.2014 um 04:10 schrieb Tyler Grummett: > Hello fieldtrippers, > > I am trying to create a layout file that has the positions of the beamformer sources. > > The output of my beamformer analysis was 1400 channels and I am trying to create a layout file with certain position which correspond to certain sources. > > For example, if I wanted to plot 30 sources and all I had were the x y z position. > > I am hoping that this made sense, I cant quite work out what I should be asking for. I have worked out how to plot the power of the sources, but > ft_topoplotIC is asking for a layout file (after I ran an ICA over it), which I cant work out how to make. > > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Fri May 23 10:04:12 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Fri, 23 May 2014 08:04:12 +0000 Subject: [FieldTrip] layout file from beamformer In-Reply-To: <53A25C84-5000-471D-A96B-A1EEF293ACAD@gmail.com> References: <1400811002490.44354@flinders.edu.au>, <53A25C84-5000-471D-A96B-A1EEF293ACAD@gmail.com> Message-ID: <13054238-2E21-4214-851F-F6481F0860B0@flinders.edu.au> Hey Julian, That sounds good, it would be awesome if you could give me an example. Also though, what are the steps of using ft_prepare_layout with beamformer data. I am away it gives you permissions, but how do you enter that into ft_prepare_layout. This is only for using in trentool, otherwise I would be using your method Tyler On 23 May 2014, at 4:40 pm, "Julian Keil" > wrote: Dear Tyler, I recently had a similar problem. I solved this by plotting the x,y,z-coordinates of all dipoles within the BEM-Model and assign a color value depending on the power value to the dipole markers. In short: use ft_triplot to plot the mesh of the BEM. Then select the .pos-field of the dipoles inside your volume and plot them with plot3. In the plot3-step, you can assign each dipole a 'Color'-property based on your power or stats value. Alternatively, you can use ft_prepare_layout to get a planar projection of your sources, but at least in my case it did not look too good. Hope that helps, if you want to, I can send you an example of what the plots look like. Best, Julian Am 23.05.2014 um 04:10 schrieb Tyler Grummett: Hello fieldtrippers, I am trying to create a layout file that has the positions of the beamformer sources. The output of my beamformer analysis was 1400 channels and I am trying to create a layout file with certain position which correspond to certain sources. For example, if I wanted to plot 30 sources and all I had were the x y z position. I am hoping that this made sense, I cant quite work out what I should be asking for. I have worked out how to plot the power of the sources, but ft_topoplotIC is asking for a layout file (after I ran an ICA over it), which I cant work out how to make. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.herring at fcdonders.ru.nl Fri May 23 10:42:58 2014 From: j.herring at fcdonders.ru.nl (Herring, J.D. (Jim)) Date: Fri, 23 May 2014 10:42:58 +0200 (CEST) Subject: [FieldTrip] layout file from beamformer In-Reply-To: <13054238-2E21-4214-851F-F6481F0860B0@flinders.edu.au> References: <1400811002490.44354@flinders.edu.au>, <53A25C84-5000-471D-A96B-A1EEF293ACAD@gmail.com> <13054238-2E21-4214-851F-F6481F0860B0@flinders.edu.au> Message-ID: <010201cf7663$002490f0$006db2d0$@herring@fcdonders.ru.nl> Hi Tyler, What would you like to plot? It seems like you want to plot the spatial weights of independent components after running ICA on your source data. Ft_topoplotIC plots data on a 2D-layout of your sensors/electrodes, I do not think you want this. It seems to me you should have a look at ft_sourceplot and add a field to your source data structure that, for each IC, represents the weights per gridpoint. Then you should be able to plot the IC weights in 3D (with anatomy if you wish). Best, Jim From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Tyler Grummett Sent: vrijdag 23 mei 2014 10:04 To: FieldTrip discussion list Subject: Re: [FieldTrip] layout file from beamformer Hey Julian, That sounds good, it would be awesome if you could give me an example. Also though, what are the steps of using ft_prepare_layout with beamformer data. I am away it gives you permissions, but how do you enter that into ft_prepare_layout. This is only for using in trentool, otherwise I would be using your method Tyler On 23 May 2014, at 4:40 pm, "Julian Keil" wrote: Dear Tyler, I recently had a similar problem. I solved this by plotting the x,y,z-coordinates of all dipoles within the BEM-Model and assign a color value depending on the power value to the dipole markers. In short: use ft_triplot to plot the mesh of the BEM. Then select the .pos-field of the dipoles inside your volume and plot them with plot3. In the plot3-step, you can assign each dipole a 'Color'-property based on your power or stats value. Alternatively, you can use ft_prepare_layout to get a planar projection of your sources, but at least in my case it did not look too good. Hope that helps, if you want to, I can send you an example of what the plots look like. Best, Julian Am 23.05.2014 um 04:10 schrieb Tyler Grummett: Hello fieldtrippers, I am trying to create a layout file that has the positions of the beamformer sources. The output of my beamformer analysis was 1400 channels and I am trying to create a layout file with certain position which correspond to certain sources. For example, if I wanted to plot 30 sources and all I had were the x y z position. I am hoping that this made sense, I cant quite work out what I should be asking for. I have worked out how to plot the power of the sources, but ft_topoplotIC is asking for a layout file (after I ran an ICA over it), which I cant work out how to make. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Fri May 23 10:45:20 2014 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 23 May 2014 10:45:20 +0200 Subject: [FieldTrip] layout file from beamformer In-Reply-To: <13054238-2E21-4214-851F-F6481F0860B0@flinders.edu.au> References: <1400811002490.44354@flinders.edu.au> <53A25C84-5000-471D-A96B-A1EEF293ACAD@gmail.com> <13054238-2E21-4214-851F-F6481F0860B0@flinders.edu.au> Message-ID: Hi Tyler, I attached 2 plots for you, one with evoked ERF activity, and one of the same activity but masked for the maximum. As you can see, you get information about the activity for each dipole as well as the location within the volume. As for the layout, here's how it works for me: % Sourcedummy in this case is a source structure containing the grid .pos % and .inside field elec = []; elec.elecpos = sourcedummy.pos(sourcedummy.inside,:); elec.chanpos = sourcedummy.pos(sourcedummy.inside,:); tmp = num2cell(sourcedummy.inside); elec.label = cellfun(@num2str,tmp,'UniformOutput',0); cfg = []; cfg.elec = elec; cfg.projection = 'polar'; example_lay = ft_prepare_layout(cfg); cfg=[]; cfg.layout = example_lay; ft_layoutplot(cfg); Please be careful with the 2D-projection of 3D-data. I'm not sure how accurate the projection is and some grid points might overlap. Good Luck, Julian On Fri, May 23, 2014 at 10:04 AM, Tyler Grummett < tyler.grummett at flinders.edu.au> wrote: > Hey Julian, > > That sounds good, it would be awesome if you could give me an example. > > Also though, what are the steps of using ft_prepare_layout with > beamformer data. I am away it gives you permissions, but how do you enter > that into ft_prepare_layout. > > This is only for using in trentool, otherwise I would be using your > method > > Tyler > > > On 23 May 2014, at 4:40 pm, "Julian Keil" wrote: > > Dear Tyler, > > I recently had a similar problem. > > I solved this by plotting the x,y,z-coordinates of all dipoles within > the BEM-Model and assign a color value depending on the power value to the > dipole markers. > > In short: use ft_triplot to plot the mesh of the BEM. Then select the > .pos-field of the dipoles inside your volume and plot them with plot3. > In the plot3-step, you can assign each dipole a 'Color'-property based on > your power or stats value. > > Alternatively, you can use ft_prepare_layout to get a planar projection > of your sources, but at least in my case it did not look too good. > > Hope that helps, if you want to, I can send you an example of what the > plots look like. > > Best, > > Julian > > Am 23.05.2014 um 04:10 schrieb Tyler Grummett: > > Hello fieldtrippers, > > I am trying to create a layout file that has the positions of the > beamformer sources. > > The output of my beamformer analysis was 1400 channels and I am trying > to create a layout file with certain position which correspond to certain > sources. > > For example, if I wanted to plot 30 sources and all I had were the x y z > position. > > I am hoping that this made sense, I cant quite work out what I should be > asking for. I have worked out how to plot the power of the sources, but > ft_topoplotIC is asking for a layout file (after I ran an ICA over it), > which I cant work out how to make. > > Tyler > > ************************* > > *Tyler Grummett ( BBSc, BSc(Hons I))* > *PhD Candidate* > *Brain Signals Laboratory* > *Flinders University* > *Rm 5A301* > *Ext 66124* > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: wirebrain_example_mask.png Type: image/png Size: 37668 bytes Desc: not available URL: From s.hassel at aston.ac.uk Fri May 23 13:06:23 2014 From: s.hassel at aston.ac.uk (Hassel, Stefanie) Date: Fri, 23 May 2014 11:06:23 +0000 Subject: [FieldTrip] PhD Studentship at Aston University, Birmingham, UK Message-ID: <282D53FEFCF0B44EA5D1E7977E0C32E61FACE2E5@exch-mb-g50-02.campus.aston.ac.uk> Dear all, Please see below for information on a PhD Studentship available in the School of Life & Health Sciences at Aston University, Birmingham, UK Using Response Inhibition and Reward Responsiveness to Investigate Risk for Psychopathology Dr Stefanie Hassel and Prof. Klaus Kessler Biological predisposition towards psychopathology as well as environmental events may influence whether and when symptoms surface among individuals, who are at an increased risk for psychopathology. Individuals differ in their degree of responsiveness to cues of reward or cues of threat, in goal-seeking behaviours and/or anxiety. A high degree of responsiveness to cues of reward or threat may play an additional role in placing individuals at risk for psychopathologies, especially mood disorders. For instance, high reward responsiveness on a specific behavioural task, individual characteristics like impulsivity or extreme appraisals of social approval as well as family history of psychopathology may all aid in predicting future diagnoses. This project will address the underlying mechanisms that control fluctuations in mood and behaviour, specific sensitivities which may determine the strength of a person's emotional reaction to reward or threat and investigate potential relationships between sensitivity levels to cues of reward and threat and sub-threshold symptoms of (hypo)mania and depression in individuals at increased risk for a mood disorder (or other psychopathology), compared to undergraduate students classified as not at risk. Multi-modal experimental methods will be used to examine these issues, such as behavioural task-based and questionnaire measures, as well as structural and functional neuroimaging (Magnetic Resonance Imaging (MRI), Diffusion Tensor Imaging, functional MRI and Magnetoencephalography). Outcomes from this research may be used to help inform early identification of risk factors for general psychopathology and mood disorders (depression and bipolar disorder) in particular. The high quality of research in Aston's School of Life and Health Sciences was confirmed in the last Research Assessment Exercise (RAE): research in Allied Health Professions and Studies ranked 3rd out of 63 UK Higher Education Institutions. Additional information about research in the School can be found at http://www1.aston.ac.uk/lhs/research/ Financial Support: The studentship comprises of a tax-free stipend of £13,863 p.a. and payment of Home/EU tuition fees only. The studentship is available for three years, subject to satisfactory progress review at the end of the first year with an anticipated Registration date of 1st October 2014. Application Requirements: * Eligible Applicants should hold at least a Bachelor (Hons.) Degree of either First Class/Upper Second Class or hold a Master's Degree in Psychology or related discipline. A demonstrable interest in affective neuroscience and/or clinical psychology is a requirement. (Supervisors are based at Aston University, and draw on expertise with experimental and neuroimaging research with healthy and clinical populations). * EU Applicants will need to demonstrate adequate proficiency in English Language skills, with a minimum overall score of 101 (Internet Based) (with a minimum score in each section of: R: 23, W: 26, L: 23 and S: 22) in TOEFL or IELTS with minimum marks of 6.5 in each section and an overall band of 7.0. * Informal enquiries should be addressed to the Project Supervisor, Dr Stefanie Hassel (E-mail:s.hassel at aston.ac.uk). Closing Date: Monday 09 June 2014 Reference: R140127 To apply please complete the on-line application form athttps://map.aston.ac.uk/urd/sits.urd/run/siw_ipp_lgn.login?process=siw_ipp_app&&code1=LHS029PR&code2=0014 Email details to a friend --- --- --- Stefanie Hassel, PhD Department of Psychology School of Life and Health Sciences Aston University Birmingham B4 7ET Email: s.hassel at aston.ac.uk Phone: 0121 204 4003 Students can make an appointment with me by following this link: https://wass.aston.ac.uk/pages/login.page.php Adjunct Assistant Professor: Dept. of Psychiatry, Faculty of Medicine, University of Calgary, Calgary, AB, Canada Adjunct Instructor: Western Psychiatric Institute and Clinic, University of Pittsburgh, Pittsburgh, PA, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: From diezmartini at gmail.com Mon May 26 02:30:57 2014 From: diezmartini at gmail.com (Ana Laura Diez Martini) Date: Mon, 26 May 2014 12:30:57 +1200 Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW Message-ID: Hi all! This is the .BDF file of one of my EEG subjects. For my last experiment I used a Biosemi system and now I'm using an EGI system which gives me .RAW files. I exported the .RAW file with EEGlab to .BDF format and I tried using the scripts I use to analise the data of my previous experiment but I realised that it was not reading the events: cfg = []; cfg.dataset = ' (location)'; cfg.trialdef.eventtype = '?'; definetrial(cfg); Warning: no trialfun was specified, using trialfun_general > In definetrial at 79 evaluating trialfunction 'trialfun_general' no events were found in the datafile no trials have been defined yet, see DEFINETRIAL for further help found 0 events created 0 trials EEGlab does read them. Any idea of what could be wrong? Thank you all!! -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Mon May 26 08:59:13 2014 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Mon, 26 May 2014 08:59:13 +0200 Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW In-Reply-To: References: Message-ID: Hi Ana Laura, Have you tried importing the .RAW file directly? That is, by specifying cfg.dataset = 'XXX.raw'? Best regards, Arjen 2014-05-26 2:30 GMT+02:00 Ana Laura Diez Martini : > Hi all! > > This is the .BDF file > of one of > my EEG subjects. For my last experiment I used a Biosemi system and now I'm > using an EGI system which gives me .RAW files. I exported the .RAW file > with EEGlab to .BDF format and I tried using the scripts I use to analise > the data of my previous experiment but I realised that it was not reading > the events: > > cfg = []; > cfg.dataset = ' (location)'; > cfg.trialdef.eventtype = '?'; > definetrial(cfg); > Warning: no trialfun was specified, using trialfun_general > > In definetrial at 79 > evaluating trialfunction 'trialfun_general' > no events were found in the datafile > no trials have been defined yet, see DEFINETRIAL for further help > found 0 events > created 0 trials > > EEGlab does read them. Any idea of what could be wrong? > > Thank you all!! > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Mon May 26 09:03:09 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 26 May 2014 09:03:09 +0200 Subject: [FieldTrip] Fwd: summer school on stress & cognition Message-ID: Forwarding on behalf of a colleague. ---------- Forwarded message ---------- From: Vogel, S. (Susanne) Date: 23 May 2014 11:38 Subject: fieldtrip and MEG mailing lists To: Eelke Spaak Dear colleague, Each year, the Donders Institute for Brain, Cognition and Behaviour organizes a highly prestigious international summer school in cognitive neuroscience, bringing together world-leading scientists and outstanding MSc students, PhD students, and postdocs. The topic of this year's summer school is STRESS & COGNITION: FROM BASIC MECHANISMS TO PSYCHOPATHOLOGY. The event will take place in the week of August 11-15, 2014, on the campus of Radboud University in Nijmegen. With a list of highly renowned international experts in the interdisciplinary field of stress and cognition, we are convinced that our summer school will be of great interest to your research group and/or department. In addition to lectures, we will organize group discussions, a poster session for students to get feedback on their work, lab tours at the Donders' research facilities, and a range of social activities. There is optional accommodation available on campus. Currently, the application procedure is in full swing. We are proud to inform you that thus far we have accepted students from 17 different countries: Belgium, Brazil, Bulgaria, Chili, China, Denmark, Germany, Greece, Italy, Korea, Netherlands, Poland, Romania, Russia, Scotland, Spain, and the United States. Please note that we are rapidly approaching the maximum number of participants. Registration will close on JUNE 15, 2014. More information can be found on our website: HTTP://WWW.RU.NL/DONDERS/SUMMERSCHOOL We would like to ask you to kindly bring this to the attention of MSc students, PhD students, and postdocs who might be interested. With warm regards, Benno Roozendaal Erno Hermans (Organizers) From d.lozanosoldevilla at fcdonders.ru.nl Mon May 26 10:58:01 2014 From: d.lozanosoldevilla at fcdonders.ru.nl (Diego Lozano Soldevilla) Date: Mon, 26 May 2014 10:58:01 +0200 Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW In-Reply-To: References: Message-ID: Hi Ana, Fieldtrip does not read events in BDF format. Take a look to our wiki: http://fieldtrip.fcdonders.nl/getting_started/egi - *EDF+* (.edf) All channels, including PIB channels, are read in correctly, including channel labels. However, the events, which are stored on the annotation channel, are written in a way by Net Station that is not compatible with the edf+ reading implementation in FieldTrip. So, events do not come out properly. Also discontinuous epochs are “glued” together as one “continuous” data stream. As Arjen suggested, with *.RAW you shouldn't have any problem. event = ft_read_event('*.RAW') If you encounter it, please let us know. best, Diego On 26 May 2014 08:59, Arjen Stolk wrote: > Hi Ana Laura, > > Have you tried importing the .RAW file directly? That is, by specifying > cfg.dataset = 'XXX.raw'? > > Best regards, > Arjen > > > 2014-05-26 2:30 GMT+02:00 Ana Laura Diez Martini : > >> Hi all! >> >> This is the .BDF file >> of one of >> my EEG subjects. For my last experiment I used a Biosemi system and now I'm >> using an EGI system which gives me .RAW files. I exported the .RAW file >> with EEGlab to .BDF format and I tried using the scripts I use to analise >> the data of my previous experiment but I realised that it was not reading >> the events: >> >> cfg = []; >> cfg.dataset = ' (location)'; >> cfg.trialdef.eventtype = '?'; >> definetrial(cfg); >> Warning: no trialfun was specified, using trialfun_general >> > In definetrial at 79 >> evaluating trialfunction 'trialfun_general' >> no events were found in the datafile >> no trials have been defined yet, see DEFINETRIAL for further help >> found 0 events >> created 0 trials >> >> EEGlab does read them. Any idea of what could be wrong? >> >> Thank you all!! >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dr.chungki.lee at gmail.com Mon May 26 11:18:34 2014 From: dr.chungki.lee at gmail.com (Chungki Lee) Date: Mon, 26 May 2014 18:18:34 +0900 Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW In-Reply-To: References: Message-ID: Dear all Fieldtrip can read events in BDF format ! Hear simple examples example #1 %% cfg = []; cfg.dataset = '~~~ '; % your filename with file extension; cfg.trialdef.eventtype = 'STATUS'; % Status notation maybe Biosemi's tigger name cfg.trialdef.eventvalue = 1; % your event value cfg.trialdef.prestim = 4; % before stimulation (sec), only use positive value cfg.trialdef.poststim = 8; % after stimulation (sec) , only use positive value cfg = ft_definetrial(cfg); cfg.method = 'trial'; data = ft_preprocessing(cfg); %% example #2 %% % if you executed these command lines cfg = []; cfg.dataset = '~~~ '; % your filename with file extension; cfg.trialdef.eventtype = '?'; % Status notation maybe Biosemi's tigger name cfg = ft_definetrial(cfg); % result example #2 the following events were found in the datafile event type: 'CM_in_range' with event values: event type: 'Epoch' with event values: event type: 'STATUS' with event values: 1 2 3 4 255 <----------- "this indicate your file configuration for trigger information" no trials have been defined yet, see FT_DEFINETRIAL for further help found 255 events created 0 trials the call to "ft_definetrial" took 8 seconds have fun~!! 2014-05-26 17:58 GMT+09:00 Diego Lozano Soldevilla < d.lozanosoldevilla at fcdonders.ru.nl>: > Hi Ana, > > Fieldtrip does not read events in BDF format. Take a look to our wiki: > > http://fieldtrip.fcdonders.nl/getting_started/egi > > > - *EDF+* (.edf) All channels, including PIB channels, are read in > correctly, including channel labels. However, the events, which are stored > on the annotation channel, are written in a way by Net Station that is not > compatible with the edf+ reading implementation in FieldTrip. So, events do > not come out properly. Also discontinuous epochs are “glued” together as > one “continuous” data stream. > > As Arjen suggested, with *.RAW you shouldn't have any problem. > > event = ft_read_event('*.RAW') > > If you encounter it, please let us know. > > best, > > Diego > > > On 26 May 2014 08:59, Arjen Stolk wrote: > >> Hi Ana Laura, >> >> Have you tried importing the .RAW file directly? That is, by specifying >> cfg.dataset = 'XXX.raw'? >> >> Best regards, >> Arjen >> >> >> 2014-05-26 2:30 GMT+02:00 Ana Laura Diez Martini : >> >>> Hi all! >>> >>> This is the .BDF file >>> of one of >>> my EEG subjects. For my last experiment I used a Biosemi system and now I'm >>> using an EGI system which gives me .RAW files. I exported the .RAW file >>> with EEGlab to .BDF format and I tried using the scripts I use to analise >>> the data of my previous experiment but I realised that it was not reading >>> the events: >>> >>> cfg = []; >>> cfg.dataset = ' (location)'; >>> cfg.trialdef.eventtype = '?'; >>> definetrial(cfg); >>> Warning: no trialfun was specified, using trialfun_general >>> > In definetrial at 79 >>> evaluating trialfunction 'trialfun_general' >>> no events were found in the datafile >>> no trials have been defined yet, see DEFINETRIAL for further help >>> found 0 events >>> created 0 trials >>> >>> EEGlab does read them. Any idea of what could be wrong? >>> >>> Thank you all!! >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ---------------------------------------------------------------- Chungki Lee, Ph.D. Post-doc Biomedical Research Institute Korea Institute of Science and Technology E-mail: chungki at kist.re.kr Tel:+82-2-958-5636, C.P: +82-10-5223-7309 ---------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.lozanosoldevilla at fcdonders.ru.nl Mon May 26 11:44:13 2014 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Mon, 26 May 2014 11:44:13 +0200 (CEST) Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW In-Reply-To: Message-ID: <222446912.7087267.1401097453356.JavaMail.root@sculptor.zimbra.ru.nl> Dear Ana, Sorry for my file extension confusion: edf instead of bdf. However, I don't know a way to read events coded in BDF format exported by NETSTATION. I encounter this problem in the past but I had no problems with RAW file format Dear Chungki , Fieldtrip can read events in *.bdf but from BIOSEMI eeg system but Ana was refering to a different eeg system that has the same fileformat extension. best, Diego ----- Original Message ----- > From: "Chungki Lee" > To: "FieldTrip discussion list" > Sent: Monday, 26 May, 2014 11:18:34 AM > Subject: Re: [FieldTrip] Cannot read the events of a .BDF file > exported from an EGI .RAW > Dear all > Fieldtrip can read events in BDF format ! > Hear simple examples > example #1 > %% > cfg = []; > cfg.dataset = '~~~ '; % your filename with file extension; > cfg.trialdef.eventtype = 'STATUS'; % Status notation maybe Biosemi's > tigger name > cfg.trialdef.eventvalue = 1; % your event value > cfg.trialdef.prestim = 4; % before stimulation (sec), only use > positive value > cfg.trialdef.poststim = 8; % after stimulation (sec) , only use > positive value > cfg = ft_definetrial(cfg); > cfg.method = 'trial'; > data = ft_preprocessing(cfg); > %% > example #2 > %% > % if you executed these command lines > cfg = []; > cfg.dataset = '~~~ '; % your filename with file extension; > cfg.trialdef.eventtype = '?'; % Status notation maybe Biosemi's tigger > name > cfg = ft_definetrial(cfg); > % result example #2 > the following events were found in the datafile > event type: 'CM_in_range' with event values: > event type: 'Epoch' with event values: > event type: 'STATUS' with event values: 1 2 3 4 255 <----------- "this > indicate your file configuration for trigger information" > no trials have been defined yet, see FT_DEFINETRIAL for further help > found 255 events > created 0 trials > the call to "ft_definetrial" took 8 seconds > have fun~!! > 2014-05-26 17:58 GMT+09:00 Diego Lozano Soldevilla < > d.lozanosoldevilla at fcdonders.ru.nl > : > > Hi Ana, > > Fieldtrip does not read events in BDF format. Take a look to our > > wiki: > > http://fieldtrip.fcdonders.nl/getting_started/egi > > • > > EDF+ (.edf) All channels, including PIB channels, are read in > > correctly, including channel labels. However, the events, which are > > stored on the annotation channel, are written in a way by Net > > Station > > that is not compatible with the edf+ reading implementation in > > FieldTrip. So, events do not come out properly. Also discontinuous > > epochs are “glued” together as one “continuous” data stream. > > As Arjen suggested, with *.RAW you shouldn't have any problem. > > event = ft_read_event('*.RAW') > > If you encounter it, please let us know. > > best, > > Diego > > On 26 May 2014 08:59, Arjen Stolk < a.stolk8 at gmail.com > wrote: > > > Hi Ana Laura, > > > Have you tried importing the .RAW file directly? That is, by > > > specifying cfg.dataset = 'XXX.raw'? > > > Best regards, > > > Arjen > > > 2014-05-26 2:30 GMT+02:00 Ana Laura Diez Martini < > > > diezmartini at gmail.com > : > > > > Hi all! > > > > This is the .BDF file of one of my EEG subjects. For my last > > > > experiment I used a Biosemi system and now I'm using an EGI > > > > system > > > > which gives me .RAW files. I exported the .RAW file with EEGlab > > > > to > > > > .BDF format and I tried using the scripts I use to analise the > > > > data > > > > of > > > > my previous experiment but I realised that it was not reading > > > > the > > > > events: > > > > cfg = []; > > > > cfg.dataset = ' (location)'; > > > > cfg.trialdef.eventtype = '?'; > > > > definetrial(cfg); > > > > Warning: no trialfun was specified, using trialfun_general > > > > > In definetrial at 79 > > > > evaluating trialfunction 'trialfun_general' > > > > no events were found in the datafile > > > > no trials have been defined yet, see DEFINETRIAL for further > > > > help > > > > found 0 events > > > > created 0 trials > > > > EEGlab does read them. Any idea of what could be wrong? > > > > Thank you all!! > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- > ---------------------------------------------------------------- > Chungki Lee, Ph.D. > Post-doc > Biomedical Research Institute > Korea Institute of Science and Technology > E-mail: chungki at kist.re.kr > Tel:+82-2-958-5636, C.P: +82-10-5223-7309 > ---------------------------------------------------------------- > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- PhD Student Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen NL-6525 EN Nijmegen The Netherlands http://www.ru.nl/people/donders/lozano-soldevilla-d/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahjoory86 at gmail.com Mon May 26 13:42:51 2014 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Mon, 26 May 2014 13:42:51 +0200 Subject: [FieldTrip] Template for Electrode Positions Message-ID: Dear all, I want to do EEG source reconstruction. The EEG cap we used is the standard 10-20 system with 64 channels, but the MRI and electrode positions of subjects are not available. I'm thinking of using Fieldtrip templates. For head model I used: load standard_bem.mat cfg.vol=vol; But for Electrode positions I checked all options at this link: http://fieldtrip.fcdonders.nl/template/electrode the only option with 64 channel is GSN-HydroCel-64_1.0.sfp. It includes labels in this format: E1 E2 E3... So, How can I use it for my work? Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From i.e.j.de.vries at student.vu.nl Mon May 26 14:20:44 2014 From: i.e.j.de.vries at student.vu.nl (Vries, I.E.J. de) Date: Mon, 26 May 2014 12:20:44 +0000 Subject: [FieldTrip] Template for Electrode Positions In-Reply-To: References: Message-ID: <19DD7427D34B7E47B33093FB4C3CFDD2010950FF81@PEXMB001B.vu.local> Hi Keyvan, I also used a 64 channel EEG cap and used the Fieldtrip template standard_1020.elc. Although this template has more electrodes, Fieldtrip automatically only uses the electrodes from that template that are also present in your data (it checks the labels, so make sure your electrode labels agree with the ones in the template when it comes to upper/lower case). The 64 electrodes that I used in my experiment are all present in the standard_1020.elc template and they are on the same position as in my cap. Good luck! Ingmar ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Keyvan Mahjoory [mahjoory86 at gmail.com] Sent: 26 May 2014 13:42 To: FieldTrip discussion list Subject: [FieldTrip] Template for Electrode Positions Dear all, I want to do EEG source reconstruction. The EEG cap we used is the standard 10-20 system with 64 channels, but the MRI and electrode positions of subjects are not available. I'm thinking of using Fieldtrip templates. For head model I used: load standard_bem.mat cfg.vol=vol; But for Electrode positions I checked all options at this link: http://fieldtrip.fcdonders.nl/template/electrode the only option with 64 channel is GSN-HydroCel-64_1.0.sfp. It includes labels in this format: E1 E2 E3... So, How can I use it for my work? Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.herring at fcdonders.ru.nl Mon May 26 14:22:10 2014 From: j.herring at fcdonders.ru.nl (Herring, J.D. (Jim)) Date: Mon, 26 May 2014 14:22:10 +0200 (CEST) Subject: [FieldTrip] Template for Electrode Positions In-Reply-To: References: Message-ID: <005c01cf78dd$1d9519d0$58bf4d70$@herring@fcdonders.ru.nl> Dear Keyvan, As is stated on http://fieldtrip.fcdonders.nl/template/electrode, Fieldtrip also has electrode positions for the standard 10-20 system, namely: standard_1020.elc. To read in the sensor positions you would have to do something like: Filename = 'c:\fieldtrip\template\electrode\standard_1020.elc'; sens = ft_read_sens(filename); Best, Jim From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Keyvan Mahjoory Sent: maandag 26 mei 2014 13:43 To: FieldTrip discussion list Subject: [FieldTrip] Template for Electrode Positions Dear all, I want to do EEG source reconstruction. The EEG cap we used is the standard 10-20 system with 64 channels, but the MRI and electrode positions of subjects are not available. I'm thinking of using Fieldtrip templates. For head model I used: load standard_bem.mat cfg.vol=vol; But for Electrode positions I checked all options at this link: http://fieldtrip.fcdonders.nl/template/electrode the only option with 64 channel is GSN-HydroCel-64_1.0.sfp. It includes labels in this format: E1 E2 E3... So, How can I use it for my work? Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From frsantos at fpce.up.pt Mon May 26 18:08:41 2014 From: frsantos at fpce.up.pt (Fernando Ferreira-Santos) Date: Mon, 26 May 2014 16:08:41 +0000 Subject: [FieldTrip] Porto III CAN: 3rd Cognitive and Affective Neurophysiology Summer School Message-ID: <2BAB036A9BAEA44984A131DFCE44610801099FB3BD@SRVMBX01.fpceup.psi.up.pt> Dear colleagues, The Laboratory of Neuropsychopsysiology of the University of Porto (http://www.fpce.up.pt/labpsi/) is pleased to announce the 3rd edition of the International Cognitive and Affective Neurophysiology Summer School: Acquisition, processing and analysis of EEG signal. This summer school is focused on the application of Electroencephalography (EEG) and Event Related Potential (ERP) techniques to the study of cognitive and affective processes. The course will be fully taught in English and is aimed at an introductory level, so no previous experience with EEG or ERP is required. This event will take place from 8-13 of September in the lovely city of Porto, recently elected as the Best European Destination of 2014 (http://www.europeanbestdestinations.org/top/europe-best-destinations-2014/#PORTO). In last year’s edition the course was fully booked and, as such, we recommend early registration (course places are attributed by order of registration). For additional details and instructions on how to register, please consult our website (http://www.fpce.up.pt/labpsi/summerschool/). Please feel free to pass this information along to students or researchers that may be potentially interested. Thanks you and best wishes, -- Fernando Ferreira-Santos, PhD Laboratory of Neuropsychophysiology Faculty of Psychology and Education Sciences University of Porto Rua Alfredo Allen, 4200-135 Porto (Portugal) Tel.: +351 226079700 (ext. 301) Email: frsantos at fpce.up.pt http://www.fpce.up.pt/labpsi/ -- Fernando Ferreira-Santos, PhD Laboratory of Neuropsychophysiology Faculty of Psychology and Education Sciences University of Porto Rua Alfredo Allen, 4200-135 Porto (Portugal) Tel.: +351 226079700 (ext. 301) Email: frsantos at fpce.up.pt http://www.fpce.up.pt/labpsi/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahjoory86 at gmail.com Mon May 26 18:14:17 2014 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Mon, 26 May 2014 18:14:17 +0200 Subject: [FieldTrip] Error in source analysis Message-ID: Dear All, Here is my scripts for source analysis, when I run it, I face with error mentioned below, load 'standard_bem.mat' cfg = []; cfg.method = 'dics'; cfg.frequency = 10; cfg.grid = grid; cfg.elec=ft_read_sens('standard_1020.elc'); cfg.vol = vol; sourcePost_nocon = ft_sourceanalysis(cfg,freq); ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> beamformer_dics>pinv at 650 [U,S,V] = svd(A,0); Error in ==> beamformer_dics at 339 filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ==> ft_sourceanalysis at 567 dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Thank you in advance, Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From diezmartini at gmail.com Tue May 27 00:25:39 2014 From: diezmartini at gmail.com (Ana Laura Diez Martini) Date: Tue, 27 May 2014 10:25:39 +1200 Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW In-Reply-To: <222446912.7087267.1401097453356.JavaMail.root@sculptor.zimbra.ru.nl> References: <222446912.7087267.1401097453356.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Thank you Arjen, Diego and Chungki Lee! I tried with the .RAW and it reads the event. The problem is that my triggers have the following format "11,12,13,14,15,21,22...." . Netstation instead of saving them as they are, returns them in this way: say my trigger is 12, I get "DIN4" and "DIN8". or 11 is DIN1 + DIN8 + DIN2. so I had to convert them into my original triggers. After that I can either save the set (I tried this but it didn't work) or export it to bdf. When I open the exported file in EEGlab, it reads the events correctly, but fieldtrip doesn't. Any ideas? Thanks!! On Mon, May 26, 2014 at 9:44 PM, Lozano Soldevilla, D. (Diego) < d.lozanosoldevilla at fcdonders.ru.nl> wrote: > Dear Ana, > > Sorry for my file extension confusion: edf instead of bdf. However, I > don't know a way to read events coded in BDF format exported by NETSTATION. > I encounter this problem in the past but I had no problems with RAW file > format > > Dear Chungki, > > Fieldtrip can read events in *.bdf but from BIOSEMI eeg system but Ana was > refering to a different eeg system that has the same fileformat extension. > > best, > > Diego > > ------------------------------ > > *From: *"Chungki Lee" > *To: *"FieldTrip discussion list" > *Sent: *Monday, 26 May, 2014 11:18:34 AM > *Subject: *Re: [FieldTrip] Cannot read the events of a .BDF file exported > from an EGI .RAW > > > Dear all > > Fieldtrip can read events in BDF format ! > > Hear simple examples > > example #1 > %% > cfg = []; > cfg.dataset = '~~~ '; % your filename with file extension; > cfg.trialdef.eventtype = 'STATUS'; % Status notation maybe Biosemi's > tigger name > cfg.trialdef.eventvalue = 1; % your event value > cfg.trialdef.prestim = 4; % before stimulation (sec), only use > positive value > cfg.trialdef.poststim = 8; % after stimulation (sec) , only use > positive value > cfg = ft_definetrial(cfg); > cfg.method = 'trial'; > data = ft_preprocessing(cfg); > %% > > example #2 > %% > % if you executed these command lines > cfg = []; > cfg.dataset = '~~~ '; % your filename with file extension; > cfg.trialdef.eventtype = '?'; % Status notation maybe Biosemi's > tigger name > cfg = ft_definetrial(cfg); > > % result example #2 > the following events were found in the datafile > event type: 'CM_in_range' with event values: > event type: 'Epoch' with event values: > event type: 'STATUS' with event values: 1 2 3 4 255 <----------- > "this indicate your file configuration for trigger information" > no trials have been defined yet, see FT_DEFINETRIAL for further help > found 255 events > created 0 trials > the call to "ft_definetrial" took 8 seconds > > have fun~!! > > > > 2014-05-26 17:58 GMT+09:00 Diego Lozano Soldevilla < > d.lozanosoldevilla at fcdonders.ru.nl>: > >> Hi Ana, >> >> Fieldtrip does not read events in BDF format. Take a look to our wiki: >> >> http://fieldtrip.fcdonders.nl/getting_started/egi >> >> >> - *EDF+* (.edf) All channels, including PIB channels, are read in >> correctly, including channel labels. However, the events, which are stored >> on the annotation channel, are written in a way by Net Station that is not >> compatible with the edf+ reading implementation in FieldTrip. So, events do >> not come out properly. Also discontinuous epochs are “glued” together as >> one “continuous” data stream. >> >> As Arjen suggested, with *.RAW you shouldn't have any problem. >> >> event = ft_read_event('*.RAW') >> >> If you encounter it, please let us know. >> >> best, >> >> Diego >> >> >> On 26 May 2014 08:59, Arjen Stolk wrote: >> >>> Hi Ana Laura, >>> >>> Have you tried importing the .RAW file directly? That is, by specifying >>> cfg.dataset = 'XXX.raw'? >>> >>> Best regards, >>> Arjen >>> >>> >>> 2014-05-26 2:30 GMT+02:00 Ana Laura Diez Martini >>> : >>> >>>> Hi all! >>>> >>>> This is the .BDF file >>>> of one >>>> of my EEG subjects. For my last experiment I used a Biosemi system and now >>>> I'm using an EGI system which gives me .RAW files. I exported the .RAW file >>>> with EEGlab to .BDF format and I tried using the scripts I use to analise >>>> the data of my previous experiment but I realised that it was not reading >>>> the events: >>>> >>>> cfg = []; >>>> cfg.dataset = ' (location)'; >>>> cfg.trialdef.eventtype = '?'; >>>> definetrial(cfg); >>>> Warning: no trialfun was specified, using trialfun_general >>>> > In definetrial at 79 >>>> evaluating trialfunction 'trialfun_general' >>>> no events were found in the datafile >>>> no trials have been defined yet, see DEFINETRIAL for further help >>>> found 0 events >>>> created 0 trials >>>> >>>> EEGlab does read them. Any idea of what could be wrong? >>>> >>>> Thank you all!! >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > ---------------------------------------------------------------- > Chungki Lee, Ph.D. > Post-doc > Biomedical Research Institute > Korea Institute of Science and Technology > E-mail: chungki at kist.re.kr > Tel:+82-2-958-5636, C.P: +82-10-5223-7309 > ---------------------------------------------------------------- > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > PhD Student > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > NL-6525 EN Nijmegen > The Netherlands > http://www.ru.nl/people/donders/lozano-soldevilla-d/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Tue May 27 07:44:49 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Tue, 27 May 2014 05:44:49 +0000 Subject: [FieldTrip] granger causality on beamformer data Message-ID: <1401169475061.32086@flinders.edu.au> ?Hello fieldtrippers, I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. Or should you do a PCA reduction of some description beforehand. I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. Im open to all suggestions. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ulrich.Pomper at charite.de Tue May 27 15:18:57 2014 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Tue, 27 May 2014 15:18:57 +0200 Subject: [FieldTrip] TF transform, data length + padding Message-ID: Dear community, I have a question regarding time-frequency transformation. The data I want to analyse last from -800 to -200 ms before stimulus onset, I'm using a 400 ms taper. Importantly, want to make sure that no stimulus-evoked activity leaks into my prestim analysis. I first tried to cut the segment down to -1000 to 0 ms and used (zero) padding (see figure attached, top row). This would mean that the taper, at the last samplepoint of interest (-200ms), would include data up to 0ms Suprisingly, I get quite different looking results when using a longer data segment (-1200 to 0 ms) (fig. bottom row) without padding. Can someone explain to me what is going on here, and which approach would be more correct? Either, the padding in the first variant introduces artificial low frequency activity, or the taper in the second variant uses more than 400ms, at least for the low frequencies. Note that the difference between conditions (left coloumn) look almost identical, so whatever happens, it happens to both conditions very similarly. I hope someone can educate me on that matter. Cheers, Ulrich %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% TF transform %% cfg = []; cfg.continuous = 'no'; cfg.channel = 'all'; cfg.output = 'pow'; cfg.method = 'mtmconvol'; cfg.foi = 2:0.5:35; cfg.toi = -1:0.01:0; cfg.taper = 'hanning'; cfg.tapsmofrq = 2; cfg.t_ftimwin = 400 % cfg.pad = 5; ... -------------- next part -------------- A non-text attachment was scrubbed... Name: Bild5.png Type: image/png Size: 128717 bytes Desc: Bild5.png URL: From litvak.vladimir at gmail.com Tue May 27 15:29:33 2014 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Tue, 27 May 2014 14:29:33 +0100 Subject: [FieldTrip] Head model for a phantom Message-ID: Dear all, I need to to do source reconstruction of activity generated with current dipole phantom in CTF MEG. The HPI coils were at the front and sides as they would be for a subject. I was thinking I could just make a single sphere vol with origin set at [0 0 0] as that would coincide with the center of the phantom in this case. The radius shouldn't matter anyway if we are not fitting it to anything, right? Please let me know if you think this is the right approach. Thanks, Vladimir -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcgoiv0 at wfu.edu Tue May 27 16:18:28 2014 From: mcgoiv0 at wfu.edu (McGowin, Inna) Date: Tue, 27 May 2014 10:18:28 -0400 Subject: [FieldTrip] Head model for a phantom In-Reply-To: References: Message-ID: Hello Vladimir, According to the CTF MEG tech support to apply DipFit or SAM to the Current Dipole phantom recordings you need to change (0,0,4) sphere center to (0,0,0) and multiple spheres to a single sphere model for SAM.Thus you are correct. To view the results of SAM any MRI can be used. Cheers, Inna On Tue, May 27, 2014 at 9:29 AM, Vladimir Litvak wrote: > Dear all, > > I need to to do source reconstruction of activity generated with current > dipole phantom in CTF MEG. The HPI coils were at the front and sides as > they would be for a subject. I was thinking I could just make a single > sphere vol with origin set at [0 0 0] as that would coincide with the > center of the phantom in this case. The radius shouldn't matter anyway if > we are not fitting it to anything, right? > > Please let me know if you think this is the right approach. > > Thanks, > > Vladimir > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Tue May 27 18:10:24 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Tue, 27 May 2014 18:10:24 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? Message-ID: Dear all, my name is Katrin Heimann, I am phd student at the University of Parma. New to Fieldtrip. I am doing an EEG analysis, still in the preprocessing phase. It is a within trials design. I would like to compare a baseline period with an experimental condition (visual stimulus). I have a trigger after a fixation cross, then a baseline period (approx 1 sec) , then the period of my stimulus (1 sec- starting with a bottom press (trigger)). As I would like to apply the same baseline correction for both (the fixationcross period) I planned to first define my trials as long trials including the timewindows of baseline and the stimulus period, applying filter and baselinecorrection on those long pieces. However, as I do not wanna do the artifact detection on the whole pieces (but seperately for baseline and stimulus, to avoid that I have to throw away too many trials) I would like to redefine my trials then, cutting out only baseline period and only stimulus period (starting with another trigger (triggervalue=resp).. *Unfortunately I do not understand how I can change the trigger used with ft redefine trial. * Anybody who could give me an example how that is done? Thanks a million Katrin -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Tue May 27 18:25:18 2014 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 27 May 2014 18:25:18 +0200 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: <1401169475061.32086@flinders.edu.au> References: <1401169475061.32086@flinders.edu.au> Message-ID: Hi Tyler, I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 connections, so I hope you have a fast computer. As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website: http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). I hope that helps, if you have specific questions, feel free to ask. Best, Julian On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett < tyler.grummett at flinders.edu.au> wrote: > ​Hello fieldtrippers, > > > I was just wondering whether it would be sensible to do granger > causality on all 1400 virtual channels, as calculated using beamformer. > > > Or should you do a PCA reduction of some description beforehand. > > > I was also wondering how to create regions of interest. Some of my > colleagues think that we should use some kind of spatial ICA technique. > > > Im open to all suggestions. > > > Tyler > > > ************************* > > *Tyler Grummett ( BBSc, BSc(Hons I))* > *PhD Candidate* > *Brain Signals Laboratory* > *Flinders University* > *Rm 5A301* > *Ext 66124* > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcantor at umich.edu Tue May 27 18:58:32 2014 From: mcantor at umich.edu (Max Cantor) Date: Tue, 27 May 2014 12:58:32 -0400 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Hi Katrin, It may help to see your code, but hopefully this will help. It should be as simple as taking your epoched data from ft_definetrial and ft_preprocessing, then creating two configurations for your timewindows and running ft_redefinetrial. For example (from the fieldtrip tutorial, slightly simplified by me for explanatory purposes): *** % find the interesting segments of data cfg = []; % empty configuration cfg.dataset = 'Subject01.ds'; % name of CTF dataset cfg.trialdef.eventtype = 'backpanel trigger'; cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 2; cfg.trialdef.eventvalue = 3; % event value of FIC cfg = ft_definetrial(cfg); % preprocess the data cfg.channel = {'MEG'}; dataFIC = ft_preprocessing(cfg); % define time window cfg = []; cfg.toilim = [-0.5 0]; dataPre = ft_redefinetrial(cfg, dataFIC); cfg.toilim = [0.8 1.3]; dataPost = ft_redefinetrial(cfg, dataFIC); *** So if your code resembles this, you are defining in cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that encompasses both your baseline period and stimulus period, then for cfg.toilim in the ft_redefinetrial section you are setting one to your baseline period and the other to your stimulus period, and outputting them into separate variables. Hopefully this helps. Also, if you haven't done so already, I would strongly recommend you run through the tutorial, as it may help answer questions like this in the future (assuming I've properly identified the issue). Good luck, Max On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann wrote: > Dear all, > > my name is Katrin Heimann, I am phd student at the University of Parma. > New to Fieldtrip. > I am doing an EEG analysis, still in the preprocessing phase. > It is a within trials design. I would like to compare a baseline period > with an experimental condition (visual stimulus). > > I have a trigger after a fixation cross, then a baseline period (approx 1 > sec) , then the period of my stimulus (1 sec- starting with a bottom press > (trigger)). > > As I would like to apply the same baseline correction for both (the > fixationcross period) I planned to first define my trials as long trials > including the timewindows of baseline and the stimulus period, applying > filter and baselinecorrection on those long pieces. However, as I do not > wanna do the artifact detection on the whole pieces (but seperately for > baseline and stimulus, to avoid that I have to throw away too many trials) > I would like to redefine my trials then, cutting out only baseline period > and only stimulus period (starting with another trigger > (triggervalue=resp).. > > *Unfortunately I do not understand how I can change the trigger used with > ft redefine trial. * > > Anybody who could give me an example how that is done? > Thanks a million > Katrin > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Research Assistant Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Tue May 27 20:30:14 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Tue, 27 May 2014 20:30:14 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Dear Max, thanks a lot for your prompt answer. Unfortunately this is not what I am looking for (I found an example like this in the tutorial). I would like to change the trigger for one of the two conditions, let it be now the response of the subject, as this is where the stimulus actually starts... Defining two different timewindows is not enough... Can you also help me with that? Thanks a million! Katrin 2014-05-27 18:58 GMT+02:00 Max Cantor : > Hi Katrin, > > It may help to see your code, but hopefully this will help. It should be > as simple as taking your epoched data from ft_definetrial and > ft_preprocessing, then creating two configurations for your timewindows and > running ft_redefinetrial. > > For example (from the fieldtrip tutorial, slightly simplified by me for > explanatory purposes): > > *** > > % find the interesting segments of data > > cfg = []; > % empty configuration > cfg.dataset = 'Subject01.ds'; > % name of CTF dataset > cfg.trialdef.eventtype = 'backpanel trigger'; > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 2; > cfg.trialdef.eventvalue = 3; > % event value of FIC > cfg = ft_definetrial(cfg); > > % preprocess the data > > cfg.channel = {'MEG'}; > dataFIC = ft_preprocessing(cfg); > > % define time window > > cfg = []; > > cfg.toilim = [-0.5 0]; > dataPre = ft_redefinetrial(cfg, dataFIC); > > cfg.toilim = [0.8 1.3]; > dataPost = ft_redefinetrial(cfg, dataFIC); > > *** > > So if your code resembles this, you are defining in cfg.trialdef.prestim > and cfg.trialdef.poststim a timewindow that encompasses both your baseline > period and stimulus period, then for cfg.toilim in the ft_redefinetrial > section you are setting one to your baseline period and the other to your > stimulus period, and outputting them into separate variables. > > Hopefully this helps. Also, if you haven't done so already, I would > strongly recommend you run through the tutorial, as it may help answer > questions like this in the future (assuming I've properly identified the > issue). > > Good luck, > > Max > > > > > On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann > wrote: > >> Dear all, >> >> my name is Katrin Heimann, I am phd student at the University of Parma. >> New to Fieldtrip. >> I am doing an EEG analysis, still in the preprocessing phase. >> It is a within trials design. I would like to compare a baseline period >> with an experimental condition (visual stimulus). >> >> I have a trigger after a fixation cross, then a baseline period (approx >> 1 sec) , then the period of my stimulus (1 sec- starting with a bottom >> press (trigger)). >> >> As I would like to apply the same baseline correction for both (the >> fixationcross period) I planned to first define my trials as long trials >> including the timewindows of baseline and the stimulus period, applying >> filter and baselinecorrection on those long pieces. However, as I do not >> wanna do the artifact detection on the whole pieces (but seperately for >> baseline and stimulus, to avoid that I have to throw away too many trials) >> I would like to redefine my trials then, cutting out only baseline period >> and only stimulus period (starting with another trigger >> (triggervalue=resp).. >> >> *Unfortunately I do not understand how I can change the trigger used with >> ft redefine trial. * >> >> Anybody who could give me an example how that is done? >> Thanks a million >> Katrin >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Max Cantor > Research Assistant > Computational Neurolinguistics Lab > University of Michigan > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathykousik at gmail.com Tue May 27 20:44:15 2014 From: sarathykousik at gmail.com (kousik sarathy) Date: Tue, 27 May 2014 20:44:15 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Hey Katrin, It seems to me that Max's suggestion would suffice. But you seem to be looking for something else. Could you elaborate a little bit as to what you need? -- Regards, Kousik Sarathy, S On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann wrote: > Dear Max, thanks a lot for your prompt answer. Unfortunately this is not > what I am looking for (I found an example like this in the tutorial). I > would like to change the trigger for one of the two conditions, let it be > now the response of the subject, as this is where the stimulus actually > starts... Defining two different timewindows is not enough... Can you also > help me with that? Thanks a million! Katrin > > > 2014-05-27 18:58 GMT+02:00 Max Cantor : > > Hi Katrin, >> >> It may help to see your code, but hopefully this will help. It should be >> as simple as taking your epoched data from ft_definetrial and >> ft_preprocessing, then creating two configurations for your timewindows and >> running ft_redefinetrial. >> >> For example (from the fieldtrip tutorial, slightly simplified by me for >> explanatory purposes): >> >> *** >> >> % find the interesting segments of data >> >> cfg = []; >> % empty configuration >> cfg.dataset = 'Subject01.ds'; >> % name of CTF dataset >> cfg.trialdef.eventtype = 'backpanel trigger'; >> cfg.trialdef.prestim = 1; >> cfg.trialdef.poststim = 2; >> cfg.trialdef.eventvalue = 3; >> % event value of FIC >> cfg = ft_definetrial(cfg); >> >> % preprocess the data >> >> cfg.channel = {'MEG'}; >> dataFIC = ft_preprocessing(cfg); >> >> % define time window >> >> cfg = []; >> >> cfg.toilim = [-0.5 0]; >> dataPre = ft_redefinetrial(cfg, dataFIC); >> >> cfg.toilim = [0.8 1.3]; >> dataPost = ft_redefinetrial(cfg, dataFIC); >> >> *** >> >> So if your code resembles this, you are defining in cfg.trialdef.prestim >> and cfg.trialdef.poststim a timewindow that encompasses both your baseline >> period and stimulus period, then for cfg.toilim in the ft_redefinetrial >> section you are setting one to your baseline period and the other to your >> stimulus period, and outputting them into separate variables. >> >> Hopefully this helps. Also, if you haven't done so already, I would >> strongly recommend you run through the tutorial, as it may help answer >> questions like this in the future (assuming I've properly identified the >> issue). >> >> Good luck, >> >> Max >> >> >> >> >> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >> katrinheimann at gmail.com> wrote: >> >>> Dear all, >>> >>> my name is Katrin Heimann, I am phd student at the University of Parma. >>> New to Fieldtrip. >>> I am doing an EEG analysis, still in the preprocessing phase. >>> It is a within trials design. I would like to compare a baseline period >>> with an experimental condition (visual stimulus). >>> >>> I have a trigger after a fixation cross, then a baseline period (approx >>> 1 sec) , then the period of my stimulus (1 sec- starting with a bottom >>> press (trigger)). >>> >>> As I would like to apply the same baseline correction for both (the >>> fixationcross period) I planned to first define my trials as long trials >>> including the timewindows of baseline and the stimulus period, applying >>> filter and baselinecorrection on those long pieces. However, as I do not >>> wanna do the artifact detection on the whole pieces (but seperately for >>> baseline and stimulus, to avoid that I have to throw away too many trials) >>> I would like to redefine my trials then, cutting out only baseline period >>> and only stimulus period (starting with another trigger >>> (triggervalue=resp).. >>> >>> *Unfortunately I do not understand how I can change the trigger used >>> with ft redefine trial. * >>> >>> Anybody who could give me an example how that is done? >>> Thanks a million >>> Katrin >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Max Cantor >> Research Assistant >> Computational Neurolinguistics Lab >> University of Michigan >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcantor at umich.edu Tue May 27 21:05:17 2014 From: mcantor at umich.edu (Max Cantor) Date: Tue, 27 May 2014 15:05:17 -0400 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Ya, it would definitely help if we could see your code, but I might have another idea. When you say you have a fixation cross trigger, is this trigger being recorded from your EEG recording equipment in such a way that it can be represented as an event value in cfg.trialdef for ft_definetrial? If so, I think you may be right that it can't be changed through ft_redefinetrial (at least, as far as I can tell, no mention of this is made in the help section of the function). That being said, if you run ft_definetrial separately for both event values that should work. That being said, I may still be slightly confused about what you mean when you say you want to change the trigger. Do you mean you want to create a new trigger for your data off-line? I think it may be possible to create custom triggers off-line through fieldtrip, but it's not something I've tried personally, but if that is what you are trying to do, I could look into it. On Tue, May 27, 2014 at 2:44 PM, kousik sarathy wrote: > Hey Katrin, > > It seems to me that Max's suggestion would suffice. But you seem to be > looking for something else. Could you elaborate a little bit as to what you > need? > > -- > Regards, > Kousik Sarathy, S > > > > On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann wrote: > >> Dear Max, thanks a lot for your prompt answer. Unfortunately this is not >> what I am looking for (I found an example like this in the tutorial). I >> would like to change the trigger for one of the two conditions, let it be >> now the response of the subject, as this is where the stimulus actually >> starts... Defining two different timewindows is not enough... Can you also >> help me with that? Thanks a million! Katrin >> >> >> 2014-05-27 18:58 GMT+02:00 Max Cantor : >> >> Hi Katrin, >>> >>> It may help to see your code, but hopefully this will help. It should be >>> as simple as taking your epoched data from ft_definetrial and >>> ft_preprocessing, then creating two configurations for your timewindows and >>> running ft_redefinetrial. >>> >>> For example (from the fieldtrip tutorial, slightly simplified by me for >>> explanatory purposes): >>> >>> *** >>> >>> % find the interesting segments of data >>> >>> cfg = []; >>> % empty configuration >>> cfg.dataset = 'Subject01.ds'; >>> % name of CTF dataset >>> cfg.trialdef.eventtype = 'backpanel trigger'; >>> cfg.trialdef.prestim = 1; >>> cfg.trialdef.poststim = 2; >>> cfg.trialdef.eventvalue = 3; >>> % event value of FIC >>> cfg = ft_definetrial(cfg); >>> >>> % preprocess the data >>> >>> cfg.channel = {'MEG'}; >>> dataFIC = ft_preprocessing(cfg); >>> >>> % define time window >>> >>> cfg = []; >>> >>> cfg.toilim = [-0.5 0]; >>> dataPre = ft_redefinetrial(cfg, dataFIC); >>> >>> cfg.toilim = [0.8 1.3]; >>> dataPost = ft_redefinetrial(cfg, dataFIC); >>> >>> *** >>> >>> So if your code resembles this, you are defining in cfg.trialdef.prestim >>> and cfg.trialdef.poststim a timewindow that encompasses both your baseline >>> period and stimulus period, then for cfg.toilim in the ft_redefinetrial >>> section you are setting one to your baseline period and the other to your >>> stimulus period, and outputting them into separate variables. >>> >>> Hopefully this helps. Also, if you haven't done so already, I would >>> strongly recommend you run through the tutorial, as it may help answer >>> questions like this in the future (assuming I've properly identified the >>> issue). >>> >>> Good luck, >>> >>> Max >>> >>> >>> >>> >>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >>> katrinheimann at gmail.com> wrote: >>> >>>> Dear all, >>>> >>>> my name is Katrin Heimann, I am phd student at the University of Parma. >>>> New to Fieldtrip. >>>> I am doing an EEG analysis, still in the preprocessing phase. >>>> It is a within trials design. I would like to compare a baseline period >>>> with an experimental condition (visual stimulus). >>>> >>>> I have a trigger after a fixation cross, then a baseline period >>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a >>>> bottom press (trigger)). >>>> >>>> As I would like to apply the same baseline correction for both (the >>>> fixationcross period) I planned to first define my trials as long trials >>>> including the timewindows of baseline and the stimulus period, applying >>>> filter and baselinecorrection on those long pieces. However, as I do not >>>> wanna do the artifact detection on the whole pieces (but seperately for >>>> baseline and stimulus, to avoid that I have to throw away too many trials) >>>> I would like to redefine my trials then, cutting out only baseline period >>>> and only stimulus period (starting with another trigger >>>> (triggervalue=resp).. >>>> >>>> *Unfortunately I do not understand how I can change the trigger used >>>> with ft redefine trial. * >>>> >>>> Anybody who could give me an example how that is done? >>>> Thanks a million >>>> Katrin >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> Max Cantor >>> Research Assistant >>> Computational Neurolinguistics Lab >>> University of Michigan >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Research Assistant Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Tue May 27 23:02:41 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Tue, 27 May 2014 23:02:41 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Hi! Guys, your help is so much appreciated! So I try to be more clear!: So, yeah, Max, you are right! At the end I would like to use two different triggervalues. If I would use twice ft_definetrial then it would look like this: cfg = []; cfg.dataset = '1.raw'; cfg.trialfun = 'ft_trialfun_general'; cfg.trialdef.eventtype = 'trigger'; cfg.trialdef.eventvalue = 'stim'; % the value of the stimulus trigger for the beginning of baseline cfg.trialdef.prestim = 0.5; %the time of the fixation cross cfg.trialdef.poststim = 1.5; %the time of the baseline (plus 0.5 buffer) cfg = ft_redefinetrial(cfg); This baselinedata I could easily baselinecorrect using 100 ms of the fixationcrossperiod: cfg.channel = 'all'; cfg.preproc.demean = 'yes'; cfg.preproc.baselinewindow = [-0.1 0] cfg.preproc.bpfilter = 'yes'; cfg.preproc.bpfreq = [6 32]; The stimulusdata would be defined using a trigger that corresponds to a button press: cfg = []; cfg.dataset = '1.raw'; cfg.trialfun = 'ft_trialfun_general'; cfg.trialdef.eventtype = 'trigger'; cfg.trialdef.eventvalue = 'resp'; % the value of the stimulus trigger for the beginning of baseline cfg.trialdef.prestim = 0.5; % 0.5 sec before button press cfg.trialdef.poststim = 1.5; % 1.5 sec after button press (time that I wanna analyse) cfg = ft_redefinetrial(cfg); However here I have the problem that I cannot correct with the same baseline than before as the buttonpress is not always at the same time so I don't know when the fixationcrossperiod is located... So I thought I could first "cut" bigger pieces and then redefine trials by cutting again (after the preprocessing), then with different eventvalues ... But you say that is not possible? Thanks a lot for your help!!! Katrin 2014-05-27 21:05 GMT+02:00 Max Cantor : > Ya, it would definitely help if we could see your code, but I might have > another idea. > > When you say you have a fixation cross trigger, is this trigger being > recorded from your EEG recording equipment in such a way that it can be > represented as an event value in cfg.trialdef for ft_definetrial? If so, I > think you may be right that it can't be changed through ft_redefinetrial > (at least, as far as I can tell, no mention of this is made in the help > section of the function). That being said, if you run ft_definetrial > separately for both event values that should work. > > That being said, I may still be slightly confused about what you mean when > you say you want to change the trigger. Do you mean you want to create a > new trigger for your data off-line? I think it may be possible to create > custom triggers off-line through fieldtrip, but it's not something I've > tried personally, but if that is what you are trying to do, I could look > into it. > > > On Tue, May 27, 2014 at 2:44 PM, kousik sarathy wrote: > >> Hey Katrin, >> >> It seems to me that Max's suggestion would suffice. But you seem to be >> looking for something else. Could you elaborate a little bit as to what you >> need? >> >> -- >> Regards, >> Kousik Sarathy, S >> >> >> >> On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann > > wrote: >> >>> Dear Max, thanks a lot for your prompt answer. Unfortunately this is not >>> what I am looking for (I found an example like this in the tutorial). I >>> would like to change the trigger for one of the two conditions, let it be >>> now the response of the subject, as this is where the stimulus actually >>> starts... Defining two different timewindows is not enough... Can you also >>> help me with that? Thanks a million! Katrin >>> >>> >>> 2014-05-27 18:58 GMT+02:00 Max Cantor : >>> >>> Hi Katrin, >>>> >>>> It may help to see your code, but hopefully this will help. It should >>>> be as simple as taking your epoched data from ft_definetrial and >>>> ft_preprocessing, then creating two configurations for your timewindows and >>>> running ft_redefinetrial. >>>> >>>> For example (from the fieldtrip tutorial, slightly simplified by me for >>>> explanatory purposes): >>>> >>>> *** >>>> >>>> % find the interesting segments of data >>>> >>>> cfg = []; >>>> % empty configuration >>>> cfg.dataset = 'Subject01.ds'; >>>> % name of CTF dataset >>>> cfg.trialdef.eventtype = 'backpanel trigger'; >>>> cfg.trialdef.prestim = 1; >>>> cfg.trialdef.poststim = 2; >>>> cfg.trialdef.eventvalue = 3; >>>> % event value of FIC >>>> cfg = ft_definetrial(cfg); >>>> >>>> % preprocess the data >>>> >>>> cfg.channel = {'MEG'}; >>>> dataFIC = ft_preprocessing(cfg); >>>> >>>> % define time window >>>> >>>> cfg = []; >>>> >>>> cfg.toilim = [-0.5 0]; >>>> dataPre = ft_redefinetrial(cfg, dataFIC); >>>> >>>> cfg.toilim = [0.8 1.3]; >>>> dataPost = ft_redefinetrial(cfg, dataFIC); >>>> >>>> *** >>>> >>>> So if your code resembles this, you are defining in >>>> cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that >>>> encompasses both your baseline period and stimulus period, then for >>>> cfg.toilim in the ft_redefinetrial section you are setting one to your >>>> baseline period and the other to your stimulus period, and outputting them >>>> into separate variables. >>>> >>>> Hopefully this helps. Also, if you haven't done so already, I would >>>> strongly recommend you run through the tutorial, as it may help answer >>>> questions like this in the future (assuming I've properly identified the >>>> issue). >>>> >>>> Good luck, >>>> >>>> Max >>>> >>>> >>>> >>>> >>>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >>>> katrinheimann at gmail.com> wrote: >>>> >>>>> Dear all, >>>>> >>>>> my name is Katrin Heimann, I am phd student at the University of >>>>> Parma. New to Fieldtrip. >>>>> I am doing an EEG analysis, still in the preprocessing phase. >>>>> It is a within trials design. I would like to compare a baseline >>>>> period with an experimental condition (visual stimulus). >>>>> >>>>> I have a trigger after a fixation cross, then a baseline period >>>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a >>>>> bottom press (trigger)). >>>>> >>>>> As I would like to apply the same baseline correction for both (the >>>>> fixationcross period) I planned to first define my trials as long trials >>>>> including the timewindows of baseline and the stimulus period, applying >>>>> filter and baselinecorrection on those long pieces. However, as I do not >>>>> wanna do the artifact detection on the whole pieces (but seperately for >>>>> baseline and stimulus, to avoid that I have to throw away too many trials) >>>>> I would like to redefine my trials then, cutting out only baseline period >>>>> and only stimulus period (starting with another trigger >>>>> (triggervalue=resp).. >>>>> >>>>> *Unfortunately I do not understand how I can change the trigger used >>>>> with ft redefine trial. * >>>>> >>>>> Anybody who could give me an example how that is done? >>>>> Thanks a million >>>>> Katrin >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>> >>>> >>>> >>>> >>>> -- >>>> Max Cantor >>>> Research Assistant >>>> Computational Neurolinguistics Lab >>>> University of Michigan >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Max Cantor > Research Assistant > Computational Neurolinguistics Lab > University of Michigan > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcantor at umich.edu Tue May 27 23:39:31 2014 From: mcantor at umich.edu (Max Cantor) Date: Tue, 27 May 2014 17:39:31 -0400 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: I'm hesitant to say impossible, but I'm not sure how to do it off-hand. Also, there may be some other complications, now that I think I understand your situation better. If you're trying to cut based on the buttonpresses, which are inconsistent/unreliable, any large number of trials would make it impractical to define/redefine your epoch for each one, especially since this process would need to be customized for each subject. It might be better to keep it in a larger window, or come up with a few general windows to encompass, for instance 'early', 'on target', and 'late' button press windows. For all of the experiments I've worked on in which we've used / are using fieldtrip for our data analysis pipeline, we've never used behavioral responses for anything other than a control (as in, lack of response or incorrect response leads to rejecting the trial), so I don't really know if there is a particular systematic way to incorporate behavioral or floating triggers like what you seem to be looking to do. I might suggest, though keep in mind this is entirely speculative, rather than trying to create a pinpoint window around the response, that instead you use a wide window, and then either by viewing the data, or perhaps using independent component analysis, try to pinpoint for each subject when the button press may have occurred based on some kind of muscle artifact, and then in later timelock/time-frequency/statistical analyses specify that time window. Again, that is just me spitballing, but something post-processing may be a better solution, if the behavioral response is pivotal to the analysis of your experiment and not just for making sure the subject was paying attention / understands the prompt, as in the experiments I've worked on. On Tue, May 27, 2014 at 5:02 PM, KatrinH Heimann wrote: > Hi! Guys, your help is so much appreciated! > So I try to be more clear!: > So, yeah, Max, you are right! At the end I would like to use two different > triggervalues. > > If I would use twice ft_definetrial then it would look like this: > > cfg = []; > > cfg.dataset = '1.raw'; > > cfg.trialfun = 'ft_trialfun_general'; > > cfg.trialdef.eventtype = 'trigger'; > > cfg.trialdef.eventvalue = 'stim'; % the value of the stimulus trigger for > the beginning of baseline > > cfg.trialdef.prestim = 0.5; %the time of the fixation cross > > cfg.trialdef.poststim = 1.5; %the time of the baseline (plus 0.5 buffer) > > cfg = ft_redefinetrial(cfg); > > > This baselinedata I could easily baselinecorrect using 100 ms of the > fixationcrossperiod: > > > cfg.channel = 'all'; > > cfg.preproc.demean = 'yes'; > > cfg.preproc.baselinewindow = [-0.1 0] > > cfg.preproc.bpfilter = 'yes'; > > cfg.preproc.bpfreq = [6 32]; > > > The stimulusdata would be defined using a trigger that corresponds to a > button press: > > > cfg = []; > > cfg.dataset = '1.raw'; > > cfg.trialfun = 'ft_trialfun_general'; > > cfg.trialdef.eventtype = 'trigger'; > > cfg.trialdef.eventvalue = 'resp'; % the value of the stimulus trigger for > the beginning of baseline > > cfg.trialdef.prestim = 0.5; % 0.5 sec before button press > > cfg.trialdef.poststim = 1.5; % 1.5 sec after button press (time that I > wanna analyse) > > cfg = ft_redefinetrial(cfg); > > > However here I have the problem that I cannot correct with the same > baseline than before as the buttonpress is not always at the same time so I > don't know when the fixationcrossperiod is located... > > > So I thought I could first "cut" bigger pieces and then redefine trials by > cutting again (after the preprocessing), then with different eventvalues > ... > > But you say that is not possible? > > > > Thanks a lot for your help!!! > > > Katrin > > > > 2014-05-27 21:05 GMT+02:00 Max Cantor : > > Ya, it would definitely help if we could see your code, but I might have >> another idea. >> >> When you say you have a fixation cross trigger, is this trigger being >> recorded from your EEG recording equipment in such a way that it can be >> represented as an event value in cfg.trialdef for ft_definetrial? If so, I >> think you may be right that it can't be changed through ft_redefinetrial >> (at least, as far as I can tell, no mention of this is made in the help >> section of the function). That being said, if you run ft_definetrial >> separately for both event values that should work. >> >> That being said, I may still be slightly confused about what you mean >> when you say you want to change the trigger. Do you mean you want to create >> a new trigger for your data off-line? I think it may be possible to create >> custom triggers off-line through fieldtrip, but it's not something I've >> tried personally, but if that is what you are trying to do, I could look >> into it. >> >> >> On Tue, May 27, 2014 at 2:44 PM, kousik sarathy wrote: >> >>> Hey Katrin, >>> >>> It seems to me that Max's suggestion would suffice. But you seem to be >>> looking for something else. Could you elaborate a little bit as to what you >>> need? >>> >>> -- >>> Regards, >>> Kousik Sarathy, S >>> >>> >>> >>> On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann < >>> katrinheimann at gmail.com> wrote: >>> >>>> Dear Max, thanks a lot for your prompt answer. Unfortunately this is >>>> not what I am looking for (I found an example like this in the tutorial). I >>>> would like to change the trigger for one of the two conditions, let it be >>>> now the response of the subject, as this is where the stimulus actually >>>> starts... Defining two different timewindows is not enough... Can you also >>>> help me with that? Thanks a million! Katrin >>>> >>>> >>>> 2014-05-27 18:58 GMT+02:00 Max Cantor : >>>> >>>> Hi Katrin, >>>>> >>>>> It may help to see your code, but hopefully this will help. It should >>>>> be as simple as taking your epoched data from ft_definetrial and >>>>> ft_preprocessing, then creating two configurations for your timewindows and >>>>> running ft_redefinetrial. >>>>> >>>>> For example (from the fieldtrip tutorial, slightly simplified by me >>>>> for explanatory purposes): >>>>> >>>>> *** >>>>> >>>>> % find the interesting segments of data >>>>> >>>>> cfg = []; >>>>> % empty configuration >>>>> cfg.dataset = 'Subject01.ds'; >>>>> % name of CTF dataset >>>>> cfg.trialdef.eventtype = 'backpanel trigger'; >>>>> cfg.trialdef.prestim = 1; >>>>> cfg.trialdef.poststim = 2; >>>>> cfg.trialdef.eventvalue = 3; >>>>> % event value of FIC >>>>> cfg = ft_definetrial(cfg); >>>>> >>>>> % preprocess the data >>>>> >>>>> cfg.channel = {'MEG'}; >>>>> dataFIC = ft_preprocessing(cfg); >>>>> >>>>> % define time window >>>>> >>>>> cfg = []; >>>>> >>>>> cfg.toilim = [-0.5 0]; >>>>> dataPre = ft_redefinetrial(cfg, dataFIC); >>>>> >>>>> cfg.toilim = [0.8 1.3]; >>>>> dataPost = ft_redefinetrial(cfg, dataFIC); >>>>> >>>>> *** >>>>> >>>>> So if your code resembles this, you are defining in >>>>> cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that >>>>> encompasses both your baseline period and stimulus period, then for >>>>> cfg.toilim in the ft_redefinetrial section you are setting one to your >>>>> baseline period and the other to your stimulus period, and outputting them >>>>> into separate variables. >>>>> >>>>> Hopefully this helps. Also, if you haven't done so already, I would >>>>> strongly recommend you run through the tutorial, as it may help answer >>>>> questions like this in the future (assuming I've properly identified the >>>>> issue). >>>>> >>>>> Good luck, >>>>> >>>>> Max >>>>> >>>>> >>>>> >>>>> >>>>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >>>>> katrinheimann at gmail.com> wrote: >>>>> >>>>>> Dear all, >>>>>> >>>>>> my name is Katrin Heimann, I am phd student at the University of >>>>>> Parma. New to Fieldtrip. >>>>>> I am doing an EEG analysis, still in the preprocessing phase. >>>>>> It is a within trials design. I would like to compare a baseline >>>>>> period with an experimental condition (visual stimulus). >>>>>> >>>>>> I have a trigger after a fixation cross, then a baseline period >>>>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a >>>>>> bottom press (trigger)). >>>>>> >>>>>> As I would like to apply the same baseline correction for both (the >>>>>> fixationcross period) I planned to first define my trials as long trials >>>>>> including the timewindows of baseline and the stimulus period, applying >>>>>> filter and baselinecorrection on those long pieces. However, as I do not >>>>>> wanna do the artifact detection on the whole pieces (but seperately for >>>>>> baseline and stimulus, to avoid that I have to throw away too many trials) >>>>>> I would like to redefine my trials then, cutting out only baseline period >>>>>> and only stimulus period (starting with another trigger >>>>>> (triggervalue=resp).. >>>>>> >>>>>> *Unfortunately I do not understand how I can change the trigger used >>>>>> with ft redefine trial. * >>>>>> >>>>>> Anybody who could give me an example how that is done? >>>>>> Thanks a million >>>>>> Katrin >>>>>> >>>>>> _______________________________________________ >>>>>> fieldtrip mailing list >>>>>> fieldtrip at donders.ru.nl >>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Max Cantor >>>>> Research Assistant >>>>> Computational Neurolinguistics Lab >>>>> University of Michigan >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>> >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Max Cantor >> Research Assistant >> Computational Neurolinguistics Lab >> University of Michigan >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Research Assistant Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Wed May 28 03:06:47 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Wed, 28 May 2014 01:06:47 +0000 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: References: <1401169475061.32086@flinders.edu.au>, Message-ID: <1401239195251.79033@flinders.edu.au> ?Hey Julian, Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense. Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it? Regards, Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil Sent: Wednesday, 28 May 2014 1:55 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data Hi Tyler, I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 connections, so I hope you have a fast computer. As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website: http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). I hope that helps, if you have specific questions, feel free to ask. Best, Julian On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett > wrote: ?Hello fieldtrippers, I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. Or should you do a PCA reduction of some description beforehand. I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. Im open to all suggestions. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Wed May 28 05:56:58 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Wed, 28 May 2014 03:56:58 +0000 Subject: [FieldTrip] ft_networkanalysis over many subjects, between groups etc Message-ID: <1401249406137.6651@flinders.edu.au> ?Hello fieldtrippers, I was just wondering how to run the ft_networkanalysis function with input of many subjects. Would you run the analysis over each subject individually or can you combine subjects/groups of subjects. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Wed May 28 08:23:42 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Wed, 28 May 2014 06:23:42 +0000 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: <1401239195251.79033@flinders.edu.au> References: <1401169475061.32086@flinders.edu.au>, , <1401239195251.79033@flinders.edu.au> Message-ID: <1401258209971.36904@flinders.edu.au> Hello Julian, I think I got a few steps further into what I am trying to do, except I dont know whether I have done the correct thing or not, could you check it? % interpolate sources mri = ft_read_mri('Subject01.mri'); mri = ft_volumereslice([], mri); % read in atlas from fieldtrip template afni = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/afni/TTatlas+tlrc.HEAD')); % construct grid that lies only in grey matter cfg = []; cfg.mri = mri; cfg.grid.warpmni = 'yes'; cfg.grid = afni; grid = ft_prepare_sourcemodel( cfg); % Source Analysis: without contrasting condition cfg = []; cfg.channel = 'EEG'; cfg.method = 'lcmv'; cfg.grid = grid; cfg.vol = vol; cfg.keepfilter = 'yes'; source = ft_sourceanalysis( cfg, timelock); ? Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Tyler Grummett Sent: Wednesday, 28 May 2014 10:36 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data ?Hey Julian, Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense. Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it? Regards, Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil Sent: Wednesday, 28 May 2014 1:55 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data Hi Tyler, I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 connections, so I hope you have a fast computer. As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website: http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). I hope that helps, if you have specific questions, feel free to ask. Best, Julian On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett > wrote: ?Hello fieldtrippers, I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. Or should you do a PCA reduction of some description beforehand. I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. Im open to all suggestions. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed May 28 09:04:01 2014 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 28 May 2014 09:04:01 +0200 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: <1401239195251.79033@flinders.edu.au> References: <1401169475061.32086@flinders.edu.au>, <1401239195251.79033@flinders.edu.au> Message-ID: <8AB768DB-56A0-4081-9A58-44286BB0F9BB@gmail.com> Hi Tyler, if you follow the link, you get to the "Volumes of Interest" Data base. You can browse through the volumes by then clicking on "Alphabetic index" (http://neuro.imm.dtu.dk/services/jerne/ninf/voi/index-alphabetic.html) If you then click on a volume (e.g. "amygdala" http://neuro.imm.dtu.dk/services/jerne/ninf/voi/amygdala.html) you get to a definition of that VOI. Here, you can now download .hdr and .img files. These are ANALYZE volumes with 1s for all voxels inside a VOI and 0s outside. You can read these with ft_read_mri and normalize to the MNI brain. tl;dr You don't need any functions, just the .hdr and .img files defining the volumes Best, Julian Am 28.05.2014 um 03:06 schrieb Tyler Grummett: > ​Hey Julian, > > Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense. > > Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it? > > Regards, > > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil > Sent: Wednesday, 28 May 2014 1:55 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] granger causality on beamformer data > > Hi Tyler, > > I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 > connections, so I hope you have a fast computer. > > As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website:http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html > > The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. > > In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). > > I hope that helps, if you have specific questions, feel free to ask. > > Best, > > Julian > > > On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett wrote: > ​Hello fieldtrippers, > > I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. > > Or should you do a PCA reduction of some description beforehand. > > I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. > > Im open to all suggestions. > > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Wed May 28 09:05:52 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Wed, 28 May 2014 07:05:52 +0000 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: <1401258209971.36904@flinders.edu.au> References: <1401169475061.32086@flinders.edu.au>, , <1401239195251.79033@flinders.edu.au>,<1401258209971.36904@flinders.edu.au> Message-ID: <1401260739200.88415@flinders.edu.au> I then do the following: % look up which virtual channels correspond to particular areas % of the brain cfg = []; cfg.atlas = afni; cfg.inputcoord = 'mni'; cfg.maskparameter = 'inside'; labels = ft_volumelookup( cfg, source); % how many sources found in grey matter [tmp ind] = sort(labels.count,1,'descend'); sel = find(tmp); for j = 1:length(sel) found_areas{j,1} = [num2str(labels.count(ind(j))) ': ' labels.name{ind(j)}]; end​ However I dont know how to find out what sources are the 'found_areas', after that I dont know how to cluster the source in a particular area. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Tyler Grummett Sent: Wednesday, 28 May 2014 3:53 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data Hello Julian, I think I got a few steps further into what I am trying to do, except I dont know whether I have done the correct thing or not, could you check it? % interpolate sources mri = ft_read_mri('Subject01.mri'); mri = ft_volumereslice([], mri); % read in atlas from fieldtrip template afni = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/afni/TTatlas+tlrc.HEAD')); % construct grid that lies only in grey matter cfg = []; cfg.mri = mri; cfg.grid.warpmni = 'yes'; cfg.grid = afni; grid = ft_prepare_sourcemodel( cfg); % Source Analysis: without contrasting condition cfg = []; cfg.channel = 'EEG'; cfg.method = 'lcmv'; cfg.grid = grid; cfg.vol = vol; cfg.keepfilter = 'yes'; source = ft_sourceanalysis( cfg, timelock); ​ Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Tyler Grummett Sent: Wednesday, 28 May 2014 10:36 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data ​Hey Julian, Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense. Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it? Regards, Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil Sent: Wednesday, 28 May 2014 1:55 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data Hi Tyler, I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 connections, so I hope you have a fast computer. As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website: http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). I hope that helps, if you have specific questions, feel free to ask. Best, Julian On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett > wrote: ​Hello fieldtrippers, I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. Or should you do a PCA reduction of some description beforehand. I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. Im open to all suggestions. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Wed May 28 10:00:49 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Wed, 28 May 2014 08:00:49 +0000 Subject: [FieldTrip] ft_volumelookup source reconstruction (?) Message-ID: <1401264036357.85337@flinders.edu.au> Hello fieldtrippers, I would like to know if it is possible to determine the sources that correspond to a brain region as found by ft_volumelookup. I have used the following code: % interpolate sources mri = ft_read_mri('Subject01.mri'); mri = ft_volumereslice([], mri); % read in atlas from fieldtrip template afni = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/afni/TTatlas+tlrc.HEAD')); % construct grid that lies only in grey matter cfg = []; cfg.mri = mri; cfg.grid.warpmni = 'yes'; cfg.grid = afni; grid = ft_prepare_sourcemodel( cfg);? % Source Analysis: without contrasting condition cfg = []; cfg.channel = 'EEG'; cfg.method = 'lcmv'; cfg.grid = grid; cfg.grid.outside = []; cfg.vol = vol; cfg.keepfilter = 'yes'; source = ft_sourceanalysis( cfg, timelock); source.pos = source.pos( source.inside( :), :); % look up which virtual channels correspond to particular areas % of the brain cfg = []; cfg.atlas = afni; cfg.inputcoord = 'mni'; cfg.maskparameter = 'inside'; labels = ft_volumelookup( cfg, source); It gives me a set of labels, but I dont know what sources are located in the brain regions found. I would like to somehow combine the sources in these brain regions, so that I am left with one source per brain region. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed May 28 10:13:03 2014 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 28 May 2014 10:13:03 +0200 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: <1401260739200.88415@flinders.edu.au> References: <1401169475061.32086@flinders.edu.au>, , <1401239195251.79033@flinders.edu.au>, <1401258209971.36904@flinders.edu.au> <1401260739200.88415@flinders.edu.au> Message-ID: Hi Tyler, sorry if my description was a bit brief, so here's a bit more information. You need: 1) Virtual Electrodes (you have your 1400 electrodes, so I assume you got that far) and the .pos field with the XYZ-coordinates of the virtual electrodes. 2) A grid with a grid point for each voxel of the MNI brain (That's what you do using ft_prepare_sourcemodel) 3) A "inside" definition for your VOI (That's what you do with ft_volumelookup). Now, given that your steps 1-3 all are in the same coordinate system, you can simply use pythagoras (s = sqrt((X2-X1)^2 + (Y2-Y1)^2 + (Z2-Z1)^2) to find the minimum distance between each virtual channels of step 1 and all grid points of step 2. From the min (find the minimum distance) step, you can get the index of closest virtual channel to each grid point. You then apply this index to the output of ft_volumelookup and you have the virtual electrodes inside your ROI. Best, Julian Am 28.05.2014 um 09:05 schrieb Tyler Grummett: > I then do the following: > > % look up which virtual channels correspond to particular areas > % of the brain > cfg = []; > cfg.atlas = afni; > cfg.inputcoord = 'mni'; > cfg.maskparameter = 'inside'; > labels = ft_volumelookup( cfg, source); > > % how many sources found in grey matter > [tmp ind] = sort(labels.count,1,'descend'); > sel = find(tmp); > for j = 1:length(sel) > found_areas{j,1} = [num2str(labels.count(ind(j))) ': ' labels.name{ind(j)}]; > end​ > > However I dont know how to find out what sources are the 'found_areas', after that I dont know how to cluster the source in a particular area. > > Tyler > > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > From: fieldtrip-bounces at science.ru.nl on behalf of Tyler Grummett > Sent: Wednesday, 28 May 2014 3:53 PM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] granger causality on beamformer data > > Hello Julian, > > I think I got a few steps further into what I am trying to do, except I dont know whether I have done the correct thing or not, could you check it? > > % interpolate sources > mri = ft_read_mri('Subject01.mri'); > mri = ft_volumereslice([], mri); > > % read in atlas from fieldtrip template > afni = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/afni/TTatlas+tlrc.HEAD')); > > % construct grid that lies only in grey matter > cfg = []; > cfg.mri = mri; > cfg.grid.warpmni = 'yes'; > cfg.grid = afni; > grid = ft_prepare_sourcemodel( cfg); > > % Source Analysis: without contrasting condition > cfg = []; > cfg.channel = 'EEG'; > cfg.method = 'lcmv'; > cfg.grid = grid; > cfg.vol = vol; > cfg.keepfilter = 'yes'; > source = ft_sourceanalysis( cfg, timelock); > ​ > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > From: fieldtrip-bounces at science.ru.nl on behalf of Tyler Grummett > Sent: Wednesday, 28 May 2014 10:36 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] granger causality on beamformer data > > ​Hey Julian, > > Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense. > > Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it? > > Regards, > > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil > Sent: Wednesday, 28 May 2014 1:55 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] granger causality on beamformer data > > Hi Tyler, > > I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 > connections, so I hope you have a fast computer. > > As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website:http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html > > The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. > > In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). > > I hope that helps, if you have specific questions, feel free to ask. > > Best, > > Julian > > > On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett wrote: > ​Hello fieldtrippers, > > I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. > > Or should you do a PCA reduction of some description beforehand. > > I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. > > Im open to all suggestions. > > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From elmeri.syrjanen at gmail.com Wed May 28 12:04:33 2014 From: elmeri.syrjanen at gmail.com (=?UTF-8?Q?Elmeri_Syrj=C3=A4nen?=) Date: Wed, 28 May 2014 12:04:33 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Dear Katrin, I have recently done exactly what you are asking for unfortunately I don't have access to my code right now but basically you can do it manually if you familiarize yourself with the structure how FieldTrip stores your data. The idea is to have two trial functions, one where you define only the baseline, and one without a baseline, I created a variable cfg.trigoffset where i set the time that you wan't to epoch before the trigger and then the rest of the trialfun is as normal. I then manually in Matlab join the baseline and button press preceding structures to a new data structure. Make sure that you remove the last column in data.time and data.trial in the baseline epoch. You may also wan't to create your own data.sampleinfo with "fake" sample points (1 641, 642 1282..) because some functions (ft_channelrepair) will use sampleinfo instead of fsample to calculate your sample rate which will give you head aches down the road. Best Regards Elmeri Syrjänen On Tue, May 27, 2014 at 11:39 PM, Max Cantor wrote: > I'm hesitant to say impossible, but I'm not sure how to do it off-hand. > Also, there may be some other complications, now that I think I understand > your situation better. > > If you're trying to cut based on the buttonpresses, which are > inconsistent/unreliable, any large number of trials would make it > impractical to define/redefine your epoch for each one, especially since > this process would need to be customized for each subject. It might be > better to keep it in a larger window, or come up with a few general windows > to encompass, for instance 'early', 'on target', and 'late' button press > windows. > > For all of the experiments I've worked on in which we've used / are using > fieldtrip for our data analysis pipeline, we've never used behavioral > responses for anything other than a control (as in, lack of response or > incorrect response leads to rejecting the trial), so I don't really know if > there is a particular systematic way to incorporate behavioral or floating > triggers like what you seem to be looking to do. > > I might suggest, though keep in mind this is entirely speculative, rather > than trying to create a pinpoint window around the response, that instead > you use a wide window, and then either by viewing the data, or perhaps > using independent component analysis, try to pinpoint for each subject when > the button press may have occurred based on some kind of muscle artifact, > and then in later timelock/time-frequency/statistical analyses specify that > time window. Again, that is just me spitballing, but something > post-processing may be a better solution, if the behavioral response is > pivotal to the analysis of your experiment and not just for making sure the > subject was paying attention / understands the prompt, as in the > experiments I've worked on. > > > On Tue, May 27, 2014 at 5:02 PM, KatrinH Heimann wrote: > >> Hi! Guys, your help is so much appreciated! >> So I try to be more clear!: >> So, yeah, Max, you are right! At the end I would like to use two >> different triggervalues. >> >> If I would use twice ft_definetrial then it would look like this: >> >> cfg = []; >> >> cfg.dataset = '1.raw'; >> >> cfg.trialfun = 'ft_trialfun_general'; >> >> cfg.trialdef.eventtype = 'trigger'; >> >> cfg.trialdef.eventvalue = 'stim'; % the value of the stimulus trigger for >> the beginning of baseline >> >> cfg.trialdef.prestim = 0.5; %the time of the fixation cross >> >> cfg.trialdef.poststim = 1.5; %the time of the baseline (plus 0.5 >> buffer) >> >> cfg = ft_redefinetrial(cfg); >> >> >> This baselinedata I could easily baselinecorrect using 100 ms of the >> fixationcrossperiod: >> >> >> cfg.channel = 'all'; >> >> cfg.preproc.demean = 'yes'; >> >> cfg.preproc.baselinewindow = [-0.1 0] >> >> cfg.preproc.bpfilter = 'yes'; >> >> cfg.preproc.bpfreq = [6 32]; >> >> >> The stimulusdata would be defined using a trigger that corresponds to a >> button press: >> >> >> cfg = []; >> >> cfg.dataset = '1.raw'; >> >> cfg.trialfun = 'ft_trialfun_general'; >> >> cfg.trialdef.eventtype = 'trigger'; >> >> cfg.trialdef.eventvalue = 'resp'; % the value of the stimulus trigger for >> the beginning of baseline >> >> cfg.trialdef.prestim = 0.5; % 0.5 sec before button press >> >> cfg.trialdef.poststim = 1.5; % 1.5 sec after button press (time that I >> wanna analyse) >> >> cfg = ft_redefinetrial(cfg); >> >> >> However here I have the problem that I cannot correct with the same >> baseline than before as the buttonpress is not always at the same time so I >> don't know when the fixationcrossperiod is located... >> >> >> So I thought I could first "cut" bigger pieces and then redefine trials >> by cutting again (after the preprocessing), then with different eventvalues >> ... >> >> But you say that is not possible? >> >> >> >> Thanks a lot for your help!!! >> >> >> Katrin >> >> >> >> 2014-05-27 21:05 GMT+02:00 Max Cantor : >> >> Ya, it would definitely help if we could see your code, but I might have >>> another idea. >>> >>> When you say you have a fixation cross trigger, is this trigger being >>> recorded from your EEG recording equipment in such a way that it can be >>> represented as an event value in cfg.trialdef for ft_definetrial? If so, I >>> think you may be right that it can't be changed through ft_redefinetrial >>> (at least, as far as I can tell, no mention of this is made in the help >>> section of the function). That being said, if you run ft_definetrial >>> separately for both event values that should work. >>> >>> That being said, I may still be slightly confused about what you mean >>> when you say you want to change the trigger. Do you mean you want to create >>> a new trigger for your data off-line? I think it may be possible to create >>> custom triggers off-line through fieldtrip, but it's not something I've >>> tried personally, but if that is what you are trying to do, I could look >>> into it. >>> >>> >>> On Tue, May 27, 2014 at 2:44 PM, kousik sarathy >> > wrote: >>> >>>> Hey Katrin, >>>> >>>> It seems to me that Max's suggestion would suffice. But you seem to be >>>> looking for something else. Could you elaborate a little bit as to what you >>>> need? >>>> >>>> -- >>>> Regards, >>>> Kousik Sarathy, S >>>> >>>> >>>> >>>> On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann < >>>> katrinheimann at gmail.com> wrote: >>>> >>>>> Dear Max, thanks a lot for your prompt answer. Unfortunately this is >>>>> not what I am looking for (I found an example like this in the tutorial). I >>>>> would like to change the trigger for one of the two conditions, let it be >>>>> now the response of the subject, as this is where the stimulus actually >>>>> starts... Defining two different timewindows is not enough... Can you also >>>>> help me with that? Thanks a million! Katrin >>>>> >>>>> >>>>> 2014-05-27 18:58 GMT+02:00 Max Cantor : >>>>> >>>>> Hi Katrin, >>>>>> >>>>>> It may help to see your code, but hopefully this will help. It should >>>>>> be as simple as taking your epoched data from ft_definetrial and >>>>>> ft_preprocessing, then creating two configurations for your timewindows and >>>>>> running ft_redefinetrial. >>>>>> >>>>>> For example (from the fieldtrip tutorial, slightly simplified by me >>>>>> for explanatory purposes): >>>>>> >>>>>> *** >>>>>> >>>>>> % find the interesting segments of data >>>>>> >>>>>> cfg = []; >>>>>> % empty configuration >>>>>> cfg.dataset = 'Subject01.ds'; >>>>>> % name of CTF dataset >>>>>> cfg.trialdef.eventtype = 'backpanel trigger'; >>>>>> cfg.trialdef.prestim = 1; >>>>>> cfg.trialdef.poststim = 2; >>>>>> cfg.trialdef.eventvalue = 3; >>>>>> % event value of FIC >>>>>> cfg = ft_definetrial(cfg); >>>>>> >>>>>> % preprocess the data >>>>>> >>>>>> cfg.channel = {'MEG'}; >>>>>> dataFIC = ft_preprocessing(cfg); >>>>>> >>>>>> % define time window >>>>>> >>>>>> cfg = []; >>>>>> >>>>>> cfg.toilim = [-0.5 0]; >>>>>> dataPre = ft_redefinetrial(cfg, dataFIC); >>>>>> >>>>>> cfg.toilim = [0.8 1.3]; >>>>>> dataPost = ft_redefinetrial(cfg, dataFIC); >>>>>> >>>>>> *** >>>>>> >>>>>> So if your code resembles this, you are defining in >>>>>> cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that >>>>>> encompasses both your baseline period and stimulus period, then for >>>>>> cfg.toilim in the ft_redefinetrial section you are setting one to your >>>>>> baseline period and the other to your stimulus period, and outputting them >>>>>> into separate variables. >>>>>> >>>>>> Hopefully this helps. Also, if you haven't done so already, I would >>>>>> strongly recommend you run through the tutorial, as it may help answer >>>>>> questions like this in the future (assuming I've properly identified the >>>>>> issue). >>>>>> >>>>>> Good luck, >>>>>> >>>>>> Max >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >>>>>> katrinheimann at gmail.com> wrote: >>>>>> >>>>>>> Dear all, >>>>>>> >>>>>>> my name is Katrin Heimann, I am phd student at the University of >>>>>>> Parma. New to Fieldtrip. >>>>>>> I am doing an EEG analysis, still in the preprocessing phase. >>>>>>> It is a within trials design. I would like to compare a baseline >>>>>>> period with an experimental condition (visual stimulus). >>>>>>> >>>>>>> I have a trigger after a fixation cross, then a baseline period >>>>>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a >>>>>>> bottom press (trigger)). >>>>>>> >>>>>>> As I would like to apply the same baseline correction for both (the >>>>>>> fixationcross period) I planned to first define my trials as long trials >>>>>>> including the timewindows of baseline and the stimulus period, applying >>>>>>> filter and baselinecorrection on those long pieces. However, as I do not >>>>>>> wanna do the artifact detection on the whole pieces (but seperately for >>>>>>> baseline and stimulus, to avoid that I have to throw away too many trials) >>>>>>> I would like to redefine my trials then, cutting out only baseline period >>>>>>> and only stimulus period (starting with another trigger >>>>>>> (triggervalue=resp).. >>>>>>> >>>>>>> *Unfortunately I do not understand how I can change the trigger used >>>>>>> with ft redefine trial. * >>>>>>> >>>>>>> Anybody who could give me an example how that is done? >>>>>>> Thanks a million >>>>>>> Katrin >>>>>>> >>>>>>> _______________________________________________ >>>>>>> fieldtrip mailing list >>>>>>> fieldtrip at donders.ru.nl >>>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Max Cantor >>>>>> Research Assistant >>>>>> Computational Neurolinguistics Lab >>>>>> University of Michigan >>>>>> >>>>>> _______________________________________________ >>>>>> fieldtrip mailing list >>>>>> fieldtrip at donders.ru.nl >>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>> >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> Max Cantor >>> Research Assistant >>> Computational Neurolinguistics Lab >>> University of Michigan >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Max Cantor > Research Assistant > Computational Neurolinguistics Lab > University of Michigan > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Wed May 28 12:09:00 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Wed, 28 May 2014 12:09:00 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Dear Max, dear Elmeri! Thanks a million, that was really really helpful! :) Katrin 2014-05-28 12:04 GMT+02:00 Elmeri Syrjänen : > Dear Katrin, > > I have recently done exactly what you are asking for unfortunately I don't > have access to my code right now but basically you can do it manually if > you familiarize yourself with the structure how FieldTrip stores your data. > The idea is to have two trial functions, one where you define only the > baseline, and one without a baseline, I created a variable cfg.trigoffset > where i set the time that you wan't to epoch before the trigger and then > the rest of the trialfun is as normal. > > I then manually in Matlab join the baseline and button press preceding > structures to a new data structure. Make sure that you remove the last > column in data.time and data.trial in the baseline epoch. You may also > wan't to create your own data.sampleinfo with "fake" sample points (1 641, > 642 1282..) because some functions (ft_channelrepair) will use sampleinfo > instead of fsample to calculate your sample rate which will give you head > aches down the road. > > Best Regards > Elmeri Syrjänen > > > On Tue, May 27, 2014 at 11:39 PM, Max Cantor wrote: > >> I'm hesitant to say impossible, but I'm not sure how to do it off-hand. >> Also, there may be some other complications, now that I think I understand >> your situation better. >> >> If you're trying to cut based on the buttonpresses, which are >> inconsistent/unreliable, any large number of trials would make it >> impractical to define/redefine your epoch for each one, especially since >> this process would need to be customized for each subject. It might be >> better to keep it in a larger window, or come up with a few general windows >> to encompass, for instance 'early', 'on target', and 'late' button press >> windows. >> >> For all of the experiments I've worked on in which we've used / are using >> fieldtrip for our data analysis pipeline, we've never used behavioral >> responses for anything other than a control (as in, lack of response or >> incorrect response leads to rejecting the trial), so I don't really know if >> there is a particular systematic way to incorporate behavioral or floating >> triggers like what you seem to be looking to do. >> >> I might suggest, though keep in mind this is entirely speculative, rather >> than trying to create a pinpoint window around the response, that instead >> you use a wide window, and then either by viewing the data, or perhaps >> using independent component analysis, try to pinpoint for each subject when >> the button press may have occurred based on some kind of muscle artifact, >> and then in later timelock/time-frequency/statistical analyses specify that >> time window. Again, that is just me spitballing, but something >> post-processing may be a better solution, if the behavioral response is >> pivotal to the analysis of your experiment and not just for making sure the >> subject was paying attention / understands the prompt, as in the >> experiments I've worked on. >> >> >> On Tue, May 27, 2014 at 5:02 PM, KatrinH Heimann > > wrote: >> >>> Hi! Guys, your help is so much appreciated! >>> So I try to be more clear!: >>> So, yeah, Max, you are right! At the end I would like to use two >>> different triggervalues. >>> >>> If I would use twice ft_definetrial then it would look like this: >>> >>> cfg = []; >>> >>> cfg.dataset = '1.raw'; >>> >>> cfg.trialfun = 'ft_trialfun_general'; >>> >>> cfg.trialdef.eventtype = 'trigger'; >>> >>> cfg.trialdef.eventvalue = 'stim'; % the value of the stimulus trigger for >>> the beginning of baseline >>> >>> cfg.trialdef.prestim = 0.5; %the time of the fixation cross >>> >>> cfg.trialdef.poststim = 1.5; %the time of the baseline (plus 0.5 >>> buffer) >>> >>> cfg = ft_redefinetrial(cfg); >>> >>> >>> This baselinedata I could easily baselinecorrect using 100 ms of the >>> fixationcrossperiod: >>> >>> >>> cfg.channel = 'all'; >>> >>> cfg.preproc.demean = 'yes'; >>> >>> cfg.preproc.baselinewindow = [-0.1 0] >>> >>> cfg.preproc.bpfilter = 'yes'; >>> >>> cfg.preproc.bpfreq = [6 32]; >>> >>> >>> The stimulusdata would be defined using a trigger that corresponds to a >>> button press: >>> >>> >>> cfg = []; >>> >>> cfg.dataset = '1.raw'; >>> >>> cfg.trialfun = 'ft_trialfun_general'; >>> >>> cfg.trialdef.eventtype = 'trigger'; >>> >>> cfg.trialdef.eventvalue = 'resp'; % the value of the stimulus trigger for >>> the beginning of baseline >>> >>> cfg.trialdef.prestim = 0.5; % 0.5 sec before button press >>> >>> cfg.trialdef.poststim = 1.5; % 1.5 sec after button press (time that >>> I wanna analyse) >>> >>> cfg = ft_redefinetrial(cfg); >>> >>> >>> However here I have the problem that I cannot correct with the same >>> baseline than before as the buttonpress is not always at the same time so I >>> don't know when the fixationcrossperiod is located... >>> >>> >>> So I thought I could first "cut" bigger pieces and then redefine trials >>> by cutting again (after the preprocessing), then with different eventvalues >>> ... >>> >>> But you say that is not possible? >>> >>> >>> >>> Thanks a lot for your help!!! >>> >>> >>> Katrin >>> >>> >>> >>> 2014-05-27 21:05 GMT+02:00 Max Cantor : >>> >>> Ya, it would definitely help if we could see your code, but I might have >>>> another idea. >>>> >>>> When you say you have a fixation cross trigger, is this trigger being >>>> recorded from your EEG recording equipment in such a way that it can be >>>> represented as an event value in cfg.trialdef for ft_definetrial? If so, I >>>> think you may be right that it can't be changed through ft_redefinetrial >>>> (at least, as far as I can tell, no mention of this is made in the help >>>> section of the function). That being said, if you run ft_definetrial >>>> separately for both event values that should work. >>>> >>>> That being said, I may still be slightly confused about what you mean >>>> when you say you want to change the trigger. Do you mean you want to create >>>> a new trigger for your data off-line? I think it may be possible to create >>>> custom triggers off-line through fieldtrip, but it's not something I've >>>> tried personally, but if that is what you are trying to do, I could look >>>> into it. >>>> >>>> >>>> On Tue, May 27, 2014 at 2:44 PM, kousik sarathy < >>>> sarathykousik at gmail.com> wrote: >>>> >>>>> Hey Katrin, >>>>> >>>>> It seems to me that Max's suggestion would suffice. But you seem to be >>>>> looking for something else. Could you elaborate a little bit as to what you >>>>> need? >>>>> >>>>> -- >>>>> Regards, >>>>> Kousik Sarathy, S >>>>> >>>>> >>>>> >>>>> On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann < >>>>> katrinheimann at gmail.com> wrote: >>>>> >>>>>> Dear Max, thanks a lot for your prompt answer. Unfortunately this is >>>>>> not what I am looking for (I found an example like this in the tutorial). I >>>>>> would like to change the trigger for one of the two conditions, let it be >>>>>> now the response of the subject, as this is where the stimulus actually >>>>>> starts... Defining two different timewindows is not enough... Can you also >>>>>> help me with that? Thanks a million! Katrin >>>>>> >>>>>> >>>>>> 2014-05-27 18:58 GMT+02:00 Max Cantor : >>>>>> >>>>>> Hi Katrin, >>>>>>> >>>>>>> It may help to see your code, but hopefully this will help. It >>>>>>> should be as simple as taking your epoched data from ft_definetrial and >>>>>>> ft_preprocessing, then creating two configurations for your timewindows and >>>>>>> running ft_redefinetrial. >>>>>>> >>>>>>> For example (from the fieldtrip tutorial, slightly simplified by me >>>>>>> for explanatory purposes): >>>>>>> >>>>>>> *** >>>>>>> >>>>>>> % find the interesting segments of data >>>>>>> >>>>>>> cfg = []; >>>>>>> % empty configuration >>>>>>> cfg.dataset = 'Subject01.ds'; >>>>>>> % name of CTF dataset >>>>>>> cfg.trialdef.eventtype = 'backpanel trigger'; >>>>>>> cfg.trialdef.prestim = 1; >>>>>>> cfg.trialdef.poststim = 2; >>>>>>> cfg.trialdef.eventvalue = 3; >>>>>>> % event value of FIC >>>>>>> cfg = ft_definetrial(cfg); >>>>>>> >>>>>>> % preprocess the data >>>>>>> >>>>>>> cfg.channel = {'MEG'}; >>>>>>> dataFIC = ft_preprocessing(cfg); >>>>>>> >>>>>>> % define time window >>>>>>> >>>>>>> cfg = []; >>>>>>> >>>>>>> cfg.toilim = [-0.5 0]; >>>>>>> dataPre = ft_redefinetrial(cfg, dataFIC); >>>>>>> >>>>>>> cfg.toilim = [0.8 1.3]; >>>>>>> dataPost = ft_redefinetrial(cfg, dataFIC); >>>>>>> >>>>>>> *** >>>>>>> >>>>>>> So if your code resembles this, you are defining in >>>>>>> cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that >>>>>>> encompasses both your baseline period and stimulus period, then for >>>>>>> cfg.toilim in the ft_redefinetrial section you are setting one to your >>>>>>> baseline period and the other to your stimulus period, and outputting them >>>>>>> into separate variables. >>>>>>> >>>>>>> Hopefully this helps. Also, if you haven't done so already, I would >>>>>>> strongly recommend you run through the tutorial, as it may help answer >>>>>>> questions like this in the future (assuming I've properly identified the >>>>>>> issue). >>>>>>> >>>>>>> Good luck, >>>>>>> >>>>>>> Max >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >>>>>>> katrinheimann at gmail.com> wrote: >>>>>>> >>>>>>>> Dear all, >>>>>>>> >>>>>>>> my name is Katrin Heimann, I am phd student at the University of >>>>>>>> Parma. New to Fieldtrip. >>>>>>>> I am doing an EEG analysis, still in the preprocessing phase. >>>>>>>> It is a within trials design. I would like to compare a baseline >>>>>>>> period with an experimental condition (visual stimulus). >>>>>>>> >>>>>>>> I have a trigger after a fixation cross, then a baseline period >>>>>>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a >>>>>>>> bottom press (trigger)). >>>>>>>> >>>>>>>> As I would like to apply the same baseline correction for both >>>>>>>> (the fixationcross period) I planned to first define my trials as long >>>>>>>> trials including the timewindows of baseline and the stimulus period, >>>>>>>> applying filter and baselinecorrection on those long pieces. However, as I >>>>>>>> do not wanna do the artifact detection on the whole pieces (but seperately >>>>>>>> for baseline and stimulus, to avoid that I have to throw away too many >>>>>>>> trials) I would like to redefine my trials then, cutting out only baseline >>>>>>>> period and only stimulus period (starting with another trigger >>>>>>>> (triggervalue=resp).. >>>>>>>> >>>>>>>> *Unfortunately I do not understand how I can change the trigger >>>>>>>> used with ft redefine trial. * >>>>>>>> >>>>>>>> Anybody who could give me an example how that is done? >>>>>>>> Thanks a million >>>>>>>> Katrin >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> fieldtrip mailing list >>>>>>>> fieldtrip at donders.ru.nl >>>>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Max Cantor >>>>>>> Research Assistant >>>>>>> Computational Neurolinguistics Lab >>>>>>> University of Michigan >>>>>>> >>>>>>> _______________________________________________ >>>>>>> fieldtrip mailing list >>>>>>> fieldtrip at donders.ru.nl >>>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> fieldtrip mailing list >>>>>> fieldtrip at donders.ru.nl >>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>> >>>> >>>> >>>> >>>> -- >>>> Max Cantor >>>> Research Assistant >>>> Computational Neurolinguistics Lab >>>> University of Michigan >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Max Cantor >> Research Assistant >> Computational Neurolinguistics Lab >> University of Michigan >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed May 28 12:36:15 2014 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 28 May 2014 12:36:15 +0200 Subject: [FieldTrip] TF transform, data length + padding In-Reply-To: References: Message-ID: Hi Ulrich, one possible explanation for this could be the subtraction of the mean when calling ft_freqanalysis. If you don't specify cfg.polyremoval explicitly, the mean is removed. Of course, changing the time-dimension will change the mean and therefore result in a different value used in the ft_preproc_polyremoval - step. I tried this with a dataset, setting cfg.polyremoval to -1, thereby avoiding the demean results in virtually identical time-freq results for a short (800ms) or long (1000ms) interval. However, setting cfg.polyremoval to 0 (the default) will change the output. Also, setting the padding to 5, as you did in your code, will increase the frequency resolution which again might influence the way the low frequencies contribute to your output. If someone has a more in-depth explanation or if I got this completely wrong, please correct me! Best, Julian ******************** *Dr. Julian Keil* AG Multisensorische Integration Psychiatrische Universitätsklinik der Charité im St. Hedwig-Krankenhaus Große Hamburger Straße 5-11, Raum E 307 10115 Berlin Telefon: +49-30-2311-1879 Fax: +49-30-2311-2209 http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration On Tue, May 27, 2014 at 3:18 PM, Pomper, Ulrich wrote: > Dear community, > I have a question regarding time-frequency transformation. > The data I want to analyse last from -800 to -200 ms before stimulus > onset, I'm using a 400 ms taper. > Importantly, want to make sure that no stimulus-evoked activity leaks into > my prestim analysis. > > I first tried to cut the segment down to -1000 to 0 ms and used (zero) > padding (see figure attached, top row). This would mean that the taper, at > the last samplepoint of interest (-200ms), would include data up to 0ms > Suprisingly, I get quite different looking results when using a longer > data segment (-1200 to 0 ms) (fig. bottom row) without padding. > > Can someone explain to me what is going on here, and which approach would > be more correct? > Either, the padding in the first variant introduces artificial low > frequency activity, or the taper in the second variant uses more than > 400ms, at least for the low frequencies. > Note that the difference between conditions (left coloumn) look almost > identical, so whatever happens, it happens to both conditions very > similarly. > > I hope someone can educate me on that matter. > Cheers, Ulrich > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %% TF transform %% > > cfg = []; > cfg.continuous = 'no'; > cfg.channel = 'all'; > cfg.output = 'pow'; > cfg.method = 'mtmconvol'; > cfg.foi = 2:0.5:35; > cfg.toi = -1:0.01:0; > cfg.taper = 'hanning'; > cfg.tapsmofrq = 2; > cfg.t_ftimwin = 400 > % cfg.pad = 5; > ... > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: poly_vs_nopoly.png Type: image/png Size: 32330 bytes Desc: not available URL: From Ulrich.Pomper at charite.de Wed May 28 12:50:31 2014 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Wed, 28 May 2014 12:50:31 +0200 Subject: [FieldTrip] TF transform, data length + padding In-Reply-To: References: , Message-ID: Hey Julian, Thanks a lot for your help! Both explanations seem quite plausible. I think I will try to avoid the padding and stick with the longer data segments. Cheers, Ulrich ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] On Behalf Of Julian Keil [julian.keil at gmail.com] Sent: Wednesday, May 28, 2014 12:36 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] TF transform, data length + padding Hi Ulrich, one possible explanation for this could be the subtraction of the mean when calling ft_freqanalysis. If you don't specify cfg.polyremoval explicitly, the mean is removed. Of course, changing the time-dimension will change the mean and therefore result in a different value used in the ft_preproc_polyremoval - step. I tried this with a dataset, setting cfg.polyremoval to -1, thereby avoiding the demean results in virtually identical time-freq results for a short (800ms) or long (1000ms) interval. However, setting cfg.polyremoval to 0 (the default) will change the output. Also, setting the padding to 5, as you did in your code, will increase the frequency resolution which again might influence the way the low frequencies contribute to your output. If someone has a more in-depth explanation or if I got this completely wrong, please correct me! Best, Julian ******************** Dr. Julian Keil AG Multisensorische Integration Psychiatrische Universitätsklinik der Charité im St. Hedwig-Krankenhaus Große Hamburger Straße 5-11, Raum E 307 10115 Berlin Telefon: +49-30-2311-1879 Fax: +49-30-2311-2209 http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration On Tue, May 27, 2014 at 3:18 PM, Pomper, Ulrich > wrote: Dear community, I have a question regarding time-frequency transformation. The data I want to analyse last from -800 to -200 ms before stimulus onset, I'm using a 400 ms taper. Importantly, want to make sure that no stimulus-evoked activity leaks into my prestim analysis. I first tried to cut the segment down to -1000 to 0 ms and used (zero) padding (see figure attached, top row). This would mean that the taper, at the last samplepoint of interest (-200ms), would include data up to 0ms Suprisingly, I get quite different looking results when using a longer data segment (-1200 to 0 ms) (fig. bottom row) without padding. Can someone explain to me what is going on here, and which approach would be more correct? Either, the padding in the first variant introduces artificial low frequency activity, or the taper in the second variant uses more than 400ms, at least for the low frequencies. Note that the difference between conditions (left coloumn) look almost identical, so whatever happens, it happens to both conditions very similarly. I hope someone can educate me on that matter. Cheers, Ulrich %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% TF transform %% cfg = []; cfg.continuous = 'no'; cfg.channel = 'all'; cfg.output = 'pow'; cfg.method = 'mtmconvol'; cfg.foi = 2:0.5:35; cfg.toi = -1:0.01:0; cfg.taper = 'hanning'; cfg.tapsmofrq = 2; cfg.t_ftimwin = 400 % cfg.pad = 5; ... _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From katrinheimann at gmail.com Wed May 28 12:59:38 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Wed, 28 May 2014 12:59:38 +0200 Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? Message-ID: Dear all, another question: Is it possible to visualize the Activity power spectrum of the single components after an ICA by using ft_databrowser (or something else). I like this feature from EEG lab as I find it easier to detect artifactual components. Thanks a lot for your help Katrin -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.lozanosoldevilla at fcdonders.ru.nl Wed May 28 14:24:06 2014 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Wed, 28 May 2014 14:24:06 +0200 (CEST) Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? In-Reply-To: Message-ID: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> Hi Katrin, First, to display the independent components: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% cfg = []; cfg.layout = 'CTF151.lay'; % specify the layout file that should be used for plotting cfg.viewmode = 'component' ft_databrowser(cfg, comp) Take a look to the following example script: http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts Second, you'll have to compute the power spectrum for each independent component with ft_freqanalaysis: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% cfg = []; cfg.output = 'pow'; cfg.channel = 'all';%compute the power spectrum in all ICs cfg.method = 'mtmfft'; cfg.taper = 'hanning'; cfg.foi = 2:2:30; freq = ft_freqanalysis(cfg, comp); And you can plot the spectra: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% nsubplots = 25; nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals, type doc subplot Nfigs = ceil(size(comp.topo,1)/nsubplots); tot = Nfigs*nsubplots; rptvect = 1:size(comp.topo,1); rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post'); rptvect = reshape(rptvect,nsubplots,Nfigs)'; for r=1:size(rptvect,1); figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full screen k=0; for j=1:size(rptvect,2); if~(rptvect(r,j)==0); k=k+1; cfg=[]; cfg.channel = rptvect(r,j); subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq); end end end For the IC topos you'll follow the same logic as above but with: figure cfg = []; cfg.component = [1:20]; % specify the component(s) that should be plotted cfg.layout = 'GSN-HydroCel-129.sfp'; cfg.comment = 'no'; ft_topoplotIC(cfg, comp) I hope it helps Diego ----- Original Message ----- > From: "KatrinH Heimann" > To: "FieldTrip discussion list" > Sent: Wednesday, 28 May, 2014 12:59:38 PM > Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of > single components? > Dear all, > another question: > Is it possible to visualize the Activity power spectrum of the single > components after an ICA by using ft_databrowser (or something else). I > like this feature from EEG lab as I find it easier to detect > artifactual components. > Thanks a lot for your help > Katrin > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- PhD Student Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen NL-6525 EN Nijmegen The Netherlands http://www.ru.nl/people/donders/lozano-soldevilla-d/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Wed May 28 15:02:23 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Wed, 28 May 2014 15:02:23 +0200 Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? In-Reply-To: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> References: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Wonderfull! Thanks Diego!!!! Cheers k 2014-05-28 14:24 GMT+02:00 Lozano Soldevilla, D. (Diego) < d.lozanosoldevilla at fcdonders.ru.nl>: > Hi Katrin, > > First, to display the independent components: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > cfg = []; > cfg.layout = 'CTF151.lay'; % specify the layout file that should be used > for plotting > cfg.viewmode = 'component' > ft_databrowser(cfg, comp) > > Take a look to the following example script: > > http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts > > Second, you'll have to compute the power spectrum for each independent > component with ft_freqanalaysis: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'all';%compute the power spectrum in all ICs > cfg.method = 'mtmfft'; > cfg.taper = 'hanning'; > cfg.foi = 2:2:30; > freq = ft_freqanalysis(cfg, comp); > > And you can plot the spectra: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > nsubplots = 25; > nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals, type > doc subplot > > Nfigs = ceil(size(comp.topo,1)/nsubplots); > tot = Nfigs*nsubplots; > > rptvect = 1:size(comp.topo,1); > rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post'); > rptvect = reshape(rptvect,nsubplots,Nfigs)'; > > for r=1:size(rptvect,1); > figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full > screen > k=0; > for j=1:size(rptvect,2); > if~(rptvect(r,j)==0); > k=k+1; > cfg=[]; > cfg.channel = rptvect(r,j); > subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq); > end > end > end > > For the IC topos you'll follow the same logic as above but with: > > figure > cfg = []; > cfg.component = [1:20]; % specify the component(s) that should be > plotted > cfg.layout = 'GSN-HydroCel-129.sfp'; > cfg.comment = 'no'; > ft_topoplotIC(cfg, comp) > > I hope it helps > > Diego > ------------------------------ > > *From: *"KatrinH Heimann" > *To: *"FieldTrip discussion list" > *Sent: *Wednesday, 28 May, 2014 12:59:38 PM > *Subject: *[FieldTrip] ICA - Can I visualize Activity power spectrum of > single components? > > > Dear all, > another question: > Is it possible to visualize the Activity power spectrum of the single > components after an ICA by using ft_databrowser (or something else). I like > this feature from EEG lab as I find it easier to detect artifactual > components. > Thanks a lot for your help > Katrin > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > PhD Student > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > NL-6525 EN Nijmegen > The Netherlands > http://www.ru.nl/people/donders/lozano-soldevilla-d/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Wed May 28 15:54:24 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Wed, 28 May 2014 15:54:24 +0200 Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? In-Reply-To: References: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Diego, can I ask you another advice- this time more conceptually? I am playing with the ICA now and experience, that I get very different components depending on the artifact detection that I do beforehand. So my idea (due to the literature) was, that the ICA works better on already cleaned data. Now, as I want to do a frequency analysis afterwards, I did not want to reject parts of trials. Therefore I deleted a relatively big amount of trials in which I found muscle artifacts/drifts (Say 25% of the whole amount of trials). However, in fact I see that the ICA then does not give me easily to interpret components anymore - actually the results are better (that is easier to interpret which is artifact, which not) if I include all trials. If I only reject parts of the trials it gets even a bit better. So my question is: Shell I a) do the (stricter) artifact detection rather after the ICA or b) perform it on data with parts of trials marked as bad - in which case I also ask: can I then still reject those components in the uncleaned data (saved beforehand) so that I do not get problems with the frequency analysis afterwards...?! Thanks a lot for your help!!! Katrin 2014-05-28 15:02 GMT+02:00 KatrinH Heimann : > Wonderfull! Thanks Diego!!!! > Cheers k > > > 2014-05-28 14:24 GMT+02:00 Lozano Soldevilla, D. (Diego) < > d.lozanosoldevilla at fcdonders.ru.nl>: > > Hi Katrin, >> >> First, to display the independent components: >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> cfg = []; >> cfg.layout = 'CTF151.lay'; % specify the layout file that should be used >> for plotting >> cfg.viewmode = 'component' >> ft_databrowser(cfg, comp) >> >> Take a look to the following example script: >> >> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts >> >> Second, you'll have to compute the power spectrum for each independent >> component with ft_freqanalaysis: >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> cfg = []; >> cfg.output = 'pow'; >> cfg.channel = 'all';%compute the power spectrum in all ICs >> cfg.method = 'mtmfft'; >> cfg.taper = 'hanning'; >> cfg.foi = 2:2:30; >> freq = ft_freqanalysis(cfg, comp); >> >> And you can plot the spectra: >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> nsubplots = 25; >> nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals, >> type doc subplot >> >> Nfigs = ceil(size(comp.topo,1)/nsubplots); >> tot = Nfigs*nsubplots; >> >> rptvect = 1:size(comp.topo,1); >> rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post'); >> rptvect = reshape(rptvect,nsubplots,Nfigs)'; >> >> for r=1:size(rptvect,1); >> figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full >> screen >> k=0; >> for j=1:size(rptvect,2); >> if~(rptvect(r,j)==0); >> k=k+1; >> cfg=[]; >> cfg.channel = rptvect(r,j); >> subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq); >> end >> end >> end >> >> For the IC topos you'll follow the same logic as above but with: >> >> figure >> cfg = []; >> cfg.component = [1:20]; % specify the component(s) that should be >> plotted >> cfg.layout = 'GSN-HydroCel-129.sfp'; >> cfg.comment = 'no'; >> ft_topoplotIC(cfg, comp) >> >> I hope it helps >> >> Diego >> ------------------------------ >> >> *From: *"KatrinH Heimann" >> *To: *"FieldTrip discussion list" >> *Sent: *Wednesday, 28 May, 2014 12:59:38 PM >> *Subject: *[FieldTrip] ICA - Can I visualize Activity power spectrum of >> single components? >> >> >> Dear all, >> another question: >> Is it possible to visualize the Activity power spectrum of the single >> components after an ICA by using ft_databrowser (or something else). I like >> this feature from EEG lab as I find it easier to detect artifactual >> components. >> Thanks a lot for your help >> Katrin >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -- >> PhD Student >> Neuronal Oscillations Group >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> NL-6525 EN Nijmegen >> The Netherlands >> http://www.ru.nl/people/donders/lozano-soldevilla-d/ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Laura.Rueda at faber.kuleuven.be Wed May 28 16:29:08 2014 From: Laura.Rueda at faber.kuleuven.be (Laura Rueda Delgado) Date: Wed, 28 May 2014 14:29:08 +0000 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS Message-ID: Dear Fieldtrip users, I'm following the tutorial of beamformers (Source Analysis: Contrast activity to another interval) to estimate oscillatory sources using DICS. I've checked the surface created after segmentation and the grid generated from the electrode positions and the headmodel. That seems to work ok. However, at the step of source analysis, I get the following error: Error using * Inner matrix dimensions must agree. Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Does anybody have an idea of what I'm doing wrong? Thank you in advance for any help or suggestion! ----------------------------------------------------------------- This is my code: %% 1 - Preparation of MRI- source space % Read MRI mrifile = 'Subject01\Subject01.mri'; mri = ft_read_mri(mrifile); % Reslice to reorient images cfg = []; cfg.dim = [256 256 256]; mri = ft_volumereslice(cfg,mri); % Segment compartments cfg = []; cfg.output = {'brain','skull','scalp'}; segmentedmri = ft_volumesegment(cfg, mri); % Prepare mesh cfg=[]; cfg.tissue={'brain', 'skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); % Prepare headmodel cfg = []; cfg.method ='bemcp'; vol = ft_prepare_headmodel(cfg, bnd); %% 2- Prepare leadfield - Creating grid load elec_aligned2 % Obtained after adjusting electrodes on scalp surface interactively % Three fiducial markers were added to the electrode file, and now they're % removed so that the electrode structure has the same number of channels as the data elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); elec_aligned2.label = elec_aligned2.label(1:128, :); cfg =[]; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.grid.resolution = 10; cfg.grid.unit = 'mm'; [grid] = ft_prepare_leadfield(cfg); %% 3- Join rest and task data % data_rs: resting state data % data4: data during task dataAll = ft_appenddata([], data_rs, data4); cfg = []; cfg.method = 'mtmfft'; cfg.output = 'powandcsd'; cfg.tapsmofrq = 4; cfg.foilim = [18 18]; freqAll = ft_freqanalysis(cfg, dataAll); %---------------------------------- % all seems normal until here %---------------------------------- %% 4- Estimate source of all data cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAll = ft_sourceanalysis(cfg, freqAll); Cheers, Laura Rueda Delgado -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at gmail.com Wed May 28 16:41:54 2014 From: johanna.zumer at gmail.com (Johanna Zumer) Date: Wed, 28 May 2014 15:41:54 +0100 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Hi Laura, Does your data have the same channels as the leadfield (as the electrodes that went in to compute the leadfield)? I often see that error when there is a mismatch of channels in that way. Best, Johanna 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado < Laura.Rueda at faber.kuleuven.be>: > Dear Fieldtrip users, > > > > I’m following the tutorial of beamformers (Source Analysis: Contrast > activity to another interval) > to estimate oscillatory sources using DICS. I’ve checked the surface > created after segmentation and the grid generated from the electrode > positions and the headmodel. That seems to work ok. However, at the step of > source analysis, I get the following error: > > > > Error using * > > Inner matrix dimensions must agree. > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > Does anybody have an idea of what I’m doing wrong? > > Thank you in advance for any help or suggestion! > > > > ----------------------------------------------------------------- > > This is my code: > > %% 1 - Preparation of MRI- source space > > % Read MRI > > mrifile = 'Subject01\Subject01.mri'; > > mri = ft_read_mri(mrifile); > > % Reslice to reorient images > > cfg = []; > > cfg.dim = [256 256 256]; > > mri = ft_volumereslice(cfg,mri); > > % Segment compartments > > cfg = []; > > cfg.output = {'brain','skull','scalp'}; > > segmentedmri = ft_volumesegment(cfg, mri); > > % Prepare mesh > > cfg=[]; > > cfg.tissue={'brain', 'skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > % Prepare headmodel > > cfg = []; > > cfg.method ='bemcp'; > > vol = ft_prepare_headmodel(cfg, bnd); > > %% 2- Prepare leadfield - Creating grid > > load elec_aligned2 % Obtained after adjusting electrodes on scalp surface > interactively > > % Three fiducial markers were added to the electrode file, and now they're > > % removed so that the electrode structure has the same number of channels > as the data > > elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); > > elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); > > elec_aligned2.label = elec_aligned2.label(1:128, :); > > cfg =[]; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.grid.resolution = 10; > > cfg.grid.unit = 'mm'; > > [grid] = ft_prepare_leadfield(cfg); > > %% 3- Join rest and task data > > % data_rs: resting state data > > % data4: data during task > > dataAll = ft_appenddata([], data_rs, data4); > > cfg = []; > > cfg.method = 'mtmfft'; > > cfg.output = 'powandcsd'; > > cfg.tapsmofrq = 4; > > cfg.foilim = [18 18]; > > freqAll = ft_freqanalysis(cfg, dataAll); > > %---------------------------------- > > % all seems normal until here > > %---------------------------------- > > %% 4- Estimate source of all data > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 18; > > cfg.grid = grid; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > sourceAll = ft_sourceanalysis(cfg, freqAll); > > > > > > Cheers, > > > > Laura Rueda Delgado > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Laura.Rueda at faber.kuleuven.be Wed May 28 16:51:27 2014 From: Laura.Rueda at faber.kuleuven.be (Laura Rueda Delgado) Date: Wed, 28 May 2014 14:51:27 +0000 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Dear Johanna, Thank you for your suggestion. On step 2 in the code, I select from the elec structure the channels that are included in the frequency data. So the elec structure used for preparing the leadfield has 128 electrodes, the same as the data (data_rs, data 4, and therefore freqAll). I checked this precisely because I read a previous thread discussing that issue. Best regards, Laura Rueda Delgado From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer Sent: woensdag 28 mei 2014 16:42 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Hi Laura, Does your data have the same channels as the leadfield (as the electrodes that went in to compute the leadfield)? I often see that error when there is a mismatch of channels in that way. Best, Johanna 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado >: Dear Fieldtrip users, I’m following the tutorial of beamformers (Source Analysis: Contrast activity to another interval) to estimate oscillatory sources using DICS. I’ve checked the surface created after segmentation and the grid generated from the electrode positions and the headmodel. That seems to work ok. However, at the step of source analysis, I get the following error: Error using * Inner matrix dimensions must agree. Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Does anybody have an idea of what I’m doing wrong? Thank you in advance for any help or suggestion! ----------------------------------------------------------------- This is my code: %% 1 - Preparation of MRI- source space % Read MRI mrifile = 'Subject01\Subject01.mri'; mri = ft_read_mri(mrifile); % Reslice to reorient images cfg = []; cfg.dim = [256 256 256]; mri = ft_volumereslice(cfg,mri); % Segment compartments cfg = []; cfg.output = {'brain','skull','scalp'}; segmentedmri = ft_volumesegment(cfg, mri); % Prepare mesh cfg=[]; cfg.tissue={'brain', 'skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); % Prepare headmodel cfg = []; cfg.method ='bemcp'; vol = ft_prepare_headmodel(cfg, bnd); %% 2- Prepare leadfield - Creating grid load elec_aligned2 % Obtained after adjusting electrodes on scalp surface interactively % Three fiducial markers were added to the electrode file, and now they're % removed so that the electrode structure has the same number of channels as the data elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); elec_aligned2.label = elec_aligned2.label(1:128, :); cfg =[]; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.grid.resolution = 10; cfg.grid.unit = 'mm'; [grid] = ft_prepare_leadfield(cfg); %% 3- Join rest and task data % data_rs: resting state data % data4: data during task dataAll = ft_appenddata([], data_rs, data4); cfg = []; cfg.method = 'mtmfft'; cfg.output = 'powandcsd'; cfg.tapsmofrq = 4; cfg.foilim = [18 18]; freqAll = ft_freqanalysis(cfg, dataAll); %---------------------------------- % all seems normal until here %---------------------------------- %% 4- Estimate source of all data cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAll = ft_sourceanalysis(cfg, freqAll); Cheers, Laura Rueda Delgado _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcantor at umich.edu Wed May 28 16:24:38 2014 From: mcantor at umich.edu (Max Cantor) Date: Wed, 28 May 2014 10:24:38 -0400 Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? In-Reply-To: References: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: What we usually do before ICA is a rough pass removing the most extremely artifactual trials or channels. For instance, if you see artifacts that are not systematic and are affecting multiple sensors, it may be something like a head scratch that is affecting multiple sensors independently, and so would be turned into multiple ICA components, and so removing these would be beneficial. That being said, anything that might be, for instance, an ECG or EOG artifact, is best not cleaned before ICA, because the whole point of ICA components is to find artifacts that are independent from each other, but dependent to the source (in other words, a systematic artifact as the result of a blink) and remove them without having to throw away the rest of the good data within that trial/channel. In other words, if you're doing a comprehensive artifact rejection before ICA, it makes sense that you aren't necessarily picking up artifactual components, since you might already be removing the data that would be turned into an artifactual component. On Wed, May 28, 2014 at 9:54 AM, KatrinH Heimann wrote: > Diego, can I ask you another advice- this time more conceptually? I am > playing with the ICA now and experience, that I get very different > components depending on the artifact detection that I do beforehand. So my > idea (due to the literature) was, that the ICA works better on already > cleaned data. Now, as I want to do a frequency analysis afterwards, I did > not want to reject parts of trials. Therefore I deleted a relatively big > amount of trials in which I found muscle artifacts/drifts (Say 25% of the > whole amount of trials). However, in fact I see that the ICA then does not > give me easily to interpret components anymore - actually the results are > better (that is easier to interpret which is artifact, which not) if I > include all trials. If I only reject parts of the trials it gets even a bit > better. So my question is: Shell I a) do the (stricter) artifact detection > rather after the ICA or b) perform it on data with parts of trials marked > as bad - in which case I also ask: can I then still reject those components > in the uncleaned data (saved beforehand) so that I do not get problems with > the frequency analysis afterwards...?! > Thanks a lot for your help!!! Katrin > > > 2014-05-28 15:02 GMT+02:00 KatrinH Heimann : > > Wonderfull! Thanks Diego!!!! >> Cheers k >> >> >> 2014-05-28 14:24 GMT+02:00 Lozano Soldevilla, D. (Diego) < >> d.lozanosoldevilla at fcdonders.ru.nl>: >> >> Hi Katrin, >>> >>> First, to display the independent components: >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> cfg = []; >>> cfg.layout = 'CTF151.lay'; % specify the layout file that should be used >>> for plotting >>> cfg.viewmode = 'component' >>> ft_databrowser(cfg, comp) >>> >>> Take a look to the following example script: >>> >>> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts >>> >>> Second, you'll have to compute the power spectrum for each independent >>> component with ft_freqanalaysis: >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> cfg = []; >>> cfg.output = 'pow'; >>> cfg.channel = 'all';%compute the power spectrum in all ICs >>> cfg.method = 'mtmfft'; >>> cfg.taper = 'hanning'; >>> cfg.foi = 2:2:30; >>> freq = ft_freqanalysis(cfg, comp); >>> >>> And you can plot the spectra: >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> nsubplots = 25; >>> nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals, >>> type doc subplot >>> >>> Nfigs = ceil(size(comp.topo,1)/nsubplots); >>> tot = Nfigs*nsubplots; >>> >>> rptvect = 1:size(comp.topo,1); >>> rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post'); >>> rptvect = reshape(rptvect,nsubplots,Nfigs)'; >>> >>> for r=1:size(rptvect,1); >>> figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full >>> screen >>> k=0; >>> for j=1:size(rptvect,2); >>> if~(rptvect(r,j)==0); >>> k=k+1; >>> cfg=[]; >>> cfg.channel = rptvect(r,j); >>> subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq); >>> end >>> end >>> end >>> >>> For the IC topos you'll follow the same logic as above but with: >>> >>> figure >>> cfg = []; >>> cfg.component = [1:20]; % specify the component(s) that should be >>> plotted >>> cfg.layout = 'GSN-HydroCel-129.sfp'; >>> cfg.comment = 'no'; >>> ft_topoplotIC(cfg, comp) >>> >>> I hope it helps >>> >>> Diego >>> ------------------------------ >>> >>> *From: *"KatrinH Heimann" >>> *To: *"FieldTrip discussion list" >>> *Sent: *Wednesday, 28 May, 2014 12:59:38 PM >>> *Subject: *[FieldTrip] ICA - Can I visualize Activity power spectrum of >>> single components? >>> >>> >>> Dear all, >>> another question: >>> Is it possible to visualize the Activity power spectrum of the single >>> components after an ICA by using ft_databrowser (or something else). I like >>> this feature from EEG lab as I find it easier to detect artifactual >>> components. >>> Thanks a lot for your help >>> Katrin >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> -- >>> PhD Student >>> Neuronal Oscillations Group >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognitive Neuroimaging >>> Radboud University Nijmegen >>> NL-6525 EN Nijmegen >>> The Netherlands >>> http://www.ru.nl/people/donders/lozano-soldevilla-d/ >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Research Assistant Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathykousik at gmail.com Wed May 28 17:09:37 2014 From: sarathykousik at gmail.com (kousik sarathy) Date: Wed, 28 May 2014 17:09:37 +0200 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Hey Laura, I too had the same suggestion as Johanna's. Another thing to check would be if the labels that you used for the leadfield estimation are the same as the freq data. I guess FT at some point would also check this to extract the indices. -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 4:51 PM, Laura Rueda Delgado < Laura.Rueda at faber.kuleuven.be> wrote: > Dear Johanna, > > > > Thank you for your suggestion. > > > > On step 2 in the code, I select from the elec structure the channels that > are included in the frequency data. So the elec structure used for > preparing the leadfield has 128 electrodes, the same as the data (data_rs, > data 4, and therefore freqAll). I checked this precisely because I read a > previous thread discussing that issue. > > > > Best regards, > > > > Laura Rueda Delgado > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *Johanna Zumer > *Sent:* woensdag 28 mei 2014 16:42 > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Hi Laura, > > > > Does your data have the same channels as the leadfield (as the electrodes > that went in to compute the leadfield)? I often see that error when there > is a mismatch of channels in that way. > > > > Best, > > Johanna > > > > 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be>: > > Dear Fieldtrip users, > > > > I’m following the tutorial of beamformers (Source Analysis: Contrast > activity to another interval) > to estimate oscillatory sources using DICS. I’ve checked the surface > created after segmentation and the grid generated from the electrode > positions and the headmodel. That seems to work ok. However, at the step of > source analysis, I get the following error: > > > > Error using * > > Inner matrix dimensions must agree. > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > Does anybody have an idea of what I’m doing wrong? > > Thank you in advance for any help or suggestion! > > > > ----------------------------------------------------------------- > > This is my code: > > %% 1 - Preparation of MRI- source space > > % Read MRI > > mrifile = 'Subject01\Subject01.mri'; > > mri = ft_read_mri(mrifile); > > % Reslice to reorient images > > cfg = []; > > cfg.dim = [256 256 256]; > > mri = ft_volumereslice(cfg,mri); > > % Segment compartments > > cfg = []; > > cfg.output = {'brain','skull','scalp'}; > > segmentedmri = ft_volumesegment(cfg, mri); > > % Prepare mesh > > cfg=[]; > > cfg.tissue={'brain', 'skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > % Prepare headmodel > > cfg = []; > > cfg.method ='bemcp'; > > vol = ft_prepare_headmodel(cfg, bnd); > > %% 2- Prepare leadfield - Creating grid > > load elec_aligned2 % Obtained after adjusting electrodes on scalp surface > interactively > > % Three fiducial markers were added to the electrode file, and now they're > > % removed so that the electrode structure has the same number of channels > as the data > > elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); > > elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); > > elec_aligned2.label = elec_aligned2.label(1:128, :); > > cfg =[]; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.grid.resolution = 10; > > cfg.grid.unit = 'mm'; > > [grid] = ft_prepare_leadfield(cfg); > > %% 3- Join rest and task data > > % data_rs: resting state data > > % data4: data during task > > dataAll = ft_appenddata([], data_rs, data4); > > cfg = []; > > cfg.method = 'mtmfft'; > > cfg.output = 'powandcsd'; > > cfg.tapsmofrq = 4; > > cfg.foilim = [18 18]; > > freqAll = ft_freqanalysis(cfg, dataAll); > > %---------------------------------- > > % all seems normal until here > > %---------------------------------- > > %% 4- Estimate source of all data > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 18; > > cfg.grid = grid; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > sourceAll = ft_sourceanalysis(cfg, freqAll); > > > > > > Cheers, > > > > Laura Rueda Delgado > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Laura.Rueda at faber.kuleuven.be Wed May 28 17:31:40 2014 From: Laura.Rueda at faber.kuleuven.be (Laura Rueda Delgado) Date: Wed, 28 May 2014 15:31:40 +0000 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Dear Kousik, I checked the labels and they were the same, except for whether they were in capital letters. So I added the following before ft_sourceanalysis: freqAll.label=cellfun(@upper, freqAll.label, 'UniformOutput', 0); freqAll.labelcmb=cellfun(@upper, freqAll.labelcmb, 'UniformOutput', 0); This way the labels of the elec structure and freqAll are in capital letters. And now I get a different error (although still within the function beamformer_dics): Error using svd Input to SVD must not contain NaN or Inf. Error in beamformer_dics>pinv (line 650) [U,S,V] = svd(A,0); Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); What could it be? Best regards, Laura From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of kousik sarathy Sent: woensdag 28 mei 2014 17:10 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Hey Laura, I too had the same suggestion as Johanna's. Another thing to check would be if the labels that you used for the leadfield estimation are the same as the freq data. I guess FT at some point would also check this to extract the indices. -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 4:51 PM, Laura Rueda Delgado > wrote: Dear Johanna, Thank you for your suggestion. On step 2 in the code, I select from the elec structure the channels that are included in the frequency data. So the elec structure used for preparing the leadfield has 128 electrodes, the same as the data (data_rs, data 4, and therefore freqAll). I checked this precisely because I read a previous thread discussing that issue. Best regards, Laura Rueda Delgado From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer Sent: woensdag 28 mei 2014 16:42 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Hi Laura, Does your data have the same channels as the leadfield (as the electrodes that went in to compute the leadfield)? I often see that error when there is a mismatch of channels in that way. Best, Johanna 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado >: Dear Fieldtrip users, I’m following the tutorial of beamformers (Source Analysis: Contrast activity to another interval) to estimate oscillatory sources using DICS. I’ve checked the surface created after segmentation and the grid generated from the electrode positions and the headmodel. That seems to work ok. However, at the step of source analysis, I get the following error: Error using * Inner matrix dimensions must agree. Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Does anybody have an idea of what I’m doing wrong? Thank you in advance for any help or suggestion! ----------------------------------------------------------------- This is my code: %% 1 - Preparation of MRI- source space % Read MRI mrifile = 'Subject01\Subject01.mri'; mri = ft_read_mri(mrifile); % Reslice to reorient images cfg = []; cfg.dim = [256 256 256]; mri = ft_volumereslice(cfg,mri); % Segment compartments cfg = []; cfg.output = {'brain','skull','scalp'}; segmentedmri = ft_volumesegment(cfg, mri); % Prepare mesh cfg=[]; cfg.tissue={'brain', 'skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); % Prepare headmodel cfg = []; cfg.method ='bemcp'; vol = ft_prepare_headmodel(cfg, bnd); %% 2- Prepare leadfield - Creating grid load elec_aligned2 % Obtained after adjusting electrodes on scalp surface interactively % Three fiducial markers were added to the electrode file, and now they're % removed so that the electrode structure has the same number of channels as the data elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); elec_aligned2.label = elec_aligned2.label(1:128, :); cfg =[]; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.grid.resolution = 10; cfg.grid.unit = 'mm'; [grid] = ft_prepare_leadfield(cfg); %% 3- Join rest and task data % data_rs: resting state data % data4: data during task dataAll = ft_appenddata([], data_rs, data4); cfg = []; cfg.method = 'mtmfft'; cfg.output = 'powandcsd'; cfg.tapsmofrq = 4; cfg.foilim = [18 18]; freqAll = ft_freqanalysis(cfg, dataAll); %---------------------------------- % all seems normal until here %---------------------------------- %% 4- Estimate source of all data cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAll = ft_sourceanalysis(cfg, freqAll); Cheers, Laura Rueda Delgado _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From ayobimpe2004 at hotmail.com Wed May 28 17:36:39 2014 From: ayobimpe2004 at hotmail.com (Azeez Adebimpe) Date: Wed, 28 May 2014 16:36:39 +0100 Subject: [FieldTrip] source resampling Message-ID: Dear all I calculated my leadfield or grid with 8 mm resolution. Please is there anyway after or before source interpolation or before to resample the source to 1 mm resolution. merci! Azeez A. Adebimpe "Knowledge and good manner, the beauty of a man" -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathykousik at gmail.com Wed May 28 17:37:17 2014 From: sarathykousik at gmail.com (kousik sarathy) Date: Wed, 28 May 2014 17:37:17 +0200 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Ah. Interesting. Good that error changes. So that was the problem before. Now, can you check if your Freq matrices contain any NaN's (isnan(freqAll))? It can happen sometimes. -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 5:31 PM, Laura Rueda Delgado < Laura.Rueda at faber.kuleuven.be> wrote: > Dear Kousik, > > > > I checked the labels and they were the same, except for whether they were > in capital letters. So I added the following before ft_sourceanalysis: > > > > freqAll.label=cellfun(@upper, freqAll.label, 'UniformOutput', 0); > > freqAll.labelcmb=cellfun(@upper, freqAll.labelcmb, 'UniformOutput', 0); > > > > This way the labels of the elec structure and freqAll are in capital > letters. > > > > And now I get a different error (although still within the function > beamformer_dics): > > > > Error using svd > > Input to SVD must not contain NaN or Inf. > > > > Error in beamformer_dics>pinv (line 650) > > [U,S,V] = svd(A,0); > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > > > What could it be? > > > > Best regards, > > Laura > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *kousik sarathy > *Sent:* woensdag 28 mei 2014 17:10 > > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Hey Laura, > > > > I too had the same suggestion as Johanna's. > > > > Another thing to check would be if the labels that you used for the > leadfield estimation are the same as the freq data. I guess FT at some > point would also check this to extract the indices. > > > -- > > Regards, > > Kousik Sarathy, S > > > > > > On Wed, May 28, 2014 at 4:51 PM, Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be> wrote: > > Dear Johanna, > > > > Thank you for your suggestion. > > > > On step 2 in the code, I select from the elec structure the channels that > are included in the frequency data. So the elec structure used for > preparing the leadfield has 128 electrodes, the same as the data (data_rs, > data 4, and therefore freqAll). I checked this precisely because I read a > previous thread discussing that issue. > > > > Best regards, > > > > Laura Rueda Delgado > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *Johanna Zumer > *Sent:* woensdag 28 mei 2014 16:42 > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Hi Laura, > > > > Does your data have the same channels as the leadfield (as the electrodes > that went in to compute the leadfield)? I often see that error when there > is a mismatch of channels in that way. > > > > Best, > > Johanna > > > > 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be>: > > Dear Fieldtrip users, > > > > I’m following the tutorial of beamformers (Source Analysis: Contrast > activity to another interval) > to estimate oscillatory sources using DICS. I’ve checked the surface > created after segmentation and the grid generated from the electrode > positions and the headmodel. That seems to work ok. However, at the step of > source analysis, I get the following error: > > > > Error using * > > Inner matrix dimensions must agree. > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > Does anybody have an idea of what I’m doing wrong? > > Thank you in advance for any help or suggestion! > > > > ----------------------------------------------------------------- > > This is my code: > > %% 1 - Preparation of MRI- source space > > % Read MRI > > mrifile = 'Subject01\Subject01.mri'; > > mri = ft_read_mri(mrifile); > > % Reslice to reorient images > > cfg = []; > > cfg.dim = [256 256 256]; > > mri = ft_volumereslice(cfg,mri); > > % Segment compartments > > cfg = []; > > cfg.output = {'brain','skull','scalp'}; > > segmentedmri = ft_volumesegment(cfg, mri); > > % Prepare mesh > > cfg=[]; > > cfg.tissue={'brain', 'skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > % Prepare headmodel > > cfg = []; > > cfg.method ='bemcp'; > > vol = ft_prepare_headmodel(cfg, bnd); > > %% 2- Prepare leadfield - Creating grid > > load elec_aligned2 % Obtained after adjusting electrodes on scalp surface > interactively > > % Three fiducial markers were added to the electrode file, and now they're > > % removed so that the electrode structure has the same number of channels > as the data > > elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); > > elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); > > elec_aligned2.label = elec_aligned2.label(1:128, :); > > cfg =[]; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.grid.resolution = 10; > > cfg.grid.unit = 'mm'; > > [grid] = ft_prepare_leadfield(cfg); > > %% 3- Join rest and task data > > % data_rs: resting state data > > % data4: data during task > > dataAll = ft_appenddata([], data_rs, data4); > > cfg = []; > > cfg.method = 'mtmfft'; > > cfg.output = 'powandcsd'; > > cfg.tapsmofrq = 4; > > cfg.foilim = [18 18]; > > freqAll = ft_freqanalysis(cfg, dataAll); > > %---------------------------------- > > % all seems normal until here > > %---------------------------------- > > %% 4- Estimate source of all data > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 18; > > cfg.grid = grid; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > sourceAll = ft_sourceanalysis(cfg, freqAll); > > > > > > Cheers, > > > > Laura Rueda Delgado > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Wed May 28 17:50:09 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Wed, 28 May 2014 17:50:09 +0200 Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? In-Reply-To: References: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Thanks Max! :) Katrin 2014-05-28 16:24 GMT+02:00 Max Cantor : > What we usually do before ICA is a rough pass removing the most extremely > artifactual trials or channels. For instance, if you see artifacts that are > not systematic and are affecting multiple sensors, it may be something like > a head scratch that is affecting multiple sensors independently, and so > would be turned into multiple ICA components, and so removing these would > be beneficial. That being said, anything that might be, for instance, an > ECG or EOG artifact, is best not cleaned before ICA, because the whole > point of ICA components is to find artifacts that are independent from each > other, but dependent to the source (in other words, a systematic artifact > as the result of a blink) and remove them without having to throw away the > rest of the good data within that trial/channel. In other words, if you're > doing a comprehensive artifact rejection before ICA, it makes sense that > you aren't necessarily picking up artifactual components, since you might > already be removing the data that would be turned into an artifactual > component. > > > On Wed, May 28, 2014 at 9:54 AM, KatrinH Heimann wrote: > >> Diego, can I ask you another advice- this time more conceptually? I am >> playing with the ICA now and experience, that I get very different >> components depending on the artifact detection that I do beforehand. So my >> idea (due to the literature) was, that the ICA works better on already >> cleaned data. Now, as I want to do a frequency analysis afterwards, I did >> not want to reject parts of trials. Therefore I deleted a relatively big >> amount of trials in which I found muscle artifacts/drifts (Say 25% of the >> whole amount of trials). However, in fact I see that the ICA then does not >> give me easily to interpret components anymore - actually the results are >> better (that is easier to interpret which is artifact, which not) if I >> include all trials. If I only reject parts of the trials it gets even a bit >> better. So my question is: Shell I a) do the (stricter) artifact detection >> rather after the ICA or b) perform it on data with parts of trials marked >> as bad - in which case I also ask: can I then still reject those components >> in the uncleaned data (saved beforehand) so that I do not get problems with >> the frequency analysis afterwards...?! >> Thanks a lot for your help!!! Katrin >> >> >> 2014-05-28 15:02 GMT+02:00 KatrinH Heimann : >> >> Wonderfull! Thanks Diego!!!! >>> Cheers k >>> >>> >>> 2014-05-28 14:24 GMT+02:00 Lozano Soldevilla, D. (Diego) < >>> d.lozanosoldevilla at fcdonders.ru.nl>: >>> >>> Hi Katrin, >>>> >>>> First, to display the independent components: >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> cfg = []; >>>> cfg.layout = 'CTF151.lay'; % specify the layout file that should be >>>> used for plotting >>>> cfg.viewmode = 'component' >>>> ft_databrowser(cfg, comp) >>>> >>>> Take a look to the following example script: >>>> >>>> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts >>>> >>>> Second, you'll have to compute the power spectrum for each independent >>>> component with ft_freqanalaysis: >>>> >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> cfg = []; >>>> cfg.output = 'pow'; >>>> cfg.channel = 'all';%compute the power spectrum in all ICs >>>> cfg.method = 'mtmfft'; >>>> cfg.taper = 'hanning'; >>>> cfg.foi = 2:2:30; >>>> freq = ft_freqanalysis(cfg, comp); >>>> >>>> And you can plot the spectra: >>>> >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> nsubplots = 25; >>>> nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals, >>>> type doc subplot >>>> >>>> Nfigs = ceil(size(comp.topo,1)/nsubplots); >>>> tot = Nfigs*nsubplots; >>>> >>>> rptvect = 1:size(comp.topo,1); >>>> rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post'); >>>> rptvect = reshape(rptvect,nsubplots,Nfigs)'; >>>> >>>> for r=1:size(rptvect,1); >>>> figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full >>>> screen >>>> k=0; >>>> for j=1:size(rptvect,2); >>>> if~(rptvect(r,j)==0); >>>> k=k+1; >>>> cfg=[]; >>>> cfg.channel = rptvect(r,j); >>>> subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq); >>>> end >>>> end >>>> end >>>> >>>> For the IC topos you'll follow the same logic as above but with: >>>> >>>> figure >>>> cfg = []; >>>> cfg.component = [1:20]; % specify the component(s) that should be >>>> plotted >>>> cfg.layout = 'GSN-HydroCel-129.sfp'; >>>> cfg.comment = 'no'; >>>> ft_topoplotIC(cfg, comp) >>>> >>>> I hope it helps >>>> >>>> Diego >>>> ------------------------------ >>>> >>>> *From: *"KatrinH Heimann" >>>> *To: *"FieldTrip discussion list" >>>> *Sent: *Wednesday, 28 May, 2014 12:59:38 PM >>>> *Subject: *[FieldTrip] ICA - Can I visualize Activity power spectrum >>>> of single components? >>>> >>>> >>>> Dear all, >>>> another question: >>>> Is it possible to visualize the Activity power spectrum of the single >>>> components after an ICA by using ft_databrowser (or something else). I like >>>> this feature from EEG lab as I find it easier to detect artifactual >>>> components. >>>> Thanks a lot for your help >>>> Katrin >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> >>>> >>>> -- >>>> PhD Student >>>> Neuronal Oscillations Group >>>> Donders Institute for Brain, Cognition and Behaviour >>>> Centre for Cognitive Neuroimaging >>>> Radboud University Nijmegen >>>> NL-6525 EN Nijmegen >>>> The Netherlands >>>> http://www.ru.nl/people/donders/lozano-soldevilla-d/ >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Max Cantor > Research Assistant > Computational Neurolinguistics Lab > University of Michigan > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Laura.Rueda at faber.kuleuven.be Wed May 28 18:01:52 2014 From: Laura.Rueda at faber.kuleuven.be (Laura Rueda Delgado) Date: Wed, 28 May 2014 16:01:52 +0000 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Dear Kousik, I checked for NaN and Inf values in powspctrm and crsspctrm of freqAll. There are none. However, I checked for NaN values in grid.leadfield and it has some. I thought that these were NaN values in the points of the grid outside a brain region, but I might be mistaken. grid = xgrid: [-58 -48 -38 -28 -18 -8 2 12 22 32 42 52 62 72 82 92 102] ygrid: [-61 -51 -41 -31 -21 -11 -1 9 19 29 39 49 59] zgrid: [-13 -3 7 17 27 37 47 57 67 77 87 97 107 117] dim: [17 13 14] pos: [3094x3 double] unit: 'mm' inside: [1x1516 double] outside: [1x1578 double] cfg: [1x1 struct] leadfield: {1x3094 cell} Best regards, Laura Rueda Delgado From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of kousik sarathy Sent: woensdag 28 mei 2014 17:37 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Ah. Interesting. Good that error changes. So that was the problem before. Now, can you check if your Freq matrices contain any NaN's (isnan(freqAll))? It can happen sometimes. -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 5:31 PM, Laura Rueda Delgado > wrote: Dear Kousik, I checked the labels and they were the same, except for whether they were in capital letters. So I added the following before ft_sourceanalysis: freqAll.label=cellfun(@upper, freqAll.label, 'UniformOutput', 0); freqAll.labelcmb=cellfun(@upper, freqAll.labelcmb, 'UniformOutput', 0); This way the labels of the elec structure and freqAll are in capital letters. And now I get a different error (although still within the function beamformer_dics): Error using svd Input to SVD must not contain NaN or Inf. Error in beamformer_dics>pinv (line 650) [U,S,V] = svd(A,0); Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); What could it be? Best regards, Laura From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of kousik sarathy Sent: woensdag 28 mei 2014 17:10 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Hey Laura, I too had the same suggestion as Johanna's. Another thing to check would be if the labels that you used for the leadfield estimation are the same as the freq data. I guess FT at some point would also check this to extract the indices. -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 4:51 PM, Laura Rueda Delgado > wrote: Dear Johanna, Thank you for your suggestion. On step 2 in the code, I select from the elec structure the channels that are included in the frequency data. So the elec structure used for preparing the leadfield has 128 electrodes, the same as the data (data_rs, data 4, and therefore freqAll). I checked this precisely because I read a previous thread discussing that issue. Best regards, Laura Rueda Delgado From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer Sent: woensdag 28 mei 2014 16:42 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Hi Laura, Does your data have the same channels as the leadfield (as the electrodes that went in to compute the leadfield)? I often see that error when there is a mismatch of channels in that way. Best, Johanna 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado >: Dear Fieldtrip users, I’m following the tutorial of beamformers (Source Analysis: Contrast activity to another interval) to estimate oscillatory sources using DICS. I’ve checked the surface created after segmentation and the grid generated from the electrode positions and the headmodel. That seems to work ok. However, at the step of source analysis, I get the following error: Error using * Inner matrix dimensions must agree. Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Does anybody have an idea of what I’m doing wrong? Thank you in advance for any help or suggestion! ----------------------------------------------------------------- This is my code: %% 1 - Preparation of MRI- source space % Read MRI mrifile = 'Subject01\Subject01.mri'; mri = ft_read_mri(mrifile); % Reslice to reorient images cfg = []; cfg.dim = [256 256 256]; mri = ft_volumereslice(cfg,mri); % Segment compartments cfg = []; cfg.output = {'brain','skull','scalp'}; segmentedmri = ft_volumesegment(cfg, mri); % Prepare mesh cfg=[]; cfg.tissue={'brain', 'skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); % Prepare headmodel cfg = []; cfg.method ='bemcp'; vol = ft_prepare_headmodel(cfg, bnd); %% 2- Prepare leadfield - Creating grid load elec_aligned2 % Obtained after adjusting electrodes on scalp surface interactively % Three fiducial markers were added to the electrode file, and now they're % removed so that the electrode structure has the same number of channels as the data elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); elec_aligned2.label = elec_aligned2.label(1:128, :); cfg =[]; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.grid.resolution = 10; cfg.grid.unit = 'mm'; [grid] = ft_prepare_leadfield(cfg); %% 3- Join rest and task data % data_rs: resting state data % data4: data during task dataAll = ft_appenddata([], data_rs, data4); cfg = []; cfg.method = 'mtmfft'; cfg.output = 'powandcsd'; cfg.tapsmofrq = 4; cfg.foilim = [18 18]; freqAll = ft_freqanalysis(cfg, dataAll); %---------------------------------- % all seems normal until here %---------------------------------- %% 4- Estimate source of all data cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAll = ft_sourceanalysis(cfg, freqAll); Cheers, Laura Rueda Delgado _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathykousik at gmail.com Wed May 28 18:09:31 2014 From: sarathykousik at gmail.com (kousik sarathy) Date: Wed, 28 May 2014 18:09:31 +0200 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Oh. Yes. FT puts NaN's into sourcespace points outside the brain. You can constrain FT to only calculate leadfields for sourcespace points inside the brain. I generally do this. I don't know how FT handles those outside the brain source points really. You could give this a try. Check this tutorial/code: http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#forward_solution -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 6:01 PM, Laura Rueda Delgado < Laura.Rueda at faber.kuleuven.be> wrote: > Dear Kousik, > > > > I checked for NaN and Inf values in powspctrm and crsspctrm of freqAll. > There are none. However, I checked for NaN values in grid.leadfield and it > has some. I thought that these were NaN values in the points of the grid > outside a brain region, but I might be mistaken. > > > > > > grid = > > > > xgrid: [-58 -48 -38 -28 -18 -8 2 12 22 32 42 52 62 72 82 92 102] > > ygrid: [-61 -51 -41 -31 -21 -11 -1 9 19 29 39 49 59] > > zgrid: [-13 -3 7 17 27 37 47 57 67 77 87 97 107 117] > > dim: [17 13 14] > > pos: [3094x3 double] > > unit: 'mm' > > inside: [1x1516 double] > > outside: [1x1578 double] > > cfg: [1x1 struct] > > leadfield: {1x3094 cell} > > > > Best regards, > > > > Laura Rueda Delgado > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *kousik sarathy > *Sent:* woensdag 28 mei 2014 17:37 > > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Ah. Interesting. Good that error changes. So that was the problem before. > > > > Now, can you check if your Freq matrices contain any NaN's > (isnan(freqAll))? It can happen sometimes. > > > -- > > Regards, > > Kousik Sarathy, S > > > > > > On Wed, May 28, 2014 at 5:31 PM, Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be> wrote: > > Dear Kousik, > > > > I checked the labels and they were the same, except for whether they were > in capital letters. So I added the following before ft_sourceanalysis: > > > > freqAll.label=cellfun(@upper, freqAll.label, 'UniformOutput', 0); > > freqAll.labelcmb=cellfun(@upper, freqAll.labelcmb, 'UniformOutput', 0); > > > > This way the labels of the elec structure and freqAll are in capital > letters. > > > > And now I get a different error (although still within the function > beamformer_dics): > > > > Error using svd > > Input to SVD must not contain NaN or Inf. > > > > Error in beamformer_dics>pinv (line 650) > > [U,S,V] = svd(A,0); > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > > > What could it be? > > > > Best regards, > > Laura > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *kousik sarathy > *Sent:* woensdag 28 mei 2014 17:10 > > > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Hey Laura, > > > > I too had the same suggestion as Johanna's. > > > > Another thing to check would be if the labels that you used for the > leadfield estimation are the same as the freq data. I guess FT at some > point would also check this to extract the indices. > > > -- > > Regards, > > Kousik Sarathy, S > > > > > > On Wed, May 28, 2014 at 4:51 PM, Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be> wrote: > > Dear Johanna, > > > > Thank you for your suggestion. > > > > On step 2 in the code, I select from the elec structure the channels that > are included in the frequency data. So the elec structure used for > preparing the leadfield has 128 electrodes, the same as the data (data_rs, > data 4, and therefore freqAll). I checked this precisely because I read a > previous thread discussing that issue. > > > > Best regards, > > > > Laura Rueda Delgado > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *Johanna Zumer > *Sent:* woensdag 28 mei 2014 16:42 > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Hi Laura, > > > > Does your data have the same channels as the leadfield (as the electrodes > that went in to compute the leadfield)? I often see that error when there > is a mismatch of channels in that way. > > > > Best, > > Johanna > > > > 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be>: > > Dear Fieldtrip users, > > > > I’m following the tutorial of beamformers (Source Analysis: Contrast > activity to another interval) > to estimate oscillatory sources using DICS. I’ve checked the surface > created after segmentation and the grid generated from the electrode > positions and the headmodel. That seems to work ok. However, at the step of > source analysis, I get the following error: > > > > Error using * > > Inner matrix dimensions must agree. > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > Does anybody have an idea of what I’m doing wrong? > > Thank you in advance for any help or suggestion! > > > > ----------------------------------------------------------------- > > This is my code: > > %% 1 - Preparation of MRI- source space > > % Read MRI > > mrifile = 'Subject01\Subject01.mri'; > > mri = ft_read_mri(mrifile); > > % Reslice to reorient images > > cfg = []; > > cfg.dim = [256 256 256]; > > mri = ft_volumereslice(cfg,mri); > > % Segment compartments > > cfg = []; > > cfg.output = {'brain','skull','scalp'}; > > segmentedmri = ft_volumesegment(cfg, mri); > > % Prepare mesh > > cfg=[]; > > cfg.tissue={'brain', 'skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > % Prepare headmodel > > cfg = []; > > cfg.method ='bemcp'; > > vol = ft_prepare_headmodel(cfg, bnd); > > %% 2- Prepare leadfield - Creating grid > > load elec_aligned2 % Obtained after adjusting electrodes on scalp surface > interactively > > % Three fiducial markers were added to the electrode file, and now they're > > % removed so that the electrode structure has the same number of channels > as the data > > elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); > > elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); > > elec_aligned2.label = elec_aligned2.label(1:128, :); > > cfg =[]; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.grid.resolution = 10; > > cfg.grid.unit = 'mm'; > > [grid] = ft_prepare_leadfield(cfg); > > %% 3- Join rest and task data > > % data_rs: resting state data > > % data4: data during task > > dataAll = ft_appenddata([], data_rs, data4); > > cfg = []; > > cfg.method = 'mtmfft'; > > cfg.output = 'powandcsd'; > > cfg.tapsmofrq = 4; > > cfg.foilim = [18 18]; > > freqAll = ft_freqanalysis(cfg, dataAll); > > %---------------------------------- > > % all seems normal until here > > %---------------------------------- > > %% 4- Estimate source of all data > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 18; > > cfg.grid = grid; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > sourceAll = ft_sourceanalysis(cfg, freqAll); > > > > > > Cheers, > > > > Laura Rueda Delgado > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahjoory86 at gmail.com Wed May 28 23:47:14 2014 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Wed, 28 May 2014 23:47:14 +0200 Subject: [FieldTrip] NaN Values in grid.liedfield Message-ID: Dear all, I want to do EEG source reconstruction. The EEG cap is t 10-20 standard, with 64 channels, but the MRI and electrode positions of subjects are not available. I used Fieldtrip templates for my work. my scripts are as below: cfg = []; cfg.elec=ft_read_sens('standard_1020.elc'); cfg.vol = load('standard_bem.mat'); cfg.channel = epo.clab; [grid] = ft_prepare_leadfield(cfg); But the output for grid.liedfield includes NAN values. I hope someone can give me comments on this matter. Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Thu May 29 03:56:15 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Thu, 29 May 2014 01:56:15 +0000 Subject: [FieldTrip] possible bug with either ft_volumelookup or AAL atlas Message-ID: <1401328562572.43734@flinders.edu.au> Hello fieldtrippers, I just wanted to check if this is a bug or not. When running the following code: atlas = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/aal/ROI_MNI_V4.nii')) It gives you the following: dim: [91 109 91] hdr: [1x1 struct] transform: [4x4 double] unit: 'mm' tissue: [91x109x91 double] tissuelabel: {1x116 cell} coordsys: 'mni' Take note that tissuelabel is 1x116 When running the following code through ft_volumelookup: cfg = []; cfg.atlas = atlas; cfg.inputcoord = 'mni'; cfg.maskparameter = 'inside'; labels = ft_volumelookup( cfg, source); An error occurs: Error using cat Dimensions of matrices being concatenated are not consistent. Error in ft_volumelookup (line 313) labels.name = cat(1, labels.name, atlas.([fn{k},'label'])); If you invert tissuelabel, so that it becomes 116x1, then the code works. For some reason ft_volumelookup doesnt like a 1xY cell. Thank you, Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathykousik at gmail.com Thu May 29 07:29:52 2014 From: sarathykousik at gmail.com (kousik sarathy) Date: Thu, 29 May 2014 07:29:52 +0200 Subject: [FieldTrip] NaN Values in grid.liedfield In-Reply-To: References: Message-ID: Hey Keyvan, When leadfield structure has NaN it generally means the grid points lie outside the brain. Please have a look at this: http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 11:47 PM, Keyvan Mahjoory wrote: > Dear all, > > I want to do EEG source reconstruction. The EEG cap is t 10-20 standard, > with 64 channels, but the MRI and electrode positions of subjects are not > available. I used Fieldtrip templates for my work. my scripts are as below: > > cfg = []; > cfg.elec=ft_read_sens('standard_1020.elc'); > cfg.vol = load('standard_bem.mat'); > cfg.channel = epo.clab; > [grid] = ft_prepare_leadfield(cfg); > > But the output for grid.liedfield includes NAN values. > I hope someone can give me comments on this matter. > > Best, > Keyvan > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu May 29 09:00:40 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 29 May 2014 09:00:40 +0200 Subject: [FieldTrip] possible bug with either ft_volumelookup or AAL atlas In-Reply-To: <1401328562572.43734@flinders.edu.au> References: <1401328562572.43734@flinders.edu.au> Message-ID: Hi Tyler, That sounds like a bug to me. I've filed it on our bugzilla: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2594 Best, Eelke On 29 May 2014 03:56, Tyler Grummett wrote: > Hello fieldtrippers, > > > I just wanted to check if this is a bug or not. > > > When running the following code: atlas = ft_read_atlas( fullfile( > matlabrootpath, 'Matlab/fieldtrip/template/atlas/aal/ROI_MNI_V4.nii')) > > > It gives you the following: > > > dim: [91 109 91] > hdr: [1x1 struct] > transform: [4x4 double] > unit: 'mm' > tissue: [91x109x91 double] > tissuelabel: {1x116 cell} > coordsys: 'mni' > > Take note that tissuelabel is 1x116 > > When running the following code through ft_volumelookup: > > cfg = []; > cfg.atlas = atlas; > cfg.inputcoord = 'mni'; > cfg.maskparameter = 'inside'; > labels = ft_volumelookup( cfg, source); > > An error occurs: > > Error using cat > Dimensions of matrices being concatenated are not consistent. > > Error in ft_volumelookup (line 313) > labels.name = cat(1, labels.name, atlas.([fn{k},'label'])); > > If you invert tissuelabel, so that it becomes 116x1, then the code works. > > For some reason ft_volumelookup doesnt like a 1xY cell. > > Thank you, > > Tyler > > > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From tyler.grummett at flinders.edu.au Thu May 29 09:26:39 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Thu, 29 May 2014 07:26:39 +0000 Subject: [FieldTrip] possible bug with either ft_volumelookup or AAL atlas In-Reply-To: References: <1401328562572.43734@flinders.edu.au>, Message-ID: <1401348385612.16930@flinders.edu.au> Thank you Eelke, I also noticed that with the AFNI atlas, the labels in the file dont match up to the labels that come out of ft_prepare_sourcemodel. when I say label I mean data.( label) I tested it with the AAL atlas and the labels in the file and the data.( label) match up perfectly. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Eelke Spaak Sent: Thursday, 29 May 2014 4:30 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] possible bug with either ft_volumelookup or AAL atlas Hi Tyler, That sounds like a bug to me. I've filed it on our bugzilla: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2594 Best, Eelke On 29 May 2014 03:56, Tyler Grummett wrote: > Hello fieldtrippers, > > > I just wanted to check if this is a bug or not. > > > When running the following code: atlas = ft_read_atlas( fullfile( > matlabrootpath, 'Matlab/fieldtrip/template/atlas/aal/ROI_MNI_V4.nii')) > > > It gives you the following: > > > dim: [91 109 91] > hdr: [1x1 struct] > transform: [4x4 double] > unit: 'mm' > tissue: [91x109x91 double] > tissuelabel: {1x116 cell} > coordsys: 'mni' > > Take note that tissuelabel is 1x116 > > When running the following code through ft_volumelookup: > > cfg = []; > cfg.atlas = atlas; > cfg.inputcoord = 'mni'; > cfg.maskparameter = 'inside'; > labels = ft_volumelookup( cfg, source); > > An error occurs: > > Error using cat > Dimensions of matrices being concatenated are not consistent. > > Error in ft_volumelookup (line 313) > labels.name = cat(1, labels.name, atlas.([fn{k},'label'])); > > If you invert tissuelabel, so that it becomes 116x1, then the code works. > > For some reason ft_volumelookup doesnt like a 1xY cell. > > Thank you, > > Tyler > > > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From katrinheimann at gmail.com Thu May 29 11:55:35 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Thu, 29 May 2014 11:55:35 +0200 Subject: [FieldTrip] which baseline correction to choose for frequency analysis Message-ID: Hey together, another rather conceptual question: I am wondering about the baselinecorrection for the frequencyanalysis. I want to compare two timeperiods of one second each, lying right after each other. In the preprocessing I have baseline corrected them using 100 ms before the first piece (last part of a fixationcross period). Do I use the same part for the frequencyanalysis? Will say, do I run the analysis let's say from -0.5 (0 point is end of fixation cross) to 2.5 s, correcting with [-0.1 0] and then extract the two different conditions by statistical extraction (each 1 second long) ? Or do I run two analysis on (a bit more than) one second each, using the whole trial as baseline? thanks a lot for your advice again! Best Katrin -------------- next part -------------- An HTML attachment was scrubbed... URL: From nickwan at aggiemail.usu.edu Thu May 29 12:12:20 2014 From: nickwan at aggiemail.usu.edu (Nick Wan) Date: Thu, 29 May 2014 04:12:20 -0600 Subject: [FieldTrip] which baseline correction to choose for frequency analysis In-Reply-To: References: Message-ID: The most common event-related ​preprocessing is baseline correction for each event (in your case, 100ms baseline correction unique to each 1000ms epoch) -- at least, in my review of event-related imaging. On Thu, May 29, 2014 at 3:55 AM, KatrinH Heimann wrote: > Hey together, > another rather conceptual question: > I am wondering about the baselinecorrection for the frequencyanalysis. > I want to compare two timeperiods of one second each, lying right after > each other. > In the preprocessing I have baseline corrected them using 100 ms before > the first piece (last part of a fixationcross period). > Do I use the same part for the frequencyanalysis? Will say, do I run the > analysis let's say from -0.5 (0 point is end of fixation cross) to 2.5 s, > correcting with [-0.1 0] and then extract the two different conditions by > statistical extraction (each 1 second long) ? Or do I run two analysis on > (a bit more than) one second each, using the whole trial as baseline? > > thanks a lot for your advice again! Best > Katrin > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Nick Wan Graduate Student Utah State University Psychology Department 2810 Old Main Hill Logan, UT 84322 Office: HSRC 004 Phone: 435-554-8788 Blog: truebra.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Thu May 29 12:20:12 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 29 May 2014 10:20:12 +0000 Subject: [FieldTrip] which baseline correction to choose for frequency analysis In-Reply-To: <23434_1401357818_538705FA_23434_514_1_CACnHcBdHMpYa6PGGz6=c2Cd9FfD1bR3Cgk+OGkTesrgpsR=apA@mail.gmail.com> References: <23434_1401357818_538705FA_23434_514_1_CACnHcBdHMpYa6PGGz6=c2Cd9FfD1bR3Cgk+OGkTesrgpsR=apA@mail.gmail.com> Message-ID: Hi Katrin, it sounds like you will end up using 'depsamplesT' as your statistic (because you compare repeated measures = 2 consecutive time intervals from the same subject or trial) - why do you need to use baseline-correction then? The pairing should already account for differences in baseline power between subjects (or trials). If you do need a baseline correction, I would not choose such a short baseline in the frequency domain, but go for an average over a much longer (.5 to 1 second) interval, particularly if you intend to baseline-correct single trials (because a short baseline is more likely to project noise from the baseline into your interval of interest). Also, keep in mind that ft_freqanalysis computes power across a time window (specified by you in cfg.t_ftimwin), so that power between -.1 and 0 may not only reflect "baseline" power. Best Max ________________________________ Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" im Auftrag von "KatrinH Heimann [katrinheimann at gmail.com] Gesendet: Donnerstag, 29. Mai 2014 11:55 An: FieldTrip discussion list Betreff: [FieldTrip] which baseline correction to choose for frequency analysis Hey together, another rather conceptual question: I am wondering about the baselinecorrection for the frequencyanalysis. I want to compare two timeperiods of one second each, lying right after each other. In the preprocessing I have baseline corrected them using 100 ms before the first piece (last part of a fixationcross period). Do I use the same part for the frequencyanalysis? Will say, do I run the analysis let's say from -0.5 (0 point is end of fixation cross) to 2.5 s, correcting with [-0.1 0] and then extract the two different conditions by statistical extraction (each 1 second long) ? Or do I run two analysis on (a bit more than) one second each, using the whole trial as baseline? thanks a lot for your advice again! Best Katrin From katrinheimann at gmail.com Thu May 29 13:38:53 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Thu, 29 May 2014 13:38:53 +0200 Subject: [FieldTrip] which baseline correction to choose for frequency analysis In-Reply-To: References: <23434_1401357818_538705FA_23434_514_1_CACnHcBdHMpYa6PGGz6=c2Cd9FfD1bR3Cgk+OGkTesrgpsR=apA@mail.gmail.com> Message-ID: Thanks Max! That helped! I will indeed not do the baseline correction! k 2014-05-29 12:20 GMT+02:00 Stenner, Max-Philipp < max-philipp.stenner at med.ovgu.de>: > Hi Katrin, > > it sounds like you will end up using 'depsamplesT' as your statistic > (because you compare repeated measures = 2 consecutive time intervals from > the same subject or trial) - why do you need to use baseline-correction > then? The pairing should already account for differences in baseline power > between subjects (or trials). If you do need a baseline correction, I would > not choose such a short baseline in the frequency domain, but go for an > average over a much longer (.5 to 1 second) interval, particularly if you > intend to baseline-correct single trials (because a short baseline is more > likely to project noise from the baseline into your interval of interest). > Also, keep in mind that ft_freqanalysis computes power across a time window > (specified by you in cfg.t_ftimwin), so that power between -.1 and 0 may > not only reflect "baseline" power. > > Best > > Max > > > > ________________________________ > > Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" > im Auftrag von "KatrinH Heimann [katrinheimann at gmail.com] > Gesendet: Donnerstag, 29. Mai 2014 11:55 > An: FieldTrip discussion list > Betreff: [FieldTrip] which baseline correction to choose for frequency > analysis > > Hey together, > another rather conceptual question: > I am wondering about the baselinecorrection for the frequencyanalysis. > I want to compare two timeperiods of one second each, lying right after > each other. > In the preprocessing I have baseline corrected them using 100 ms before > the first piece (last part of a fixationcross period). > Do I use the same part for the frequencyanalysis? Will say, do I run the > analysis let's say from -0.5 (0 point is end of fixation cross) to 2.5 s, > correcting with [-0.1 0] and then extract the two different conditions by > statistical extraction (each 1 second long) ? Or do I run two analysis on > (a bit more than) one second each, using the whole trial as baseline? > > thanks a lot for your advice again! Best > Katrin > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Fri May 30 04:09:09 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Fri, 30 May 2014 02:09:09 +0000 Subject: [FieldTrip] ft_mvaranalysis Message-ID: <1401415735027.24988@flinders.edu.au> Hello fieldtrippers, Recently when I ran the following code: cfg = []; cfg.order = 5; cfg.toolbox = 'biosig'; mdata = ft_mvaranalysis( cfg, vchan); with this data: vchan = fsample: 500 sampleinfo: [14x2 double] trial: {1x14 cell} time: {1x14 cell} label: {1x116 cell} cfg: [1x1 struct] ?I got this error : Undefined function 'mvar' for input arguments of type 'double'. Error in ft_mvaranalysis (line 385) [ar, rc, pe] = mvar(dat', cfg.order, cfg.mvarmethod); I dont really know what has gone wrong, considering I have ran this code before with 1400 channels. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Fri May 30 04:15:01 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Fri, 30 May 2014 02:15:01 +0000 Subject: [FieldTrip] ft_networkanalysis Message-ID: <1401416086248.33062@flinders.edu.au> Hello fieldtrippers, Really interesting in running ft_networkanalysis and getting the most out of the function. Firstly, what types of analyses are recommended? and in what order... Ive tried looking on the brain connectivity toolbox website, but as it is already incorporated into fieldtrip so I thought I would ask on this forum if there is a recommended flow of processes. I am happy to be told to just look on the website. Also is there a between network comparison? Or is that another thing to just get from the website ( I believe they do it with the 'network based statistic' toolbox). Secondly,? when do you think there will be support for global efficiency, I am mainly interesting in calculating small-worldedness. Kind regards, Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From yingli.ucla at gmail.com Fri May 30 09:14:09 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Fri, 30 May 2014 00:14:09 -0700 Subject: [FieldTrip] Mesh genration error using the template MRI Message-ID: Dear all, Fieldtrip provided a template headmodel “standard_bem.mat" and a template MRI "standard_mri.mat". I tried to use the template MRI to create the BEM head model by myself. But it seems that the scalp mesh generated by myself looks a little weird (attached). I have no idea why the scalp mesh generated by myself looks different from the one provided by the template headmodel. Does anyone know the reason? The code I used is: cfg=[]; cfg.tissue={'brain','skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,seg); Thanks a lot! Ying -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: scalp mesh.fig Type: application/x-matlab-figure Size: 14678 bytes Desc: not available URL: From michelecolombo at live.it Fri May 30 17:19:24 2014 From: michelecolombo at live.it (michele colombo) Date: Fri, 30 May 2014 17:19:24 +0200 Subject: [FieldTrip] how to specify each channel-color in a topoplot Message-ID: Dear all, My goal is to make a double plot: 1) a subplot with a topoplot of channel-values that are color-mapped, 2) a sorted stem-plot where the stem color is mapped to its height., and represent the channel values The outcome should be more easily interpretable than a colorbar, because it would allow to appreciate the whole distribution at a glance, and provide spatial info about the distance between colors. The first step would be to visualize a 1*num_channels vector plotted on the eeg scalp, with the usual topoplot style, and with colors that I define. I compute these values outside of fieldtrip, so I need to re-create the expected fieldtrip structure. Question: how to properly preserve the value-color mapping? all the intuitive options I tried fail with this respect. somehow the colormap given is used as the range of possible color-rgb-values, and subsequently the colors are chosen from this map. Instead, I would want to actually give the channel-by-channel color value to be plotted on the scalp, (interpolating as usual in the space across channels). attached, you can see a failed attempt: the colormap plotted is flattened to a very narrow sub-range of the colomap given. relevant parts of the used code: ---- hh=axes('Position',[.62 .6 .3 .3],'Layer','top'); % overlay on plot % the way i define the colormap. I tried also with a simple: winter(number_of_channels) cfg.colormap= rgbslide(all_chan_stat,'low_color',[0 0 0.75],'low_val',min(all_chan_stat), ... 'zero_color',[0 0.75 0.75],'zero_val',median(all_chan_stat), ... 'high_color',[1 0.9 0],'res',numel(all_chan_stat)); if ~isempty([bads_max bads_min]) cfg.highlight=sort([bads_max bads_min]); % hilight some outliers. this works fine. end cfg.interpolation='v4'; cfg.style='straight'; cfg.maplimits='maxmin'; fieldtrippath='/data1/toolbox/fieldtrip/compat/'; addpath(fieldtrippath); topoplot(cfg,[all_chan_stat']); % all_chan_stat is my 1*num_channels = 257 channels from the EGI system. % the old-deprecated topoplot function seems more easily accessible than the current one, provided I just use fieldtrip to plot, not to compute, the values. sorted=sort(all_chan_stat) for cc= 1: length(channels) stem(cc, sorted(cc), 'Color', cfg.colormap(cc,:), 'MarkerFaceColor', cfg.colormap(cc,:)) ; hold on; end --- Another option would be to first do the topoplot, given a colormap, then to retrieve the color plotted at each channel (but I don't know how), and use these colors to plot the stem --- another attempted option: set(gca,'colororder',cfg.colormap); plot(channels, all_chan_stat) -------------- next part -------------- A non-text attachment was scrubbed... Name: topoplot_and_stem-colors.png Type: image/png Size: 39798 bytes Desc: not available URL: From pgoodin at swin.edu.au Thu May 1 07:30:41 2014 From: pgoodin at swin.edu.au (Peter Goodin) Date: Thu, 1 May 2014 05:30:41 +0000 Subject: [FieldTrip] Multiple source inversion problems for group MNE analysis Message-ID: Hi Fieldtrip list, I'm trying to do group source analysis using MNE but have run into a bit of a snag. After running ft_sourceanalysis (data is 1600ms / 901 data points, source model has been made via SPM (8196 verticies), head model through segmentation of the individual's MRI - all looks to be aligned, similar to the output of SPM (see and plots sensibly using ft_sourcemovie) I've tried running ft_sourceinterpolation using the data on an individual's MRI (freshly read in using ft_read_mri) or the SPM T1 template (also using ft_read_mri). If using the individual's MRI (dimensions = 256 256 176), with or without downsampling, after an hour or so I get an out of memory error and that's that. Running it with the template works fine and is finished ~90 seconds. The results using ft_sourceplot (ortho method) however don't look right (see interp.jpg). Additionally there's no field in the interpolated's cfg about anatomy afterward. So taking another route and just trying to use ft_sourcegrandaverage on the output of ft_sourcelocalisation I'm met with "??? Error using ==> ft_sourcegrandaverage at 111 different grid locations in source reconstructions" I have absolutely no idea what I'm doing wrong and would appreciate any help. An abridged version of the script I'm using for mass conversion to source space is below: sourcemodel = ft_read_headshape(gii_list(i,:)); <-- this is the ...2cortex_8196.surf.gii mesh from spm mri = ft_read_mri([structdir mri_list(i,1:end-2)]); <--- individual participant's raw MRI in nii form. cfg = []; cfg.coordsys = 'spm'; cfg.output = {'brain'}; seg = ft_volumesegment(cfg, mri); cfg = []; cfg.method = 'singleshell'; conductionmodel = ft_prepare_headmodel(cfg, seg); conductionmodel = ft_convert_units(conductionmodel,'cm'); conductionmodel = ft_convert_units(conductionmodel,'mm'); %%Check everything's aligned correctly: figure;hold on; subplot(1,2,1), ft_plot_vol(conductionmodel, 'facecolor', [0 0 1]);alpha 0.5; ft_plot_mesh(sourcemodel, 'edgecolor', [0 1 0]); camlight ft_plot_sens(sens, 'style', 'r*'); subplot(1,2,2), ft_plot_vol(conductionmodel, 'facecolor', [0 0 1]);alpha 0.5; ft_plot_mesh(sourcemodel, 'edgecolor', [0 1 0]); camlight ft_plot_sens(sens, 'style', 'r*'); view([90 0]); view([90 0]) gcf; suptitle([gii_list(i,2:5) ' source model']); saveas(gcf, [gii_list(i,2:6) 'source model.tiff']); close(gcf); assignin('base', [gii_list(i,2:6) 'sourcemodel'], sourcemodel); <--- rename hold variable to participant number assignin('base', [gii_list(i,2:6) 'conductionmodel'], conductionmodel); <--- ditto save([gii_list(i,2:6) 'model'], [gii_list(i,2:6) 'sourcemodel'], [gii_list(i,2:6) 'conductionmodel'], '-v6'); %% CREATE LEADFIELD & LOCALISED DATA load(sens_data_list(i,:)); <--- Load sensor space condition data conds_list = (who('*nback*av')) <--- Create participant specific list datcm = eval(conds_list{1,1}); dat = datcm; dat.grad = ft_convert_units(datcm.grad, 'mm'); %Leadfield goes here <--- Mostly taken from the tutorial cfg = []; cfg.grad = dat.grad; % sensor positions cfg.channel = 'MEG'; % the used channels cfg.grid.pos = sourcemodel.pnt; % source points <---Does this have something to do with the problem? cfg.grid.inside = 1:size(sourcemodel.pnt,1); % all source points are inside of the brain <--- Or this? cfg.vol = conductionmodel; % volume conduction model leadfield = ft_prepare_leadfield(cfg); assignin('base', [conds_list{1,1} '_leadfield'], leadfield); save([gii_list(i,2:6) 'model'], [conds_list{1,1} '_leadfield'], '-v6', '-append'); clear dat; for k = 1:size(conds_list,1); disp('---'); disp(['Creating source data for ' conds_list{k,1}]); disp('---'); datcm = eval(conds_list{k,1}); dat = datcm; dat.grad = ft_convert_units(datcm.grad, 'mm'); %Inversion goes here <--- Mostly taken from the tutorial cfg = []; cfg.method = 'mne'; cfg.grid = leadfield; cfg.vol = conductionmodel; cfg.mne.prewhiten = 'yes'; cfg.mne.lambda = 3; cfg.mne.scalesourcecov = 'yes'; sourcedat = ft_sourceanalysis(cfg,dat); assignin('base', [conds_list{k,1} '_source'], sourcedat); k = k + 1; end %%General saving stuff a = who('*C_av_source'); b = a(1:2:end,1); save([sourcedatadir gii_list(i,2:6) 'condep_conds'], char(b(1,1)), '-v6'); for l = 2:size(b,1); save([sourcedatadir gii_list(i,2:6) 'condep_conds'], char(b(l,1)), '-append', '-v6'); l = l + 1; end save([sourcedatadir gii_list(i,2:6) 'source'], '*_source', '-v6'); Thanks again, Peter __________________________ Peter Goodin, BSc (Hons), Ph.D Candidate. Brain and Psychological Sciences Research Centre (BPsych) Swinburne University, Hawthorn, Vic, 3122 http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149 Monash Alfred Psychiatry Research Centre (MAPrc) Level 4, 607 St Kilda Road, Melbourne 3004 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: interp.jpg Type: image/jpeg Size: 17514 bytes Desc: interp.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: c112_source model.tiff Type: image/tiff Size: 233110 bytes Desc: c112_source model.tiff URL: From pierpaolo12croce at gmail.com Thu May 1 14:56:59 2014 From: pierpaolo12croce at gmail.com (Pierpaolo Croce) Date: Thu, 1 May 2014 14:56:59 +0200 Subject: [FieldTrip] Undefined function 'mtimes' for input arguments of type 'cell'. Message-ID: Undefined function 'mtimes' for input arguments of type 'cell'. I have this error in using "ft_databrowser" like im the tutorial web page. can someone help me? -- PC -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu May 1 15:01:58 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 1 May 2014 15:01:58 +0200 Subject: [FieldTrip] Undefined function 'mtimes' for input arguments of type 'cell'. In-Reply-To: References: Message-ID: Hi Pierpaolo, Could you show us what input data and cfg you are providing for ft_databrowser? Best, Eelke On 1 May 2014 14:56, Pierpaolo Croce wrote: > Undefined function 'mtimes' for input arguments of type 'cell'. > > I have this error in using "ft_databrowser" like im the tutorial web page. > > can someone help me? > > > -- > PC > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From eliasc at live.it Thu May 1 23:54:32 2014 From: eliasc at live.it (Elias P. Casula) Date: Thu, 1 May 2014 23:54:32 +0200 Subject: [FieldTrip] ft_preproc_dftfilter function In-Reply-To: References: Message-ID: Dear all,I found some problems with the ft_preproc_dftfilter function. This function should remove the 50hz noise from the signal. But when I call the function with [filt] = ft_preproc_dftfilter(mymatrixdata, 1024, 50) the 50hz noise is still in the filtered signal. Does anyone else had the same problem?Thanks a lot, Elias -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Fri May 2 08:51:11 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 02 May 2014 08:51:11 +0200 Subject: [FieldTrip] ft_preproc_dftfilter function In-Reply-To: References: Message-ID: <5363405F.3010802@donders.ru.nl> Hi Elias, please see http://fieldtrip.fcdonders.nl/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter that should enlighten you :) Best, Jörn On 5/1/2014 11:54 PM, Elias P. Casula wrote: > > Dear all, > I found some problems with the ft_preproc_dftfilter function. This > function should remove the 50hz noise from the signal. But when I call > the function with > > [filt] = ft_preproc_dftfilter(mymatrixdata, 1024, 50) > > the 50hz noise is still in the filtered signal. Does anyone else had > the same problem? > Thanks a lot, > > Elias > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From eliasc at live.it Fri May 2 09:36:35 2014 From: eliasc at live.it (Elias P. Casula) Date: Fri, 2 May 2014 09:36:35 +0200 Subject: [FieldTrip] ft_preproc_dftfilter function In-Reply-To: <5363405F.3010802@donders.ru.nl> References: , , <5363405F.3010802@donders.ru.nl> Message-ID: Thanks Jorn, Unfortunately in my case the signal remains exactly the same after the dft filter. Maybe there is something that I'm missing in the procedure? When I call the function I just insert my data matrix, the sampling frequency (1024) and the frequency band that I want to filter (50). The function generates a new file but apparently nothing changes. > Date: Fri, 2 May 2014 08:51:11 +0200 > From: jm.horschig at donders.ru.nl > To: fieldtrip at science.ru.nl > Subject: Re: [FieldTrip] ft_preproc_dftfilter function > > Hi Elias, > > please see > http://fieldtrip.fcdonders.nl/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter > that should enlighten you :) > > Best, > Jörn > > On 5/1/2014 11:54 PM, Elias P. Casula wrote: > > > > Dear all, > > I found some problems with the ft_preproc_dftfilter function. This > > function should remove the 50hz noise from the signal. But when I call > > the function with > > > > [filt] = ft_preproc_dftfilter(mymatrixdata, 1024, 50) > > > > the 50hz noise is still in the filtered signal. Does anyone else had > > the same problem? > > Thanks a lot, > > > > Elias > > > > > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Fri May 2 10:27:35 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Fri, 2 May 2014 08:27:35 +0000 Subject: [FieldTrip] clustering of bipolar referenced data Message-ID: Hi all, I would just like to confirm that I am not missing something. I am using cluster-based permutation stats for an intracranial dataset consisting of three bipolar channels. These are derived from four neighbouring contacts on the same electrode (i.e., channel 1 = contact 1 vs. contact 2, channel 2 = contact 2 vs. contact 3, etc.). For clustering in space, I've defined 2 to be a neighbour of 1 (and 3), and vice versa (etc. for the other channels). Since bipolar referencing means looking at differences between contacts, the fact that channels 1 and 2, for example, are partially derived from the same contact (contact 2), should not prevent me from clustering across these two channels when running stats - is that correct? Thanks! Best Max From martine.vanschouwenburg at ucsf.edu Fri May 2 20:16:29 2014 From: martine.vanschouwenburg at ucsf.edu (Martine van Schouwenburg) Date: Fri, 2 May 2014 11:16:29 -0700 Subject: [FieldTrip] ft_databrowser crashes Matlab Message-ID: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> Hi Fieldtrip experts, I am experiencing a problem with the ft_databrowser routine. Matlab crashes when I'm trying to run it, forcing me to end the Matlab session. ('Matlab has encountered an internal problem and needs to close.'). It seems more like a Matlab/Windows related issue when looking at the crash report (see below), but I am posting it here because it also seems to depend on the data that I use as input. When I run the routine on the 'raw' data (after defining the trials) it is working fine, but after I ran ICA and try to use the databrowser to look at the components, it crashes at line 676. This is the part where it calls the subfunction redraw_cb. Does anyone might have a clue what in the component data might cause this problem? Maybe some of you have experienced this before? I also send a request for Tech Support to Matlab. Best, Martine Here is the Matlab crash report if that is of any help: ------------------------------------------------------------------------ Segmentation violation detected at Thu May 01 22:28:30 2014 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Default Encoding: windows-1252 MATLAB Root : C:\Program Files\MATLAB\R2012b MATLAB Version : 8.0.0.783 (R2012b) Operating System: Microsoft Windows 7 Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode Window System : Version 6.1 (Build 7601: Service Pack 1) Fault Count: 1 Abnormal termination: Segmentation violation Register State (from fault): RAX = 00000000000001a4 RBX = 000000007a8425c0 RCX = 00000000000262de RDX = 00000000000001b2 RSP = 0000000004110a50 RBP = 000000000000007e RSI = 000000007a75cab0 RDI = 000000013942b996 R8 = 00000000000262de R9 = 0000000000000230 R10 = 0000000000000000 R11 = 0000000004110b28 R12 = 0000000000f206cd R13 = 0000000077ce4060 R14 = 000000000002635c R15 = 00000000000006c8 RIP = 000000006000d341 EFL = 00010216 CS = 0033 FS = 0053 GS = 002b Stack Trace (from fault): [ 0] 0x000000006000d341 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( RenderEngineBase::~RenderEngineBase+171553 ) [ 1] 0x000000005ff83130 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) [ 2] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) [ 3] 0x000000005fede587 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( renderAnimatedKids+000519 ) [ 4] 0x000000005fee3788 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) [ 5] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) [ 6] 0x000000005ff04729 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( FigureSetVisualAutoMode+001561 ) [ 7] 0x000000005ff0abbd C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( UIJ_CreatePeerWindow+001597 ) [ 8] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) [ 9] 0x0000000060013548 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( RenderEngineBase::~RenderEngineBase+196648 ) [ 10] 0x000000005ff06b87 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( FigureSetVisualAutoMode+010871 ) [ 11] 0x000000005ff06c0d C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( FigureSetVisualAutoMode+011005 ) [ 12] 0x0000000063425006 C:\Program Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( wm_ExposeFcn_Pre_Optional+000374 ) [ 13] 0x0000000064c8c694 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) [ 14] 0x0000000064c8e456 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( UIJ_IsWindowShowing+000438 ) [ 15] 0x0000000064c8f943 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( UIJ_clearWaitForResize+002067 ) [ 16] 0x0000000064c8fa61 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) [ 17] 0x0000000064c707ae C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( UIJ_MarkEventFinished+005838 ) [ 18] 0x0000000064c70800 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( UIJ_MarkEventFinished+005920 ) [ 19] 0x0000000064c892ac C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( uij::JavaDraw2D::paintQuadStrip+001324 ) [ 20] 0x0000000064d4e808 C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( uddSetListenerRecursionWarning+000680 ) [ 21] 0x0000000064d4ee6c C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( UDListenerManagerHost::notifyEvent+000076 ) [ 22] 0x0000000064d4697d C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( UDEventInfo::send+000093 ) [ 23] 0x000000005fb9cedb C:\Program Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( MErrorException::operator=+047675 ) [ 24] 0x00000000055ce0b6 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( UIW_IsUserMessage+000086 ) [ 25] 0x00000000055ce7b9 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( UIW_SetGLIMUserMsg+000153 ) [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( GetMenuBarInfo+000638 ) [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( SystemParametersInfoW+000235 ) [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( IsProcessDPIAware+000465 ) [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( KiUserCallbackDispatcher+000031 ) [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( PeekMessageW+000186 ) [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( GetKeyState+000238 ) [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( PeekMessageA+000087 ) [ 33] 0x00000000055a8f4b C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( UIW_SetCurrentDialog+000731 ) [ 34] 0x00000000055cfbe2 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( ws_FreeSystemFont+000546 ) [ 35] 0x000000000485e6a3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( sysq::removeCommitDatabaseUpdatesHook+002131 ) [ 36] 0x000000000485fe18 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( sysq::removeCommitDatabaseUpdatesHook+008136 ) [ 37] 0x0000000004861a20 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( sysq::addProcessPendingEventsUnitTestHook+000240 ) [ 38] 0x0000000004861ae8 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( sysq::addProcessPendingEventsUnitTestHook+000440 ) [ 39] 0x0000000004861ca3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( sysq::addProcessPendingEventsUnitTestHook+000883 ) [ 40] 0x0000000004861d76 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( sysq::addProcessPendingEventsUnitTestHook+001094 ) [ 41] 0x000000005ff0c4fe C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) [ 42] 0x0000000074e8d17f C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( Mfunction_handle::dispatch+001023 ) [ 43] 0x0000000074e8cf82 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( Mfunction_handle::dispatch+000514 ) [ 44] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) [ 45] 0x000007feef3a5ca4 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( inFunctionHandleInterface::DestroyWorkspace+295012 ) [ 46] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) [ 47] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) [ 48] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) [ 49] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) [ 50] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) [ 51] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) [ 52] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) [ 53] 0x000007feef38210b C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( inFunctionHandleInterface::DestroyWorkspace+148683 ) [ 54] 0x000007feef393edf C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( inFunctionHandleInterface::DestroyWorkspace+221855 ) [ 55] 0x000007feef3b0ae8 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( inFunctionHandleInterface::DestroyWorkspace+339624 ) [ 56] 0x000007feef398d94 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( inFunctionHandleInterface::DestroyWorkspace+242004 ) [ 57] 0x000007feef3a2978 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( inFunctionHandleInterface::DestroyWorkspace+281912 ) [ 58] 0x000007feef3a5a8b C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( inFunctionHandleInterface::DestroyWorkspace+294475 ) [ 59] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) [ 60] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) [ 61] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) [ 62] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) [ 63] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) [ 64] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) [ 65] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) [ 66] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) [ 67] 0x000007feef43318f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( inEachVisibleName+014415 ) [ 68] 0x000007feef3a74ca C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( inFunctionHandleInterface::DestroyWorkspace+301194 ) [ 69] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) [ 70] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) [ 71] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) [ 72] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) [ 73] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) [ 74] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) [ 75] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) [ 76] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) [ 77] 0x000007feef43318f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( inEachVisibleName+014415 ) [ 78] 0x000007feef3a74ca C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( inFunctionHandleInterface::DestroyWorkspace+301194 ) [ 79] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) [ 80] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) [ 81] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) [ 82] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) [ 83] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) [ 84] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) [ 85] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) [ 86] 0x000007feef4451e5 C:\Program 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URL: From mcantor at umich.edu Fri May 2 20:58:06 2014 From: mcantor at umich.edu (Max Cantor) Date: Fri, 2 May 2014 14:58:06 -0400 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: <5363e841.061d2a0a.2297.ffffb0e2SMTPIN_ADDED_BROKEN@mx.google.com> References: <5363e841.061d2a0a.2297.ffffb0e2SMTPIN_ADDED_BROKEN@mx.google.com> Message-ID: Hi Martine, I can't say for sure, but I believe it's because ft_databrowser is only designed to take channel data, not component data. To view component data, you should use ft_componentbrowser. Hope that helps, Max Cantor Research Assistant Computational Neurolinguistics Lab University of Michigan On Fri, May 2, 2014 at 2:16 PM, Martine van Schouwenburg < martine.vanschouwenburg at ucsf.edu> wrote: > Hi Fieldtrip experts, > > > > I am experiencing a problem with the ft_databrowser routine. Matlab > crashes when I’m trying to run it, forcing me to end the Matlab session. > (‘Matlab has encountered an internal problem and needs to close.’). It > seems more like a Matlab/Windows related issue when looking at the crash > report (see below), but I am posting it here because it also seems to > depend on the data that I use as input. When I run the routine on the ‘raw’ > data (after defining the trials) it is working fine, but after I ran ICA > and try to use the databrowser to look at the components, it crashes at > line 676. > > This is the part where it calls the subfunction redraw_cb. Does anyone > might have a clue what in the component data might cause this problem? > Maybe some of you have experienced this before? I also send a request for > Tech Support to Matlab. > > > > Best, Martine > > > > Here is the Matlab crash report if that is of any help: > > > > > > > > ------------------------------------------------------------------------ > > Segmentation violation detected at Thu May 01 22:28:30 2014 > > ------------------------------------------------------------------------ > > > > Configuration: > > Crash Decoding : Disabled > > Default Encoding: windows-1252 > > MATLAB Root : C:\Program Files\MATLAB\R2012b > > MATLAB Version : 8.0.0.783 (R2012b) > > Operating System: Microsoft Windows 7 > > Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD > > Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java > HotSpot(TM) 64-Bit Server VM mixed mode > > Window System : Version 6.1 (Build 7601: Service Pack 1) > > > > Fault Count: 1 > > > > > > Abnormal termination: > > Segmentation violation > > > > Register State (from fault): > > RAX = 00000000000001a4 RBX = 000000007a8425c0 > > RCX = 00000000000262de RDX = 00000000000001b2 > > RSP = 0000000004110a50 RBP = 000000000000007e > > RSI = 000000007a75cab0 RDI = 000000013942b996 > > > > R8 = 00000000000262de R9 = 0000000000000230 > > R10 = 0000000000000000 R11 = 0000000004110b28 > > R12 = 0000000000f206cd R13 = 0000000077ce4060 > > R14 = 000000000002635c R15 = 00000000000006c8 > > > > RIP = 000000006000d341 EFL = 00010216 > > > > CS = 0033 FS = 0053 GS = 002b > > > > Stack Trace (from fault): > > [ 0] 0x000000006000d341 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( > RenderEngineBase::~RenderEngineBase+171553 ) > > [ 1] 0x000000005ff83130 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) > > [ 2] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 3] 0x000000005fede587 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( renderAnimatedKids+000519 ) > > [ 4] 0x000000005fee3788 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) > > [ 5] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 6] 0x000000005ff04729 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( > FigureSetVisualAutoMode+001561 ) > > [ 7] 0x000000005ff0abbd C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( UIJ_CreatePeerWindow+001597 > ) > > [ 8] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 9] 0x0000000060013548 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( > RenderEngineBase::~RenderEngineBase+196648 ) > > [ 10] 0x000000005ff06b87 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( > FigureSetVisualAutoMode+010871 ) > > [ 11] 0x000000005ff06c0d C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( > FigureSetVisualAutoMode+011005 ) > > [ 12] 0x0000000063425006 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( > wm_ExposeFcn_Pre_Optional+000374 ) > > [ 13] 0x0000000064c8c694 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) > > [ 14] 0x0000000064c8e456 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( > UIJ_IsWindowShowing+000438 ) > > [ 15] 0x0000000064c8f943 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( > UIJ_clearWaitForResize+002067 ) > > [ 16] 0x0000000064c8fa61 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) > > [ 17] 0x0000000064c707ae C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( > UIJ_MarkEventFinished+005838 ) > > [ 18] 0x0000000064c70800 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( > UIJ_MarkEventFinished+005920 ) > > [ 19] 0x0000000064c892ac C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( > uij::JavaDraw2D::paintQuadStrip+001324 ) > > [ 20] 0x0000000064d4e808 C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( > uddSetListenerRecursionWarning+000680 ) > > [ 21] 0x0000000064d4ee6c C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( > UDListenerManagerHost::notifyEvent+000076 ) > > [ 22] 0x0000000064d4697d C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( UDEventInfo::send+000093 ) > > [ 23] 0x000000005fb9cedb C:\Program > Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( > MErrorException::operator=+047675 ) > > [ 24] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( UIW_IsUserMessage+000086 ) > > [ 25] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( UIW_SetGLIMUserMsg+000153 ) > > [ 26] 0x00000000774a87fe > C:\Windows\system32\USER32.dll+00165886 ( GetMenuBarInfo+000638 ) > > [ 27] 0x000000007748f5fb > C:\Windows\system32\USER32.dll+00062971 ( SystemParametersInfoW+000235 ) > > [ 28] 0x0000000077494895 > C:\Windows\system32\USER32.dll+00084117 ( IsProcessDPIAware+000465 ) > > [ 29] 0x00000000775d11f5 > C:\Windows\SYSTEM32\ntdll.dll+00332277 ( KiUserCallbackDispatcher+000031 ) > > [ 30] 0x000000007749908a > C:\Windows\system32\USER32.dll+00102538 ( PeekMessageW+000186 ) > > [ 31] 0x00000000774950fe > C:\Windows\system32\USER32.dll+00086270 ( GetKeyState+000238 ) > > [ 32] 0x0000000077493a6f > C:\Windows\system32\USER32.dll+00080495 ( PeekMessageA+000087 ) > > [ 33] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [ 34] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( ws_FreeSystemFont+000546 ) > > [ 35] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [ 36] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [ 37] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [ 38] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [ 39] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [ 40] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [ 41] 0x000000005ff0c4fe C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) > > [ 42] 0x0000000074e8d17f C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( > Mfunction_handle::dispatch+001023 ) > > [ 43] 0x0000000074e8cf82 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( > Mfunction_handle::dispatch+000514 ) > > [ 44] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 45] 0x000007feef3a5ca4 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( > inFunctionHandleInterface::DestroyWorkspace+295012 ) > > [ 46] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 47] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 48] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 49] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 50] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 51] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 52] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 53] 0x000007feef38210b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( > inFunctionHandleInterface::DestroyWorkspace+148683 ) > > [ 54] 0x000007feef393edf C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( > inFunctionHandleInterface::DestroyWorkspace+221855 ) > > [ 55] 0x000007feef3b0ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( > inFunctionHandleInterface::DestroyWorkspace+339624 ) > > [ 56] 0x000007feef398d94 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( > inFunctionHandleInterface::DestroyWorkspace+242004 ) > > [ 57] 0x000007feef3a2978 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( > inFunctionHandleInterface::DestroyWorkspace+281912 ) > > [ 58] 0x000007feef3a5a8b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( > inFunctionHandleInterface::DestroyWorkspace+294475 ) > > [ 59] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 60] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 61] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 62] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 63] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 64] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 65] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 66] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 67] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 68] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 69] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 70] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 71] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 72] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 73] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 74] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 75] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 76] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 77] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 78] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 79] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 80] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 81] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 82] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 83] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 84] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 85] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 86] 0x000007feef4451e5 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( > inValidateLoadedObject+001893 ) > > [ 87] 0x000007feef454595 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( > init_cleaner+015541 ) > > [ 88] 0x000007feef457b75 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( > inSetMaxFrameCount+002261 ) > > [ 89] 0x000007feef457b48 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( > inSetMaxFrameCount+002216 ) > > [ 90] 0x000007feef457b07 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( > inSetMaxFrameCount+002151 ) > > [ 91] 0x000007feef340213 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( > inPathNotification::function_clear_notification+004019 ) > > [ 92] 0x000007feef44aed0 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( > inEvalCmdWithLocalReturn+000416 ) > > [ 93] 0x000007feef44ae2c C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( > inEvalCmdWithLocalReturn+000252 ) > > [ 94] 0x000007feef44ad71 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( > inEvalCmdWithLocalReturn+000065 ) > > [ 95] 0x0000000079fbf90d C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( > mnDebugPrompt+000109 ) > > [ 96] 0x0000000079fc0471 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( mnParser+000593 ) > > [ 97] 0x00000000749a64a4 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( > mcrInstance::mnParser_on_interpreter_thread+000036 ) > > [ 98] 0x000000007498681f C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( > mcr::setInterpreterThreadToCurrent+029887 ) > > [ 99] 0x0000000074986881 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( > mcr::setInterpreterThreadToCurrent+029985 ) > > [100] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( UIW_IsUserMessage+000086 ) > > [101] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( UIW_SetGLIMUserMsg+000153 ) > > [102] 0x00000000774a87fe > C:\Windows\system32\USER32.dll+00165886 ( GetMenuBarInfo+000638 ) > > [103] 0x000000007748f5fb > C:\Windows\system32\USER32.dll+00062971 ( SystemParametersInfoW+000235 ) > > [104] 0x0000000077494895 > C:\Windows\system32\USER32.dll+00084117 ( IsProcessDPIAware+000465 ) > > [105] 0x00000000775d11f5 > C:\Windows\SYSTEM32\ntdll.dll+00332277 ( KiUserCallbackDispatcher+000031 ) > > [106] 0x000000007749908a > C:\Windows\system32\USER32.dll+00102538 ( PeekMessageW+000186 ) > > [107] 0x00000000774950fe > C:\Windows\system32\USER32.dll+00086270 ( GetKeyState+000238 ) > > [108] 0x0000000077493a6f > C:\Windows\system32\USER32.dll+00080495 ( PeekMessageA+000087 ) > > [109] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [110] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( ws_FreeSystemFont+000546 ) > > [111] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [112] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [113] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [114] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [115] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [116] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [117] 0x000000007498837e C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( > mcr::setInterpreterThreadToCurrent+036894 ) > > [118] 0x0000000074988665 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( > mcr::setInterpreterThreadToCurrent+037637 ) > > [119] 0x000000007497b166 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( > DepfunRules::postWarning+003430 ) > > [120] 0x000000013fc78a33 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) > > [121] 0x000000013fc78c97 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) > > [122] 0x000000013fc79163 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) > > [123] 0x00000000773759ed > C:\Windows\system32\kernel32.dll+00088557 ( BaseThreadInitThunk+000013 ) > > [124] 0x00000000775ac541 > C:\Windows\SYSTEM32\ntdll.dll+00181569 ( > RtlUserThreadStart+000033 ) > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri May 2 21:15:00 2014 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 2 May 2014 21:15:00 +0200 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: References: <5363e841.061d2a0a.2297.ffffb0e2SMTPIN_ADDED_BROKEN@mx.google.com> Message-ID: <1B783442-BFEC-4625-AB21-F59A3ABF1011@donders.ru.nl> Dear Martine, Although I don't have a solution right now, the error message indeed suggest a very low level crash of MATLAB. Therefore, I don't think it is likely that it is related to the fact that you are trying to visualize 'component'-data (which in principle should be possible with ft_databrowser). It's more likely that it's a platform dependent issue, likely related to (compiled) mex-files, or a graphics issue. I remember that occasionally in the past people reported crashes specifically with ft_databrowser, but I don't remember the technical details about this. Could I suggest you to create an account on our bugzilla.fcdonders.nl site, and file this as a new bug, with as much information about it as possible? It would even be better to browse around a bit (use the search functionality, and search for ft_databrowser), you may be able to add this issue as a comment to an already existing bug with the same content. Best, JM On May 2, 2014, at 8:58 PM, Max Cantor wrote: > Hi Martine, > > I can't say for sure, but I believe it's because ft_databrowser is only designed to take channel data, not component data. To view component data, you should use ft_componentbrowser. > > Hope that helps, > > Max Cantor > Research Assistant > Computational Neurolinguistics Lab > University of Michigan > > > > On Fri, May 2, 2014 at 2:16 PM, Martine van Schouwenburg wrote: > Hi Fieldtrip experts, > > > > I am experiencing a problem with the ft_databrowser routine. Matlab crashes when I’m trying to run it, forcing me to end the Matlab session. (‘Matlab has encountered an internal problem and needs to close.’). It seems more like a Matlab/Windows related issue when looking at the crash report (see below), but I am posting it here because it also seems to depend on the data that I use as input. When I run the routine on the ‘raw’ data (after defining the trials) it is working fine, but after I ran ICA and try to use the databrowser to look at the components, it crashes at line 676. > > This is the part where it calls the subfunction redraw_cb. Does anyone might have a clue what in the component data might cause this problem? Maybe some of you have experienced this before? I also send a request for Tech Support to Matlab. > > > > Best, Martine > > > > Here is the Matlab crash report if that is of any help: > > > > > > > > ------------------------------------------------------------------------ > > Segmentation violation detected at Thu May 01 22:28:30 2014 > > ------------------------------------------------------------------------ > > > > Configuration: > > Crash Decoding : Disabled > > Default Encoding: windows-1252 > > MATLAB Root : C:\Program Files\MATLAB\R2012b > > MATLAB Version : 8.0.0.783 (R2012b) > > Operating System: Microsoft Windows 7 > > Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD > > Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode > > Window System : Version 6.1 (Build 7601: Service Pack 1) > > > > Fault Count: 1 > > > > > > Abnormal termination: > > Segmentation violation > > > > Register State (from fault): > > RAX = 00000000000001a4 RBX = 000000007a8425c0 > > RCX = 00000000000262de RDX = 00000000000001b2 > > RSP = 0000000004110a50 RBP = 000000000000007e > > RSI = 000000007a75cab0 RDI = 000000013942b996 > > > > R8 = 00000000000262de R9 = 0000000000000230 > > R10 = 0000000000000000 R11 = 0000000004110b28 > > R12 = 0000000000f206cd R13 = 0000000077ce4060 > > R14 = 000000000002635c R15 = 00000000000006c8 > > > > RIP = 000000006000d341 EFL = 00010216 > > > > CS = 0033 FS = 0053 GS = 002b > > > > Stack Trace (from fault): > > [ 0] 0x000000006000d341 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( RenderEngineBase::~RenderEngineBase+171553 ) > > [ 1] 0x000000005ff83130 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) > > [ 2] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 3] 0x000000005fede587 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( renderAnimatedKids+000519 ) > > [ 4] 0x000000005fee3788 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) > > [ 5] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 6] 0x000000005ff04729 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( FigureSetVisualAutoMode+001561 ) > > [ 7] 0x000000005ff0abbd C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( UIJ_CreatePeerWindow+001597 ) > > [ 8] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 9] 0x0000000060013548 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( RenderEngineBase::~RenderEngineBase+196648 ) > > [ 10] 0x000000005ff06b87 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( FigureSetVisualAutoMode+010871 ) > > [ 11] 0x000000005ff06c0d C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( FigureSetVisualAutoMode+011005 ) > > [ 12] 0x0000000063425006 C:\Program Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( wm_ExposeFcn_Pre_Optional+000374 ) > > [ 13] 0x0000000064c8c694 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) > > [ 14] 0x0000000064c8e456 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( UIJ_IsWindowShowing+000438 ) > > [ 15] 0x0000000064c8f943 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( UIJ_clearWaitForResize+002067 ) > > [ 16] 0x0000000064c8fa61 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) > > [ 17] 0x0000000064c707ae C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( UIJ_MarkEventFinished+005838 ) > > [ 18] 0x0000000064c70800 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( UIJ_MarkEventFinished+005920 ) > > [ 19] 0x0000000064c892ac C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( uij::JavaDraw2D::paintQuadStrip+001324 ) > > [ 20] 0x0000000064d4e808 C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( uddSetListenerRecursionWarning+000680 ) > > [ 21] 0x0000000064d4ee6c C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( UDListenerManagerHost::notifyEvent+000076 ) > > [ 22] 0x0000000064d4697d C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( UDEventInfo::send+000093 ) > > [ 23] 0x000000005fb9cedb C:\Program Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( MErrorException::operator=+047675 ) > > [ 24] 0x00000000055ce0b6 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( UIW_IsUserMessage+000086 ) > > [ 25] 0x00000000055ce7b9 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( UIW_SetGLIMUserMsg+000153 ) > > [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( GetMenuBarInfo+000638 ) > > [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( SystemParametersInfoW+000235 ) > > [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( IsProcessDPIAware+000465 ) > > [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( KiUserCallbackDispatcher+000031 ) > > [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( PeekMessageW+000186 ) > > [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( GetKeyState+000238 ) > > [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( PeekMessageA+000087 ) > > [ 33] 0x00000000055a8f4b C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( UIW_SetCurrentDialog+000731 ) > > [ 34] 0x00000000055cfbe2 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( ws_FreeSystemFont+000546 ) > > [ 35] 0x000000000485e6a3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [ 36] 0x000000000485fe18 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [ 37] 0x0000000004861a20 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [ 38] 0x0000000004861ae8 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [ 39] 0x0000000004861ca3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [ 40] 0x0000000004861d76 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [ 41] 0x000000005ff0c4fe C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) > > [ 42] 0x0000000074e8d17f C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( Mfunction_handle::dispatch+001023 ) > > [ 43] 0x0000000074e8cf82 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( Mfunction_handle::dispatch+000514 ) > > [ 44] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 45] 0x000007feef3a5ca4 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( inFunctionHandleInterface::DestroyWorkspace+295012 ) > > [ 46] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 47] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 48] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 49] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 50] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 51] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) > > [ 52] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) > > [ 53] 0x000007feef38210b C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( inFunctionHandleInterface::DestroyWorkspace+148683 ) > > [ 54] 0x000007feef393edf C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( inFunctionHandleInterface::DestroyWorkspace+221855 ) > > [ 55] 0x000007feef3b0ae8 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( inFunctionHandleInterface::DestroyWorkspace+339624 ) > > [ 56] 0x000007feef398d94 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( inFunctionHandleInterface::DestroyWorkspace+242004 ) > > [ 57] 0x000007feef3a2978 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( inFunctionHandleInterface::DestroyWorkspace+281912 ) > > [ 58] 0x000007feef3a5a8b C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( inFunctionHandleInterface::DestroyWorkspace+294475 ) > > [ 59] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 60] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 61] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 62] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 63] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 64] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) > > [ 65] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) > > [ 66] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 67] 0x000007feef43318f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( inEachVisibleName+014415 ) > > [ 68] 0x000007feef3a74ca C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 69] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 70] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 71] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 72] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 73] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 74] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) > > [ 75] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) > > [ 76] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 77] 0x000007feef43318f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( inEachVisibleName+014415 ) > > [ 78] 0x000007feef3a74ca C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 79] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 80] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 81] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 82] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 83] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 84] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) > > [ 85] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) > > [ 86] 0x000007feef4451e5 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( inValidateLoadedObject+001893 ) > > [ 87] 0x000007feef454595 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( init_cleaner+015541 ) > > [ 88] 0x000007feef457b75 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( inSetMaxFrameCount+002261 ) > > [ 89] 0x000007feef457b48 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( inSetMaxFrameCount+002216 ) > > [ 90] 0x000007feef457b07 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( inSetMaxFrameCount+002151 ) > > [ 91] 0x000007feef340213 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( inPathNotification::function_clear_notification+004019 ) > > [ 92] 0x000007feef44aed0 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( inEvalCmdWithLocalReturn+000416 ) > > [ 93] 0x000007feef44ae2c C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( inEvalCmdWithLocalReturn+000252 ) > > [ 94] 0x000007feef44ad71 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( inEvalCmdWithLocalReturn+000065 ) > > [ 95] 0x0000000079fbf90d C:\Program Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( mnDebugPrompt+000109 ) > > [ 96] 0x0000000079fc0471 C:\Program Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( mnParser+000593 ) > > [ 97] 0x00000000749a64a4 C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( mcrInstance::mnParser_on_interpreter_thread+000036 ) > > [ 98] 0x000000007498681f C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( mcr::setInterpreterThreadToCurrent+029887 ) > > [ 99] 0x0000000074986881 C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( mcr::setInterpreterThreadToCurrent+029985 ) > > [100] 0x00000000055ce0b6 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( UIW_IsUserMessage+000086 ) > > [101] 0x00000000055ce7b9 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( UIW_SetGLIMUserMsg+000153 ) > > [102] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( GetMenuBarInfo+000638 ) > > [103] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( SystemParametersInfoW+000235 ) > > [104] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( IsProcessDPIAware+000465 ) > > [105] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( KiUserCallbackDispatcher+000031 ) > > [106] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( PeekMessageW+000186 ) > > [107] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( GetKeyState+000238 ) > > [108] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( PeekMessageA+000087 ) > > [109] 0x00000000055a8f4b C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( UIW_SetCurrentDialog+000731 ) > > [110] 0x00000000055cfbe2 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( ws_FreeSystemFont+000546 ) > > [111] 0x000000000485e6a3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [112] 0x000000000485fe18 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [113] 0x0000000004861a20 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [114] 0x0000000004861ae8 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [115] 0x0000000004861ca3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [116] 0x0000000004861d76 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [117] 0x000000007498837e C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( mcr::setInterpreterThreadToCurrent+036894 ) > > [118] 0x0000000074988665 C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( mcr::setInterpreterThreadToCurrent+037637 ) > > [119] 0x000000007497b166 C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( DepfunRules::postWarning+003430 ) > > [120] 0x000000013fc78a33 C:\Program Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) > > [121] 0x000000013fc78c97 C:\Program Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) > > [122] 0x000000013fc79163 C:\Program Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) > > [123] 0x00000000773759ed C:\Windows\system32\kernel32.dll+00088557 ( BaseThreadInitThunk+000013 ) > > [124] 0x00000000775ac541 C:\Windows\SYSTEM32\ntdll.dll+00181569 ( RtlUserThreadStart+000033 ) > > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl 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URL: From kkb268 at nyu.edu Fri May 2 22:41:24 2014 From: kkb268 at nyu.edu (Kristen Berry) Date: Fri, 2 May 2014 16:41:24 -0400 Subject: [FieldTrip] ft_timelockstatistics cluster correction using ECoG data Message-ID: Dear all, I am using an intracranial EEG dataset to compare average high gamma power waveforms between conditions. I want to correct for multiple comparisons across time, but not across number of electrodes. Here is my input code: cfg=[]; cfg.latency = [0.05 .5]; cfg.parameter = 'trial'; cfg.method = 'montecarlo'; cfg.correctm = 'cluster'; cfg.neighbours = []; cfg.numrandomization = 1000; cfg.statistic = 'indepsamplesT'; cfg.channel = ‘all’; cfg.alpha = 0.05; cfg.clusteralpha = 0.05; cfg.tail = 0; stats = ft_timelockstatistics(cfg, data,control); Fieldtrip’s montecarlo reference page ( http://fieldtrip.fcdonders.nl/reference/ft_statistics_montecarlo) says, “If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels.” However, my input code corrects for the number of channels as well. As an example, when cfg.channel = ‘all’ for ft_timelockstatistics, then Elec11 is not significant. However, if the analysis is limited to Elec11 (cfg.channel = 11), then Elec11 has a significant cluster. Is there a mistake in my code that is causing this? Or is there an older version of fieldtrip that doesn’t correct for # of channels, when cfg.neighbours is empty? Thank you for your input! Best regards, Kristen Kristen Berry Research Assistant NYU School of Medicine -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Sat May 3 11:04:42 2014 From: jm.horschig at donders.ru.nl (=?windows-1252?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Sat, 03 May 2014 11:04:42 +0200 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> References: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> Message-ID: <5364B12A.80807@donders.ru.nl> Hi Martine, great to hear that you are using FieldTrip ;) hope you like it. As JM said, it is indeed some low-level problem with Windows 7, Matlab and the databrowser. The only way to escape this is to use another OS... in the past we have not been successful in tracing this down, because it is such a low-level error on only happens on some PCs with Win7, but not on all. There is already a bug on bugzilla for this. Maybe we need to ask Mathworks for support on this ;) @Max: The databrowser is specifically designed to also show components if you set cfg.viewmode = 'components'. The error also has nothing to do with showing components, as it also happens for plotting channel-level data. Best, Jörn On 5/2/2014 8:16 PM, Martine van Schouwenburg wrote: > > Hi Fieldtrip experts, > > I am experiencing a problem with the ft_databrowser routine. Matlab > crashes when I’m trying to run it, forcing me to end the Matlab > session. (‘Matlab has encountered an internal problem and needs to > close.’). It seems more like a Matlab/Windows related issue when > looking at the crash report (see below), but I am posting it here > because it also seems to depend on the data that I use as input. When > I run the routine on the ‘raw’ data (after defining the trials) it is > working fine, but after I ran ICA and try to use the databrowser to > look at the components, it crashes at line 676. > > This is the part where it calls the subfunction redraw_cb. Does anyone > might have a clue what in the component data might cause this problem? > Maybe some of you have experienced this before? I also send a request > for Tech Support to Matlab. > > Best, Martine > > Here is the Matlab crash report if that is of any help: > > ------------------------------------------------------------------------ > > Segmentation violation detected at Thu May 01 22:28:30 2014 > > ------------------------------------------------------------------------ > > Configuration: > > Crash Decoding : Disabled > > Default Encoding: windows-1252 > > MATLAB Root : C:\Program Files\MATLAB\R2012b > > MATLAB Version : 8.0.0.783 (R2012b) > > Operating System: Microsoft Windows 7 > > Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD > > Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java > HotSpot(TM) 64-Bit Server VM mixed mode > > Window System : Version 6.1 (Build 7601: Service Pack 1) > > Fault Count: 1 > > Abnormal termination: > > Segmentation violation > > Register State (from fault): > > RAX = 00000000000001a4 RBX = 000000007a8425c0 > > RCX = 00000000000262de RDX = 00000000000001b2 > > RSP = 0000000004110a50 RBP = 000000000000007e > > RSI = 000000007a75cab0 RDI = 000000013942b996 > > R8 = 00000000000262de R9 = 0000000000000230 > > R10 = 0000000000000000 R11 = 0000000004110b28 > > R12 = 0000000000f206cd R13 = 0000000077ce4060 > > R14 = 000000000002635c R15 = 00000000000006c8 > > RIP = 000000006000d341 EFL = 00010216 > > CS = 0033 FS = 0053 GS = 002b > > Stack Trace (from fault): > > [ 0] 0x000000006000d341 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( > RenderEngineBase::~RenderEngineBase+171553 ) > > [ 1] 0x000000005ff83130 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) > > [ 2] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 3] 0x000000005fede587 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( > renderAnimatedKids+000519 ) > > [ 4] 0x000000005fee3788 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) > > [ 5] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 6] 0x000000005ff04729 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( > FigureSetVisualAutoMode+001561 ) > > [ 7] 0x000000005ff0abbd C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( > UIJ_CreatePeerWindow+001597 ) > > [ 8] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 9] 0x0000000060013548 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( > RenderEngineBase::~RenderEngineBase+196648 ) > > [ 10] 0x000000005ff06b87 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( > FigureSetVisualAutoMode+010871 ) > > [ 11] 0x000000005ff06c0d C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( > FigureSetVisualAutoMode+011005 ) > > [ 12] 0x0000000063425006 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( > wm_ExposeFcn_Pre_Optional+000374 ) > > [ 13] 0x0000000064c8c694 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) > > [ 14] 0x0000000064c8e456 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( > UIJ_IsWindowShowing+000438 ) > > [ 15] 0x0000000064c8f943 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( > UIJ_clearWaitForResize+002067 ) > > [ 16] 0x0000000064c8fa61 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) > > [ 17] 0x0000000064c707ae C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( > UIJ_MarkEventFinished+005838 ) > > [ 18] 0x0000000064c70800 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( > UIJ_MarkEventFinished+005920 ) > > [ 19] 0x0000000064c892ac C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( > uij::JavaDraw2D::paintQuadStrip+001324 ) > > [ 20] 0x0000000064d4e808 C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( > uddSetListenerRecursionWarning+000680 ) > > [ 21] 0x0000000064d4ee6c C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( > UDListenerManagerHost::notifyEvent+000076 ) > > [ 22] 0x0000000064d4697d C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( > UDEventInfo::send+000093 ) > > [ 23] 0x000000005fb9cedb C:\Program > Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( > MErrorException::operator=+047675 ) > > [ 24] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( > UIW_IsUserMessage+000086 ) > > [ 25] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( > UIW_SetGLIMUserMsg+000153 ) > > [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( > GetMenuBarInfo+000638 ) > > [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( > SystemParametersInfoW+000235 ) > > [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( > IsProcessDPIAware+000465 ) > > [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( > KiUserCallbackDispatcher+000031 ) > > [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( > PeekMessageW+000186 ) > > [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( > GetKeyState+000238 ) > > [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( > PeekMessageA+000087 ) > > [ 33] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [ 34] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( > ws_FreeSystemFont+000546 ) > > [ 35] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [ 36] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [ 37] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [ 38] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [ 39] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [ 40] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [ 41] 0x000000005ff0c4fe C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) > > [ 42] 0x0000000074e8d17f C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( > Mfunction_handle::dispatch+001023 ) > > [ 43] 0x0000000074e8cf82 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( > Mfunction_handle::dispatch+000514 ) > > [ 44] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 45] 0x000007feef3a5ca4 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( > inFunctionHandleInterface::DestroyWorkspace+295012 ) > > [ 46] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 47] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 48] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 49] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 50] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 51] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 52] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 53] 0x000007feef38210b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( > inFunctionHandleInterface::DestroyWorkspace+148683 ) > > [ 54] 0x000007feef393edf C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( > inFunctionHandleInterface::DestroyWorkspace+221855 ) > > [ 55] 0x000007feef3b0ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( > inFunctionHandleInterface::DestroyWorkspace+339624 ) > > [ 56] 0x000007feef398d94 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( > inFunctionHandleInterface::DestroyWorkspace+242004 ) > > [ 57] 0x000007feef3a2978 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( > inFunctionHandleInterface::DestroyWorkspace+281912 ) > > [ 58] 0x000007feef3a5a8b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( > inFunctionHandleInterface::DestroyWorkspace+294475 ) > > [ 59] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 60] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 61] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 62] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 63] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 64] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 65] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 66] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 67] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 68] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 69] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 70] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 71] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 72] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 73] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 74] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 75] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 76] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 77] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 78] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 79] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 80] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 81] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 82] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 83] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 84] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 85] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 86] 0x000007feef4451e5 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( > inValidateLoadedObject+001893 ) > > [ 87] 0x000007feef454595 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( > init_cleaner+015541 ) > > [ 88] 0x000007feef457b75 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( > inSetMaxFrameCount+002261 ) > > [ 89] 0x000007feef457b48 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( > inSetMaxFrameCount+002216 ) > > [ 90] 0x000007feef457b07 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( > inSetMaxFrameCount+002151 ) > > [ 91] 0x000007feef340213 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( > inPathNotification::function_clear_notification+004019 ) > > [ 92] 0x000007feef44aed0 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( > inEvalCmdWithLocalReturn+000416 ) > > [ 93] 0x000007feef44ae2c C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( > inEvalCmdWithLocalReturn+000252 ) > > [ 94] 0x000007feef44ad71 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( > inEvalCmdWithLocalReturn+000065 ) > > [ 95] 0x0000000079fbf90d C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( > mnDebugPrompt+000109 ) > > [ 96] 0x0000000079fc0471 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( mnParser+000593 ) > > [ 97] 0x00000000749a64a4 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( > mcrInstance::mnParser_on_interpreter_thread+000036 ) > > [ 98] 0x000000007498681f C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( > mcr::setInterpreterThreadToCurrent+029887 ) > > [ 99] 0x0000000074986881 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( > mcr::setInterpreterThreadToCurrent+029985 ) > > [100] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( > UIW_IsUserMessage+000086 ) > > [101] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( > UIW_SetGLIMUserMsg+000153 ) > > [102] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( > GetMenuBarInfo+000638 ) > > [103] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( > SystemParametersInfoW+000235 ) > > [104] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( > IsProcessDPIAware+000465 ) > > [105] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( > KiUserCallbackDispatcher+000031 ) > > [106] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( > PeekMessageW+000186 ) > > [107] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( > GetKeyState+000238 ) > > [108] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( > PeekMessageA+000087 ) > > [109] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [110] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( > ws_FreeSystemFont+000546 ) > > [111] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [112] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [113] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [114] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [115] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [116] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [117] 0x000000007498837e C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( > mcr::setInterpreterThreadToCurrent+036894 ) > > [118] 0x0000000074988665 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( > mcr::setInterpreterThreadToCurrent+037637 ) > > [119] 0x000000007497b166 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( > DepfunRules::postWarning+003430 ) > > [120] 0x000000013fc78a33 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) > > [121] 0x000000013fc78c97 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) > > [122] 0x000000013fc79163 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) > > [123] 0x00000000773759ed C:\Windows\system32\kernel32.dll+00088557 ( > BaseThreadInitThunk+000013 ) > > [124] 0x00000000775ac541 C:\Windows\SYSTEM32\ntdll.dll+00181569 ( > RtlUserThreadStart+000033 ) > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From martine.vanschouwenburg at ucsf.edu Sat May 3 23:16:43 2014 From: martine.vanschouwenburg at ucsf.edu (Martine van Schouwenburg) Date: Sat, 3 May 2014 14:16:43 -0700 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: <5364B12A.80807@donders.ru.nl> References: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> <5364B12A.80807@donders.ru.nl> Message-ID: <009501cf6714$fbc5e110$f351a330$@vanschouwenburg@ucsf.edu> Hi all, Thank you for all of your quick replies! I have traced the problem down to the ft_plot_topo script, specifically when it calls the 'surf' function. I have been in touch with someone from Mathworks, and I have send him the script and all the variables he needs to run it, and he is looking into the issue. I'll let you know once he gets back to me. Hopefully, with a solution. :) Best, Martine -----Original Message----- From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" Sent: Saturday, May 03, 2014 2:05 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] ft_databrowser crashes Matlab Hi Martine, great to hear that you are using FieldTrip ;) hope you like it. As JM said, it is indeed some low-level problem with Windows 7, Matlab and the databrowser. The only way to escape this is to use another OS... in the past we have not been successful in tracing this down, because it is such a low-level error on only happens on some PCs with Win7, but not on all. There is already a bug on bugzilla for this. Maybe we need to ask Mathworks for support on this ;) @Max: The databrowser is specifically designed to also show components if you set cfg.viewmode = 'components'. The error also has nothing to do with showing components, as it also happens for plotting channel-level data. Best, Jörn On 5/2/2014 8:16 PM, Martine van Schouwenburg wrote: > > Hi Fieldtrip experts, > > I am experiencing a problem with the ft_databrowser routine. Matlab > crashes when I’m trying to run it, forcing me to end the Matlab > session. (‘Matlab has encountered an internal problem and needs to > close.’). It seems more like a Matlab/Windows related issue when > looking at the crash report (see below), but I am posting it here > because it also seems to depend on the data that I use as input. When > I run the routine on the ‘raw’ data (after defining the trials) it is > working fine, but after I ran ICA and try to use the databrowser to > look at the components, it crashes at line 676. > > This is the part where it calls the subfunction redraw_cb. Does anyone > might have a clue what in the component data might cause this problem? > Maybe some of you have experienced this before? I also send a request > for Tech Support to Matlab. > > Best, Martine > > Here is the Matlab crash report if that is of any help: > > ---------------------------------------------------------------------- > -- > > Segmentation violation detected at Thu May 01 22:28:30 2014 > > ---------------------------------------------------------------------- > -- > > Configuration: > > Crash Decoding : Disabled > > Default Encoding: windows-1252 > > MATLAB Root : C:\Program Files\MATLAB\R2012b > > MATLAB Version : 8.0.0.783 (R2012b) > > Operating System: Microsoft Windows 7 > > Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD > > Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java > HotSpot(TM) 64-Bit Server VM mixed mode > > Window System : Version 6.1 (Build 7601: Service Pack 1) > > Fault Count: 1 > > Abnormal termination: > > Segmentation violation > > Register State (from fault): > > RAX = 00000000000001a4 RBX = 000000007a8425c0 > > RCX = 00000000000262de RDX = 00000000000001b2 > > RSP = 0000000004110a50 RBP = 000000000000007e > > RSI = 000000007a75cab0 RDI = 000000013942b996 > > R8 = 00000000000262de R9 = 0000000000000230 > > R10 = 0000000000000000 R11 = 0000000004110b28 > > R12 = 0000000000f206cd R13 = 0000000077ce4060 > > R14 = 000000000002635c R15 = 00000000000006c8 > > RIP = 000000006000d341 EFL = 00010216 > > CS = 0033 FS = 0053 GS = 002b > > Stack Trace (from fault): > > [ 0] 0x000000006000d341 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( > RenderEngineBase::~RenderEngineBase+171553 ) > > [ 1] 0x000000005ff83130 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) > > [ 2] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 3] 0x000000005fede587 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( > renderAnimatedKids+000519 ) > > [ 4] 0x000000005fee3788 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) > > [ 5] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 6] 0x000000005ff04729 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( > FigureSetVisualAutoMode+001561 ) > > [ 7] 0x000000005ff0abbd C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( > UIJ_CreatePeerWindow+001597 ) > > [ 8] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 9] 0x0000000060013548 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( > RenderEngineBase::~RenderEngineBase+196648 ) > > [ 10] 0x000000005ff06b87 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( > FigureSetVisualAutoMode+010871 ) > > [ 11] 0x000000005ff06c0d C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( > FigureSetVisualAutoMode+011005 ) > > [ 12] 0x0000000063425006 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( > wm_ExposeFcn_Pre_Optional+000374 ) > > [ 13] 0x0000000064c8c694 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) > > [ 14] 0x0000000064c8e456 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( > UIJ_IsWindowShowing+000438 ) > > [ 15] 0x0000000064c8f943 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( > UIJ_clearWaitForResize+002067 ) > > [ 16] 0x0000000064c8fa61 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) > > [ 17] 0x0000000064c707ae C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( > UIJ_MarkEventFinished+005838 ) > > [ 18] 0x0000000064c70800 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( > UIJ_MarkEventFinished+005920 ) > > [ 19] 0x0000000064c892ac C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( > uij::JavaDraw2D::paintQuadStrip+001324 ) > > [ 20] 0x0000000064d4e808 C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( > uddSetListenerRecursionWarning+000680 ) > > [ 21] 0x0000000064d4ee6c C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( > UDListenerManagerHost::notifyEvent+000076 ) > > [ 22] 0x0000000064d4697d C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( > UDEventInfo::send+000093 ) > > [ 23] 0x000000005fb9cedb C:\Program > Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( > MErrorException::operator=+047675 ) > > [ 24] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( > UIW_IsUserMessage+000086 ) > > [ 25] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( > UIW_SetGLIMUserMsg+000153 ) > > [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( > GetMenuBarInfo+000638 ) > > [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( > SystemParametersInfoW+000235 ) > > [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( > IsProcessDPIAware+000465 ) > > [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( > KiUserCallbackDispatcher+000031 ) > > [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( > PeekMessageW+000186 ) > > [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( > GetKeyState+000238 ) > > [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( > PeekMessageA+000087 ) > > [ 33] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [ 34] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( > ws_FreeSystemFont+000546 ) > > [ 35] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [ 36] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [ 37] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [ 38] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [ 39] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [ 40] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [ 41] 0x000000005ff0c4fe C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) > > [ 42] 0x0000000074e8d17f C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( > Mfunction_handle::dispatch+001023 ) > > [ 43] 0x0000000074e8cf82 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( > Mfunction_handle::dispatch+000514 ) > > [ 44] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 45] 0x000007feef3a5ca4 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( > inFunctionHandleInterface::DestroyWorkspace+295012 ) > > [ 46] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 47] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 48] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 49] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 50] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 51] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 52] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 53] 0x000007feef38210b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( > inFunctionHandleInterface::DestroyWorkspace+148683 ) > > [ 54] 0x000007feef393edf C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( > inFunctionHandleInterface::DestroyWorkspace+221855 ) > > [ 55] 0x000007feef3b0ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( > inFunctionHandleInterface::DestroyWorkspace+339624 ) > > [ 56] 0x000007feef398d94 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( > inFunctionHandleInterface::DestroyWorkspace+242004 ) > > [ 57] 0x000007feef3a2978 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( > inFunctionHandleInterface::DestroyWorkspace+281912 ) > > [ 58] 0x000007feef3a5a8b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( > inFunctionHandleInterface::DestroyWorkspace+294475 ) > > [ 59] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 60] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 61] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 62] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 63] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 64] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 65] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 66] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 67] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 68] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 69] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 70] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 71] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 72] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 73] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 74] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 75] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 76] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 77] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 78] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 79] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 80] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 81] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 82] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 83] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 84] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 85] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 86] 0x000007feef4451e5 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( > inValidateLoadedObject+001893 ) > > [ 87] 0x000007feef454595 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( > init_cleaner+015541 ) > > [ 88] 0x000007feef457b75 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( > inSetMaxFrameCount+002261 ) > > [ 89] 0x000007feef457b48 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( > inSetMaxFrameCount+002216 ) > > [ 90] 0x000007feef457b07 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( > inSetMaxFrameCount+002151 ) > > [ 91] 0x000007feef340213 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( > inPathNotification::function_clear_notification+004019 ) > > [ 92] 0x000007feef44aed0 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( > inEvalCmdWithLocalReturn+000416 ) > > [ 93] 0x000007feef44ae2c C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( > inEvalCmdWithLocalReturn+000252 ) > > [ 94] 0x000007feef44ad71 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( > inEvalCmdWithLocalReturn+000065 ) > > [ 95] 0x0000000079fbf90d C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( > mnDebugPrompt+000109 ) > > [ 96] 0x0000000079fc0471 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( mnParser+000593 ) > > [ 97] 0x00000000749a64a4 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( > mcrInstance::mnParser_on_interpreter_thread+000036 ) > > [ 98] 0x000000007498681f C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( > mcr::setInterpreterThreadToCurrent+029887 ) > > [ 99] 0x0000000074986881 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( > mcr::setInterpreterThreadToCurrent+029985 ) > > [100] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( > UIW_IsUserMessage+000086 ) > > [101] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( > UIW_SetGLIMUserMsg+000153 ) > > [102] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( > GetMenuBarInfo+000638 ) > > [103] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( > SystemParametersInfoW+000235 ) > > [104] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( > IsProcessDPIAware+000465 ) > > [105] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( > KiUserCallbackDispatcher+000031 ) > > [106] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( > PeekMessageW+000186 ) > > [107] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( > GetKeyState+000238 ) > > [108] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( > PeekMessageA+000087 ) > > [109] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [110] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( > ws_FreeSystemFont+000546 ) > > [111] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [112] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [113] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [114] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [115] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [116] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [117] 0x000000007498837e C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( > mcr::setInterpreterThreadToCurrent+036894 ) > > [118] 0x0000000074988665 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( > mcr::setInterpreterThreadToCurrent+037637 ) > > [119] 0x000000007497b166 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( > DepfunRules::postWarning+003430 ) > > [120] 0x000000013fc78a33 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) > > [121] 0x000000013fc78c97 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) > > [122] 0x000000013fc79163 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) > > [123] 0x00000000773759ed C:\Windows\system32\kernel32.dll+00088557 ( > BaseThreadInitThunk+000013 ) > > [124] 0x00000000775ac541 C:\Windows\SYSTEM32\ntdll.dll+00181569 ( > RtlUserThreadStart+000033 ) > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From e.maris at psych.ru.nl Sun May 4 12:33:35 2014 From: e.maris at psych.ru.nl (Eric Maris) Date: Sun, 4 May 2014 12:33:35 +0200 (CEST) Subject: [FieldTrip] ft_timelockstatistics cluster correction using ECoG data In-Reply-To: References: Message-ID: <036d01cf6784$4b2602c0$e1720840$@maris@psych.ru.nl> Hi Kristen, If you supply ft_timelockstatistics with data containing multiple channels it will always “correct” (this is not the best word to denote what the method does, but let’s use it anyhow) for the number of channels. By requesting not to do clustering in space you just achieve that a clusters are computed in a different way (ie, assuming that the channels measure functionally independent signals). If you do not want correction for multiple channels, then you must analyze the data per channel, as you did for Elec11. If you have a low number of channels, then you could combine the permutation-based p-value with regular Bonferroni correction (dividing the critical alpha-level by the number of channels). Good luck, Eric Maris From: Kristen Berry [mailto:kkb268 at nyu.edu] Sent: vrijdag 2 mei 2014 22:41 To: fieldtrip at science.ru.nl Subject: [FieldTrip] ft_timelockstatistics cluster correction using ECoG data Dear all, I am using an intracranial EEG dataset to compare average high gamma power waveforms between conditions. I want to correct for multiple comparisons across time, but not across number of electrodes. Here is my input code: cfg=[]; cfg.latency = [0.05 .5]; cfg.parameter = 'trial'; cfg.method = 'montecarlo'; cfg.correctm = 'cluster'; cfg.neighbours = []; cfg.numrandomization = 1000; cfg.statistic = 'indepsamplesT'; cfg.channel = ‘all’; cfg.alpha = 0.05; cfg.clusteralpha = 0.05; cfg.tail = 0; stats = ft_timelockstatistics(cfg, data,control); Fieldtrip’s montecarlo reference page ( http://fieldtrip.fcdonders.nl/reference/ft_statistics_montecarlo) says, “If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels.” However, my input code corrects for the number of channels as well. As an example, when cfg.channel = ‘all’ for ft_timelockstatistics, then Elec11 is not significant. However, if the analysis is limited to Elec11 (cfg.channel = 11), then Elec11 has a significant cluster. Is there a mistake in my code that is causing this? Or is there an older version of fieldtrip that doesn’t correct for # of channels, when cfg.neighbours is empty? Thank you for your input! Best regards, Kristen Kristen Berry Research Assistant NYU School of Medicine -------------- next part -------------- An HTML attachment was scrubbed... URL: From lmelloni at gmail.com Mon May 5 01:10:07 2014 From: lmelloni at gmail.com (Lucia Melloni) Date: Sun, 4 May 2014 19:10:07 -0400 Subject: [FieldTrip] deadline extended for the Neurobiology of Cognition GRC/GRS! Message-ID: Dear colleagues, The deadline for application and abstract submission for the Gordon Research Seminar has been extended to the *15th of May*. Please submit your application and abstract soon!. We are very much looking forward to receiving your contributions and to a vibrant seminar. We have also added a mentorship component which promises to provide us with important tips for a successful transition from postdoc to PI. Looking forward to seeing you at the GRS/GRC! Lucia Melloni. Ayelet A. Landau [image: Gordon Research Conferences] Join us at the 2014 *Gordon Conference* and *Seminar* On *Neurobiology of Cognition* Circuits, Dynamics, Action and Perception We are meeting *July 20-25, 2014 -*New GRC site: *Sunday River Resort* Newry, Maine Click *here*to see the *GRC* program. There is also an associated *GRS* *July 19-20 *for students and postdocs Click *here*to see the *GRS* website. *GRS* application & abstract deadline to be considered for oral presentation- *May 15* *Please use attached **flyer **to help spread the word! * The Neurobiology of Cognition is a recently-inaugurated GRC designed to foster convergence of traditional neuroscience investigations with more recent developments in systems, cellular and molecular neurobiology, in engineering and imaging and in computational sciences. Cognition is construed broadly to embrace empirical findings in a range of species including humans, and there is a strong focus on integration of findings and principles across species and levels of analysis. In the opening Keynote Session, two leading neuroscientists with provide an experimental and computational perspective on the recent initiative, termed Brain Research through Advancing Innovative Neurotechnologies (BRAIN). This initiative, spearheaded by the President and NIH, is aimed at developing innovative methodologies to study how complex systems of neurons interact in time and in space during complex behaviors. Along with recent findings in a few traditional "core" areas, formal sessions will then explore several new themes, including: 1) the neuroanatomy and 2) coordination of cognitive circuits in the brain, 3) motor cognition and brain-computer interfaces, 4) music and language, and 5) learning and plasticity. The program juxtaposes human psychophysical, neuroimaging and electrophysiological studies with parallel investigations in rodents and non-human primates, and with computational approaches that explicate empirical findings and construct robust, detailed models to represent the developing picture and guide future experimentation. The program also underscores novel experimental and theoretical approaches that promise to define fundamental principles that guide and integrate the understanding of cognition at a fundamental level, and to extend these to improved treatment of brain dysfunction. The format of the meeting promotes intensive interactions among investigators and trainees from different perspectives and analytic levels, and in particular, between experimentalists and theorists. There is a linked Gordon Research Seminar for trainees, most of whom also attend the GRC. All that is missing now is your *application* to attend. Click *here*for the *GRC*. Click* here*for the *GRS*. (You must apply to both to attend both.) Best regards, GRC Chair: *Charles E. Schroeder* GRC V. Chair:*Tatiana Pasternak* GRS Chair: *Lucia Melloni* GRS Assoc. Chair: *Ayelet N. Landau* *Apply* now and see why our attendees consistently rate GRCs "the best conference I've attended this year"! [image: Like us on Facebook] [image: Follow us on Twitter] [image: View our profile on LinkedIn] *Forward this email * This email was sent to htobin at grc.org by announcements at grc.org | Instant removal with SafeUnsubscribe™ | Privacy Policy . Gordon Research Conferences | 512 Liberty Lane | West Kingston | RI | 02892 Follow GRC: Facebook | Twitter Call Send SMS Add to Skype You'll need Skype CreditFree via Skype -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue May 6 08:26:21 2014 From: jm.horschig at donders.ru.nl (=?windows-1252?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 06 May 2014 08:26:21 +0200 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: <009501cf6714$fbc5e110$f351a330$@vanschouwenburg@ucsf.edu> References: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> <5364B12A.80807@donders.ru.nl> <009501cf6714$fbc5e110$f351a330$@vanschouwenburg@ucsf.edu> Message-ID: <5368808D.4000803@donders.ru.nl> Hi Martine, that's great, thanks. Looking forward to hearing what they say. @Max: then it seems like Martine's problem really is specific to viewing components, sorry :) Best, Jörn On 5/3/2014 11:16 PM, Martine van Schouwenburg wrote: > Hi all, > > Thank you for all of your quick replies! I have traced the problem down to > the ft_plot_topo script, specifically when it calls the 'surf' function. I > have been in touch with someone from Mathworks, and I have send him the > script and all the variables he needs to run it, and he is looking into the > issue. I'll let you know once he gets back to me. Hopefully, with a > solution. :) > > Best, Martine > > > > > -----Original Message----- > From: fieldtrip-bounces at science.ru.nl > [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" > Sent: Saturday, May 03, 2014 2:05 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] ft_databrowser crashes Matlab > > Hi Martine, > > great to hear that you are using FieldTrip ;) hope you like it. > As JM said, it is indeed some low-level problem with Windows 7, Matlab and > the databrowser. The only way to escape this is to use another OS... > in the past we have not been successful in tracing this down, because it is > such a low-level error on only happens on some PCs with Win7, but not on > all. There is already a bug on bugzilla for this. Maybe we need to ask > Mathworks for support on this ;) > > @Max: The databrowser is specifically designed to also show components if > you set cfg.viewmode = 'components'. The error also has nothing to do with > showing components, as it also happens for plotting channel-level data. > > Best, > Jörn > > On 5/2/2014 8:16 PM, Martine van Schouwenburg wrote: >> Hi Fieldtrip experts, >> >> I am experiencing a problem with the ft_databrowser routine. Matlab >> crashes when I’m trying to run it, forcing me to end the Matlab >> session. (‘Matlab has encountered an internal problem and needs to >> close.’). It seems more like a Matlab/Windows related issue when >> looking at the crash report (see below), but I am posting it here >> because it also seems to depend on the data that I use as input. When >> I run the routine on the ‘raw’ data (after defining the trials) it is >> working fine, but after I ran ICA and try to use the databrowser to >> look at the components, it crashes at line 676. >> >> This is the part where it calls the subfunction redraw_cb. Does anyone >> might have a clue what in the component data might cause this problem? >> Maybe some of you have experienced this before? I also send a request >> for Tech Support to Matlab. >> >> Best, Martine >> >> Here is the Matlab crash report if that is of any help: >> >> ---------------------------------------------------------------------- >> -- >> >> Segmentation violation detected at Thu May 01 22:28:30 2014 >> >> ---------------------------------------------------------------------- >> -- >> >> Configuration: >> >> Crash Decoding : Disabled >> >> Default Encoding: windows-1252 >> >> MATLAB Root : C:\Program Files\MATLAB\R2012b >> >> MATLAB Version : 8.0.0.783 (R2012b) >> >> Operating System: Microsoft Windows 7 >> >> Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD >> >> Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java >> HotSpot(TM) 64-Bit Server VM mixed mode >> >> Window System : Version 6.1 (Build 7601: Service Pack 1) >> >> Fault Count: 1 >> >> Abnormal termination: >> >> Segmentation violation >> >> Register State (from fault): >> >> RAX = 00000000000001a4 RBX = 000000007a8425c0 >> >> RCX = 00000000000262de RDX = 00000000000001b2 >> >> RSP = 0000000004110a50 RBP = 000000000000007e >> >> RSI = 000000007a75cab0 RDI = 000000013942b996 >> >> R8 = 00000000000262de R9 = 0000000000000230 >> >> R10 = 0000000000000000 R11 = 0000000004110b28 >> >> R12 = 0000000000f206cd R13 = 0000000077ce4060 >> >> R14 = 000000000002635c R15 = 00000000000006c8 >> >> RIP = 000000006000d341 EFL = 00010216 >> >> CS = 0033 FS = 0053 GS = 002b >> >> Stack Trace (from fault): >> >> [ 0] 0x000000006000d341 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( >> RenderEngineBase::~RenderEngineBase+171553 ) >> >> [ 1] 0x000000005ff83130 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) >> >> [ 2] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 3] 0x000000005fede587 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( >> renderAnimatedKids+000519 ) >> >> [ 4] 0x000000005fee3788 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) >> >> [ 5] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 6] 0x000000005ff04729 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( >> FigureSetVisualAutoMode+001561 ) >> >> [ 7] 0x000000005ff0abbd C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( >> UIJ_CreatePeerWindow+001597 ) >> >> [ 8] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 9] 0x0000000060013548 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( >> RenderEngineBase::~RenderEngineBase+196648 ) >> >> [ 10] 0x000000005ff06b87 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( >> FigureSetVisualAutoMode+010871 ) >> >> [ 11] 0x000000005ff06c0d C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( >> FigureSetVisualAutoMode+011005 ) >> >> [ 12] 0x0000000063425006 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( >> wm_ExposeFcn_Pre_Optional+000374 ) >> >> [ 13] 0x0000000064c8c694 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) >> >> [ 14] 0x0000000064c8e456 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( >> UIJ_IsWindowShowing+000438 ) >> >> [ 15] 0x0000000064c8f943 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( >> UIJ_clearWaitForResize+002067 ) >> >> [ 16] 0x0000000064c8fa61 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) >> >> [ 17] 0x0000000064c707ae C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( >> UIJ_MarkEventFinished+005838 ) >> >> [ 18] 0x0000000064c70800 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( >> UIJ_MarkEventFinished+005920 ) >> >> [ 19] 0x0000000064c892ac C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( >> uij::JavaDraw2D::paintQuadStrip+001324 ) >> >> [ 20] 0x0000000064d4e808 C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( >> uddSetListenerRecursionWarning+000680 ) >> >> [ 21] 0x0000000064d4ee6c C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( >> UDListenerManagerHost::notifyEvent+000076 ) >> >> [ 22] 0x0000000064d4697d C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( >> UDEventInfo::send+000093 ) >> >> [ 23] 0x000000005fb9cedb C:\Program >> Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( >> MErrorException::operator=+047675 ) >> >> [ 24] 0x00000000055ce0b6 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( >> UIW_IsUserMessage+000086 ) >> >> [ 25] 0x00000000055ce7b9 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( >> UIW_SetGLIMUserMsg+000153 ) >> >> [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( >> GetMenuBarInfo+000638 ) >> >> [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( >> SystemParametersInfoW+000235 ) >> >> [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( >> IsProcessDPIAware+000465 ) >> >> [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( >> KiUserCallbackDispatcher+000031 ) >> >> [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( >> PeekMessageW+000186 ) >> >> [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( >> GetKeyState+000238 ) >> >> [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( >> PeekMessageA+000087 ) >> >> [ 33] 0x00000000055a8f4b C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( >> UIW_SetCurrentDialog+000731 ) >> >> [ 34] 0x00000000055cfbe2 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( >> ws_FreeSystemFont+000546 ) >> >> [ 35] 0x000000000485e6a3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( >> sysq::removeCommitDatabaseUpdatesHook+002131 ) >> >> [ 36] 0x000000000485fe18 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( >> sysq::removeCommitDatabaseUpdatesHook+008136 ) >> >> [ 37] 0x0000000004861a20 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( >> sysq::addProcessPendingEventsUnitTestHook+000240 ) >> >> [ 38] 0x0000000004861ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( >> sysq::addProcessPendingEventsUnitTestHook+000440 ) >> >> [ 39] 0x0000000004861ca3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( >> sysq::addProcessPendingEventsUnitTestHook+000883 ) >> >> [ 40] 0x0000000004861d76 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( >> sysq::addProcessPendingEventsUnitTestHook+001094 ) >> >> [ 41] 0x000000005ff0c4fe C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) >> >> [ 42] 0x0000000074e8d17f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( >> Mfunction_handle::dispatch+001023 ) >> >> [ 43] 0x0000000074e8cf82 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( >> Mfunction_handle::dispatch+000514 ) >> >> [ 44] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 45] 0x000007feef3a5ca4 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( >> inFunctionHandleInterface::DestroyWorkspace+295012 ) >> >> [ 46] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 47] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 48] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 49] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 50] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 51] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 52] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 53] 0x000007feef38210b C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( >> inFunctionHandleInterface::DestroyWorkspace+148683 ) >> >> [ 54] 0x000007feef393edf C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( >> inFunctionHandleInterface::DestroyWorkspace+221855 ) >> >> [ 55] 0x000007feef3b0ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( >> inFunctionHandleInterface::DestroyWorkspace+339624 ) >> >> [ 56] 0x000007feef398d94 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( >> inFunctionHandleInterface::DestroyWorkspace+242004 ) >> >> [ 57] 0x000007feef3a2978 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( >> inFunctionHandleInterface::DestroyWorkspace+281912 ) >> >> [ 58] 0x000007feef3a5a8b C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( >> inFunctionHandleInterface::DestroyWorkspace+294475 ) >> >> [ 59] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 60] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 61] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 62] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 63] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 64] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 65] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 66] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 67] 0x000007feef43318f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( >> inEachVisibleName+014415 ) >> >> [ 68] 0x000007feef3a74ca C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( >> inFunctionHandleInterface::DestroyWorkspace+301194 ) >> >> [ 69] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 70] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 71] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 72] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 73] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 74] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 75] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 76] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 77] 0x000007feef43318f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( >> inEachVisibleName+014415 ) >> >> [ 78] 0x000007feef3a74ca C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( >> inFunctionHandleInterface::DestroyWorkspace+301194 ) >> >> [ 79] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 80] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 81] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 82] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 83] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 84] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 85] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 86] 0x000007feef4451e5 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( >> inValidateLoadedObject+001893 ) >> >> [ 87] 0x000007feef454595 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( >> init_cleaner+015541 ) >> >> [ 88] 0x000007feef457b75 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( >> inSetMaxFrameCount+002261 ) >> >> [ 89] 0x000007feef457b48 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( >> inSetMaxFrameCount+002216 ) >> >> [ 90] 0x000007feef457b07 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( >> inSetMaxFrameCount+002151 ) >> >> [ 91] 0x000007feef340213 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( >> inPathNotification::function_clear_notification+004019 ) >> >> [ 92] 0x000007feef44aed0 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( >> inEvalCmdWithLocalReturn+000416 ) >> >> [ 93] 0x000007feef44ae2c C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( >> inEvalCmdWithLocalReturn+000252 ) >> >> [ 94] 0x000007feef44ad71 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( >> inEvalCmdWithLocalReturn+000065 ) >> >> [ 95] 0x0000000079fbf90d C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( >> mnDebugPrompt+000109 ) >> >> [ 96] 0x0000000079fc0471 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( mnParser+000593 ) >> >> [ 97] 0x00000000749a64a4 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( >> mcrInstance::mnParser_on_interpreter_thread+000036 ) >> >> [ 98] 0x000000007498681f C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( >> mcr::setInterpreterThreadToCurrent+029887 ) >> >> [ 99] 0x0000000074986881 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( >> mcr::setInterpreterThreadToCurrent+029985 ) >> >> [100] 0x00000000055ce0b6 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( >> UIW_IsUserMessage+000086 ) >> >> [101] 0x00000000055ce7b9 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( >> UIW_SetGLIMUserMsg+000153 ) >> >> [102] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( >> GetMenuBarInfo+000638 ) >> >> [103] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( >> SystemParametersInfoW+000235 ) >> >> [104] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( >> IsProcessDPIAware+000465 ) >> >> [105] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( >> KiUserCallbackDispatcher+000031 ) >> >> [106] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( >> PeekMessageW+000186 ) >> >> [107] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( >> GetKeyState+000238 ) >> >> [108] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( >> PeekMessageA+000087 ) >> >> [109] 0x00000000055a8f4b C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( >> UIW_SetCurrentDialog+000731 ) >> >> [110] 0x00000000055cfbe2 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( >> ws_FreeSystemFont+000546 ) >> >> [111] 0x000000000485e6a3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( >> sysq::removeCommitDatabaseUpdatesHook+002131 ) >> >> [112] 0x000000000485fe18 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( >> sysq::removeCommitDatabaseUpdatesHook+008136 ) >> >> [113] 0x0000000004861a20 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( >> sysq::addProcessPendingEventsUnitTestHook+000240 ) >> >> [114] 0x0000000004861ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( >> sysq::addProcessPendingEventsUnitTestHook+000440 ) >> >> [115] 0x0000000004861ca3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( >> sysq::addProcessPendingEventsUnitTestHook+000883 ) >> >> [116] 0x0000000004861d76 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( >> sysq::addProcessPendingEventsUnitTestHook+001094 ) >> >> [117] 0x000000007498837e C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( >> mcr::setInterpreterThreadToCurrent+036894 ) >> >> [118] 0x0000000074988665 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( >> mcr::setInterpreterThreadToCurrent+037637 ) >> >> [119] 0x000000007497b166 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( >> DepfunRules::postWarning+003430 ) >> >> [120] 0x000000013fc78a33 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) >> >> [121] 0x000000013fc78c97 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) >> >> [122] 0x000000013fc79163 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) >> >> [123] 0x00000000773759ed C:\Windows\system32\kernel32.dll+00088557 ( >> BaseThreadInitThunk+000013 ) >> >> [124] 0x00000000775ac541 C:\Windows\SYSTEM32\ntdll.dll+00181569 ( >> RtlUserThreadStart+000033 ) >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From Gregor.Volberg at psychologie.uni-regensburg.de Tue May 6 11:03:52 2014 From: Gregor.Volberg at psychologie.uni-regensburg.de (Gregor Volberg) Date: Tue, 06 May 2014 11:03:52 +0200 Subject: [FieldTrip] PhD Job offer in Visual Neuroscience, University of Regensburg (Germany) Message-ID: <5368C198020000570001653B@gwsmtp1.uni-regensburg.de> Dear colleagues, please find below a job offer for a PhD position at the University of Regensburg, Germany. You might send it to interested students if you like. Best regards, Gregor **** The University of Regensburg (Germany), Institute for Psychology, Workgroup Experimental Psychology offers a 65 % position for a three-year PhD project starting in October 2014 (Chair: Prof. Dr. Mark Greenlee; Principal Investigator: PD Dr. G. Volberg). The salary will be according to German TV-L E 13 (65 % position) payment plan. The DFG-funded research project is on the neural basis of grapheme-color synesthesia, a perceptual phenomenon where achromatic letters or numbers produce a simultaneous sensation of color. Methods include electroencephalography (EEG) and functional magnetic resonance imaging (fMRI). Eligible job applicants must hold a masters degree (or comparable) in psychology or neighboring disciplines. They should have an academic background in visual neuroscience, especially in the acquisition and analysis of EEG and/or fMRI data. Programming experience in MatLab is advantageous. Job holders will need to recruit and test synesthetic participants from the local student population. Good skills in German are therefore necessary. We can offer an active research environment, an interesting topic for your PhD thesis, a friendly team and a UNESCO-heritage city located on the Danube River. We are looking forward to receiving your application! The University of Regensburg supports the reconcilability between family and career (see http://www.uni-regensburg.de/chancengleichheit). Physically challenged applicants will be preferred in cases of equivalent qualification. If applicable, please convey extend and type of disability in your résumé. Please note that the university does not refund costs ensuing from job interviews. Please send your application by June 1st, 2014 to PD Dr. Volberg, gregor.volberg at ur.de. The application should hold pertinent information about your academic career. Please send in the application in an electronic form (pdf) and use the subject matter „Application Synesthesia“ in the e-mail. The contact person is PD Dr. Gregor Volberg (office hours, Wednesday 10-12, Tel. +49 941 943 3862; http://www.uni-regensburg.de/psychologie-paedagogik-sport/psychologie-greenlee/team/volberg/index.html). -- PD Dr. rer. nat. Gregor Volberg gregor.volberg at ur.deUniversity of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From martine.vanschouwenburg at ucsf.edu Tue May 6 18:59:06 2014 From: martine.vanschouwenburg at ucsf.edu (Martine van Schouwenburg) Date: Tue, 6 May 2014 09:59:06 -0700 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: <5368808D.4000803@donders.ru.nl> References: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> <5364B12A.80807@donders.ru.nl> <009501cf6714$fbc5e110$f351a330$@vanschouwenburg@ucsf.edu> <5368808D.4000803@donders.ru.nl> Message-ID: <00ff01cf694c$7d847f20$788d7d60$@vanschouwenburg@ucsf.edu> Hi all, Problem is solved! I have had great help from the Mathworks support team and it turns out it was a rendering issue (see below part of the email that I got from Mathworks). Setting the renderer to 'Paintings' did the trick for me, so I have now added this line [set(gcf,'renderer','painters');] to the script, just before it calls the 'surf' function (line 242 of ft_plot_topo). This issue seems to depend strongly on OS, graphics card, software version etc, but if anyone runs into a similar problem you could try to see if changing the renderer works for you too. Best, Martine EMAIL SUPPORT TEAM MATHWORKS: "I have a feeling that the crash might be because of the renderer being chosen by MATLAB to plot the surface plot. MATLAB has three renderers- OpenGL, Painters and Z-Buffer. Each of these renderers has its own merits and limitations. MATLAB chooses the correct renderer based on the type of figure that you are plotting. Here is a documentation page that talks more about the three renderers in MATLAB: http://www.mathworks.com/help/matlab/creating_plots/changing-a-figures-setti ngs.html#f3-102410 Of the three renderers OpenGL has the ability to use the graphics hardware on your system to help render the graphics. This can occasionally cause incompatibilities due to the many different graphics cards out there and also the many different driver versions that exist for each of these cards. So, you can try and switch to the software implementation of OpenGL by executing the following command in the command window: >>opengl software This setting is retained for the current session of MATLAB. If you want MATLAB to remember this setting across settings, then I would suggest that you add this command to your "startup.m". Please use the above command and then run your code to see if the crash still occurs. IF THE ABOVE PROCEDURE DOES NOT WORK: We can try and change the renderer to one of the other two and see if this helps. You can change the renderer by using the "set" command: >> set(gcf,'renderer','painters'); OR >>set(gcf,'renderer','zbuffer'); OR >>set(gcf,'renderer','opengl'); Here "gcf" refers to the currently active figure window. I would suggest that you try changing the renderer just before the "surf" command is executed and see if the crash stops happening when using a particular renderer." -----Original Message----- From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" Sent: Monday, May 05, 2014 11:26 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] ft_databrowser crashes Matlab Hi Martine, that's great, thanks. Looking forward to hearing what they say. @Max: then it seems like Martine's problem really is specific to viewing components, sorry :) Best, Jörn On 5/3/2014 11:16 PM, Martine van Schouwenburg wrote: > Hi all, > > Thank you for all of your quick replies! I have traced the problem > down to the ft_plot_topo script, specifically when it calls the 'surf' > function. I have been in touch with someone from Mathworks, and I have > send him the script and all the variables he needs to run it, and he > is looking into the issue. I'll let you know once he gets back to me. > Hopefully, with a solution. :) > > Best, Martine > > > > > -----Original Message----- > From: fieldtrip-bounces at science.ru.nl > [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" > Sent: Saturday, May 03, 2014 2:05 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] ft_databrowser crashes Matlab > > Hi Martine, > > great to hear that you are using FieldTrip ;) hope you like it. > As JM said, it is indeed some low-level problem with Windows 7, Matlab > and the databrowser. The only way to escape this is to use another OS... > in the past we have not been successful in tracing this down, because > it is such a low-level error on only happens on some PCs with Win7, > but not on all. There is already a bug on bugzilla for this. Maybe we > need to ask Mathworks for support on this ;) > > @Max: The databrowser is specifically designed to also show components > if you set cfg.viewmode = 'components'. The error also has nothing to > do with showing components, as it also happens for plotting channel-level data. > > Best, > Jörn > > On 5/2/2014 8:16 PM, Martine van Schouwenburg wrote: >> Hi Fieldtrip experts, >> >> I am experiencing a problem with the ft_databrowser routine. Matlab >> crashes when I’m trying to run it, forcing me to end the Matlab >> session. (‘Matlab has encountered an internal problem and needs to >> close.’). It seems more like a Matlab/Windows related issue when >> looking at the crash report (see below), but I am posting it here >> because it also seems to depend on the data that I use as input. When >> I run the routine on the ‘raw’ data (after defining the trials) it is >> working fine, but after I ran ICA and try to use the databrowser to >> look at the components, it crashes at line 676. >> >> This is the part where it calls the subfunction redraw_cb. Does >> anyone might have a clue what in the component data might cause this problem? >> Maybe some of you have experienced this before? I also send a request >> for Tech Support to Matlab. >> >> Best, Martine >> >> Here is the Matlab crash report if that is of any help: >> >> --------------------------------------------------------------------- >> - >> -- >> >> Segmentation violation detected at Thu May 01 22:28:30 2014 >> >> --------------------------------------------------------------------- >> - >> -- >> >> Configuration: >> >> Crash Decoding : Disabled >> >> Default Encoding: windows-1252 >> >> MATLAB Root : C:\Program Files\MATLAB\R2012b >> >> MATLAB Version : 8.0.0.783 (R2012b) >> >> Operating System: Microsoft Windows 7 >> >> Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD >> >> Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java >> HotSpot(TM) 64-Bit Server VM mixed mode >> >> Window System : Version 6.1 (Build 7601: Service Pack 1) >> >> Fault Count: 1 >> >> Abnormal termination: >> >> Segmentation violation >> >> Register State (from fault): >> >> RAX = 00000000000001a4 RBX = 000000007a8425c0 >> >> RCX = 00000000000262de RDX = 00000000000001b2 >> >> RSP = 0000000004110a50 RBP = 000000000000007e >> >> RSI = 000000007a75cab0 RDI = 000000013942b996 >> >> R8 = 00000000000262de R9 = 0000000000000230 >> >> R10 = 0000000000000000 R11 = 0000000004110b28 >> >> R12 = 0000000000f206cd R13 = 0000000077ce4060 >> >> R14 = 000000000002635c R15 = 00000000000006c8 >> >> RIP = 000000006000d341 EFL = 00010216 >> >> CS = 0033 FS = 0053 GS = 002b >> >> Stack Trace (from fault): >> >> [ 0] 0x000000006000d341 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( >> RenderEngineBase::~RenderEngineBase+171553 ) >> >> [ 1] 0x000000005ff83130 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 >> ) >> >> [ 2] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 3] 0x000000005fede587 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( >> renderAnimatedKids+000519 ) >> >> [ 4] 0x000000005fee3788 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) >> >> [ 5] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 6] 0x000000005ff04729 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( >> FigureSetVisualAutoMode+001561 ) >> >> [ 7] 0x000000005ff0abbd C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( >> UIJ_CreatePeerWindow+001597 ) >> >> [ 8] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 9] 0x0000000060013548 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( >> RenderEngineBase::~RenderEngineBase+196648 ) >> >> [ 10] 0x000000005ff06b87 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( >> FigureSetVisualAutoMode+010871 ) >> >> [ 11] 0x000000005ff06c0d C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( >> FigureSetVisualAutoMode+011005 ) >> >> [ 12] 0x0000000063425006 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( >> wm_ExposeFcn_Pre_Optional+000374 ) >> >> [ 13] 0x0000000064c8c694 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( >> GetframeJava+001332 ) >> >> [ 14] 0x0000000064c8e456 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( >> UIJ_IsWindowShowing+000438 ) >> >> [ 15] 0x0000000064c8f943 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( >> UIJ_clearWaitForResize+002067 ) >> >> [ 16] 0x0000000064c8fa61 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( >> UIJ_ExposeFcn+000145 ) >> >> [ 17] 0x0000000064c707ae C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( >> UIJ_MarkEventFinished+005838 ) >> >> [ 18] 0x0000000064c70800 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( >> UIJ_MarkEventFinished+005920 ) >> >> [ 19] 0x0000000064c892ac C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( >> uij::JavaDraw2D::paintQuadStrip+001324 ) >> >> [ 20] 0x0000000064d4e808 C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( >> uddSetListenerRecursionWarning+000680 ) >> >> [ 21] 0x0000000064d4ee6c C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( >> UDListenerManagerHost::notifyEvent+000076 ) >> >> [ 22] 0x0000000064d4697d C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( >> UDEventInfo::send+000093 ) >> >> [ 23] 0x000000005fb9cedb C:\Program >> Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( >> MErrorException::operator=+047675 ) >> >> [ 24] 0x00000000055ce0b6 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( >> UIW_IsUserMessage+000086 ) >> >> [ 25] 0x00000000055ce7b9 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( >> UIW_SetGLIMUserMsg+000153 ) >> >> [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( >> GetMenuBarInfo+000638 ) >> >> [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( >> SystemParametersInfoW+000235 ) >> >> [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( >> IsProcessDPIAware+000465 ) >> >> [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( >> KiUserCallbackDispatcher+000031 ) >> >> [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( >> PeekMessageW+000186 ) >> >> [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( >> GetKeyState+000238 ) >> >> [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( >> PeekMessageA+000087 ) >> >> [ 33] 0x00000000055a8f4b C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( >> UIW_SetCurrentDialog+000731 ) >> >> [ 34] 0x00000000055cfbe2 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( >> ws_FreeSystemFont+000546 ) >> >> [ 35] 0x000000000485e6a3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( >> sysq::removeCommitDatabaseUpdatesHook+002131 ) >> >> [ 36] 0x000000000485fe18 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( >> sysq::removeCommitDatabaseUpdatesHook+008136 ) >> >> [ 37] 0x0000000004861a20 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( >> sysq::addProcessPendingEventsUnitTestHook+000240 ) >> >> [ 38] 0x0000000004861ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( >> sysq::addProcessPendingEventsUnitTestHook+000440 ) >> >> [ 39] 0x0000000004861ca3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( >> sysq::addProcessPendingEventsUnitTestHook+000883 ) >> >> [ 40] 0x0000000004861d76 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( >> sysq::addProcessPendingEventsUnitTestHook+001094 ) >> >> [ 41] 0x000000005ff0c4fe C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) >> >> [ 42] 0x0000000074e8d17f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( >> Mfunction_handle::dispatch+001023 ) >> >> [ 43] 0x0000000074e8cf82 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( >> Mfunction_handle::dispatch+000514 ) >> >> [ 44] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 45] 0x000007feef3a5ca4 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( >> inFunctionHandleInterface::DestroyWorkspace+295012 ) >> >> [ 46] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 47] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 48] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 49] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 50] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 51] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 52] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 53] 0x000007feef38210b C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( >> inFunctionHandleInterface::DestroyWorkspace+148683 ) >> >> [ 54] 0x000007feef393edf C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( >> inFunctionHandleInterface::DestroyWorkspace+221855 ) >> >> [ 55] 0x000007feef3b0ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( >> inFunctionHandleInterface::DestroyWorkspace+339624 ) >> >> [ 56] 0x000007feef398d94 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( >> inFunctionHandleInterface::DestroyWorkspace+242004 ) >> >> [ 57] 0x000007feef3a2978 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( >> inFunctionHandleInterface::DestroyWorkspace+281912 ) >> >> [ 58] 0x000007feef3a5a8b C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( >> inFunctionHandleInterface::DestroyWorkspace+294475 ) >> >> [ 59] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 60] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 61] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 62] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 63] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 64] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 65] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 66] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 67] 0x000007feef43318f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( >> inEachVisibleName+014415 ) >> >> [ 68] 0x000007feef3a74ca C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( >> inFunctionHandleInterface::DestroyWorkspace+301194 ) >> >> [ 69] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 70] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 71] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 72] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 73] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 74] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 75] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 76] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 77] 0x000007feef43318f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( >> inEachVisibleName+014415 ) >> >> [ 78] 0x000007feef3a74ca C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( >> inFunctionHandleInterface::DestroyWorkspace+301194 ) >> >> [ 79] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 80] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 81] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 82] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 83] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 84] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 85] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 86] 0x000007feef4451e5 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( >> inValidateLoadedObject+001893 ) >> >> [ 87] 0x000007feef454595 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( >> init_cleaner+015541 ) >> >> [ 88] 0x000007feef457b75 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( >> inSetMaxFrameCount+002261 ) >> >> [ 89] 0x000007feef457b48 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( >> inSetMaxFrameCount+002216 ) >> >> [ 90] 0x000007feef457b07 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( >> inSetMaxFrameCount+002151 ) >> >> [ 91] 0x000007feef340213 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( >> inPathNotification::function_clear_notification+004019 ) >> >> [ 92] 0x000007feef44aed0 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( >> inEvalCmdWithLocalReturn+000416 ) >> >> [ 93] 0x000007feef44ae2c C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( >> inEvalCmdWithLocalReturn+000252 ) >> >> [ 94] 0x000007feef44ad71 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( >> inEvalCmdWithLocalReturn+000065 ) >> >> [ 95] 0x0000000079fbf90d C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( >> mnDebugPrompt+000109 ) >> >> [ 96] 0x0000000079fc0471 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( >> mnParser+000593 ) >> >> [ 97] 0x00000000749a64a4 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( >> mcrInstance::mnParser_on_interpreter_thread+000036 ) >> >> [ 98] 0x000000007498681f C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( >> mcr::setInterpreterThreadToCurrent+029887 ) >> >> [ 99] 0x0000000074986881 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( >> mcr::setInterpreterThreadToCurrent+029985 ) >> >> [100] 0x00000000055ce0b6 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( >> UIW_IsUserMessage+000086 ) >> >> [101] 0x00000000055ce7b9 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( >> UIW_SetGLIMUserMsg+000153 ) >> >> [102] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( >> GetMenuBarInfo+000638 ) >> >> [103] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( >> SystemParametersInfoW+000235 ) >> >> [104] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( >> IsProcessDPIAware+000465 ) >> >> [105] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( >> KiUserCallbackDispatcher+000031 ) >> >> [106] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( >> PeekMessageW+000186 ) >> >> [107] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( >> GetKeyState+000238 ) >> >> [108] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( >> PeekMessageA+000087 ) >> >> [109] 0x00000000055a8f4b C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( >> UIW_SetCurrentDialog+000731 ) >> >> [110] 0x00000000055cfbe2 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( >> ws_FreeSystemFont+000546 ) >> >> [111] 0x000000000485e6a3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( >> sysq::removeCommitDatabaseUpdatesHook+002131 ) >> >> [112] 0x000000000485fe18 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( >> sysq::removeCommitDatabaseUpdatesHook+008136 ) >> >> [113] 0x0000000004861a20 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( >> sysq::addProcessPendingEventsUnitTestHook+000240 ) >> >> [114] 0x0000000004861ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( >> sysq::addProcessPendingEventsUnitTestHook+000440 ) >> >> [115] 0x0000000004861ca3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( >> sysq::addProcessPendingEventsUnitTestHook+000883 ) >> >> [116] 0x0000000004861d76 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( >> sysq::addProcessPendingEventsUnitTestHook+001094 ) >> >> [117] 0x000000007498837e C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( >> mcr::setInterpreterThreadToCurrent+036894 ) >> >> [118] 0x0000000074988665 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( >> mcr::setInterpreterThreadToCurrent+037637 ) >> >> [119] 0x000000007497b166 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( >> DepfunRules::postWarning+003430 ) >> >> [120] 0x000000013fc78a33 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) >> >> [121] 0x000000013fc78c97 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) >> >> [122] 0x000000013fc79163 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) >> >> [123] 0x00000000773759ed C:\Windows\system32\kernel32.dll+00088557 ( >> BaseThreadInitThunk+000013 ) >> >> [124] 0x00000000775ac541 C:\Windows\SYSTEM32\ntdll.dll+00181569 ( >> RtlUserThreadStart+000033 ) >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From ahmeedzeki at yahoo.com Tue May 6 22:41:13 2014 From: ahmeedzeki at yahoo.com (ahmeedzeki at yahoo.com) Date: Tue, 6 May 2014 20:41:13 +0000 Subject: [FieldTrip] =?utf-8?q?Leadfield_Matrix?= Message-ID: <687035.72317.bm@smtp110.mail.bf1.yahoo.com> Dear leadfield Developers and Users: My name is Ahmed Al Hilli, I am a PhD student at Rutgers University. I am working on EEG source localization. I have difficulties in generating the leadfield matrix. I want to generate the leadfield matrix using just a cortex of the brain and I want to use a realistic head model. I’ve generated the cortex sheet using ft_volume_segment function, and also I have the scalp binary mask. My question is what to do next to apply BEM method? Thank you very much Sent from Windows Mail -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.rombetto at cib.na.cnr.it Wed May 7 13:00:50 2014 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Wed, 7 May 2014 13:00:50 +0200 Subject: [FieldTrip] problem occurs when using ft_timelockanalysis Message-ID: <20140507130050.cctyuq8m1w80o4g4@arco.cib.na.cnr.it> Dear fieldtrippers I'm encountering a problem when running ft_timelockanalysis in Matlab. I receive the following message: "A Undefined function 'mxSerialize_cpp' for input arguments of type 'struct' Error in mxSerialize (line 35) argout = mxSerialize_cpp(argin); Error in ft_preamble_provenance (line 67) cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); Error in ft_preamble (line 54) evalin('caller', ['ft_preamble_' cmd]); Error in ft_timelockanalysis (line 95) ft_preamble provenance data" I am using \fieldtrip-20140506 and matlab R2014a - 64 bit Any suggestion is highly appreciated. ------------------------- Dott.ssa Sara Rombetto Istituto di Cibernetica "E. Caianiello" Via Campi Flegrei, 34 80078 Pozzuoli (NA) Italy mob +39 3401689815 tel +39 0818675361 fax +39 0818675128 Lab MEG 0817483511 -------------------------- "I disapprove of what you say, but I will defend to the death your right to say it." [Evelyn Beatrice Hall, The Friends Of Voltaire] ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From yingli.ucla at gmail.com Wed May 7 23:14:22 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Wed, 7 May 2014 14:14:22 -0700 Subject: [FieldTrip] Failed to download the sample data - the links no longer exist Message-ID: Dear all, I am learning to use fieldtrip to do source localization. When I tried to download some sample data, such as 1) The MEG data: ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip 2) The MRI data: ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip . It shows that the links don't exist any more. Are there any other ways for me to download these sample data? Thanks a lot! Ying -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Thu May 8 11:00:29 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 8 May 2014 09:00:29 +0000 Subject: [FieldTrip] (no subject) Message-ID: Dear all, has anyone come across (or used) cluster-based permutation statistics for (human) LFP data obtained from DBS-electrodes? I am looking for a reference and, after a quick search, didn't find any, thanks! Best wishes Max From jm.horschig at donders.ru.nl Thu May 8 13:02:59 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 08 May 2014 13:02:59 +0200 Subject: [FieldTrip] (no subject) In-Reply-To: References: Message-ID: <536B6463.3080504@donders.ru.nl> Hi Max-Philipp, what is it that you want to do specifically? Basically, there is nothing different from doing scalp EEG statistics. Regarding a reference, if you wait for a few more months, then you can cite my paper... once I've written it down ;) Best, Jörn On 5/8/2014 11:00 AM, Stenner, Max-Philipp wrote: > Dear all, > has anyone come across (or used) cluster-based permutation statistics for (human) LFP data obtained from DBS-electrodes? I am looking for a reference and, after a quick search, didn't find any, > thanks! > Best wishes > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From max-philipp.stenner at med.ovgu.de Thu May 8 13:24:47 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 8 May 2014 11:24:47 +0000 Subject: [FieldTrip] (no subject) In-Reply-To: <536B6463.3080504@donders.ru.nl> References: , <536B6463.3080504@donders.ru.nl> Message-ID: Hi Jörn, thanks, you are right, there is no difference to any other montage with a common reference. And thanks for the prospective citation, I'll look out for it, best Max ________________________________________ Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" im Auftrag von ""Jörn M. Horschig" [jm.horschig at donders.ru.nl] Gesendet: Donnerstag, 8. Mai 2014 13:02 An: FieldTrip discussion list Betreff: Re: [FieldTrip] (no subject) Hi Max-Philipp, what is it that you want to do specifically? Basically, there is nothing different from doing scalp EEG statistics. Regarding a reference, if you wait for a few more months, then you can cite my paper... once I've written it down ;) Best, Jörn On 5/8/2014 11:00 AM, Stenner, Max-Philipp wrote: > Dear all, > has anyone come across (or used) cluster-based permutation statistics for (human) LFP data obtained from DBS-electrodes? I am looking for a reference and, after a quick search, didn't find any, > thanks! > Best wishes > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From greg at think-now.com Thu May 8 19:52:17 2014 From: greg at think-now.com (Greg Simpson) Date: Thu, 8 May 2014 10:52:17 -0700 Subject: [FieldTrip] Research Associate Position Available Message-ID: Dear Colleagues - please note our job opening below and spread the word to those that might be interested. Thank you! Greg EEG Research Associate (Data Analysis) Think Now Inc. has a Research Associate opening for an EEG data analyst for 2 NIH-funded studies being conducted with UCLA on the neurophysiological bases of sustained attention, its deficits in ADHD and the effects of computerized brain training. We are seeking candidates with direct hands-on experience in EEG data analysis. MatLab programming skills are required. We prefer strongly self-directed individuals to take on this work. The successful candidate will report directly to Gregory V. Simpson, Ph.D., Chief Scientific Officer of Think Now and will collaborate with Mark Cohen, Ph.D., Agatha Lenartowicz, Ph.D. and the team at UCLA. Think Now is located in San Francisco, so the successful candidate can be located in either San Francisco or Los Angeles. Think Now is creating EEG and mobile-app based solutions for the diagnosis and amelioration of neurological disorders with a focus on attention and its control. Please send your CV and a description of your prior experience with EEG data analysis and MatLab to *jobs at think-now.com *. Gregory V. Simpson, Ph.D. Founder & CSO Think Now, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mossa.luca86 at gmail.com Fri May 9 12:38:05 2014 From: mossa.luca86 at gmail.com (Luca Mossa) Date: Fri, 9 May 2014 12:38:05 +0200 Subject: [FieldTrip] Combine Fieldtrip with BCI2000 Message-ID: Dear community, My name is Luca Mossa and I'm working in a company in Turin (Italy) on BCI experiments. Currently I'm trying to develop some Matlab code to improve the signal processing process. I'm currently trying to use FieldTripBuffer (in matlab) as the Signal Processing module for a mu rhythm application. I have no problems to read the raw signal and states but I have trouble to find a way to sent the processing result back to Bci for the classification. Thanks to Mr. Oostenveld now I know that I must use the ft_write_event function but when I tried to use my code (with ft_write_event function) appears an error: Error using buffer events must be given as struct. Error in ft_write_event buffer('put_evt', event, host, port) Now I think that I must define some parameters, like: event.type=.... event.sample=.... event.offset=.... event.duration=.... event.value=.... but I don't understand which kind of value to insert in these field. Have you some hint? Did you make me some example? Thank you very much. Luca -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Fri May 9 15:20:04 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Fri, 9 May 2014 15:20:04 +0200 Subject: [FieldTrip] Failed to download the sample data - the links no longer exist In-Reply-To: References: Message-ID: Dear Ying, I can download the files with no problems (to an off-campus computer). Are you still having trouble? Best, Eelke On 7 May 2014 23:14, Ying Li wrote: > Dear all, > > I am learning to use fieldtrip to do source localization. When I tried to > download some sample data, such as > 1) The MEG data: ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip > 2) The MRI data: > ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip. > It shows that the links don't exist any more. > > Are there any other ways for me to download these sample data? > > Thanks a lot! > > Ying > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From t.grent-tjong at donders.ru.nl Sun May 11 11:22:14 2014 From: t.grent-tjong at donders.ru.nl (Tineke Grent-'t-Jong) Date: Sun, 11 May 2014 11:22:14 +0200 Subject: [FieldTrip] cfg.parameter definition problem in ft_sourcegrandaverage Message-ID: <30DB2C9C4EC049A4A1128699BF86E778@socrates> Dear all, I tried to grandaverage beamformer source-reconstructions of beta-coherent sources (coherent with a seed-region) this morning and received the following error message: ??? Reference to a non-existent field 'avg.coh' (refering to my specification of cfg.parameter = 'avg.coh', which is where the data truly is) This is strange given the fact that the same procedure worked just fine on comparable data (same analysis, different settings) a few weeks ago. Running the function again with cfg.parameter = 'coh' did initially seem to work, but in hindsight gave the wrong output, likely related to the fact that the field 'coh' was simply ignored (warning during running read: "skipping unknown field 'coh'). Has anyone any idea what the problem is and how to resolve it? Best, Tineke Grent-'t-Jong -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon May 12 09:14:17 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 12 May 2014 09:14:17 +0200 Subject: [FieldTrip] Combine Fieldtrip with BCI2000 In-Reply-To: References: Message-ID: <537074C9.4090303@donders.ru.nl> Hi Luca, nice to hear that you are using the FieldTrip buffer. I guess you saw the relevant pages on our wiki? Like http://fieldtrip.fcdonders.nl/faq/what_is_the_relation_between_events_such_as_triggers_and_trials http://fieldtrip.fcdonders.nl/development/realtime/buffer_protocol?s[]=event http://fieldtrip.fcdonders.nl/example/measuring_the_timing_delay_and_jitter_for_a_real-time_application?s[]=event In general for sending events, you can set all relevant fields to anything you want, so if you want to define: > event.type=.... > event.sample=.... > event.offset=.... > event.duration=.... > event.value=.... The type is a string, and you can set it to whatever you want to distinguish in your code between different types. Sample will be automatically set by the buffer. Offset and duration are, for usual purposes, not necessary in a real-time application (though you could set them to meaningful values). The event.value field is the probably most important field. This is your trigger value, in your case for example the classification outcome. Check out the pages above, especially the last one, I guess it will become clearer then. Also check out the example scripts in the realtime folder. If you have any more questions that don't become obvious from above pages, feel free to ask again here ;) Best, Jörn On 5/9/2014 12:38 PM, Luca Mossa wrote: > Dear community, > > My name is Luca Mossa and I'm working in a company in Turin (Italy) on > BCI experiments. > Currently I'm trying to develop some Matlab code to improve the signal > processing process. > > I'm currently trying to use FieldTripBuffer (in matlab) as the Signal > Processing module for a mu rhythm application. I have no problems to > read the raw signal and states but I have trouble to find a way to > sent the processing result back to Bci for the classification. > > Thanks to Mr. Oostenveld now I know that I must use the ft_write_event > function but when I tried to use my code (with ft_write_event > function) appears an error: > > Error using buffer > events must be given as struct. > > Error in ft_write_event > buffer('put_evt', event, host, port) > > Now I think that I must define some parameters, like: > > event.type=.... > event.sample=.... > event.offset=.... > event.duration=.... > event.value=.... > > but I don't understand which kind of value to insert in these field. > Have you some hint? Did you make me some example? > > Thank you very much. > > Luca > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From j.herring at fcdonders.ru.nl Mon May 12 16:02:01 2014 From: j.herring at fcdonders.ru.nl (Herring, J.D. (Jim)) Date: Mon, 12 May 2014 16:02:01 +0200 (CEST) Subject: [FieldTrip] Brain Stimulation (TMS-tCS-EEG) toolkit course at Donders, Nijmegen - registration is now open Message-ID: <003601cf6dea$bf8df480$3ea9dd80$@herring@fcdonders.ru.nl> On June 24-27, 2014, we will host the “Toolkit of Cognitive Neuroscience: Transcranial Brain Stimulation” at the Donders Institute in Nijmegen. This intensive four-day toolkit course will provide in-depth knowledge on transcranial magnetic stimulation (TMS) and transcranial current stimulation (tDCS/tACS). The course will cover both basic and advanced topics, discussing online and offline approaches of quantification, interference, and modulation of neural activity. We will specifically address multimodal applications of non-invasive brain stimulation, with a special emphasis on concurrent electroencephalography (EEG). The course involves a series of lectures and hands-on training of stimulation application, data acquisition and data analysis. These address fundamental paradigms, such as single-pulse TMS, repetitive TMS, tDCS and tACS, and advanced topics, such as paired-pulse TMS and concurrent TMS-tDCS-EEG, and MEG. Keynote lectures will be announced in the coming months. Please see the attached preliminary program for more details. The participation fee is €200 for (PhD) students and €400 for more senior researchers. This includes coffee/tea, Dutch sandwich lunches, and social events. Because of space limitations the number of participants in the hands-on sessions is limited to 30. Location: Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Kapittelweg 29, 6525 EN Nijmegen Organizers: Ian Cameron (ian.cameron at donders.ru.nl) Dilene van Campen ( a.vancampen at donders.ru.nl) Registration: http://www.ru.nl/donders/toolkit2014 ------------------------------------------------------------------------------------------------------------------------------ Jim Herring, MSc. Neuronal Oscillations Group Centre for Cognitive Neuroimaging Donders Institute for Brain, Cognition and Behaviour Radboud University Nijmegen -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: toolkittms_program2014 (2).pdf Type: application/pdf Size: 336353 bytes Desc: not available URL: From s.rombetto at cib.na.cnr.it Tue May 13 16:15:34 2014 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Tue, 13 May 2014 16:15:34 +0200 Subject: [FieldTrip] problem occurs when using ft_timelockanalysis Message-ID: <20140513161534.pe4l2mabwo8wk40k@arco.cib.na.cnr.it> Any suggestion concerning this problem? it works finewith Matlab 2013 ----- Messaggio inoltrato da s.rombetto at cib.na.cnr.it ----- Data: Wed, 7 May 2014 13:00:50 +0200 Da: s.rombetto at cib.na.cnr.it Rispondi-A:s.rombetto at cib.na.cnr.it Oggetto: problem occurs when using ft_timelockanalysis A: fieldtrip at science.ru.nl Dear fieldtrippers I'm encountering a problem when running ft_timelockanalysis in Matlab. I receive the following message: "A Undefined function 'mxSerialize_cpp' for input arguments of type 'struct' Error in mxSerialize (line 35) argout = mxSerialize_cpp(argin); Error in ft_preamble_provenance (line 67) cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); Error in ft_preamble (line 54) evalin('caller', ['ft_preamble_' cmd]); Error in ft_timelockanalysis (line 95) ft_preamble provenance data" I am using \fieldtrip-20140506 and matlab R2014a - 64 bit Any suggestion is highly appreciated. ------------------------- Dott.ssa Sara Rombetto Istituto di Cibernetica "E. Caianiello" Via Campi Flegrei, 34 80078 Pozzuoli (NA) Italy mob +39 3401689815 tel +39 0818675361 fax +39 0818675128 Lab MEG 0817483511 -------------------------- "I disapprove of what you say, but I will defend to the death your right to say it." [Evelyn Beatrice Hall, The Friends Of Voltaire] ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ----- Fine del messaggio inoltrato ----- ------------------------- Dott.ssa Sara Rombetto Istituto di Cibernetica "E. Caianiello" Via Campi Flegrei, 34 80078 Pozzuoli (NA) Italy mob +39 3401689815 tel +39 0818675361 fax +39 0818675128 Lab MEG 0817483511 -------------------------- "I disapprove of what you say, but I will defend to the death your right to say it." [Evelyn Beatrice Hall, The Friends Of Voltaire] ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From gamaliel.ghu at gmail.com Tue May 13 18:20:03 2014 From: gamaliel.ghu at gmail.com (gamaliel huerta urrea) Date: Tue, 13 May 2014 12:20:03 -0400 Subject: [FieldTrip] questions about ft_prepare_headmodel, error: the compartment nesting cannot be determined Message-ID: hi all fieldtrip my experience is limited, and attempt a head model. I analyze the documents for the user's site, and could reach the head model is presented in the official website successfully. But when trying to do the same from imr own size: 512x512x22, throws me the following errors when trying to run the function ft_headmodel. What could be the problem? because with the Subject01.mri file, the code itself works fine, but with the mri.mat (attached) file not working properly the error is as follows Warning: please specify cfg.method='projectmesh', 'iso2mesh' or 'isosurface' > In ft_prepare_mesh at 116 In ft_prepare_headmodel at 251 In fm_0 at 41 Warning: using 'projectmesh' as default > In ft_prepare_mesh at 117 In ft_prepare_headmodel at 251 In fm_0 at 41 making mesh for scalp tissue making mesh for brain tissue making mesh for skull tissue converting seg creating probabilistic representation for scalp creating probabilistic representation for brain creating probabilistic representation for skull triangulating the outer boundary of compartment 1 (scalp) with 3000 vertices triangulating the outer boundary of compartment 2 (brain) with 3000 vertices triangulating the outer boundary of compartment 3 (skull) with 3000 vertices the call to "ft_prepare_mesh" took 6 seconds Error using surface_nesting (line 26) the compartment nesting cannot be determined Error in ft_headmodel_bemcp (line 66) order = surface_nesting(vol.bnd, 'insidefirst'); Error in ft_prepare_headmodel (line 257) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in fm_0 (line 41) vol = ft_prepare_headmodel(cfg, segmentedmri); the used code is: %% load MRI data mri = ft_read_mri('IM-0001-0001.dcm'); disp(mri)%muestra informacion de mri data cfg = []; cfg.output = {'brain','skull','scalp'};%escoge las superficies segmentedmri = ft_volumesegment(cfg, mri);%Realiza la segmentacion save segmentedmri segmentedmri disp(segmentedmri) %% Mesh cfg=[]; cfg.tissue={'brain','skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); save bnd bnd disp(bnd(1)) %% Head Model cfg = []; cfg.method ='bemcp';% el tipo de modelo se puede cambiar vol = ft_prepare_headmodel(cfg, segmentedmri); save vol vol disp(vol) -- regards -- *Gamaliel Huerta* *Ingeniería Civil Biomédica* *Universidad de Valparaíso* -------------- next part -------------- An HTML attachment was scrubbed... URL: From gamaliel.ghu at gmail.com Wed May 14 08:24:32 2014 From: gamaliel.ghu at gmail.com (gamaliel huerta urrea) Date: Wed, 14 May 2014 02:24:32 -0400 Subject: [FieldTrip] questions about ft_prepare_headmodel, error: the compartment nesting cannot be determined Message-ID: hi all fieldtrip my experience is limited, and attempt a head model. I analyze the documents for the user's site, and could reach the head model is presented in the official website successfully. But when trying to do the same from imr own size: 512x512x22, throws me the following errors when trying to run the function ft_headmodel. What could be the problem? because with the Subject01.mri file, the code itself works fine, but with the mri.mat (attached) file not working properly the error is as follows Warning: please specify cfg.method='projectmesh', 'iso2mesh' or 'isosurface' > In ft_prepare_mesh at 116 In ft_prepare_headmodel at 251 In fm_0 at 41 Warning: using 'projectmesh' as default > In ft_prepare_mesh at 117 In ft_prepare_headmodel at 251 In fm_0 at 41 making mesh for scalp tissue making mesh for brain tissue making mesh for skull tissue converting seg creating probabilistic representation for scalp creating probabilistic representation for brain creating probabilistic representation for skull triangulating the outer boundary of compartment 1 (scalp) with 3000 vertices triangulating the outer boundary of compartment 2 (brain) with 3000 vertices triangulating the outer boundary of compartment 3 (skull) with 3000 vertices the call to "ft_prepare_mesh" took 6 seconds Error using surface_nesting (line 26) the compartment nesting cannot be determined Error in ft_headmodel_bemcp (line 66) order = surface_nesting(vol.bnd, 'insidefirst'); Error in ft_prepare_headmodel (line 257) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in fm_0 (line 41) vol = ft_prepare_headmodel(cfg, segmentedmri); the used code is: %% load MRI data mri = ft_read_mri('IM-0001-0001.dcm'); disp(mri)%muestra informacion de mri data cfg = []; cfg.output = {'brain','skull','scalp'};%escoge las superficies segmentedmri = ft_volumesegment(cfg, mri);%Realiza la segmentacion save segmentedmri segmentedmri disp(segmentedmri) %% Mesh cfg=[]; cfg.tissue={'brain','skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); save bnd bnd disp(bnd(1)) %% Head Model cfg = []; cfg.method ='bemcp';% el tipo de modelo se puede cambiar vol = ft_prepare_headmodel(cfg, segmentedmri); save vol vol disp(vol) -- *Gamaliel Huerta* *Ingeniería Civil Biomédica* *Universidad de Valparaíso* -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Wed May 14 10:35:03 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 14 May 2014 10:35:03 +0200 Subject: [FieldTrip] problem occurs when using ft_timelockanalysis In-Reply-To: <20140513161534.pe4l2mabwo8wk40k@arco.cib.na.cnr.it> References: <20140513161534.pe4l2mabwo8wk40k@arco.cib.na.cnr.it> Message-ID: <53732AB7.6020203@donders.ru.nl> Hi Sara, I guess you are not using a mac. What you describe concerns bug 2452 on our Bugzilla page: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2452 which pertains to some undocumented change in Matlab. Therefore it is necessary to use a different mxserialize function that from matlab 2014a onwards than before. This is a c++ function, which requires to be compiled for each platform independently. In FieldTrip, this file exists e.g. in fileio/private but only for MacOS 64-bit platforms. Apparently, we still need to compile it for MacOS 32bit, Windows and Linux platforms. I guess we should do that quite soon ;) I'll bring it up in today's FT meeting so that hopefully from tomorrow onwards it should work. btw, for you it will help to go to the FieldTrip/src directory in Matlab and type >> mex mxSerialize_cpp.cpp Then Matlab will mex (~compile) the file for you. You can then copy that file to your matlab code directory and everything should work out fine for you. I'll keep you updated on this. Best, Jörn On 5/13/2014 4:15 PM, s.rombetto at cib.na.cnr.it wrote: > Any suggestion concerning this problem? > > it works finewith Matlab 2013 > > > > ----- Messaggio inoltrato da s.rombetto at cib.na.cnr.it ----- > Data: Wed, 7 May 2014 13:00:50 +0200 > Da: s.rombetto at cib.na.cnr.it > Rispondi-A:s.rombetto at cib.na.cnr.it > Oggetto: problem occurs when using ft_timelockanalysis > A: fieldtrip at science.ru.nl > > Dear fieldtrippers > > I'm encountering a problem when running ft_timelockanalysis in Matlab. > I receive the following message: > > "A Undefined function 'mxSerialize_cpp' for input arguments of type > 'struct' > > Error in mxSerialize (line 35) > argout = mxSerialize_cpp(argin); > > Error in ft_preamble_provenance (line 67) > cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); > > Error in ft_preamble (line 54) > evalin('caller', ['ft_preamble_' cmd]); > > Error in ft_timelockanalysis (line 95) > ft_preamble provenance data" > > > I am using \fieldtrip-20140506 and matlab R2014a - 64 bit > > Any suggestion is highly appreciated. > ------------------------- > Dott.ssa Sara Rombetto > Istituto di Cibernetica > "E. Caianiello" > Via Campi Flegrei, 34 > 80078 Pozzuoli (NA) > Italy > mob +39 3401689815 > tel +39 0818675361 > fax +39 0818675128 > Lab MEG 0817483511 > -------------------------- > "I disapprove of what you say, but I will defend to the death your > right to say > it." [Evelyn Beatrice Hall, The Friends Of Voltaire] > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > ----- Fine del messaggio inoltrato ----- > > > ------------------------- > Dott.ssa Sara Rombetto > Istituto di Cibernetica > "E. Caianiello" > Via Campi Flegrei, 34 > 80078 Pozzuoli (NA) > Italy > mob +39 3401689815 > tel +39 0818675361 > fax +39 0818675128 > Lab MEG 0817483511 > -------------------------- > "I disapprove of what you say, but I will defend to the death your > right to say > it." [Evelyn Beatrice Hall, The Friends Of Voltaire] > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From max-philipp.stenner at med.ovgu.de Wed May 14 16:25:44 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Wed, 14 May 2014 14:25:44 +0000 Subject: [FieldTrip] (no subject) Message-ID: Dear fieldtrippers, I was planning to use cluster-based permutation statistics for group-level inference on the difference between two conditions (depsamplesT) for a fairly small number of subjects (as few as 5). However, this would mean a total of only 2^5=32 possible permutations (=discrete values for the non-parametric null distribution), and therefore a maximum "p-value-resolution" of only 1/32=.0313. Does this mean that group-level permutation statistics are not appropriate for small sample sizes? How do people correct for MC in these cases (using fieldtrip)? (I am specifically interested in group-level analyses, not primarily in within-subject/across-trials testing). Thanks in advance, best Max From r.oostenveld at donders.ru.nl Wed May 14 18:10:09 2014 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 14 May 2014 18:10:09 +0200 Subject: [FieldTrip] postdoc position at NatMEG, Karolinska Institute, Stockholm, Sweden Message-ID: <4B9B1EED-6A34-4E46-95B8-F8F30B155399@donders.ru.nl> Post doc, Stockholm, Sweden The Department of Clinical Neuroscience at Karolinska Institutet offers a 2 year post doc position giving the researcher an unique mix of inspiring interactions with researchers from a wide range of research areas and a freedom to pursuit one's own qualified research questions. NatMEG – the national facility for magnetoencephalography (MEG) As of September 2013 Karolinska Institutet hosts a superbly equipped MEG lab. The NatMEG lab is a national facility open for researchers from all across Sweden. Due to it being a national facility, a wide array of projects is currently ongoing or under initiation at NatMEG. We are covering areas such as next generation SQUIDS, computational modelling, epilepsy work-ups and cognitive neuroscience in the areas of memory, language, attention, perception, pain, music, decision making, emotion, autism, schizophrenia, Parkinson's and Alzheimer's disease and more. We currently have 1 post doc and 3 guest professors that supports and initiates research at NatMEG and we are now recruiting another postdoc researcher to the lab. Please visit http://www.natmeg.se for more information. Duties Your duties as a postdoc will consist of: • The postdocs own qualified research with MEG and/or simultaneous MEG & EEG. • Research at the national infrastructure for magnetoencephalography (NatMEG), including some general operation. • Scientific support to users at NatMEG, regarding methods, experimental design and analysis. • Development of routines, experimental design and analysis with MEG and EEG. Entry requirements An ideal candidate has extensive MEG experience and is experienced in psychophysiology measurements. The person has strong skills in FieldTrip, MNE or other MEG analysis tools as well as in MatLab and/or Python. We are looking for candidates with a research interest within the cognitive neuroscience domain, that master academic English, is independent and service minded. A person is eligible for a position as postdoctoral research fellow if he or she has obtained a PhD no more than seven years before the last date of employment as postdoc. Application process Read more about the application process at https://ki.mynetworkglobal.com/en/what:job/jobID:35553/. Applications are to be submitted in the recruitment system NetRecruiter. Application deadline 2014-06-15 Contact information Daniel Lundqvist, Project manager daniel.lundqvist at ki.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.rombetto at cib.na.cnr.it Thu May 15 10:29:35 2014 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Thu, 15 May 2014 10:29:35 +0200 Subject: [FieldTrip] problem occurs when using ft_timelockanalysis In-Reply-To: <53732AB7.6020203@donders.ru.nl> References: <20140513161534.pe4l2mabwo8wk40k@arco.cib.na.cnr.it> <53732AB7.6020203@donders.ru.nl> Message-ID: <20140515102935.krkki9plw4gw40k0@arco.cib.na.cnr.it> dear Jörn thanks for your answer. You were right, I am using a win 64 pc. With your trick it works now :) Sara > Hi Sara, > > I guess you are not using a mac. What you describe concerns bug 2452 on > our Bugzilla page: > http://bugzilla.fcdonders.nl/show_bug.cgi?id=2452 > which pertains to some undocumented change in Matlab. Therefore it is > necessary to use a different mxserialize function that from matlab > 2014a onwards than before. This is a c++ function, which requires to > be compiled for each platform independently. In FieldTrip, this file > exists e.g. in fileio/private but only for MacOS 64-bit platforms. > Apparently, we still need to compile it for MacOS 32bit, Windows and > Linux platforms. I guess we should do that quite soon ;) I'll bring it > up in today's FT meeting so that hopefully from tomorrow onwards it > should work. > > btw, for you it will help to go to the FieldTrip/src directory in > Matlab and type >>> mex mxSerialize_cpp.cpp > > Then Matlab will mex (~compile) the file for you. You can then copy > that file to your matlab code directory and everything should work out > fine for you. I'll keep you updated on this. > > Best, > Jörn > > On 5/13/2014 4:15 PM, s.rombetto at cib.na.cnr.it wrote: >> Any suggestion concerning this problem? >> >> it works finewith Matlab 2013 >> >> >> >> ----- Messaggio inoltrato da s.rombetto at cib.na.cnr.it ----- >> Data: Wed, 7 May 2014 13:00:50 +0200 >> Da: s.rombetto at cib.na.cnr.it >> Rispondi-A:s.rombetto at cib.na.cnr.it >> Oggetto: problem occurs when using ft_timelockanalysis >> A: fieldtrip at science.ru.nl >> >> Dear fieldtrippers >> >> I'm encountering a problem when running ft_timelockanalysis in Matlab. >> I receive the following message: >> >> "A Undefined function 'mxSerialize_cpp' for input arguments of type 'struct' >> >> Error in mxSerialize (line 35) >> argout = mxSerialize_cpp(argin); >> >> Error in ft_preamble_provenance (line 67) >> cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); >> >> Error in ft_preamble (line 54) >> evalin('caller', ['ft_preamble_' cmd]); >> >> Error in ft_timelockanalysis (line 95) >> ft_preamble provenance data" >> >> >> I am using \fieldtrip-20140506 and matlab R2014a - 64 bit >> >> Any suggestion is highly appreciated. >> ------------------------- >> Dott.ssa Sara Rombetto >> Istituto di Cibernetica >> "E. Caianiello" >> Via Campi Flegrei, 34 >> 80078 Pozzuoli (NA) >> Italy >> mob +39 3401689815 >> tel +39 0818675361 >> fax +39 0818675128 >> Lab MEG 0817483511 >> -------------------------- >> "I disapprove of what you say, but I will defend to the death your >> right to say >> it." [Evelyn Beatrice Hall, The Friends Of Voltaire] >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> >> ----- Fine del messaggio inoltrato ----- >> >> >> ------------------------- >> Dott.ssa Sara Rombetto >> Istituto di Cibernetica >> "E. Caianiello" >> Via Campi Flegrei, 34 >> 80078 Pozzuoli (NA) >> Italy >> mob +39 3401689815 >> tel +39 0818675361 >> fax +39 0818675128 >> Lab MEG 0817483511 >> -------------------------- >> "I disapprove of what you say, but I will defend to the death your >> right to say >> it." [Evelyn Beatrice Hall, The Friends Of Voltaire] >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ------------------------- Dott.ssa Sara Rombetto Istituto di Cibernetica "E. Caianiello" Via Campi Flegrei, 34 80078 Pozzuoli (NA) Italy mob +39 3401689815 tel +39 0818675361 fax +39 0818675128 Lab MEG 0817483511 -------------------------- "I disapprove of what you say, but I will defend to the death your right to say it." [Evelyn Beatrice Hall, The Friends Of Voltaire] ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From max-philipp.stenner at med.ovgu.de Thu May 15 17:09:18 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 15 May 2014 15:09:18 +0000 Subject: [FieldTrip] within-subject partition for between-subject stats Message-ID: Dear fieldtrippers, I have a question regarding permutation statistics in a mixed design with only very few subjects (5 subjects, 2 conditions/subject; this follows up on my email yesterday). Since the number of unique permutations of *trial-averaged* data is limited (2^5=32), would it make sense (is it statistically sound) to re-compute trial-averages for each subject after randomly partitioning trials *within* each of the five subjects for a large number of iterations first (since there are >>5 trials/subject the number of unique permutations is much larger than for trial-averaged data) and then re-compute cluster-statistics (e.g. maxsum) for each of these sets of re-computed trial-averages to obtain a null-distribution? Thanks very much in advance, best Max ________________________________________ Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" im Auftrag von "Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de] Gesendet: Mittwoch, 14. Mai 2014 16:25 An: FieldTrip discussion list Betreff: [FieldTrip] (no subject) Dear fieldtrippers, I was planning to use cluster-based permutation statistics for group-level inference on the difference between two conditions (depsamplesT) for a fairly small number of subjects (as few as 5). However, this would mean a total of only 2^5=32 possible permutations (=discrete values for the non-parametric null distribution), and therefore a maximum "p-value-resolution" of only 1/32=.0313. Does this mean that group-level permutation statistics are not appropriate for small sample sizes? How do people correct for MC in these cases (using fieldtrip)? (I am specifically interested in group-level analyses, not primarily in within-subject/across-trials testing). Thanks in advance, best Max _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From laura.marzetti at gmail.com Thu May 15 18:44:26 2014 From: laura.marzetti at gmail.com (Laura Marzetti) Date: Thu, 15 May 2014 18:44:26 +0200 Subject: [FieldTrip] regularized depth weighting for MNE Message-ID: Dear all, I was wondering if the leadfield depth weighting option implemented by the configuration setting cfg.normalize = 'column' or cfg.normalize = 'yes' in input to ft_prepareleadfield, also supports a way to regularize such depth weighting in order to not artificially boost low-gain locations such as the head center in MEG. Thanks, Laura -- Laura Marzetti, PhD Istituto di Tecnologie Avanzate Biomediche Università di Chieti "G. D'Annunzio" Via dei Vestini - Campus Universitario 66013 Chieti - ITALY phone: 0039-0871-3556944 fax: 0039-0871-3556930 From yingli.ucla at gmail.com Sun May 18 00:23:29 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Sat, 17 May 2014 15:23:29 -0700 Subject: [FieldTrip] EEG source reconstruction using fieldtrip (MRI not available) Message-ID: Dear all, Fieldtrip provides a great tool of using MRI to do MEG source reconstruction (http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate). Now I want to do EEG source reconstruction. The EEG cap we used is the standard 10-10 system, but the MRI of the subject is not available. I'm thinking to use another person's MRI instead (i.e. the MNI template). Does fieldtrip provide some tools to match the electrode location and the head model from another person? In addition, since MEG sensor positions are always defined relative to the fiducial coils, so we don't need to transform it into CTF coordinate system any more. When doing EEG source reconstruction, is there any extra steps needed? (i.e. transform the EEG sensor to some certain coordinate system, etc.) Thanks a lot! Best, Ying -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at gmail.com Sun May 18 10:35:34 2014 From: johanna.zumer at gmail.com (Johanna Zumer) Date: Sun, 18 May 2014 09:35:34 +0100 Subject: [FieldTrip] EEG source reconstruction using fieldtrip (MRI not available) In-Reply-To: References: Message-ID: Dear Ying, Yes, that is possible (although in an ideal world, one does have the subject's real MRI). You might gain some help from http://fieldtrip.fcdonders.nl/example/align_eeg_electrode_positions_to_bem_headmodel or http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg (which also then links you to http://fieldtrip.fcdonders.nl/template/headmodel) for the case of using the MNI brain). Best, Johanna 2014-05-17 23:23 GMT+01:00 Ying Li : > Dear all, > > Fieldtrip provides a great tool of using MRI to do MEG source > reconstruction (http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate). > Now I want to do EEG source reconstruction. The EEG cap we used is the > standard 10-10 system, but the MRI of the subject is not available. I'm > thinking to use another person's MRI instead (i.e. the MNI template). Does > fieldtrip provide some tools to match the electrode location and the head > model from another person? > > In addition, since MEG sensor positions are always defined relative to the > fiducial coils, so we don't need to transform it into CTF coordinate system > any more. When doing EEG source reconstruction, is there any extra steps > needed? (i.e. transform the EEG sensor to some certain coordinate system, > etc.) Thanks a lot! > > Best, > > Ying > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From anne.urai at gmail.com Sun May 18 19:41:05 2014 From: anne.urai at gmail.com (anne.urai at gmail.com) Date: Sun, 18 May 2014 19:41:05 +0200 Subject: [FieldTrip] efficiently handling multiple events within a trial Message-ID: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> Hi Fieldtrippers, I have a design in which every trial has several events of interest (two stimuli with a maintenance period in between, response and feedback) - all of which I’d like to analyse at some point. I started by drafting my pipeline separately for stimulus-, response- and feedback-locked trial definitions, but this leads me to do the artefact rejection and ICA multiple times for each subject. I would prefer to reject whole trials and not use any of the events in there, rather than eg. use the response for some and the stimulus for others. I was wondering if you have any advice on how to best store multiple events in one trial (which would be, say, 12 seconds long, and have 4 different evens in it, at times that would also need to be stored). Would it work better to (1) make one big trialfun and store the onset and offset of each of those events in the trl matrix, or (2) have several trl matrices for each event and redefine the trials based on this trl matrix after I applied some other analyses? For example, it would be nice to run ft_freqanalysis once on the whole trial, and then redefine which part of the trial I’m interested in for plotting. Thanks for your thoughts on this! Best, --- Anne E. Urai, MSc PhD student | Institut für Neurophysiologie und Pathophysiologie Universitätsklinikum Hamburg-Eppendorf Martinistrasse 52, 20246 Hamburg, Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From yingli.ucla at gmail.com Mon May 19 08:16:43 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Sun, 18 May 2014 23:16:43 -0700 Subject: [FieldTrip] EEG source reconstruction using fieldtrip (MRI not available) In-Reply-To: References: Message-ID: Hi Johanna, That is exactly what I want! Appreciate your help so much! : ) Best, Ying On Sun, May 18, 2014 at 1:35 AM, Johanna Zumer wrote: > Dear Ying, > > Yes, that is possible (although in an ideal world, one does have the > subject's real MRI). > > You might gain some help from > http://fieldtrip.fcdonders.nl/example/align_eeg_electrode_positions_to_bem_headmodel > or http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg (which also > then links you to http://fieldtrip.fcdonders.nl/template/headmodel) for > the case of using the MNI brain). > > Best, > Johanna > > > > 2014-05-17 23:23 GMT+01:00 Ying Li : > >> Dear all, >> >> Fieldtrip provides a great tool of using MRI to do MEG source >> reconstruction ( >> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate). Now I want >> to do EEG source reconstruction. The EEG cap we used is the standard 10-10 >> system, but the MRI of the subject is not available. I'm thinking to use >> another person's MRI instead (i.e. the MNI template). Does fieldtrip >> provide some tools to match the electrode location and the head model from >> another person? >> >> In addition, since MEG sensor positions are always defined relative to >> the fiducial coils, so we don't need to transform it into CTF coordinate >> system any more. When doing EEG source reconstruction, is there any extra >> steps needed? (i.e. transform the EEG sensor to some certain coordinate >> system, etc.) Thanks a lot! >> >> Best, >> >> Ying >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Mon May 19 09:20:26 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 19 May 2014 09:20:26 +0200 Subject: [FieldTrip] efficiently handling multiple events within a trial In-Reply-To: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> References: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> Message-ID: Hi Anne, What I usually do is segment my data initially such that a "trial" in the data structure really corresponds to a logical trial in the experiment. So, in your case, it would contain the data for both stimuli and the maintenance period. I assume you are writing your own trialfun for this (if not, see http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition). In your trialfun, you can specify arbitrary metadata for every trial by adding extra columns to the output trl-matrix. The 4th and higher columns in the trl matrix will end up in data.trialinfo in the output data. This trialinfo field is kept throughout your analysis pipeline, as long as the data still contains trials. You could, for instance, store the time index of the response as the 4th column of your trl, the time index of the feedback onset as the 5th, etc. I always make sure that at least a condition identifier and a reaction time (if applicable) appear the trialinfo field. Once this information is present in data.trialinfo, you can use ft_selectdata and ft_redefinetrial to select the appropriate trials and (if necessary) shift the time axis, respectively. Hope that helps, Best, Eelke On 18 May 2014 19:41, wrote: > Hi Fieldtrippers, > > I have a design in which every trial has several events of interest (two > stimuli with a maintenance period in between, response and feedback) - all > of which I’d like to analyse at some point. I started by drafting my > pipeline separately for stimulus-, response- and feedback-locked trial > definitions, but this leads me to do the artefact rejection and ICA multiple > times for each subject. I would prefer to reject whole trials and not use > any of the events in there, rather than eg. use the response for some and > the stimulus for others. > > I was wondering if you have any advice on how to best store multiple events > in one trial (which would be, say, 12 seconds long, and have 4 different > evens in it, at times that would also need to be stored). Would it work > better to (1) make one big trialfun and store the onset and offset of each > of those events in the trl matrix, or (2) have several trl matrices for each > event and redefine the trials based on this trl matrix after I applied some > other analyses? For example, it would be nice to run ft_freqanalysis once on > the whole trial, and then redefine which part of the trial I’m interested in > for plotting. > > Thanks for your thoughts on this! > > Best, > > --- > Anne E. Urai, MSc > PhD student | Institut für Neurophysiologie und Pathophysiologie > Universitätsklinikum Hamburg-Eppendorf > Martinistrasse 52, 20246 Hamburg, Germany > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From anne.urai at gmail.com Mon May 19 10:24:08 2014 From: anne.urai at gmail.com (Anne Urai) Date: Mon, 19 May 2014 10:24:08 +0200 Subject: [FieldTrip] efficiently handling multiple events within a trial In-Reply-To: References: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> Message-ID: I've been writing my own trialfun but so far I've gotten by with a separate one for eg. stimulus- and response locked, which seems rather inefficient indeed. Thanks for the suggestion of using ft_selectdata, didn't know that one yet! Anne Anne Urai On 19 May 2014 09:20, Eelke Spaak wrote: > Hi Anne, > > What I usually do is segment my data initially such that a "trial" in > the data structure really corresponds to a logical trial in the > experiment. So, in your case, it would contain the data for both > stimuli and the maintenance period. > > I assume you are writing your own trialfun for this (if not, see > > http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition > ). > In your trialfun, you can specify arbitrary metadata for every trial > by adding extra columns to the output trl-matrix. The 4th and higher > columns in the trl matrix will end up in data.trialinfo in the output > data. This trialinfo field is kept throughout your analysis pipeline, > as long as the data still contains trials. You could, for instance, > store the time index of the response as the 4th column of your trl, > the time index of the feedback onset as the 5th, etc. I always make > sure that at least a condition identifier and a reaction time (if > applicable) appear the trialinfo field. > > Once this information is present in data.trialinfo, you can use > ft_selectdata and ft_redefinetrial to select the appropriate trials > and (if necessary) shift the time axis, respectively. > > Hope that helps, > Best, > Eelke > > On 18 May 2014 19:41, wrote: > > Hi Fieldtrippers, > > > > I have a design in which every trial has several events of interest (two > > stimuli with a maintenance period in between, response and feedback) - > all > > of which I’d like to analyse at some point. I started by drafting my > > pipeline separately for stimulus-, response- and feedback-locked trial > > definitions, but this leads me to do the artefact rejection and ICA > multiple > > times for each subject. I would prefer to reject whole trials and not use > > any of the events in there, rather than eg. use the response for some and > > the stimulus for others. > > > > I was wondering if you have any advice on how to best store multiple > events > > in one trial (which would be, say, 12 seconds long, and have 4 different > > evens in it, at times that would also need to be stored). Would it work > > better to (1) make one big trialfun and store the onset and offset of > each > > of those events in the trl matrix, or (2) have several trl matrices for > each > > event and redefine the trials based on this trl matrix after I applied > some > > other analyses? For example, it would be nice to run ft_freqanalysis > once on > > the whole trial, and then redefine which part of the trial I’m > interested in > > for plotting. > > > > Thanks for your thoughts on this! > > > > Best, > > > > --- > > Anne E. Urai, MSc > > PhD student | Institut für Neurophysiologie und Pathophysiologie > > Universitätsklinikum Hamburg-Eppendorf > > Martinistrasse 52, 20246 Hamburg, Germany > > > > > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.piai.research at gmail.com Mon May 19 23:14:30 2014 From: v.piai.research at gmail.com (Vitoria Piai) Date: Mon, 19 May 2014 14:14:30 -0700 Subject: [FieldTrip] Error: Undefined function 'mxSerialize_cpp' In-Reply-To: References: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> Message-ID: <537A7436.3080307@gmail.com> Hello everyone, I'm getting a low-level error (below) when running ft_singleplotER to plot FFTs. I recently changed to Matlab2014a so I'm guessing that's why I'm getting the error (different FT versions give same error for as far back in time as I could come). Does anyone know a way around this issue? Thanks a lot, Vitoria Undefined function 'mxSerialize_cpp' for input arguments of type 'struct'. Error in mxSerialize (line 35) argout = mxSerialize_cpp(argin); Error in ft_preamble_provenance (line 67) cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); Error in ft_preamble (line 54) evalin('caller', ['ft_preamble_' cmd]); Error in ft_singleplotER (line 109) ft_preamble provenance varargin From jan.schoffelen at donders.ru.nl Tue May 20 11:57:59 2014 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 20 May 2014 11:57:59 +0200 Subject: [FieldTrip] Error: Undefined function 'mxSerialize_cpp' In-Reply-To: <537A7436.3080307@gmail.com> References: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> <537A7436.3080307@gmail.com> Message-ID: Hi Vitoria, Sara Rombetto asked the same question last week (or the week before) ;-), and Jörn provided an adequate answer. See below, with credits to Jörn... +++++++++++++++++++++++++++++++++++++++++++++++++++++++ Hi Sara, I guess you are not using a mac. What you describe concerns bug 2452 on our Bugzilla page: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2452 which pertains to some undocumented change in Matlab. Therefore it is necessary to use a different mxserialize function that from matlab 2014a onwards than before. This is a c++ function, which requires to be compiled for each platform independently. In FieldTrip, this file exists e.g. in fileio/private but only for MacOS 64-bit platforms. Apparently, we still need to compile it for MacOS 32bit, Windows and Linux platforms. I guess we should do that quite soon ;) I'll bring it up in today's FT meeting so that hopefully from tomorrow onwards it should work. btw, for you it will help to go to the FieldTrip/src directory in Matlab and type >> mex mxSerialize_cpp.cpp Then Matlab will mex (~compile) the file for you. You can then copy that file to your matlab code directory and everything should work out fine for you. I'll keep you updated on this. Best, Jörn +++++++++++++++++++++++++++++++++++++++++++++++++++++++ Best, JM On May 19, 2014, at 11:14 PM, Vitoria Piai wrote: > Hello everyone, > > I'm getting a low-level error (below) when running ft_singleplotER to plot FFTs. > I recently changed to Matlab2014a so I'm guessing that's why I'm getting the error (different FT versions give same error for as far back in time as I could come). Does anyone know a way around this issue? > Thanks a lot, Vitoria > > Undefined function 'mxSerialize_cpp' for input arguments of type 'struct'. > > Error in mxSerialize (line 35) > argout = mxSerialize_cpp(argin); > > Error in ft_preamble_provenance (line 67) > cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); > > Error in ft_preamble (line 54) > evalin('caller', ['ft_preamble_' cmd]); > > Error in ft_singleplotER (line 109) > ft_preamble provenance varargin > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue May 20 11:58:11 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 20 May 2014 11:58:11 +0200 Subject: [FieldTrip] Error: Undefined function 'mxSerialize_cpp' In-Reply-To: <537A7436.3080307@gmail.com> References: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> <537A7436.3080307@gmail.com> Message-ID: <537B2733.20802@donders.ru.nl> Hi Vitoria, hope you're enjoying Berkeley ;) I assume the same error will occur for more people in a bit. We'll discuss it in the next FT meeting tomorrow. In the meanwhile, check this out (I responded to Sara last week, who got the same error): > I guess you are not using a mac. What you describe concerns bug 2452 > on our Bugzilla page: > http://bugzilla.fcdonders.nl/show_bug.cgi?id=2452 > which pertains to some undocumented change in Matlab. Therefore it is > necessary to use a different mxserialize function that from matlab > 2014a onwards than before. This is a c++ function, which requires to > be compiled for each platform independently. In FieldTrip, this file > exists e.g. in fileio/private but only for MacOS 64-bit platforms. > Apparently, we still need to compile it for MacOS 32bit, Windows and > Linux platforms. I guess we should do that quite soon I'll bring it up > in today's FT meeting so that hopefully from tomorrow onwards it > should work. > > btw, for you it will help to go to the FieldTrip/src directory in > Matlab and type > >> mex mxSerialize_cpp.cpp > > Then Matlab will mex (~compile) the file for you. You can then copy > that file to your matlab code directory and everything should work out > fine for you. I'll keep you updated on this. > Best, Jörn On 5/19/2014 11:14 PM, Vitoria Piai wrote: > Hello everyone, > > I'm getting a low-level error (below) when running ft_singleplotER to > plot FFTs. > I recently changed to Matlab2014a so I'm guessing that's why I'm > getting the error (different FT versions give same error for as far > back in time as I could come). Does anyone know a way around this issue? > Thanks a lot, Vitoria > > Undefined function 'mxSerialize_cpp' for input arguments of type > 'struct'. > > Error in mxSerialize (line 35) > argout = mxSerialize_cpp(argin); > > Error in ft_preamble_provenance (line 67) > cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); > > Error in ft_preamble (line 54) > evalin('caller', ['ft_preamble_' cmd]); > > Error in ft_singleplotER (line 109) > ft_preamble provenance varargin > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From yingli.ucla at gmail.com Thu May 22 10:26:45 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Thu, 22 May 2014 01:26:45 -0700 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface Message-ID: Dear all, I tried to use fieldtrip to generate a source space and calculate lead field matrix. I found that the dipoles in the source space has x, y, z orientations. Is it possible to generate a source model where the dipole is perpendicular to the cortex surface? Actually this can be very helpful, since it will reduce the unknown variables and make the inverse problem easier to solve. Also, there are some inverse algorithms which require the dipole to be perpendicular to the cortex surface. Thanks a lot!!! Best, Ying -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu May 22 10:56:24 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 22 May 2014 10:56:24 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: References: Message-ID: <537DBBB8.600@donders.ru.nl> Hi Ying, when computing the leadfields you can set the option cfg.reducerank, which 'nulls' the dimension(s) which explain(s) the least variance (this is not quite true, but figuratively speaking). I think this is what comes closest to what you are looking for. There is no way to explicitly set desired orientations to zero apart from modifying the leadfield structure yourself. But that should be easily achievable, right? Best, Jörn On 5/22/2014 10:26 AM, Ying Li wrote: > Dear all, > > I tried to use fieldtrip to generate a source space and calculate lead > field matrix. I found that the dipoles in the source space has x, y, z > orientations. Is it possible to generate a source model where the > dipole is perpendicular to the cortex surface? > > Actually this can be very helpful, since it will reduce the unknown > variables and make the inverse problem easier to solve. Also, there > are some inverse algorithms which require the dipole to be > perpendicular to the cortex surface. > > Thanks a lot!!! > > Best, > > Ying > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From eelke.spaak at donders.ru.nl Thu May 22 11:04:04 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 22 May 2014 11:04:04 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: <537DBBB8.600@donders.ru.nl> References: <537DBBB8.600@donders.ru.nl> Message-ID: Hi Ying, In addition to this, of course first you would need a model of the cortical surface for your subjects. See http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to obtain such a model (using FreeSurfer) and getting it into FieldTrip. Best, Eelke On 22 May 2014 10:56, "Jörn M. Horschig" wrote: > Hi Ying, > > when computing the leadfields you can set the option cfg.reducerank, which > 'nulls' the dimension(s) which explain(s) the least variance (this is not > quite true, but figuratively speaking). I think this is what comes closest > to what you are looking for. There is no way to explicitly set desired > orientations to zero apart from modifying the leadfield structure yourself. > But that should be easily achievable, right? > > Best, > Jörn > > > On 5/22/2014 10:26 AM, Ying Li wrote: >> >> Dear all, >> >> I tried to use fieldtrip to generate a source space and calculate lead >> field matrix. I found that the dipoles in the source space has x, y, z >> orientations. Is it possible to generate a source model where the dipole is >> perpendicular to the cortex surface? >> >> Actually this can be very helpful, since it will reduce the unknown >> variables and make the inverse problem easier to solve. Also, there are some >> inverse algorithms which require the dipole to be perpendicular to the >> cortex surface. >> >> Thanks a lot!!! >> >> Best, >> >> Ying >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Thu May 22 11:47:03 2014 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 22 May 2014 11:47:03 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: References: <537DBBB8.600@donders.ru.nl> Message-ID: <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> Hi Ying, Yes, it's possible to constrain the dipole orientation. If you have a cortical sheet based source model that contains a triangulation that describes the topology, it's in principle possible to compute the orientation perpendicular to the sheet (this can e.g. be done by the 'normals' function which I believe should be in ~/fieldtrip/private). Subsequently, for each vertex in the cortical sheet you can multiply the leadfield matrix with this vector to get a single column leadfield vector per vertex that describes the sensor topography of a dipolar source with orientation perpendicular to the cortex. Best, Jan-Mathijs On May 22, 2014, at 11:04 AM, Eelke Spaak wrote: > Hi Ying, > > In addition to this, of course first you would need a model of the > cortical surface for your subjects. See > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to > obtain such a model (using FreeSurfer) and getting it into FieldTrip. > > Best, > Eelke > > On 22 May 2014 10:56, "Jörn M. Horschig" wrote: >> Hi Ying, >> >> when computing the leadfields you can set the option cfg.reducerank, which >> 'nulls' the dimension(s) which explain(s) the least variance (this is not >> quite true, but figuratively speaking). I think this is what comes closest >> to what you are looking for. There is no way to explicitly set desired >> orientations to zero apart from modifying the leadfield structure yourself. >> But that should be easily achievable, right? >> >> Best, >> Jörn >> >> >> On 5/22/2014 10:26 AM, Ying Li wrote: >>> >>> Dear all, >>> >>> I tried to use fieldtrip to generate a source space and calculate lead >>> field matrix. I found that the dipoles in the source space has x, y, z >>> orientations. Is it possible to generate a source model where the dipole is >>> perpendicular to the cortex surface? >>> >>> Actually this can be very helpful, since it will reduce the unknown >>> variables and make the inverse problem easier to solve. Also, there are some >>> inverse algorithms which require the dipole to be perpendicular to the >>> cortex surface. >>> >>> Thanks a lot!!! >>> >>> Best, >>> >>> Ying >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Jörn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> FieldTrip Development Team >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu May 22 13:25:58 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 22 May 2014 13:25:58 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> References: <537DBBB8.600@donders.ru.nl> <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> Message-ID: Hi Ying & JM & the rest of the list, I've never worked with cortex-constrained source reconstructions before, but one question came to mind: doesn't it make more sense to constrain the dipole orientations to *orthogonal* to the cortex, rather than perpendicular? Given that currents along the aligned dendrites of L5 pyramidal cells are (afaik) likely the most important origin of the MEG signal, and those dendrites are oriented approximately orthogonal to the cortical surface, isn't that what you would expect? Best, Eelke On 22 May 2014 11:47, jan-mathijs schoffelen wrote: > Hi Ying, > > Yes, it's possible to constrain the dipole orientation. If you have a > cortical sheet based source model that contains a triangulation that > describes the topology, it's in principle possible to compute the > orientation perpendicular to the sheet (this can e.g. be done by the > 'normals' function which I believe should be in ~/fieldtrip/private). > Subsequently, for each vertex in the cortical sheet you can multiply the > leadfield matrix with this vector to get a single column leadfield vector > per vertex that describes the sensor topography of a dipolar source with > orientation perpendicular to the cortex. > > Best, > Jan-Mathijs > > On May 22, 2014, at 11:04 AM, Eelke Spaak wrote: > > Hi Ying, > > In addition to this, of course first you would need a model of the > cortical surface for your subjects. See > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to > obtain such a model (using FreeSurfer) and getting it into FieldTrip. > > Best, > Eelke > > On 22 May 2014 10:56, "Jörn M. Horschig" wrote: > > Hi Ying, > > > when computing the leadfields you can set the option cfg.reducerank, which > > 'nulls' the dimension(s) which explain(s) the least variance (this is not > > quite true, but figuratively speaking). I think this is what comes closest > > to what you are looking for. There is no way to explicitly set desired > > orientations to zero apart from modifying the leadfield structure yourself. > > But that should be easily achievable, right? > > > Best, > > Jörn > > > > On 5/22/2014 10:26 AM, Ying Li wrote: > > > Dear all, > > > I tried to use fieldtrip to generate a source space and calculate lead > > field matrix. I found that the dipoles in the source space has x, y, z > > orientations. Is it possible to generate a source model where the dipole is > > perpendicular to the cortex surface? > > > Actually this can be very helpful, since it will reduce the unknown > > variables and make the inverse problem easier to solve. Also, there are some > > inverse algorithms which require the dipole to be perpendicular to the > > cortex surface. > > > Thanks a lot!!! > > > Best, > > > Ying > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > > Jörn M. Horschig > > PhD Student > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Neuronal Oscillations Group > > FieldTrip Development Team > > > P.O. Box 9101 > > NL-6500 HB Nijmegen > > The Netherlands > > > Contact: > > E-Mail: jm.horschig at donders.ru.nl > > Tel: +31-(0)24-36-68493 > > Web: http://www.ru.nl/donders > > > Visiting address: > > Trigon, room 2.30 > > Kapittelweg 29 > > NL-6525 EN Nijmegen > > The Netherlands > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > http://www.hettaligebrein.nl > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Thu May 22 13:42:11 2014 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 22 May 2014 13:42:11 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: References: <537DBBB8.600@donders.ru.nl> <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> Message-ID: <09B16AC6-4417-448C-8B82-1399CEFC062F@donders.ru.nl> Eelke, You're absolutely right one should take the orientation that is othogonal! In my dictionary this is exactly what the word perpendicular means ;-)... JM On May 22, 2014, at 1:25 PM, Eelke Spaak wrote: > Hi Ying & JM & the rest of the list, > > I've never worked with cortex-constrained source reconstructions > before, but one question came to mind: doesn't it make more sense to > constrain the dipole orientations to *orthogonal* to the cortex, > rather than perpendicular? Given that currents along the aligned > dendrites of L5 pyramidal cells are (afaik) likely the most important > origin of the MEG signal, and those dendrites are oriented > approximately orthogonal to the cortical surface, isn't that what you > would expect? > > Best, > Eelke > > On 22 May 2014 11:47, jan-mathijs schoffelen > wrote: >> Hi Ying, >> >> Yes, it's possible to constrain the dipole orientation. If you have a >> cortical sheet based source model that contains a triangulation that >> describes the topology, it's in principle possible to compute the >> orientation perpendicular to the sheet (this can e.g. be done by the >> 'normals' function which I believe should be in ~/fieldtrip/private). >> Subsequently, for each vertex in the cortical sheet you can multiply the >> leadfield matrix with this vector to get a single column leadfield vector >> per vertex that describes the sensor topography of a dipolar source with >> orientation perpendicular to the cortex. >> >> Best, >> Jan-Mathijs >> >> On May 22, 2014, at 11:04 AM, Eelke Spaak wrote: >> >> Hi Ying, >> >> In addition to this, of course first you would need a model of the >> cortical surface for your subjects. See >> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to >> obtain such a model (using FreeSurfer) and getting it into FieldTrip. >> >> Best, >> Eelke >> >> On 22 May 2014 10:56, "Jörn M. Horschig" wrote: >> >> Hi Ying, >> >> >> when computing the leadfields you can set the option cfg.reducerank, which >> >> 'nulls' the dimension(s) which explain(s) the least variance (this is not >> >> quite true, but figuratively speaking). I think this is what comes closest >> >> to what you are looking for. There is no way to explicitly set desired >> >> orientations to zero apart from modifying the leadfield structure yourself. >> >> But that should be easily achievable, right? >> >> >> Best, >> >> Jörn >> >> >> >> On 5/22/2014 10:26 AM, Ying Li wrote: >> >> >> Dear all, >> >> >> I tried to use fieldtrip to generate a source space and calculate lead >> >> field matrix. I found that the dipoles in the source space has x, y, z >> >> orientations. Is it possible to generate a source model where the dipole is >> >> perpendicular to the cortex surface? >> >> >> Actually this can be very helpful, since it will reduce the unknown >> >> variables and make the inverse problem easier to solve. Also, there are some >> >> inverse algorithms which require the dipole to be perpendicular to the >> >> cortex surface. >> >> >> Thanks a lot!!! >> >> >> Best, >> >> >> Ying >> >> >> >> _______________________________________________ >> >> fieldtrip mailing list >> >> fieldtrip at donders.ru.nl >> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -- >> >> Jörn M. Horschig >> >> PhD Student >> >> Donders Institute for Brain, Cognition and Behaviour >> >> Centre for Cognitive Neuroimaging >> >> Radboud University Nijmegen >> >> Neuronal Oscillations Group >> >> FieldTrip Development Team >> >> >> P.O. Box 9101 >> >> NL-6500 HB Nijmegen >> >> The Netherlands >> >> >> Contact: >> >> E-Mail: jm.horschig at donders.ru.nl >> >> Tel: +31-(0)24-36-68493 >> >> Web: http://www.ru.nl/donders >> >> >> Visiting address: >> >> Trigon, room 2.30 >> >> Kapittelweg 29 >> >> NL-6525 EN Nijmegen >> >> The Netherlands >> >> >> _______________________________________________ >> >> fieldtrip mailing list >> >> fieldtrip at donders.ru.nl >> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> http://www.hettaligebrein.nl >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu May 22 13:47:14 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 22 May 2014 13:47:14 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: <09B16AC6-4417-448C-8B82-1399CEFC062F@donders.ru.nl> References: <537DBBB8.600@donders.ru.nl> <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> <09B16AC6-4417-448C-8B82-1399CEFC062F@donders.ru.nl> Message-ID: Haha never mind, I was totally confused. "Perpendicular" and "parallel" both start with a p... On 22 May 2014 13:42, jan-mathijs schoffelen wrote: > Eelke, > > You're absolutely right one should take the orientation that is othogonal! > In my dictionary this is exactly what the word perpendicular means ;-)... > > JM > > On May 22, 2014, at 1:25 PM, Eelke Spaak wrote: > > Hi Ying & JM & the rest of the list, > > I've never worked with cortex-constrained source reconstructions > before, but one question came to mind: doesn't it make more sense to > constrain the dipole orientations to *orthogonal* to the cortex, > rather than perpendicular? Given that currents along the aligned > dendrites of L5 pyramidal cells are (afaik) likely the most important > origin of the MEG signal, and those dendrites are oriented > approximately orthogonal to the cortical surface, isn't that what you > would expect? > > Best, > Eelke > > On 22 May 2014 11:47, jan-mathijs schoffelen > wrote: > > Hi Ying, > > > Yes, it's possible to constrain the dipole orientation. If you have a > > cortical sheet based source model that contains a triangulation that > > describes the topology, it's in principle possible to compute the > > orientation perpendicular to the sheet (this can e.g. be done by the > > 'normals' function which I believe should be in ~/fieldtrip/private). > > Subsequently, for each vertex in the cortical sheet you can multiply the > > leadfield matrix with this vector to get a single column leadfield vector > > per vertex that describes the sensor topography of a dipolar source with > > orientation perpendicular to the cortex. > > > Best, > > Jan-Mathijs > > > On May 22, 2014, at 11:04 AM, Eelke Spaak wrote: > > > Hi Ying, > > > In addition to this, of course first you would need a model of the > > cortical surface for your subjects. See > > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to > > obtain such a model (using FreeSurfer) and getting it into FieldTrip. > > > Best, > > Eelke > > > On 22 May 2014 10:56, "Jörn M. Horschig" wrote: > > > Hi Ying, > > > > when computing the leadfields you can set the option cfg.reducerank, which > > > 'nulls' the dimension(s) which explain(s) the least variance (this is not > > > quite true, but figuratively speaking). I think this is what comes closest > > > to what you are looking for. There is no way to explicitly set desired > > > orientations to zero apart from modifying the leadfield structure yourself. > > > But that should be easily achievable, right? > > > > Best, > > > Jörn > > > > > On 5/22/2014 10:26 AM, Ying Li wrote: > > > > Dear all, > > > > I tried to use fieldtrip to generate a source space and calculate lead > > > field matrix. I found that the dipoles in the source space has x, y, z > > > orientations. Is it possible to generate a source model where the dipole is > > > perpendicular to the cortex surface? > > > > Actually this can be very helpful, since it will reduce the unknown > > > variables and make the inverse problem easier to solve. Also, there are some > > > inverse algorithms which require the dipole to be perpendicular to the > > > cortex surface. > > > > Thanks a lot!!! > > > > Best, > > > > Ying > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > > > Jörn M. Horschig > > > PhD Student > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Neuronal Oscillations Group > > > FieldTrip Development Team > > > > P.O. Box 9101 > > > NL-6500 HB Nijmegen > > > The Netherlands > > > > Contact: > > > E-Mail: jm.horschig at donders.ru.nl > > > Tel: +31-(0)24-36-68493 > > > Web: http://www.ru.nl/donders > > > > Visiting address: > > > Trigon, room 2.30 > > > Kapittelweg 29 > > > NL-6525 EN Nijmegen > > > The Netherlands > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > Jan-Mathijs Schoffelen, MD PhD > > > Donders Institute for Brain, Cognition and Behaviour, > > Centre for Cognitive Neuroimaging, > > Radboud University Nijmegen, The Netherlands > > > Max Planck Institute for Psycholinguistics, > > Nijmegen, The Netherlands > > > J.Schoffelen at donders.ru.nl > > Telephone: +31-24-3614793 > > > http://www.hettaligebrein.nl > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > http://www.hettaligebrein.nl > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From tyler.grummett at flinders.edu.au Fri May 23 04:10:10 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Fri, 23 May 2014 02:10:10 +0000 Subject: [FieldTrip] layout file from beamformer Message-ID: <1400811002490.44354@flinders.edu.au> Hello fieldtrippers, I am trying to create a layout file that has the positions of the beamformer sources. The output of my beamformer analysis was 1400 channels and I am trying to create a layout file with certain position which correspond to certain sources. For example, if I wanted to plot 30 sources and all I had were the x y z position. I am hoping that this made sense, I cant quite work out what I should be asking for. I have worked out how to plot the power of the sources, but ft_topoplotIC is asking for a layout file (after I ran an ICA over it), which I cant work out how to make. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From yingli.ucla at gmail.com Fri May 23 04:18:48 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Thu, 22 May 2014 19:18:48 -0700 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: References: <537DBBB8.600@donders.ru.nl> <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> <09B16AC6-4417-448C-8B82-1399CEFC062F@donders.ru.nl> Message-ID: Dear all, Thanks so much for all of your enthusiastic replies. I'll give a try to your suggestions. Best wishes, Ying On Thu, May 22, 2014 at 4:47 AM, Eelke Spaak wrote: > Haha never mind, I was totally confused. "Perpendicular" and > "parallel" both start with a p... > > On 22 May 2014 13:42, jan-mathijs schoffelen > wrote: > > Eelke, > > > > You're absolutely right one should take the orientation that is > othogonal! > > In my dictionary this is exactly what the word perpendicular means ;-)... > > > > JM > > > > On May 22, 2014, at 1:25 PM, Eelke Spaak wrote: > > > > Hi Ying & JM & the rest of the list, > > > > I've never worked with cortex-constrained source reconstructions > > before, but one question came to mind: doesn't it make more sense to > > constrain the dipole orientations to *orthogonal* to the cortex, > > rather than perpendicular? Given that currents along the aligned > > dendrites of L5 pyramidal cells are (afaik) likely the most important > > origin of the MEG signal, and those dendrites are oriented > > approximately orthogonal to the cortical surface, isn't that what you > > would expect? > > > > Best, > > Eelke > > > > On 22 May 2014 11:47, jan-mathijs schoffelen > > wrote: > > > > Hi Ying, > > > > > > Yes, it's possible to constrain the dipole orientation. If you have a > > > > cortical sheet based source model that contains a triangulation that > > > > describes the topology, it's in principle possible to compute the > > > > orientation perpendicular to the sheet (this can e.g. be done by the > > > > 'normals' function which I believe should be in ~/fieldtrip/private). > > > > Subsequently, for each vertex in the cortical sheet you can multiply the > > > > leadfield matrix with this vector to get a single column leadfield vector > > > > per vertex that describes the sensor topography of a dipolar source with > > > > orientation perpendicular to the cortex. > > > > > > Best, > > > > Jan-Mathijs > > > > > > On May 22, 2014, at 11:04 AM, Eelke Spaak wrote: > > > > > > Hi Ying, > > > > > > In addition to this, of course first you would need a model of the > > > > cortical surface for your subjects. See > > > > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to > > > > obtain such a model (using FreeSurfer) and getting it into FieldTrip. > > > > > > Best, > > > > Eelke > > > > > > On 22 May 2014 10:56, "Jörn M. Horschig" > wrote: > > > > > > Hi Ying, > > > > > > > > when computing the leadfields you can set the option cfg.reducerank, > which > > > > > > 'nulls' the dimension(s) which explain(s) the least variance (this is not > > > > > > quite true, but figuratively speaking). I think this is what comes > closest > > > > > > to what you are looking for. There is no way to explicitly set desired > > > > > > orientations to zero apart from modifying the leadfield structure > yourself. > > > > > > But that should be easily achievable, right? > > > > > > > > Best, > > > > > > Jörn > > > > > > > > > > On 5/22/2014 10:26 AM, Ying Li wrote: > > > > > > > > Dear all, > > > > > > > > I tried to use fieldtrip to generate a source space and calculate lead > > > > > > field matrix. I found that the dipoles in the source space has x, y, z > > > > > > orientations. Is it possible to generate a source model where the dipole > is > > > > > > perpendicular to the cortex surface? > > > > > > > > Actually this can be very helpful, since it will reduce the unknown > > > > > > variables and make the inverse problem easier to solve. Also, there are > some > > > > > > inverse algorithms which require the dipole to be perpendicular to the > > > > > > cortex surface. > > > > > > > > Thanks a lot!!! > > > > > > > > Best, > > > > > > > > Ying > > > > > > > > > > _______________________________________________ > > > > > > fieldtrip mailing list > > > > > > fieldtrip at donders.ru.nl > > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > -- > > > > > > Jörn M. Horschig > > > > > > PhD Student > > > > > > Donders Institute for Brain, Cognition and Behaviour > > > > > > Centre for Cognitive Neuroimaging > > > > > > Radboud University Nijmegen > > > > > > Neuronal Oscillations Group > > > > > > FieldTrip Development Team > > > > > > > > P.O. Box 9101 > > > > > > NL-6500 HB Nijmegen > > > > > > The Netherlands > > > > > > > > Contact: > > > > > > E-Mail: jm.horschig at donders.ru.nl > > > > > > Tel: +31-(0)24-36-68493 > > > > > > Web: http://www.ru.nl/donders > > > > > > > > Visiting address: > > > > > > Trigon, room 2.30 > > > > > > Kapittelweg 29 > > > > > > NL-6525 EN Nijmegen > > > > > > The Netherlands > > > > > > > > _______________________________________________ > > > > > > fieldtrip mailing list > > > > > > fieldtrip at donders.ru.nl > > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > Jan-Mathijs Schoffelen, MD PhD > > > > > > Donders Institute for Brain, Cognition and Behaviour, > > > > Centre for Cognitive Neuroimaging, > > > > Radboud University Nijmegen, The Netherlands > > > > > > Max Planck Institute for Psycholinguistics, > > > > Nijmegen, The Netherlands > > > > > > J.Schoffelen at donders.ru.nl > > > > Telephone: +31-24-3614793 > > > > > > http://www.hettaligebrein.nl > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > Jan-Mathijs Schoffelen, MD PhD > > > > Donders Institute for Brain, Cognition and Behaviour, > > Centre for Cognitive Neuroimaging, > > Radboud University Nijmegen, The Netherlands > > > > Max Planck Institute for Psycholinguistics, > > Nijmegen, The Netherlands > > > > J.Schoffelen at donders.ru.nl > > Telephone: +31-24-3614793 > > > > http://www.hettaligebrein.nl > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Fri May 23 09:01:45 2014 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 23 May 2014 09:01:45 +0200 Subject: [FieldTrip] layout file from beamformer In-Reply-To: <1400811002490.44354@flinders.edu.au> References: <1400811002490.44354@flinders.edu.au> Message-ID: <53A25C84-5000-471D-A96B-A1EEF293ACAD@gmail.com> Dear Tyler, I recently had a similar problem. I solved this by plotting the x,y,z-coordinates of all dipoles within the BEM-Model and assign a color value depending on the power value to the dipole markers. In short: use ft_triplot to plot the mesh of the BEM. Then select the .pos-field of the dipoles inside your volume and plot them with plot3. In the plot3-step, you can assign each dipole a 'Color'-property based on your power or stats value. Alternatively, you can use ft_prepare_layout to get a planar projection of your sources, but at least in my case it did not look too good. Hope that helps, if you want to, I can send you an example of what the plots look like. Best, Julian Am 23.05.2014 um 04:10 schrieb Tyler Grummett: > Hello fieldtrippers, > > I am trying to create a layout file that has the positions of the beamformer sources. > > The output of my beamformer analysis was 1400 channels and I am trying to create a layout file with certain position which correspond to certain sources. > > For example, if I wanted to plot 30 sources and all I had were the x y z position. > > I am hoping that this made sense, I cant quite work out what I should be asking for. I have worked out how to plot the power of the sources, but > ft_topoplotIC is asking for a layout file (after I ran an ICA over it), which I cant work out how to make. > > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Fri May 23 10:04:12 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Fri, 23 May 2014 08:04:12 +0000 Subject: [FieldTrip] layout file from beamformer In-Reply-To: <53A25C84-5000-471D-A96B-A1EEF293ACAD@gmail.com> References: <1400811002490.44354@flinders.edu.au>, <53A25C84-5000-471D-A96B-A1EEF293ACAD@gmail.com> Message-ID: <13054238-2E21-4214-851F-F6481F0860B0@flinders.edu.au> Hey Julian, That sounds good, it would be awesome if you could give me an example. Also though, what are the steps of using ft_prepare_layout with beamformer data. I am away it gives you permissions, but how do you enter that into ft_prepare_layout. This is only for using in trentool, otherwise I would be using your method Tyler On 23 May 2014, at 4:40 pm, "Julian Keil" > wrote: Dear Tyler, I recently had a similar problem. I solved this by plotting the x,y,z-coordinates of all dipoles within the BEM-Model and assign a color value depending on the power value to the dipole markers. In short: use ft_triplot to plot the mesh of the BEM. Then select the .pos-field of the dipoles inside your volume and plot them with plot3. In the plot3-step, you can assign each dipole a 'Color'-property based on your power or stats value. Alternatively, you can use ft_prepare_layout to get a planar projection of your sources, but at least in my case it did not look too good. Hope that helps, if you want to, I can send you an example of what the plots look like. Best, Julian Am 23.05.2014 um 04:10 schrieb Tyler Grummett: Hello fieldtrippers, I am trying to create a layout file that has the positions of the beamformer sources. The output of my beamformer analysis was 1400 channels and I am trying to create a layout file with certain position which correspond to certain sources. For example, if I wanted to plot 30 sources and all I had were the x y z position. I am hoping that this made sense, I cant quite work out what I should be asking for. I have worked out how to plot the power of the sources, but ft_topoplotIC is asking for a layout file (after I ran an ICA over it), which I cant work out how to make. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.herring at fcdonders.ru.nl Fri May 23 10:42:58 2014 From: j.herring at fcdonders.ru.nl (Herring, J.D. (Jim)) Date: Fri, 23 May 2014 10:42:58 +0200 (CEST) Subject: [FieldTrip] layout file from beamformer In-Reply-To: <13054238-2E21-4214-851F-F6481F0860B0@flinders.edu.au> References: <1400811002490.44354@flinders.edu.au>, <53A25C84-5000-471D-A96B-A1EEF293ACAD@gmail.com> <13054238-2E21-4214-851F-F6481F0860B0@flinders.edu.au> Message-ID: <010201cf7663$002490f0$006db2d0$@herring@fcdonders.ru.nl> Hi Tyler, What would you like to plot? It seems like you want to plot the spatial weights of independent components after running ICA on your source data. Ft_topoplotIC plots data on a 2D-layout of your sensors/electrodes, I do not think you want this. It seems to me you should have a look at ft_sourceplot and add a field to your source data structure that, for each IC, represents the weights per gridpoint. Then you should be able to plot the IC weights in 3D (with anatomy if you wish). Best, Jim From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Tyler Grummett Sent: vrijdag 23 mei 2014 10:04 To: FieldTrip discussion list Subject: Re: [FieldTrip] layout file from beamformer Hey Julian, That sounds good, it would be awesome if you could give me an example. Also though, what are the steps of using ft_prepare_layout with beamformer data. I am away it gives you permissions, but how do you enter that into ft_prepare_layout. This is only for using in trentool, otherwise I would be using your method Tyler On 23 May 2014, at 4:40 pm, "Julian Keil" wrote: Dear Tyler, I recently had a similar problem. I solved this by plotting the x,y,z-coordinates of all dipoles within the BEM-Model and assign a color value depending on the power value to the dipole markers. In short: use ft_triplot to plot the mesh of the BEM. Then select the .pos-field of the dipoles inside your volume and plot them with plot3. In the plot3-step, you can assign each dipole a 'Color'-property based on your power or stats value. Alternatively, you can use ft_prepare_layout to get a planar projection of your sources, but at least in my case it did not look too good. Hope that helps, if you want to, I can send you an example of what the plots look like. Best, Julian Am 23.05.2014 um 04:10 schrieb Tyler Grummett: Hello fieldtrippers, I am trying to create a layout file that has the positions of the beamformer sources. The output of my beamformer analysis was 1400 channels and I am trying to create a layout file with certain position which correspond to certain sources. For example, if I wanted to plot 30 sources and all I had were the x y z position. I am hoping that this made sense, I cant quite work out what I should be asking for. I have worked out how to plot the power of the sources, but ft_topoplotIC is asking for a layout file (after I ran an ICA over it), which I cant work out how to make. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Fri May 23 10:45:20 2014 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 23 May 2014 10:45:20 +0200 Subject: [FieldTrip] layout file from beamformer In-Reply-To: <13054238-2E21-4214-851F-F6481F0860B0@flinders.edu.au> References: <1400811002490.44354@flinders.edu.au> <53A25C84-5000-471D-A96B-A1EEF293ACAD@gmail.com> <13054238-2E21-4214-851F-F6481F0860B0@flinders.edu.au> Message-ID: Hi Tyler, I attached 2 plots for you, one with evoked ERF activity, and one of the same activity but masked for the maximum. As you can see, you get information about the activity for each dipole as well as the location within the volume. As for the layout, here's how it works for me: % Sourcedummy in this case is a source structure containing the grid .pos % and .inside field elec = []; elec.elecpos = sourcedummy.pos(sourcedummy.inside,:); elec.chanpos = sourcedummy.pos(sourcedummy.inside,:); tmp = num2cell(sourcedummy.inside); elec.label = cellfun(@num2str,tmp,'UniformOutput',0); cfg = []; cfg.elec = elec; cfg.projection = 'polar'; example_lay = ft_prepare_layout(cfg); cfg=[]; cfg.layout = example_lay; ft_layoutplot(cfg); Please be careful with the 2D-projection of 3D-data. I'm not sure how accurate the projection is and some grid points might overlap. Good Luck, Julian On Fri, May 23, 2014 at 10:04 AM, Tyler Grummett < tyler.grummett at flinders.edu.au> wrote: > Hey Julian, > > That sounds good, it would be awesome if you could give me an example. > > Also though, what are the steps of using ft_prepare_layout with > beamformer data. I am away it gives you permissions, but how do you enter > that into ft_prepare_layout. > > This is only for using in trentool, otherwise I would be using your > method > > Tyler > > > On 23 May 2014, at 4:40 pm, "Julian Keil" wrote: > > Dear Tyler, > > I recently had a similar problem. > > I solved this by plotting the x,y,z-coordinates of all dipoles within > the BEM-Model and assign a color value depending on the power value to the > dipole markers. > > In short: use ft_triplot to plot the mesh of the BEM. Then select the > .pos-field of the dipoles inside your volume and plot them with plot3. > In the plot3-step, you can assign each dipole a 'Color'-property based on > your power or stats value. > > Alternatively, you can use ft_prepare_layout to get a planar projection > of your sources, but at least in my case it did not look too good. > > Hope that helps, if you want to, I can send you an example of what the > plots look like. > > Best, > > Julian > > Am 23.05.2014 um 04:10 schrieb Tyler Grummett: > > Hello fieldtrippers, > > I am trying to create a layout file that has the positions of the > beamformer sources. > > The output of my beamformer analysis was 1400 channels and I am trying > to create a layout file with certain position which correspond to certain > sources. > > For example, if I wanted to plot 30 sources and all I had were the x y z > position. > > I am hoping that this made sense, I cant quite work out what I should be > asking for. I have worked out how to plot the power of the sources, but > ft_topoplotIC is asking for a layout file (after I ran an ICA over it), > which I cant work out how to make. > > Tyler > > ************************* > > *Tyler Grummett ( BBSc, BSc(Hons I))* > *PhD Candidate* > *Brain Signals Laboratory* > *Flinders University* > *Rm 5A301* > *Ext 66124* > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: wirebrain_example_mask.png Type: image/png Size: 37668 bytes Desc: not available URL: From s.hassel at aston.ac.uk Fri May 23 13:06:23 2014 From: s.hassel at aston.ac.uk (Hassel, Stefanie) Date: Fri, 23 May 2014 11:06:23 +0000 Subject: [FieldTrip] PhD Studentship at Aston University, Birmingham, UK Message-ID: <282D53FEFCF0B44EA5D1E7977E0C32E61FACE2E5@exch-mb-g50-02.campus.aston.ac.uk> Dear all, Please see below for information on a PhD Studentship available in the School of Life & Health Sciences at Aston University, Birmingham, UK Using Response Inhibition and Reward Responsiveness to Investigate Risk for Psychopathology Dr Stefanie Hassel and Prof. Klaus Kessler Biological predisposition towards psychopathology as well as environmental events may influence whether and when symptoms surface among individuals, who are at an increased risk for psychopathology. Individuals differ in their degree of responsiveness to cues of reward or cues of threat, in goal-seeking behaviours and/or anxiety. A high degree of responsiveness to cues of reward or threat may play an additional role in placing individuals at risk for psychopathologies, especially mood disorders. For instance, high reward responsiveness on a specific behavioural task, individual characteristics like impulsivity or extreme appraisals of social approval as well as family history of psychopathology may all aid in predicting future diagnoses. This project will address the underlying mechanisms that control fluctuations in mood and behaviour, specific sensitivities which may determine the strength of a person's emotional reaction to reward or threat and investigate potential relationships between sensitivity levels to cues of reward and threat and sub-threshold symptoms of (hypo)mania and depression in individuals at increased risk for a mood disorder (or other psychopathology), compared to undergraduate students classified as not at risk. Multi-modal experimental methods will be used to examine these issues, such as behavioural task-based and questionnaire measures, as well as structural and functional neuroimaging (Magnetic Resonance Imaging (MRI), Diffusion Tensor Imaging, functional MRI and Magnetoencephalography). Outcomes from this research may be used to help inform early identification of risk factors for general psychopathology and mood disorders (depression and bipolar disorder) in particular. The high quality of research in Aston's School of Life and Health Sciences was confirmed in the last Research Assessment Exercise (RAE): research in Allied Health Professions and Studies ranked 3rd out of 63 UK Higher Education Institutions. Additional information about research in the School can be found at http://www1.aston.ac.uk/lhs/research/ Financial Support: The studentship comprises of a tax-free stipend of £13,863 p.a. and payment of Home/EU tuition fees only. The studentship is available for three years, subject to satisfactory progress review at the end of the first year with an anticipated Registration date of 1st October 2014. Application Requirements: * Eligible Applicants should hold at least a Bachelor (Hons.) Degree of either First Class/Upper Second Class or hold a Master's Degree in Psychology or related discipline. A demonstrable interest in affective neuroscience and/or clinical psychology is a requirement. (Supervisors are based at Aston University, and draw on expertise with experimental and neuroimaging research with healthy and clinical populations). * EU Applicants will need to demonstrate adequate proficiency in English Language skills, with a minimum overall score of 101 (Internet Based) (with a minimum score in each section of: R: 23, W: 26, L: 23 and S: 22) in TOEFL or IELTS with minimum marks of 6.5 in each section and an overall band of 7.0. * Informal enquiries should be addressed to the Project Supervisor, Dr Stefanie Hassel (E-mail:s.hassel at aston.ac.uk). Closing Date: Monday 09 June 2014 Reference: R140127 To apply please complete the on-line application form athttps://map.aston.ac.uk/urd/sits.urd/run/siw_ipp_lgn.login?process=siw_ipp_app&&code1=LHS029PR&code2=0014 Email details to a friend --- --- --- Stefanie Hassel, PhD Department of Psychology School of Life and Health Sciences Aston University Birmingham B4 7ET Email: s.hassel at aston.ac.uk Phone: 0121 204 4003 Students can make an appointment with me by following this link: https://wass.aston.ac.uk/pages/login.page.php Adjunct Assistant Professor: Dept. of Psychiatry, Faculty of Medicine, University of Calgary, Calgary, AB, Canada Adjunct Instructor: Western Psychiatric Institute and Clinic, University of Pittsburgh, Pittsburgh, PA, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: From diezmartini at gmail.com Mon May 26 02:30:57 2014 From: diezmartini at gmail.com (Ana Laura Diez Martini) Date: Mon, 26 May 2014 12:30:57 +1200 Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW Message-ID: Hi all! This is the .BDF file of one of my EEG subjects. For my last experiment I used a Biosemi system and now I'm using an EGI system which gives me .RAW files. I exported the .RAW file with EEGlab to .BDF format and I tried using the scripts I use to analise the data of my previous experiment but I realised that it was not reading the events: cfg = []; cfg.dataset = ' (location)'; cfg.trialdef.eventtype = '?'; definetrial(cfg); Warning: no trialfun was specified, using trialfun_general > In definetrial at 79 evaluating trialfunction 'trialfun_general' no events were found in the datafile no trials have been defined yet, see DEFINETRIAL for further help found 0 events created 0 trials EEGlab does read them. Any idea of what could be wrong? Thank you all!! -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Mon May 26 08:59:13 2014 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Mon, 26 May 2014 08:59:13 +0200 Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW In-Reply-To: References: Message-ID: Hi Ana Laura, Have you tried importing the .RAW file directly? That is, by specifying cfg.dataset = 'XXX.raw'? Best regards, Arjen 2014-05-26 2:30 GMT+02:00 Ana Laura Diez Martini : > Hi all! > > This is the .BDF file > of one of > my EEG subjects. For my last experiment I used a Biosemi system and now I'm > using an EGI system which gives me .RAW files. I exported the .RAW file > with EEGlab to .BDF format and I tried using the scripts I use to analise > the data of my previous experiment but I realised that it was not reading > the events: > > cfg = []; > cfg.dataset = ' (location)'; > cfg.trialdef.eventtype = '?'; > definetrial(cfg); > Warning: no trialfun was specified, using trialfun_general > > In definetrial at 79 > evaluating trialfunction 'trialfun_general' > no events were found in the datafile > no trials have been defined yet, see DEFINETRIAL for further help > found 0 events > created 0 trials > > EEGlab does read them. Any idea of what could be wrong? > > Thank you all!! > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Mon May 26 09:03:09 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 26 May 2014 09:03:09 +0200 Subject: [FieldTrip] Fwd: summer school on stress & cognition Message-ID: Forwarding on behalf of a colleague. ---------- Forwarded message ---------- From: Vogel, S. (Susanne) Date: 23 May 2014 11:38 Subject: fieldtrip and MEG mailing lists To: Eelke Spaak Dear colleague, Each year, the Donders Institute for Brain, Cognition and Behaviour organizes a highly prestigious international summer school in cognitive neuroscience, bringing together world-leading scientists and outstanding MSc students, PhD students, and postdocs. The topic of this year's summer school is STRESS & COGNITION: FROM BASIC MECHANISMS TO PSYCHOPATHOLOGY. The event will take place in the week of August 11-15, 2014, on the campus of Radboud University in Nijmegen. With a list of highly renowned international experts in the interdisciplinary field of stress and cognition, we are convinced that our summer school will be of great interest to your research group and/or department. In addition to lectures, we will organize group discussions, a poster session for students to get feedback on their work, lab tours at the Donders' research facilities, and a range of social activities. There is optional accommodation available on campus. Currently, the application procedure is in full swing. We are proud to inform you that thus far we have accepted students from 17 different countries: Belgium, Brazil, Bulgaria, Chili, China, Denmark, Germany, Greece, Italy, Korea, Netherlands, Poland, Romania, Russia, Scotland, Spain, and the United States. Please note that we are rapidly approaching the maximum number of participants. Registration will close on JUNE 15, 2014. More information can be found on our website: HTTP://WWW.RU.NL/DONDERS/SUMMERSCHOOL We would like to ask you to kindly bring this to the attention of MSc students, PhD students, and postdocs who might be interested. With warm regards, Benno Roozendaal Erno Hermans (Organizers) From d.lozanosoldevilla at fcdonders.ru.nl Mon May 26 10:58:01 2014 From: d.lozanosoldevilla at fcdonders.ru.nl (Diego Lozano Soldevilla) Date: Mon, 26 May 2014 10:58:01 +0200 Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW In-Reply-To: References: Message-ID: Hi Ana, Fieldtrip does not read events in BDF format. Take a look to our wiki: http://fieldtrip.fcdonders.nl/getting_started/egi - *EDF+* (.edf) All channels, including PIB channels, are read in correctly, including channel labels. However, the events, which are stored on the annotation channel, are written in a way by Net Station that is not compatible with the edf+ reading implementation in FieldTrip. So, events do not come out properly. Also discontinuous epochs are “glued” together as one “continuous” data stream. As Arjen suggested, with *.RAW you shouldn't have any problem. event = ft_read_event('*.RAW') If you encounter it, please let us know. best, Diego On 26 May 2014 08:59, Arjen Stolk wrote: > Hi Ana Laura, > > Have you tried importing the .RAW file directly? That is, by specifying > cfg.dataset = 'XXX.raw'? > > Best regards, > Arjen > > > 2014-05-26 2:30 GMT+02:00 Ana Laura Diez Martini : > >> Hi all! >> >> This is the .BDF file >> of one of >> my EEG subjects. For my last experiment I used a Biosemi system and now I'm >> using an EGI system which gives me .RAW files. I exported the .RAW file >> with EEGlab to .BDF format and I tried using the scripts I use to analise >> the data of my previous experiment but I realised that it was not reading >> the events: >> >> cfg = []; >> cfg.dataset = ' (location)'; >> cfg.trialdef.eventtype = '?'; >> definetrial(cfg); >> Warning: no trialfun was specified, using trialfun_general >> > In definetrial at 79 >> evaluating trialfunction 'trialfun_general' >> no events were found in the datafile >> no trials have been defined yet, see DEFINETRIAL for further help >> found 0 events >> created 0 trials >> >> EEGlab does read them. Any idea of what could be wrong? >> >> Thank you all!! >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dr.chungki.lee at gmail.com Mon May 26 11:18:34 2014 From: dr.chungki.lee at gmail.com (Chungki Lee) Date: Mon, 26 May 2014 18:18:34 +0900 Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW In-Reply-To: References: Message-ID: Dear all Fieldtrip can read events in BDF format ! Hear simple examples example #1 %% cfg = []; cfg.dataset = '~~~ '; % your filename with file extension; cfg.trialdef.eventtype = 'STATUS'; % Status notation maybe Biosemi's tigger name cfg.trialdef.eventvalue = 1; % your event value cfg.trialdef.prestim = 4; % before stimulation (sec), only use positive value cfg.trialdef.poststim = 8; % after stimulation (sec) , only use positive value cfg = ft_definetrial(cfg); cfg.method = 'trial'; data = ft_preprocessing(cfg); %% example #2 %% % if you executed these command lines cfg = []; cfg.dataset = '~~~ '; % your filename with file extension; cfg.trialdef.eventtype = '?'; % Status notation maybe Biosemi's tigger name cfg = ft_definetrial(cfg); % result example #2 the following events were found in the datafile event type: 'CM_in_range' with event values: event type: 'Epoch' with event values: event type: 'STATUS' with event values: 1 2 3 4 255 <----------- "this indicate your file configuration for trigger information" no trials have been defined yet, see FT_DEFINETRIAL for further help found 255 events created 0 trials the call to "ft_definetrial" took 8 seconds have fun~!! 2014-05-26 17:58 GMT+09:00 Diego Lozano Soldevilla < d.lozanosoldevilla at fcdonders.ru.nl>: > Hi Ana, > > Fieldtrip does not read events in BDF format. Take a look to our wiki: > > http://fieldtrip.fcdonders.nl/getting_started/egi > > > - *EDF+* (.edf) All channels, including PIB channels, are read in > correctly, including channel labels. However, the events, which are stored > on the annotation channel, are written in a way by Net Station that is not > compatible with the edf+ reading implementation in FieldTrip. So, events do > not come out properly. Also discontinuous epochs are “glued” together as > one “continuous” data stream. > > As Arjen suggested, with *.RAW you shouldn't have any problem. > > event = ft_read_event('*.RAW') > > If you encounter it, please let us know. > > best, > > Diego > > > On 26 May 2014 08:59, Arjen Stolk wrote: > >> Hi Ana Laura, >> >> Have you tried importing the .RAW file directly? That is, by specifying >> cfg.dataset = 'XXX.raw'? >> >> Best regards, >> Arjen >> >> >> 2014-05-26 2:30 GMT+02:00 Ana Laura Diez Martini : >> >>> Hi all! >>> >>> This is the .BDF file >>> of one of >>> my EEG subjects. For my last experiment I used a Biosemi system and now I'm >>> using an EGI system which gives me .RAW files. I exported the .RAW file >>> with EEGlab to .BDF format and I tried using the scripts I use to analise >>> the data of my previous experiment but I realised that it was not reading >>> the events: >>> >>> cfg = []; >>> cfg.dataset = ' (location)'; >>> cfg.trialdef.eventtype = '?'; >>> definetrial(cfg); >>> Warning: no trialfun was specified, using trialfun_general >>> > In definetrial at 79 >>> evaluating trialfunction 'trialfun_general' >>> no events were found in the datafile >>> no trials have been defined yet, see DEFINETRIAL for further help >>> found 0 events >>> created 0 trials >>> >>> EEGlab does read them. Any idea of what could be wrong? >>> >>> Thank you all!! >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ---------------------------------------------------------------- Chungki Lee, Ph.D. Post-doc Biomedical Research Institute Korea Institute of Science and Technology E-mail: chungki at kist.re.kr Tel:+82-2-958-5636, C.P: +82-10-5223-7309 ---------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.lozanosoldevilla at fcdonders.ru.nl Mon May 26 11:44:13 2014 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Mon, 26 May 2014 11:44:13 +0200 (CEST) Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW In-Reply-To: Message-ID: <222446912.7087267.1401097453356.JavaMail.root@sculptor.zimbra.ru.nl> Dear Ana, Sorry for my file extension confusion: edf instead of bdf. However, I don't know a way to read events coded in BDF format exported by NETSTATION. I encounter this problem in the past but I had no problems with RAW file format Dear Chungki , Fieldtrip can read events in *.bdf but from BIOSEMI eeg system but Ana was refering to a different eeg system that has the same fileformat extension. best, Diego ----- Original Message ----- > From: "Chungki Lee" > To: "FieldTrip discussion list" > Sent: Monday, 26 May, 2014 11:18:34 AM > Subject: Re: [FieldTrip] Cannot read the events of a .BDF file > exported from an EGI .RAW > Dear all > Fieldtrip can read events in BDF format ! > Hear simple examples > example #1 > %% > cfg = []; > cfg.dataset = '~~~ '; % your filename with file extension; > cfg.trialdef.eventtype = 'STATUS'; % Status notation maybe Biosemi's > tigger name > cfg.trialdef.eventvalue = 1; % your event value > cfg.trialdef.prestim = 4; % before stimulation (sec), only use > positive value > cfg.trialdef.poststim = 8; % after stimulation (sec) , only use > positive value > cfg = ft_definetrial(cfg); > cfg.method = 'trial'; > data = ft_preprocessing(cfg); > %% > example #2 > %% > % if you executed these command lines > cfg = []; > cfg.dataset = '~~~ '; % your filename with file extension; > cfg.trialdef.eventtype = '?'; % Status notation maybe Biosemi's tigger > name > cfg = ft_definetrial(cfg); > % result example #2 > the following events were found in the datafile > event type: 'CM_in_range' with event values: > event type: 'Epoch' with event values: > event type: 'STATUS' with event values: 1 2 3 4 255 <----------- "this > indicate your file configuration for trigger information" > no trials have been defined yet, see FT_DEFINETRIAL for further help > found 255 events > created 0 trials > the call to "ft_definetrial" took 8 seconds > have fun~!! > 2014-05-26 17:58 GMT+09:00 Diego Lozano Soldevilla < > d.lozanosoldevilla at fcdonders.ru.nl > : > > Hi Ana, > > Fieldtrip does not read events in BDF format. Take a look to our > > wiki: > > http://fieldtrip.fcdonders.nl/getting_started/egi > > • > > EDF+ (.edf) All channels, including PIB channels, are read in > > correctly, including channel labels. However, the events, which are > > stored on the annotation channel, are written in a way by Net > > Station > > that is not compatible with the edf+ reading implementation in > > FieldTrip. So, events do not come out properly. Also discontinuous > > epochs are “glued” together as one “continuous” data stream. > > As Arjen suggested, with *.RAW you shouldn't have any problem. > > event = ft_read_event('*.RAW') > > If you encounter it, please let us know. > > best, > > Diego > > On 26 May 2014 08:59, Arjen Stolk < a.stolk8 at gmail.com > wrote: > > > Hi Ana Laura, > > > Have you tried importing the .RAW file directly? That is, by > > > specifying cfg.dataset = 'XXX.raw'? > > > Best regards, > > > Arjen > > > 2014-05-26 2:30 GMT+02:00 Ana Laura Diez Martini < > > > diezmartini at gmail.com > : > > > > Hi all! > > > > This is the .BDF file of one of my EEG subjects. For my last > > > > experiment I used a Biosemi system and now I'm using an EGI > > > > system > > > > which gives me .RAW files. I exported the .RAW file with EEGlab > > > > to > > > > .BDF format and I tried using the scripts I use to analise the > > > > data > > > > of > > > > my previous experiment but I realised that it was not reading > > > > the > > > > events: > > > > cfg = []; > > > > cfg.dataset = ' (location)'; > > > > cfg.trialdef.eventtype = '?'; > > > > definetrial(cfg); > > > > Warning: no trialfun was specified, using trialfun_general > > > > > In definetrial at 79 > > > > evaluating trialfunction 'trialfun_general' > > > > no events were found in the datafile > > > > no trials have been defined yet, see DEFINETRIAL for further > > > > help > > > > found 0 events > > > > created 0 trials > > > > EEGlab does read them. Any idea of what could be wrong? > > > > Thank you all!! > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- > ---------------------------------------------------------------- > Chungki Lee, Ph.D. > Post-doc > Biomedical Research Institute > Korea Institute of Science and Technology > E-mail: chungki at kist.re.kr > Tel:+82-2-958-5636, C.P: +82-10-5223-7309 > ---------------------------------------------------------------- > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- PhD Student Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen NL-6525 EN Nijmegen The Netherlands http://www.ru.nl/people/donders/lozano-soldevilla-d/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahjoory86 at gmail.com Mon May 26 13:42:51 2014 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Mon, 26 May 2014 13:42:51 +0200 Subject: [FieldTrip] Template for Electrode Positions Message-ID: Dear all, I want to do EEG source reconstruction. The EEG cap we used is the standard 10-20 system with 64 channels, but the MRI and electrode positions of subjects are not available. I'm thinking of using Fieldtrip templates. For head model I used: load standard_bem.mat cfg.vol=vol; But for Electrode positions I checked all options at this link: http://fieldtrip.fcdonders.nl/template/electrode the only option with 64 channel is GSN-HydroCel-64_1.0.sfp. It includes labels in this format: E1 E2 E3... So, How can I use it for my work? Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From i.e.j.de.vries at student.vu.nl Mon May 26 14:20:44 2014 From: i.e.j.de.vries at student.vu.nl (Vries, I.E.J. de) Date: Mon, 26 May 2014 12:20:44 +0000 Subject: [FieldTrip] Template for Electrode Positions In-Reply-To: References: Message-ID: <19DD7427D34B7E47B33093FB4C3CFDD2010950FF81@PEXMB001B.vu.local> Hi Keyvan, I also used a 64 channel EEG cap and used the Fieldtrip template standard_1020.elc. Although this template has more electrodes, Fieldtrip automatically only uses the electrodes from that template that are also present in your data (it checks the labels, so make sure your electrode labels agree with the ones in the template when it comes to upper/lower case). The 64 electrodes that I used in my experiment are all present in the standard_1020.elc template and they are on the same position as in my cap. Good luck! Ingmar ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Keyvan Mahjoory [mahjoory86 at gmail.com] Sent: 26 May 2014 13:42 To: FieldTrip discussion list Subject: [FieldTrip] Template for Electrode Positions Dear all, I want to do EEG source reconstruction. The EEG cap we used is the standard 10-20 system with 64 channels, but the MRI and electrode positions of subjects are not available. I'm thinking of using Fieldtrip templates. For head model I used: load standard_bem.mat cfg.vol=vol; But for Electrode positions I checked all options at this link: http://fieldtrip.fcdonders.nl/template/electrode the only option with 64 channel is GSN-HydroCel-64_1.0.sfp. It includes labels in this format: E1 E2 E3... So, How can I use it for my work? Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.herring at fcdonders.ru.nl Mon May 26 14:22:10 2014 From: j.herring at fcdonders.ru.nl (Herring, J.D. (Jim)) Date: Mon, 26 May 2014 14:22:10 +0200 (CEST) Subject: [FieldTrip] Template for Electrode Positions In-Reply-To: References: Message-ID: <005c01cf78dd$1d9519d0$58bf4d70$@herring@fcdonders.ru.nl> Dear Keyvan, As is stated on http://fieldtrip.fcdonders.nl/template/electrode, Fieldtrip also has electrode positions for the standard 10-20 system, namely: standard_1020.elc. To read in the sensor positions you would have to do something like: Filename = 'c:\fieldtrip\template\electrode\standard_1020.elc'; sens = ft_read_sens(filename); Best, Jim From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Keyvan Mahjoory Sent: maandag 26 mei 2014 13:43 To: FieldTrip discussion list Subject: [FieldTrip] Template for Electrode Positions Dear all, I want to do EEG source reconstruction. The EEG cap we used is the standard 10-20 system with 64 channels, but the MRI and electrode positions of subjects are not available. I'm thinking of using Fieldtrip templates. For head model I used: load standard_bem.mat cfg.vol=vol; But for Electrode positions I checked all options at this link: http://fieldtrip.fcdonders.nl/template/electrode the only option with 64 channel is GSN-HydroCel-64_1.0.sfp. It includes labels in this format: E1 E2 E3... So, How can I use it for my work? Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From frsantos at fpce.up.pt Mon May 26 18:08:41 2014 From: frsantos at fpce.up.pt (Fernando Ferreira-Santos) Date: Mon, 26 May 2014 16:08:41 +0000 Subject: [FieldTrip] Porto III CAN: 3rd Cognitive and Affective Neurophysiology Summer School Message-ID: <2BAB036A9BAEA44984A131DFCE44610801099FB3BD@SRVMBX01.fpceup.psi.up.pt> Dear colleagues, The Laboratory of Neuropsychopsysiology of the University of Porto (http://www.fpce.up.pt/labpsi/) is pleased to announce the 3rd edition of the International Cognitive and Affective Neurophysiology Summer School: Acquisition, processing and analysis of EEG signal. This summer school is focused on the application of Electroencephalography (EEG) and Event Related Potential (ERP) techniques to the study of cognitive and affective processes. The course will be fully taught in English and is aimed at an introductory level, so no previous experience with EEG or ERP is required. This event will take place from 8-13 of September in the lovely city of Porto, recently elected as the Best European Destination of 2014 (http://www.europeanbestdestinations.org/top/europe-best-destinations-2014/#PORTO). In last year’s edition the course was fully booked and, as such, we recommend early registration (course places are attributed by order of registration). For additional details and instructions on how to register, please consult our website (http://www.fpce.up.pt/labpsi/summerschool/). Please feel free to pass this information along to students or researchers that may be potentially interested. Thanks you and best wishes, -- Fernando Ferreira-Santos, PhD Laboratory of Neuropsychophysiology Faculty of Psychology and Education Sciences University of Porto Rua Alfredo Allen, 4200-135 Porto (Portugal) Tel.: +351 226079700 (ext. 301) Email: frsantos at fpce.up.pt http://www.fpce.up.pt/labpsi/ -- Fernando Ferreira-Santos, PhD Laboratory of Neuropsychophysiology Faculty of Psychology and Education Sciences University of Porto Rua Alfredo Allen, 4200-135 Porto (Portugal) Tel.: +351 226079700 (ext. 301) Email: frsantos at fpce.up.pt http://www.fpce.up.pt/labpsi/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahjoory86 at gmail.com Mon May 26 18:14:17 2014 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Mon, 26 May 2014 18:14:17 +0200 Subject: [FieldTrip] Error in source analysis Message-ID: Dear All, Here is my scripts for source analysis, when I run it, I face with error mentioned below, load 'standard_bem.mat' cfg = []; cfg.method = 'dics'; cfg.frequency = 10; cfg.grid = grid; cfg.elec=ft_read_sens('standard_1020.elc'); cfg.vol = vol; sourcePost_nocon = ft_sourceanalysis(cfg,freq); ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> beamformer_dics>pinv at 650 [U,S,V] = svd(A,0); Error in ==> beamformer_dics at 339 filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ==> ft_sourceanalysis at 567 dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Thank you in advance, Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From diezmartini at gmail.com Tue May 27 00:25:39 2014 From: diezmartini at gmail.com (Ana Laura Diez Martini) Date: Tue, 27 May 2014 10:25:39 +1200 Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW In-Reply-To: <222446912.7087267.1401097453356.JavaMail.root@sculptor.zimbra.ru.nl> References: <222446912.7087267.1401097453356.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Thank you Arjen, Diego and Chungki Lee! I tried with the .RAW and it reads the event. The problem is that my triggers have the following format "11,12,13,14,15,21,22...." . Netstation instead of saving them as they are, returns them in this way: say my trigger is 12, I get "DIN4" and "DIN8". or 11 is DIN1 + DIN8 + DIN2. so I had to convert them into my original triggers. After that I can either save the set (I tried this but it didn't work) or export it to bdf. When I open the exported file in EEGlab, it reads the events correctly, but fieldtrip doesn't. Any ideas? Thanks!! On Mon, May 26, 2014 at 9:44 PM, Lozano Soldevilla, D. (Diego) < d.lozanosoldevilla at fcdonders.ru.nl> wrote: > Dear Ana, > > Sorry for my file extension confusion: edf instead of bdf. However, I > don't know a way to read events coded in BDF format exported by NETSTATION. > I encounter this problem in the past but I had no problems with RAW file > format > > Dear Chungki, > > Fieldtrip can read events in *.bdf but from BIOSEMI eeg system but Ana was > refering to a different eeg system that has the same fileformat extension. > > best, > > Diego > > ------------------------------ > > *From: *"Chungki Lee" > *To: *"FieldTrip discussion list" > *Sent: *Monday, 26 May, 2014 11:18:34 AM > *Subject: *Re: [FieldTrip] Cannot read the events of a .BDF file exported > from an EGI .RAW > > > Dear all > > Fieldtrip can read events in BDF format ! > > Hear simple examples > > example #1 > %% > cfg = []; > cfg.dataset = '~~~ '; % your filename with file extension; > cfg.trialdef.eventtype = 'STATUS'; % Status notation maybe Biosemi's > tigger name > cfg.trialdef.eventvalue = 1; % your event value > cfg.trialdef.prestim = 4; % before stimulation (sec), only use > positive value > cfg.trialdef.poststim = 8; % after stimulation (sec) , only use > positive value > cfg = ft_definetrial(cfg); > cfg.method = 'trial'; > data = ft_preprocessing(cfg); > %% > > example #2 > %% > % if you executed these command lines > cfg = []; > cfg.dataset = '~~~ '; % your filename with file extension; > cfg.trialdef.eventtype = '?'; % Status notation maybe Biosemi's > tigger name > cfg = ft_definetrial(cfg); > > % result example #2 > the following events were found in the datafile > event type: 'CM_in_range' with event values: > event type: 'Epoch' with event values: > event type: 'STATUS' with event values: 1 2 3 4 255 <----------- > "this indicate your file configuration for trigger information" > no trials have been defined yet, see FT_DEFINETRIAL for further help > found 255 events > created 0 trials > the call to "ft_definetrial" took 8 seconds > > have fun~!! > > > > 2014-05-26 17:58 GMT+09:00 Diego Lozano Soldevilla < > d.lozanosoldevilla at fcdonders.ru.nl>: > >> Hi Ana, >> >> Fieldtrip does not read events in BDF format. Take a look to our wiki: >> >> http://fieldtrip.fcdonders.nl/getting_started/egi >> >> >> - *EDF+* (.edf) All channels, including PIB channels, are read in >> correctly, including channel labels. However, the events, which are stored >> on the annotation channel, are written in a way by Net Station that is not >> compatible with the edf+ reading implementation in FieldTrip. So, events do >> not come out properly. Also discontinuous epochs are “glued” together as >> one “continuous” data stream. >> >> As Arjen suggested, with *.RAW you shouldn't have any problem. >> >> event = ft_read_event('*.RAW') >> >> If you encounter it, please let us know. >> >> best, >> >> Diego >> >> >> On 26 May 2014 08:59, Arjen Stolk wrote: >> >>> Hi Ana Laura, >>> >>> Have you tried importing the .RAW file directly? That is, by specifying >>> cfg.dataset = 'XXX.raw'? >>> >>> Best regards, >>> Arjen >>> >>> >>> 2014-05-26 2:30 GMT+02:00 Ana Laura Diez Martini >>> : >>> >>>> Hi all! >>>> >>>> This is the .BDF file >>>> of one >>>> of my EEG subjects. For my last experiment I used a Biosemi system and now >>>> I'm using an EGI system which gives me .RAW files. I exported the .RAW file >>>> with EEGlab to .BDF format and I tried using the scripts I use to analise >>>> the data of my previous experiment but I realised that it was not reading >>>> the events: >>>> >>>> cfg = []; >>>> cfg.dataset = ' (location)'; >>>> cfg.trialdef.eventtype = '?'; >>>> definetrial(cfg); >>>> Warning: no trialfun was specified, using trialfun_general >>>> > In definetrial at 79 >>>> evaluating trialfunction 'trialfun_general' >>>> no events were found in the datafile >>>> no trials have been defined yet, see DEFINETRIAL for further help >>>> found 0 events >>>> created 0 trials >>>> >>>> EEGlab does read them. Any idea of what could be wrong? >>>> >>>> Thank you all!! >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > ---------------------------------------------------------------- > Chungki Lee, Ph.D. > Post-doc > Biomedical Research Institute > Korea Institute of Science and Technology > E-mail: chungki at kist.re.kr > Tel:+82-2-958-5636, C.P: +82-10-5223-7309 > ---------------------------------------------------------------- > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > PhD Student > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > NL-6525 EN Nijmegen > The Netherlands > http://www.ru.nl/people/donders/lozano-soldevilla-d/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Tue May 27 07:44:49 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Tue, 27 May 2014 05:44:49 +0000 Subject: [FieldTrip] granger causality on beamformer data Message-ID: <1401169475061.32086@flinders.edu.au> ?Hello fieldtrippers, I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. Or should you do a PCA reduction of some description beforehand. I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. Im open to all suggestions. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ulrich.Pomper at charite.de Tue May 27 15:18:57 2014 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Tue, 27 May 2014 15:18:57 +0200 Subject: [FieldTrip] TF transform, data length + padding Message-ID: Dear community, I have a question regarding time-frequency transformation. The data I want to analyse last from -800 to -200 ms before stimulus onset, I'm using a 400 ms taper. Importantly, want to make sure that no stimulus-evoked activity leaks into my prestim analysis. I first tried to cut the segment down to -1000 to 0 ms and used (zero) padding (see figure attached, top row). This would mean that the taper, at the last samplepoint of interest (-200ms), would include data up to 0ms Suprisingly, I get quite different looking results when using a longer data segment (-1200 to 0 ms) (fig. bottom row) without padding. Can someone explain to me what is going on here, and which approach would be more correct? Either, the padding in the first variant introduces artificial low frequency activity, or the taper in the second variant uses more than 400ms, at least for the low frequencies. Note that the difference between conditions (left coloumn) look almost identical, so whatever happens, it happens to both conditions very similarly. I hope someone can educate me on that matter. Cheers, Ulrich %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% TF transform %% cfg = []; cfg.continuous = 'no'; cfg.channel = 'all'; cfg.output = 'pow'; cfg.method = 'mtmconvol'; cfg.foi = 2:0.5:35; cfg.toi = -1:0.01:0; cfg.taper = 'hanning'; cfg.tapsmofrq = 2; cfg.t_ftimwin = 400 % cfg.pad = 5; ... -------------- next part -------------- A non-text attachment was scrubbed... Name: Bild5.png Type: image/png Size: 128717 bytes Desc: Bild5.png URL: From litvak.vladimir at gmail.com Tue May 27 15:29:33 2014 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Tue, 27 May 2014 14:29:33 +0100 Subject: [FieldTrip] Head model for a phantom Message-ID: Dear all, I need to to do source reconstruction of activity generated with current dipole phantom in CTF MEG. The HPI coils were at the front and sides as they would be for a subject. I was thinking I could just make a single sphere vol with origin set at [0 0 0] as that would coincide with the center of the phantom in this case. The radius shouldn't matter anyway if we are not fitting it to anything, right? Please let me know if you think this is the right approach. Thanks, Vladimir -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcgoiv0 at wfu.edu Tue May 27 16:18:28 2014 From: mcgoiv0 at wfu.edu (McGowin, Inna) Date: Tue, 27 May 2014 10:18:28 -0400 Subject: [FieldTrip] Head model for a phantom In-Reply-To: References: Message-ID: Hello Vladimir, According to the CTF MEG tech support to apply DipFit or SAM to the Current Dipole phantom recordings you need to change (0,0,4) sphere center to (0,0,0) and multiple spheres to a single sphere model for SAM.Thus you are correct. To view the results of SAM any MRI can be used. Cheers, Inna On Tue, May 27, 2014 at 9:29 AM, Vladimir Litvak wrote: > Dear all, > > I need to to do source reconstruction of activity generated with current > dipole phantom in CTF MEG. The HPI coils were at the front and sides as > they would be for a subject. I was thinking I could just make a single > sphere vol with origin set at [0 0 0] as that would coincide with the > center of the phantom in this case. The radius shouldn't matter anyway if > we are not fitting it to anything, right? > > Please let me know if you think this is the right approach. > > Thanks, > > Vladimir > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Tue May 27 18:10:24 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Tue, 27 May 2014 18:10:24 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? Message-ID: Dear all, my name is Katrin Heimann, I am phd student at the University of Parma. New to Fieldtrip. I am doing an EEG analysis, still in the preprocessing phase. It is a within trials design. I would like to compare a baseline period with an experimental condition (visual stimulus). I have a trigger after a fixation cross, then a baseline period (approx 1 sec) , then the period of my stimulus (1 sec- starting with a bottom press (trigger)). As I would like to apply the same baseline correction for both (the fixationcross period) I planned to first define my trials as long trials including the timewindows of baseline and the stimulus period, applying filter and baselinecorrection on those long pieces. However, as I do not wanna do the artifact detection on the whole pieces (but seperately for baseline and stimulus, to avoid that I have to throw away too many trials) I would like to redefine my trials then, cutting out only baseline period and only stimulus period (starting with another trigger (triggervalue=resp).. *Unfortunately I do not understand how I can change the trigger used with ft redefine trial. * Anybody who could give me an example how that is done? Thanks a million Katrin -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Tue May 27 18:25:18 2014 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 27 May 2014 18:25:18 +0200 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: <1401169475061.32086@flinders.edu.au> References: <1401169475061.32086@flinders.edu.au> Message-ID: Hi Tyler, I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 connections, so I hope you have a fast computer. As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website: http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). I hope that helps, if you have specific questions, feel free to ask. Best, Julian On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett < tyler.grummett at flinders.edu.au> wrote: > ​Hello fieldtrippers, > > > I was just wondering whether it would be sensible to do granger > causality on all 1400 virtual channels, as calculated using beamformer. > > > Or should you do a PCA reduction of some description beforehand. > > > I was also wondering how to create regions of interest. Some of my > colleagues think that we should use some kind of spatial ICA technique. > > > Im open to all suggestions. > > > Tyler > > > ************************* > > *Tyler Grummett ( BBSc, BSc(Hons I))* > *PhD Candidate* > *Brain Signals Laboratory* > *Flinders University* > *Rm 5A301* > *Ext 66124* > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcantor at umich.edu Tue May 27 18:58:32 2014 From: mcantor at umich.edu (Max Cantor) Date: Tue, 27 May 2014 12:58:32 -0400 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Hi Katrin, It may help to see your code, but hopefully this will help. It should be as simple as taking your epoched data from ft_definetrial and ft_preprocessing, then creating two configurations for your timewindows and running ft_redefinetrial. For example (from the fieldtrip tutorial, slightly simplified by me for explanatory purposes): *** % find the interesting segments of data cfg = []; % empty configuration cfg.dataset = 'Subject01.ds'; % name of CTF dataset cfg.trialdef.eventtype = 'backpanel trigger'; cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 2; cfg.trialdef.eventvalue = 3; % event value of FIC cfg = ft_definetrial(cfg); % preprocess the data cfg.channel = {'MEG'}; dataFIC = ft_preprocessing(cfg); % define time window cfg = []; cfg.toilim = [-0.5 0]; dataPre = ft_redefinetrial(cfg, dataFIC); cfg.toilim = [0.8 1.3]; dataPost = ft_redefinetrial(cfg, dataFIC); *** So if your code resembles this, you are defining in cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that encompasses both your baseline period and stimulus period, then for cfg.toilim in the ft_redefinetrial section you are setting one to your baseline period and the other to your stimulus period, and outputting them into separate variables. Hopefully this helps. Also, if you haven't done so already, I would strongly recommend you run through the tutorial, as it may help answer questions like this in the future (assuming I've properly identified the issue). Good luck, Max On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann wrote: > Dear all, > > my name is Katrin Heimann, I am phd student at the University of Parma. > New to Fieldtrip. > I am doing an EEG analysis, still in the preprocessing phase. > It is a within trials design. I would like to compare a baseline period > with an experimental condition (visual stimulus). > > I have a trigger after a fixation cross, then a baseline period (approx 1 > sec) , then the period of my stimulus (1 sec- starting with a bottom press > (trigger)). > > As I would like to apply the same baseline correction for both (the > fixationcross period) I planned to first define my trials as long trials > including the timewindows of baseline and the stimulus period, applying > filter and baselinecorrection on those long pieces. However, as I do not > wanna do the artifact detection on the whole pieces (but seperately for > baseline and stimulus, to avoid that I have to throw away too many trials) > I would like to redefine my trials then, cutting out only baseline period > and only stimulus period (starting with another trigger > (triggervalue=resp).. > > *Unfortunately I do not understand how I can change the trigger used with > ft redefine trial. * > > Anybody who could give me an example how that is done? > Thanks a million > Katrin > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Research Assistant Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Tue May 27 20:30:14 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Tue, 27 May 2014 20:30:14 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Dear Max, thanks a lot for your prompt answer. Unfortunately this is not what I am looking for (I found an example like this in the tutorial). I would like to change the trigger for one of the two conditions, let it be now the response of the subject, as this is where the stimulus actually starts... Defining two different timewindows is not enough... Can you also help me with that? Thanks a million! Katrin 2014-05-27 18:58 GMT+02:00 Max Cantor : > Hi Katrin, > > It may help to see your code, but hopefully this will help. It should be > as simple as taking your epoched data from ft_definetrial and > ft_preprocessing, then creating two configurations for your timewindows and > running ft_redefinetrial. > > For example (from the fieldtrip tutorial, slightly simplified by me for > explanatory purposes): > > *** > > % find the interesting segments of data > > cfg = []; > % empty configuration > cfg.dataset = 'Subject01.ds'; > % name of CTF dataset > cfg.trialdef.eventtype = 'backpanel trigger'; > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 2; > cfg.trialdef.eventvalue = 3; > % event value of FIC > cfg = ft_definetrial(cfg); > > % preprocess the data > > cfg.channel = {'MEG'}; > dataFIC = ft_preprocessing(cfg); > > % define time window > > cfg = []; > > cfg.toilim = [-0.5 0]; > dataPre = ft_redefinetrial(cfg, dataFIC); > > cfg.toilim = [0.8 1.3]; > dataPost = ft_redefinetrial(cfg, dataFIC); > > *** > > So if your code resembles this, you are defining in cfg.trialdef.prestim > and cfg.trialdef.poststim a timewindow that encompasses both your baseline > period and stimulus period, then for cfg.toilim in the ft_redefinetrial > section you are setting one to your baseline period and the other to your > stimulus period, and outputting them into separate variables. > > Hopefully this helps. Also, if you haven't done so already, I would > strongly recommend you run through the tutorial, as it may help answer > questions like this in the future (assuming I've properly identified the > issue). > > Good luck, > > Max > > > > > On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann > wrote: > >> Dear all, >> >> my name is Katrin Heimann, I am phd student at the University of Parma. >> New to Fieldtrip. >> I am doing an EEG analysis, still in the preprocessing phase. >> It is a within trials design. I would like to compare a baseline period >> with an experimental condition (visual stimulus). >> >> I have a trigger after a fixation cross, then a baseline period (approx >> 1 sec) , then the period of my stimulus (1 sec- starting with a bottom >> press (trigger)). >> >> As I would like to apply the same baseline correction for both (the >> fixationcross period) I planned to first define my trials as long trials >> including the timewindows of baseline and the stimulus period, applying >> filter and baselinecorrection on those long pieces. However, as I do not >> wanna do the artifact detection on the whole pieces (but seperately for >> baseline and stimulus, to avoid that I have to throw away too many trials) >> I would like to redefine my trials then, cutting out only baseline period >> and only stimulus period (starting with another trigger >> (triggervalue=resp).. >> >> *Unfortunately I do not understand how I can change the trigger used with >> ft redefine trial. * >> >> Anybody who could give me an example how that is done? >> Thanks a million >> Katrin >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Max Cantor > Research Assistant > Computational Neurolinguistics Lab > University of Michigan > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathykousik at gmail.com Tue May 27 20:44:15 2014 From: sarathykousik at gmail.com (kousik sarathy) Date: Tue, 27 May 2014 20:44:15 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Hey Katrin, It seems to me that Max's suggestion would suffice. But you seem to be looking for something else. Could you elaborate a little bit as to what you need? -- Regards, Kousik Sarathy, S On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann wrote: > Dear Max, thanks a lot for your prompt answer. Unfortunately this is not > what I am looking for (I found an example like this in the tutorial). I > would like to change the trigger for one of the two conditions, let it be > now the response of the subject, as this is where the stimulus actually > starts... Defining two different timewindows is not enough... Can you also > help me with that? Thanks a million! Katrin > > > 2014-05-27 18:58 GMT+02:00 Max Cantor : > > Hi Katrin, >> >> It may help to see your code, but hopefully this will help. It should be >> as simple as taking your epoched data from ft_definetrial and >> ft_preprocessing, then creating two configurations for your timewindows and >> running ft_redefinetrial. >> >> For example (from the fieldtrip tutorial, slightly simplified by me for >> explanatory purposes): >> >> *** >> >> % find the interesting segments of data >> >> cfg = []; >> % empty configuration >> cfg.dataset = 'Subject01.ds'; >> % name of CTF dataset >> cfg.trialdef.eventtype = 'backpanel trigger'; >> cfg.trialdef.prestim = 1; >> cfg.trialdef.poststim = 2; >> cfg.trialdef.eventvalue = 3; >> % event value of FIC >> cfg = ft_definetrial(cfg); >> >> % preprocess the data >> >> cfg.channel = {'MEG'}; >> dataFIC = ft_preprocessing(cfg); >> >> % define time window >> >> cfg = []; >> >> cfg.toilim = [-0.5 0]; >> dataPre = ft_redefinetrial(cfg, dataFIC); >> >> cfg.toilim = [0.8 1.3]; >> dataPost = ft_redefinetrial(cfg, dataFIC); >> >> *** >> >> So if your code resembles this, you are defining in cfg.trialdef.prestim >> and cfg.trialdef.poststim a timewindow that encompasses both your baseline >> period and stimulus period, then for cfg.toilim in the ft_redefinetrial >> section you are setting one to your baseline period and the other to your >> stimulus period, and outputting them into separate variables. >> >> Hopefully this helps. Also, if you haven't done so already, I would >> strongly recommend you run through the tutorial, as it may help answer >> questions like this in the future (assuming I've properly identified the >> issue). >> >> Good luck, >> >> Max >> >> >> >> >> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >> katrinheimann at gmail.com> wrote: >> >>> Dear all, >>> >>> my name is Katrin Heimann, I am phd student at the University of Parma. >>> New to Fieldtrip. >>> I am doing an EEG analysis, still in the preprocessing phase. >>> It is a within trials design. I would like to compare a baseline period >>> with an experimental condition (visual stimulus). >>> >>> I have a trigger after a fixation cross, then a baseline period (approx >>> 1 sec) , then the period of my stimulus (1 sec- starting with a bottom >>> press (trigger)). >>> >>> As I would like to apply the same baseline correction for both (the >>> fixationcross period) I planned to first define my trials as long trials >>> including the timewindows of baseline and the stimulus period, applying >>> filter and baselinecorrection on those long pieces. However, as I do not >>> wanna do the artifact detection on the whole pieces (but seperately for >>> baseline and stimulus, to avoid that I have to throw away too many trials) >>> I would like to redefine my trials then, cutting out only baseline period >>> and only stimulus period (starting with another trigger >>> (triggervalue=resp).. >>> >>> *Unfortunately I do not understand how I can change the trigger used >>> with ft redefine trial. * >>> >>> Anybody who could give me an example how that is done? >>> Thanks a million >>> Katrin >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Max Cantor >> Research Assistant >> Computational Neurolinguistics Lab >> University of Michigan >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcantor at umich.edu Tue May 27 21:05:17 2014 From: mcantor at umich.edu (Max Cantor) Date: Tue, 27 May 2014 15:05:17 -0400 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Ya, it would definitely help if we could see your code, but I might have another idea. When you say you have a fixation cross trigger, is this trigger being recorded from your EEG recording equipment in such a way that it can be represented as an event value in cfg.trialdef for ft_definetrial? If so, I think you may be right that it can't be changed through ft_redefinetrial (at least, as far as I can tell, no mention of this is made in the help section of the function). That being said, if you run ft_definetrial separately for both event values that should work. That being said, I may still be slightly confused about what you mean when you say you want to change the trigger. Do you mean you want to create a new trigger for your data off-line? I think it may be possible to create custom triggers off-line through fieldtrip, but it's not something I've tried personally, but if that is what you are trying to do, I could look into it. On Tue, May 27, 2014 at 2:44 PM, kousik sarathy wrote: > Hey Katrin, > > It seems to me that Max's suggestion would suffice. But you seem to be > looking for something else. Could you elaborate a little bit as to what you > need? > > -- > Regards, > Kousik Sarathy, S > > > > On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann wrote: > >> Dear Max, thanks a lot for your prompt answer. Unfortunately this is not >> what I am looking for (I found an example like this in the tutorial). I >> would like to change the trigger for one of the two conditions, let it be >> now the response of the subject, as this is where the stimulus actually >> starts... Defining two different timewindows is not enough... Can you also >> help me with that? Thanks a million! Katrin >> >> >> 2014-05-27 18:58 GMT+02:00 Max Cantor : >> >> Hi Katrin, >>> >>> It may help to see your code, but hopefully this will help. It should be >>> as simple as taking your epoched data from ft_definetrial and >>> ft_preprocessing, then creating two configurations for your timewindows and >>> running ft_redefinetrial. >>> >>> For example (from the fieldtrip tutorial, slightly simplified by me for >>> explanatory purposes): >>> >>> *** >>> >>> % find the interesting segments of data >>> >>> cfg = []; >>> % empty configuration >>> cfg.dataset = 'Subject01.ds'; >>> % name of CTF dataset >>> cfg.trialdef.eventtype = 'backpanel trigger'; >>> cfg.trialdef.prestim = 1; >>> cfg.trialdef.poststim = 2; >>> cfg.trialdef.eventvalue = 3; >>> % event value of FIC >>> cfg = ft_definetrial(cfg); >>> >>> % preprocess the data >>> >>> cfg.channel = {'MEG'}; >>> dataFIC = ft_preprocessing(cfg); >>> >>> % define time window >>> >>> cfg = []; >>> >>> cfg.toilim = [-0.5 0]; >>> dataPre = ft_redefinetrial(cfg, dataFIC); >>> >>> cfg.toilim = [0.8 1.3]; >>> dataPost = ft_redefinetrial(cfg, dataFIC); >>> >>> *** >>> >>> So if your code resembles this, you are defining in cfg.trialdef.prestim >>> and cfg.trialdef.poststim a timewindow that encompasses both your baseline >>> period and stimulus period, then for cfg.toilim in the ft_redefinetrial >>> section you are setting one to your baseline period and the other to your >>> stimulus period, and outputting them into separate variables. >>> >>> Hopefully this helps. Also, if you haven't done so already, I would >>> strongly recommend you run through the tutorial, as it may help answer >>> questions like this in the future (assuming I've properly identified the >>> issue). >>> >>> Good luck, >>> >>> Max >>> >>> >>> >>> >>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >>> katrinheimann at gmail.com> wrote: >>> >>>> Dear all, >>>> >>>> my name is Katrin Heimann, I am phd student at the University of Parma. >>>> New to Fieldtrip. >>>> I am doing an EEG analysis, still in the preprocessing phase. >>>> It is a within trials design. I would like to compare a baseline period >>>> with an experimental condition (visual stimulus). >>>> >>>> I have a trigger after a fixation cross, then a baseline period >>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a >>>> bottom press (trigger)). >>>> >>>> As I would like to apply the same baseline correction for both (the >>>> fixationcross period) I planned to first define my trials as long trials >>>> including the timewindows of baseline and the stimulus period, applying >>>> filter and baselinecorrection on those long pieces. However, as I do not >>>> wanna do the artifact detection on the whole pieces (but seperately for >>>> baseline and stimulus, to avoid that I have to throw away too many trials) >>>> I would like to redefine my trials then, cutting out only baseline period >>>> and only stimulus period (starting with another trigger >>>> (triggervalue=resp).. >>>> >>>> *Unfortunately I do not understand how I can change the trigger used >>>> with ft redefine trial. * >>>> >>>> Anybody who could give me an example how that is done? >>>> Thanks a million >>>> Katrin >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> Max Cantor >>> Research Assistant >>> Computational Neurolinguistics Lab >>> University of Michigan >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Research Assistant Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Tue May 27 23:02:41 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Tue, 27 May 2014 23:02:41 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Hi! Guys, your help is so much appreciated! So I try to be more clear!: So, yeah, Max, you are right! At the end I would like to use two different triggervalues. If I would use twice ft_definetrial then it would look like this: cfg = []; cfg.dataset = '1.raw'; cfg.trialfun = 'ft_trialfun_general'; cfg.trialdef.eventtype = 'trigger'; cfg.trialdef.eventvalue = 'stim'; % the value of the stimulus trigger for the beginning of baseline cfg.trialdef.prestim = 0.5; %the time of the fixation cross cfg.trialdef.poststim = 1.5; %the time of the baseline (plus 0.5 buffer) cfg = ft_redefinetrial(cfg); This baselinedata I could easily baselinecorrect using 100 ms of the fixationcrossperiod: cfg.channel = 'all'; cfg.preproc.demean = 'yes'; cfg.preproc.baselinewindow = [-0.1 0] cfg.preproc.bpfilter = 'yes'; cfg.preproc.bpfreq = [6 32]; The stimulusdata would be defined using a trigger that corresponds to a button press: cfg = []; cfg.dataset = '1.raw'; cfg.trialfun = 'ft_trialfun_general'; cfg.trialdef.eventtype = 'trigger'; cfg.trialdef.eventvalue = 'resp'; % the value of the stimulus trigger for the beginning of baseline cfg.trialdef.prestim = 0.5; % 0.5 sec before button press cfg.trialdef.poststim = 1.5; % 1.5 sec after button press (time that I wanna analyse) cfg = ft_redefinetrial(cfg); However here I have the problem that I cannot correct with the same baseline than before as the buttonpress is not always at the same time so I don't know when the fixationcrossperiod is located... So I thought I could first "cut" bigger pieces and then redefine trials by cutting again (after the preprocessing), then with different eventvalues ... But you say that is not possible? Thanks a lot for your help!!! Katrin 2014-05-27 21:05 GMT+02:00 Max Cantor : > Ya, it would definitely help if we could see your code, but I might have > another idea. > > When you say you have a fixation cross trigger, is this trigger being > recorded from your EEG recording equipment in such a way that it can be > represented as an event value in cfg.trialdef for ft_definetrial? If so, I > think you may be right that it can't be changed through ft_redefinetrial > (at least, as far as I can tell, no mention of this is made in the help > section of the function). That being said, if you run ft_definetrial > separately for both event values that should work. > > That being said, I may still be slightly confused about what you mean when > you say you want to change the trigger. Do you mean you want to create a > new trigger for your data off-line? I think it may be possible to create > custom triggers off-line through fieldtrip, but it's not something I've > tried personally, but if that is what you are trying to do, I could look > into it. > > > On Tue, May 27, 2014 at 2:44 PM, kousik sarathy wrote: > >> Hey Katrin, >> >> It seems to me that Max's suggestion would suffice. But you seem to be >> looking for something else. Could you elaborate a little bit as to what you >> need? >> >> -- >> Regards, >> Kousik Sarathy, S >> >> >> >> On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann > > wrote: >> >>> Dear Max, thanks a lot for your prompt answer. Unfortunately this is not >>> what I am looking for (I found an example like this in the tutorial). I >>> would like to change the trigger for one of the two conditions, let it be >>> now the response of the subject, as this is where the stimulus actually >>> starts... Defining two different timewindows is not enough... Can you also >>> help me with that? Thanks a million! Katrin >>> >>> >>> 2014-05-27 18:58 GMT+02:00 Max Cantor : >>> >>> Hi Katrin, >>>> >>>> It may help to see your code, but hopefully this will help. It should >>>> be as simple as taking your epoched data from ft_definetrial and >>>> ft_preprocessing, then creating two configurations for your timewindows and >>>> running ft_redefinetrial. >>>> >>>> For example (from the fieldtrip tutorial, slightly simplified by me for >>>> explanatory purposes): >>>> >>>> *** >>>> >>>> % find the interesting segments of data >>>> >>>> cfg = []; >>>> % empty configuration >>>> cfg.dataset = 'Subject01.ds'; >>>> % name of CTF dataset >>>> cfg.trialdef.eventtype = 'backpanel trigger'; >>>> cfg.trialdef.prestim = 1; >>>> cfg.trialdef.poststim = 2; >>>> cfg.trialdef.eventvalue = 3; >>>> % event value of FIC >>>> cfg = ft_definetrial(cfg); >>>> >>>> % preprocess the data >>>> >>>> cfg.channel = {'MEG'}; >>>> dataFIC = ft_preprocessing(cfg); >>>> >>>> % define time window >>>> >>>> cfg = []; >>>> >>>> cfg.toilim = [-0.5 0]; >>>> dataPre = ft_redefinetrial(cfg, dataFIC); >>>> >>>> cfg.toilim = [0.8 1.3]; >>>> dataPost = ft_redefinetrial(cfg, dataFIC); >>>> >>>> *** >>>> >>>> So if your code resembles this, you are defining in >>>> cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that >>>> encompasses both your baseline period and stimulus period, then for >>>> cfg.toilim in the ft_redefinetrial section you are setting one to your >>>> baseline period and the other to your stimulus period, and outputting them >>>> into separate variables. >>>> >>>> Hopefully this helps. Also, if you haven't done so already, I would >>>> strongly recommend you run through the tutorial, as it may help answer >>>> questions like this in the future (assuming I've properly identified the >>>> issue). >>>> >>>> Good luck, >>>> >>>> Max >>>> >>>> >>>> >>>> >>>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >>>> katrinheimann at gmail.com> wrote: >>>> >>>>> Dear all, >>>>> >>>>> my name is Katrin Heimann, I am phd student at the University of >>>>> Parma. New to Fieldtrip. >>>>> I am doing an EEG analysis, still in the preprocessing phase. >>>>> It is a within trials design. I would like to compare a baseline >>>>> period with an experimental condition (visual stimulus). >>>>> >>>>> I have a trigger after a fixation cross, then a baseline period >>>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a >>>>> bottom press (trigger)). >>>>> >>>>> As I would like to apply the same baseline correction for both (the >>>>> fixationcross period) I planned to first define my trials as long trials >>>>> including the timewindows of baseline and the stimulus period, applying >>>>> filter and baselinecorrection on those long pieces. However, as I do not >>>>> wanna do the artifact detection on the whole pieces (but seperately for >>>>> baseline and stimulus, to avoid that I have to throw away too many trials) >>>>> I would like to redefine my trials then, cutting out only baseline period >>>>> and only stimulus period (starting with another trigger >>>>> (triggervalue=resp).. >>>>> >>>>> *Unfortunately I do not understand how I can change the trigger used >>>>> with ft redefine trial. * >>>>> >>>>> Anybody who could give me an example how that is done? >>>>> Thanks a million >>>>> Katrin >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>> >>>> >>>> >>>> >>>> -- >>>> Max Cantor >>>> Research Assistant >>>> Computational Neurolinguistics Lab >>>> University of Michigan >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Max Cantor > Research Assistant > Computational Neurolinguistics Lab > University of Michigan > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcantor at umich.edu Tue May 27 23:39:31 2014 From: mcantor at umich.edu (Max Cantor) Date: Tue, 27 May 2014 17:39:31 -0400 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: I'm hesitant to say impossible, but I'm not sure how to do it off-hand. Also, there may be some other complications, now that I think I understand your situation better. If you're trying to cut based on the buttonpresses, which are inconsistent/unreliable, any large number of trials would make it impractical to define/redefine your epoch for each one, especially since this process would need to be customized for each subject. It might be better to keep it in a larger window, or come up with a few general windows to encompass, for instance 'early', 'on target', and 'late' button press windows. For all of the experiments I've worked on in which we've used / are using fieldtrip for our data analysis pipeline, we've never used behavioral responses for anything other than a control (as in, lack of response or incorrect response leads to rejecting the trial), so I don't really know if there is a particular systematic way to incorporate behavioral or floating triggers like what you seem to be looking to do. I might suggest, though keep in mind this is entirely speculative, rather than trying to create a pinpoint window around the response, that instead you use a wide window, and then either by viewing the data, or perhaps using independent component analysis, try to pinpoint for each subject when the button press may have occurred based on some kind of muscle artifact, and then in later timelock/time-frequency/statistical analyses specify that time window. Again, that is just me spitballing, but something post-processing may be a better solution, if the behavioral response is pivotal to the analysis of your experiment and not just for making sure the subject was paying attention / understands the prompt, as in the experiments I've worked on. On Tue, May 27, 2014 at 5:02 PM, KatrinH Heimann wrote: > Hi! Guys, your help is so much appreciated! > So I try to be more clear!: > So, yeah, Max, you are right! At the end I would like to use two different > triggervalues. > > If I would use twice ft_definetrial then it would look like this: > > cfg = []; > > cfg.dataset = '1.raw'; > > cfg.trialfun = 'ft_trialfun_general'; > > cfg.trialdef.eventtype = 'trigger'; > > cfg.trialdef.eventvalue = 'stim'; % the value of the stimulus trigger for > the beginning of baseline > > cfg.trialdef.prestim = 0.5; %the time of the fixation cross > > cfg.trialdef.poststim = 1.5; %the time of the baseline (plus 0.5 buffer) > > cfg = ft_redefinetrial(cfg); > > > This baselinedata I could easily baselinecorrect using 100 ms of the > fixationcrossperiod: > > > cfg.channel = 'all'; > > cfg.preproc.demean = 'yes'; > > cfg.preproc.baselinewindow = [-0.1 0] > > cfg.preproc.bpfilter = 'yes'; > > cfg.preproc.bpfreq = [6 32]; > > > The stimulusdata would be defined using a trigger that corresponds to a > button press: > > > cfg = []; > > cfg.dataset = '1.raw'; > > cfg.trialfun = 'ft_trialfun_general'; > > cfg.trialdef.eventtype = 'trigger'; > > cfg.trialdef.eventvalue = 'resp'; % the value of the stimulus trigger for > the beginning of baseline > > cfg.trialdef.prestim = 0.5; % 0.5 sec before button press > > cfg.trialdef.poststim = 1.5; % 1.5 sec after button press (time that I > wanna analyse) > > cfg = ft_redefinetrial(cfg); > > > However here I have the problem that I cannot correct with the same > baseline than before as the buttonpress is not always at the same time so I > don't know when the fixationcrossperiod is located... > > > So I thought I could first "cut" bigger pieces and then redefine trials by > cutting again (after the preprocessing), then with different eventvalues > ... > > But you say that is not possible? > > > > Thanks a lot for your help!!! > > > Katrin > > > > 2014-05-27 21:05 GMT+02:00 Max Cantor : > > Ya, it would definitely help if we could see your code, but I might have >> another idea. >> >> When you say you have a fixation cross trigger, is this trigger being >> recorded from your EEG recording equipment in such a way that it can be >> represented as an event value in cfg.trialdef for ft_definetrial? If so, I >> think you may be right that it can't be changed through ft_redefinetrial >> (at least, as far as I can tell, no mention of this is made in the help >> section of the function). That being said, if you run ft_definetrial >> separately for both event values that should work. >> >> That being said, I may still be slightly confused about what you mean >> when you say you want to change the trigger. Do you mean you want to create >> a new trigger for your data off-line? I think it may be possible to create >> custom triggers off-line through fieldtrip, but it's not something I've >> tried personally, but if that is what you are trying to do, I could look >> into it. >> >> >> On Tue, May 27, 2014 at 2:44 PM, kousik sarathy wrote: >> >>> Hey Katrin, >>> >>> It seems to me that Max's suggestion would suffice. But you seem to be >>> looking for something else. Could you elaborate a little bit as to what you >>> need? >>> >>> -- >>> Regards, >>> Kousik Sarathy, S >>> >>> >>> >>> On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann < >>> katrinheimann at gmail.com> wrote: >>> >>>> Dear Max, thanks a lot for your prompt answer. Unfortunately this is >>>> not what I am looking for (I found an example like this in the tutorial). I >>>> would like to change the trigger for one of the two conditions, let it be >>>> now the response of the subject, as this is where the stimulus actually >>>> starts... Defining two different timewindows is not enough... Can you also >>>> help me with that? Thanks a million! Katrin >>>> >>>> >>>> 2014-05-27 18:58 GMT+02:00 Max Cantor : >>>> >>>> Hi Katrin, >>>>> >>>>> It may help to see your code, but hopefully this will help. It should >>>>> be as simple as taking your epoched data from ft_definetrial and >>>>> ft_preprocessing, then creating two configurations for your timewindows and >>>>> running ft_redefinetrial. >>>>> >>>>> For example (from the fieldtrip tutorial, slightly simplified by me >>>>> for explanatory purposes): >>>>> >>>>> *** >>>>> >>>>> % find the interesting segments of data >>>>> >>>>> cfg = []; >>>>> % empty configuration >>>>> cfg.dataset = 'Subject01.ds'; >>>>> % name of CTF dataset >>>>> cfg.trialdef.eventtype = 'backpanel trigger'; >>>>> cfg.trialdef.prestim = 1; >>>>> cfg.trialdef.poststim = 2; >>>>> cfg.trialdef.eventvalue = 3; >>>>> % event value of FIC >>>>> cfg = ft_definetrial(cfg); >>>>> >>>>> % preprocess the data >>>>> >>>>> cfg.channel = {'MEG'}; >>>>> dataFIC = ft_preprocessing(cfg); >>>>> >>>>> % define time window >>>>> >>>>> cfg = []; >>>>> >>>>> cfg.toilim = [-0.5 0]; >>>>> dataPre = ft_redefinetrial(cfg, dataFIC); >>>>> >>>>> cfg.toilim = [0.8 1.3]; >>>>> dataPost = ft_redefinetrial(cfg, dataFIC); >>>>> >>>>> *** >>>>> >>>>> So if your code resembles this, you are defining in >>>>> cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that >>>>> encompasses both your baseline period and stimulus period, then for >>>>> cfg.toilim in the ft_redefinetrial section you are setting one to your >>>>> baseline period and the other to your stimulus period, and outputting them >>>>> into separate variables. >>>>> >>>>> Hopefully this helps. Also, if you haven't done so already, I would >>>>> strongly recommend you run through the tutorial, as it may help answer >>>>> questions like this in the future (assuming I've properly identified the >>>>> issue). >>>>> >>>>> Good luck, >>>>> >>>>> Max >>>>> >>>>> >>>>> >>>>> >>>>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >>>>> katrinheimann at gmail.com> wrote: >>>>> >>>>>> Dear all, >>>>>> >>>>>> my name is Katrin Heimann, I am phd student at the University of >>>>>> Parma. New to Fieldtrip. >>>>>> I am doing an EEG analysis, still in the preprocessing phase. >>>>>> It is a within trials design. I would like to compare a baseline >>>>>> period with an experimental condition (visual stimulus). >>>>>> >>>>>> I have a trigger after a fixation cross, then a baseline period >>>>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a >>>>>> bottom press (trigger)). >>>>>> >>>>>> As I would like to apply the same baseline correction for both (the >>>>>> fixationcross period) I planned to first define my trials as long trials >>>>>> including the timewindows of baseline and the stimulus period, applying >>>>>> filter and baselinecorrection on those long pieces. However, as I do not >>>>>> wanna do the artifact detection on the whole pieces (but seperately for >>>>>> baseline and stimulus, to avoid that I have to throw away too many trials) >>>>>> I would like to redefine my trials then, cutting out only baseline period >>>>>> and only stimulus period (starting with another trigger >>>>>> (triggervalue=resp).. >>>>>> >>>>>> *Unfortunately I do not understand how I can change the trigger used >>>>>> with ft redefine trial. * >>>>>> >>>>>> Anybody who could give me an example how that is done? >>>>>> Thanks a million >>>>>> Katrin >>>>>> >>>>>> _______________________________________________ >>>>>> fieldtrip mailing list >>>>>> fieldtrip at donders.ru.nl >>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Max Cantor >>>>> Research Assistant >>>>> Computational Neurolinguistics Lab >>>>> University of Michigan >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>> >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Max Cantor >> Research Assistant >> Computational Neurolinguistics Lab >> University of Michigan >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Research Assistant Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Wed May 28 03:06:47 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Wed, 28 May 2014 01:06:47 +0000 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: References: <1401169475061.32086@flinders.edu.au>, Message-ID: <1401239195251.79033@flinders.edu.au> ?Hey Julian, Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense. Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it? Regards, Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil Sent: Wednesday, 28 May 2014 1:55 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data Hi Tyler, I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 connections, so I hope you have a fast computer. As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website: http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). I hope that helps, if you have specific questions, feel free to ask. Best, Julian On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett > wrote: ?Hello fieldtrippers, I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. Or should you do a PCA reduction of some description beforehand. I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. Im open to all suggestions. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Wed May 28 05:56:58 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Wed, 28 May 2014 03:56:58 +0000 Subject: [FieldTrip] ft_networkanalysis over many subjects, between groups etc Message-ID: <1401249406137.6651@flinders.edu.au> ?Hello fieldtrippers, I was just wondering how to run the ft_networkanalysis function with input of many subjects. Would you run the analysis over each subject individually or can you combine subjects/groups of subjects. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Wed May 28 08:23:42 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Wed, 28 May 2014 06:23:42 +0000 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: <1401239195251.79033@flinders.edu.au> References: <1401169475061.32086@flinders.edu.au>, , <1401239195251.79033@flinders.edu.au> Message-ID: <1401258209971.36904@flinders.edu.au> Hello Julian, I think I got a few steps further into what I am trying to do, except I dont know whether I have done the correct thing or not, could you check it? % interpolate sources mri = ft_read_mri('Subject01.mri'); mri = ft_volumereslice([], mri); % read in atlas from fieldtrip template afni = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/afni/TTatlas+tlrc.HEAD')); % construct grid that lies only in grey matter cfg = []; cfg.mri = mri; cfg.grid.warpmni = 'yes'; cfg.grid = afni; grid = ft_prepare_sourcemodel( cfg); % Source Analysis: without contrasting condition cfg = []; cfg.channel = 'EEG'; cfg.method = 'lcmv'; cfg.grid = grid; cfg.vol = vol; cfg.keepfilter = 'yes'; source = ft_sourceanalysis( cfg, timelock); ? Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Tyler Grummett Sent: Wednesday, 28 May 2014 10:36 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data ?Hey Julian, Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense. Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it? Regards, Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil Sent: Wednesday, 28 May 2014 1:55 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data Hi Tyler, I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 connections, so I hope you have a fast computer. As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website: http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). I hope that helps, if you have specific questions, feel free to ask. Best, Julian On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett > wrote: ?Hello fieldtrippers, I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. Or should you do a PCA reduction of some description beforehand. I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. Im open to all suggestions. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed May 28 09:04:01 2014 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 28 May 2014 09:04:01 +0200 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: <1401239195251.79033@flinders.edu.au> References: <1401169475061.32086@flinders.edu.au>, <1401239195251.79033@flinders.edu.au> Message-ID: <8AB768DB-56A0-4081-9A58-44286BB0F9BB@gmail.com> Hi Tyler, if you follow the link, you get to the "Volumes of Interest" Data base. You can browse through the volumes by then clicking on "Alphabetic index" (http://neuro.imm.dtu.dk/services/jerne/ninf/voi/index-alphabetic.html) If you then click on a volume (e.g. "amygdala" http://neuro.imm.dtu.dk/services/jerne/ninf/voi/amygdala.html) you get to a definition of that VOI. Here, you can now download .hdr and .img files. These are ANALYZE volumes with 1s for all voxels inside a VOI and 0s outside. You can read these with ft_read_mri and normalize to the MNI brain. tl;dr You don't need any functions, just the .hdr and .img files defining the volumes Best, Julian Am 28.05.2014 um 03:06 schrieb Tyler Grummett: > ​Hey Julian, > > Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense. > > Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it? > > Regards, > > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil > Sent: Wednesday, 28 May 2014 1:55 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] granger causality on beamformer data > > Hi Tyler, > > I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 > connections, so I hope you have a fast computer. > > As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website:http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html > > The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. > > In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). > > I hope that helps, if you have specific questions, feel free to ask. > > Best, > > Julian > > > On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett wrote: > ​Hello fieldtrippers, > > I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. > > Or should you do a PCA reduction of some description beforehand. > > I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. > > Im open to all suggestions. > > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Wed May 28 09:05:52 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Wed, 28 May 2014 07:05:52 +0000 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: <1401258209971.36904@flinders.edu.au> References: <1401169475061.32086@flinders.edu.au>, , <1401239195251.79033@flinders.edu.au>,<1401258209971.36904@flinders.edu.au> Message-ID: <1401260739200.88415@flinders.edu.au> I then do the following: % look up which virtual channels correspond to particular areas % of the brain cfg = []; cfg.atlas = afni; cfg.inputcoord = 'mni'; cfg.maskparameter = 'inside'; labels = ft_volumelookup( cfg, source); % how many sources found in grey matter [tmp ind] = sort(labels.count,1,'descend'); sel = find(tmp); for j = 1:length(sel) found_areas{j,1} = [num2str(labels.count(ind(j))) ': ' labels.name{ind(j)}]; end​ However I dont know how to find out what sources are the 'found_areas', after that I dont know how to cluster the source in a particular area. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Tyler Grummett Sent: Wednesday, 28 May 2014 3:53 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data Hello Julian, I think I got a few steps further into what I am trying to do, except I dont know whether I have done the correct thing or not, could you check it? % interpolate sources mri = ft_read_mri('Subject01.mri'); mri = ft_volumereslice([], mri); % read in atlas from fieldtrip template afni = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/afni/TTatlas+tlrc.HEAD')); % construct grid that lies only in grey matter cfg = []; cfg.mri = mri; cfg.grid.warpmni = 'yes'; cfg.grid = afni; grid = ft_prepare_sourcemodel( cfg); % Source Analysis: without contrasting condition cfg = []; cfg.channel = 'EEG'; cfg.method = 'lcmv'; cfg.grid = grid; cfg.vol = vol; cfg.keepfilter = 'yes'; source = ft_sourceanalysis( cfg, timelock); ​ Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Tyler Grummett Sent: Wednesday, 28 May 2014 10:36 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data ​Hey Julian, Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense. Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it? Regards, Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil Sent: Wednesday, 28 May 2014 1:55 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data Hi Tyler, I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 connections, so I hope you have a fast computer. As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website: http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). I hope that helps, if you have specific questions, feel free to ask. Best, Julian On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett > wrote: ​Hello fieldtrippers, I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. Or should you do a PCA reduction of some description beforehand. I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. Im open to all suggestions. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Wed May 28 10:00:49 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Wed, 28 May 2014 08:00:49 +0000 Subject: [FieldTrip] ft_volumelookup source reconstruction (?) Message-ID: <1401264036357.85337@flinders.edu.au> Hello fieldtrippers, I would like to know if it is possible to determine the sources that correspond to a brain region as found by ft_volumelookup. I have used the following code: % interpolate sources mri = ft_read_mri('Subject01.mri'); mri = ft_volumereslice([], mri); % read in atlas from fieldtrip template afni = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/afni/TTatlas+tlrc.HEAD')); % construct grid that lies only in grey matter cfg = []; cfg.mri = mri; cfg.grid.warpmni = 'yes'; cfg.grid = afni; grid = ft_prepare_sourcemodel( cfg);? % Source Analysis: without contrasting condition cfg = []; cfg.channel = 'EEG'; cfg.method = 'lcmv'; cfg.grid = grid; cfg.grid.outside = []; cfg.vol = vol; cfg.keepfilter = 'yes'; source = ft_sourceanalysis( cfg, timelock); source.pos = source.pos( source.inside( :), :); % look up which virtual channels correspond to particular areas % of the brain cfg = []; cfg.atlas = afni; cfg.inputcoord = 'mni'; cfg.maskparameter = 'inside'; labels = ft_volumelookup( cfg, source); It gives me a set of labels, but I dont know what sources are located in the brain regions found. I would like to somehow combine the sources in these brain regions, so that I am left with one source per brain region. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed May 28 10:13:03 2014 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 28 May 2014 10:13:03 +0200 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: <1401260739200.88415@flinders.edu.au> References: <1401169475061.32086@flinders.edu.au>, , <1401239195251.79033@flinders.edu.au>, <1401258209971.36904@flinders.edu.au> <1401260739200.88415@flinders.edu.au> Message-ID: Hi Tyler, sorry if my description was a bit brief, so here's a bit more information. You need: 1) Virtual Electrodes (you have your 1400 electrodes, so I assume you got that far) and the .pos field with the XYZ-coordinates of the virtual electrodes. 2) A grid with a grid point for each voxel of the MNI brain (That's what you do using ft_prepare_sourcemodel) 3) A "inside" definition for your VOI (That's what you do with ft_volumelookup). Now, given that your steps 1-3 all are in the same coordinate system, you can simply use pythagoras (s = sqrt((X2-X1)^2 + (Y2-Y1)^2 + (Z2-Z1)^2) to find the minimum distance between each virtual channels of step 1 and all grid points of step 2. From the min (find the minimum distance) step, you can get the index of closest virtual channel to each grid point. You then apply this index to the output of ft_volumelookup and you have the virtual electrodes inside your ROI. Best, Julian Am 28.05.2014 um 09:05 schrieb Tyler Grummett: > I then do the following: > > % look up which virtual channels correspond to particular areas > % of the brain > cfg = []; > cfg.atlas = afni; > cfg.inputcoord = 'mni'; > cfg.maskparameter = 'inside'; > labels = ft_volumelookup( cfg, source); > > % how many sources found in grey matter > [tmp ind] = sort(labels.count,1,'descend'); > sel = find(tmp); > for j = 1:length(sel) > found_areas{j,1} = [num2str(labels.count(ind(j))) ': ' labels.name{ind(j)}]; > end​ > > However I dont know how to find out what sources are the 'found_areas', after that I dont know how to cluster the source in a particular area. > > Tyler > > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > From: fieldtrip-bounces at science.ru.nl on behalf of Tyler Grummett > Sent: Wednesday, 28 May 2014 3:53 PM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] granger causality on beamformer data > > Hello Julian, > > I think I got a few steps further into what I am trying to do, except I dont know whether I have done the correct thing or not, could you check it? > > % interpolate sources > mri = ft_read_mri('Subject01.mri'); > mri = ft_volumereslice([], mri); > > % read in atlas from fieldtrip template > afni = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/afni/TTatlas+tlrc.HEAD')); > > % construct grid that lies only in grey matter > cfg = []; > cfg.mri = mri; > cfg.grid.warpmni = 'yes'; > cfg.grid = afni; > grid = ft_prepare_sourcemodel( cfg); > > % Source Analysis: without contrasting condition > cfg = []; > cfg.channel = 'EEG'; > cfg.method = 'lcmv'; > cfg.grid = grid; > cfg.vol = vol; > cfg.keepfilter = 'yes'; > source = ft_sourceanalysis( cfg, timelock); > ​ > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > From: fieldtrip-bounces at science.ru.nl on behalf of Tyler Grummett > Sent: Wednesday, 28 May 2014 10:36 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] granger causality on beamformer data > > ​Hey Julian, > > Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense. > > Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it? > > Regards, > > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil > Sent: Wednesday, 28 May 2014 1:55 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] granger causality on beamformer data > > Hi Tyler, > > I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 > connections, so I hope you have a fast computer. > > As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website:http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html > > The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. > > In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). > > I hope that helps, if you have specific questions, feel free to ask. > > Best, > > Julian > > > On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett wrote: > ​Hello fieldtrippers, > > I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. > > Or should you do a PCA reduction of some description beforehand. > > I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. > > Im open to all suggestions. > > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From elmeri.syrjanen at gmail.com Wed May 28 12:04:33 2014 From: elmeri.syrjanen at gmail.com (=?UTF-8?Q?Elmeri_Syrj=C3=A4nen?=) Date: Wed, 28 May 2014 12:04:33 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Dear Katrin, I have recently done exactly what you are asking for unfortunately I don't have access to my code right now but basically you can do it manually if you familiarize yourself with the structure how FieldTrip stores your data. The idea is to have two trial functions, one where you define only the baseline, and one without a baseline, I created a variable cfg.trigoffset where i set the time that you wan't to epoch before the trigger and then the rest of the trialfun is as normal. I then manually in Matlab join the baseline and button press preceding structures to a new data structure. Make sure that you remove the last column in data.time and data.trial in the baseline epoch. You may also wan't to create your own data.sampleinfo with "fake" sample points (1 641, 642 1282..) because some functions (ft_channelrepair) will use sampleinfo instead of fsample to calculate your sample rate which will give you head aches down the road. Best Regards Elmeri Syrjänen On Tue, May 27, 2014 at 11:39 PM, Max Cantor wrote: > I'm hesitant to say impossible, but I'm not sure how to do it off-hand. > Also, there may be some other complications, now that I think I understand > your situation better. > > If you're trying to cut based on the buttonpresses, which are > inconsistent/unreliable, any large number of trials would make it > impractical to define/redefine your epoch for each one, especially since > this process would need to be customized for each subject. It might be > better to keep it in a larger window, or come up with a few general windows > to encompass, for instance 'early', 'on target', and 'late' button press > windows. > > For all of the experiments I've worked on in which we've used / are using > fieldtrip for our data analysis pipeline, we've never used behavioral > responses for anything other than a control (as in, lack of response or > incorrect response leads to rejecting the trial), so I don't really know if > there is a particular systematic way to incorporate behavioral or floating > triggers like what you seem to be looking to do. > > I might suggest, though keep in mind this is entirely speculative, rather > than trying to create a pinpoint window around the response, that instead > you use a wide window, and then either by viewing the data, or perhaps > using independent component analysis, try to pinpoint for each subject when > the button press may have occurred based on some kind of muscle artifact, > and then in later timelock/time-frequency/statistical analyses specify that > time window. Again, that is just me spitballing, but something > post-processing may be a better solution, if the behavioral response is > pivotal to the analysis of your experiment and not just for making sure the > subject was paying attention / understands the prompt, as in the > experiments I've worked on. > > > On Tue, May 27, 2014 at 5:02 PM, KatrinH Heimann wrote: > >> Hi! Guys, your help is so much appreciated! >> So I try to be more clear!: >> So, yeah, Max, you are right! At the end I would like to use two >> different triggervalues. >> >> If I would use twice ft_definetrial then it would look like this: >> >> cfg = []; >> >> cfg.dataset = '1.raw'; >> >> cfg.trialfun = 'ft_trialfun_general'; >> >> cfg.trialdef.eventtype = 'trigger'; >> >> cfg.trialdef.eventvalue = 'stim'; % the value of the stimulus trigger for >> the beginning of baseline >> >> cfg.trialdef.prestim = 0.5; %the time of the fixation cross >> >> cfg.trialdef.poststim = 1.5; %the time of the baseline (plus 0.5 >> buffer) >> >> cfg = ft_redefinetrial(cfg); >> >> >> This baselinedata I could easily baselinecorrect using 100 ms of the >> fixationcrossperiod: >> >> >> cfg.channel = 'all'; >> >> cfg.preproc.demean = 'yes'; >> >> cfg.preproc.baselinewindow = [-0.1 0] >> >> cfg.preproc.bpfilter = 'yes'; >> >> cfg.preproc.bpfreq = [6 32]; >> >> >> The stimulusdata would be defined using a trigger that corresponds to a >> button press: >> >> >> cfg = []; >> >> cfg.dataset = '1.raw'; >> >> cfg.trialfun = 'ft_trialfun_general'; >> >> cfg.trialdef.eventtype = 'trigger'; >> >> cfg.trialdef.eventvalue = 'resp'; % the value of the stimulus trigger for >> the beginning of baseline >> >> cfg.trialdef.prestim = 0.5; % 0.5 sec before button press >> >> cfg.trialdef.poststim = 1.5; % 1.5 sec after button press (time that I >> wanna analyse) >> >> cfg = ft_redefinetrial(cfg); >> >> >> However here I have the problem that I cannot correct with the same >> baseline than before as the buttonpress is not always at the same time so I >> don't know when the fixationcrossperiod is located... >> >> >> So I thought I could first "cut" bigger pieces and then redefine trials >> by cutting again (after the preprocessing), then with different eventvalues >> ... >> >> But you say that is not possible? >> >> >> >> Thanks a lot for your help!!! >> >> >> Katrin >> >> >> >> 2014-05-27 21:05 GMT+02:00 Max Cantor : >> >> Ya, it would definitely help if we could see your code, but I might have >>> another idea. >>> >>> When you say you have a fixation cross trigger, is this trigger being >>> recorded from your EEG recording equipment in such a way that it can be >>> represented as an event value in cfg.trialdef for ft_definetrial? If so, I >>> think you may be right that it can't be changed through ft_redefinetrial >>> (at least, as far as I can tell, no mention of this is made in the help >>> section of the function). That being said, if you run ft_definetrial >>> separately for both event values that should work. >>> >>> That being said, I may still be slightly confused about what you mean >>> when you say you want to change the trigger. Do you mean you want to create >>> a new trigger for your data off-line? I think it may be possible to create >>> custom triggers off-line through fieldtrip, but it's not something I've >>> tried personally, but if that is what you are trying to do, I could look >>> into it. >>> >>> >>> On Tue, May 27, 2014 at 2:44 PM, kousik sarathy >> > wrote: >>> >>>> Hey Katrin, >>>> >>>> It seems to me that Max's suggestion would suffice. But you seem to be >>>> looking for something else. Could you elaborate a little bit as to what you >>>> need? >>>> >>>> -- >>>> Regards, >>>> Kousik Sarathy, S >>>> >>>> >>>> >>>> On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann < >>>> katrinheimann at gmail.com> wrote: >>>> >>>>> Dear Max, thanks a lot for your prompt answer. Unfortunately this is >>>>> not what I am looking for (I found an example like this in the tutorial). I >>>>> would like to change the trigger for one of the two conditions, let it be >>>>> now the response of the subject, as this is where the stimulus actually >>>>> starts... Defining two different timewindows is not enough... Can you also >>>>> help me with that? Thanks a million! Katrin >>>>> >>>>> >>>>> 2014-05-27 18:58 GMT+02:00 Max Cantor : >>>>> >>>>> Hi Katrin, >>>>>> >>>>>> It may help to see your code, but hopefully this will help. It should >>>>>> be as simple as taking your epoched data from ft_definetrial and >>>>>> ft_preprocessing, then creating two configurations for your timewindows and >>>>>> running ft_redefinetrial. >>>>>> >>>>>> For example (from the fieldtrip tutorial, slightly simplified by me >>>>>> for explanatory purposes): >>>>>> >>>>>> *** >>>>>> >>>>>> % find the interesting segments of data >>>>>> >>>>>> cfg = []; >>>>>> % empty configuration >>>>>> cfg.dataset = 'Subject01.ds'; >>>>>> % name of CTF dataset >>>>>> cfg.trialdef.eventtype = 'backpanel trigger'; >>>>>> cfg.trialdef.prestim = 1; >>>>>> cfg.trialdef.poststim = 2; >>>>>> cfg.trialdef.eventvalue = 3; >>>>>> % event value of FIC >>>>>> cfg = ft_definetrial(cfg); >>>>>> >>>>>> % preprocess the data >>>>>> >>>>>> cfg.channel = {'MEG'}; >>>>>> dataFIC = ft_preprocessing(cfg); >>>>>> >>>>>> % define time window >>>>>> >>>>>> cfg = []; >>>>>> >>>>>> cfg.toilim = [-0.5 0]; >>>>>> dataPre = ft_redefinetrial(cfg, dataFIC); >>>>>> >>>>>> cfg.toilim = [0.8 1.3]; >>>>>> dataPost = ft_redefinetrial(cfg, dataFIC); >>>>>> >>>>>> *** >>>>>> >>>>>> So if your code resembles this, you are defining in >>>>>> cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that >>>>>> encompasses both your baseline period and stimulus period, then for >>>>>> cfg.toilim in the ft_redefinetrial section you are setting one to your >>>>>> baseline period and the other to your stimulus period, and outputting them >>>>>> into separate variables. >>>>>> >>>>>> Hopefully this helps. Also, if you haven't done so already, I would >>>>>> strongly recommend you run through the tutorial, as it may help answer >>>>>> questions like this in the future (assuming I've properly identified the >>>>>> issue). >>>>>> >>>>>> Good luck, >>>>>> >>>>>> Max >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >>>>>> katrinheimann at gmail.com> wrote: >>>>>> >>>>>>> Dear all, >>>>>>> >>>>>>> my name is Katrin Heimann, I am phd student at the University of >>>>>>> Parma. New to Fieldtrip. >>>>>>> I am doing an EEG analysis, still in the preprocessing phase. >>>>>>> It is a within trials design. I would like to compare a baseline >>>>>>> period with an experimental condition (visual stimulus). >>>>>>> >>>>>>> I have a trigger after a fixation cross, then a baseline period >>>>>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a >>>>>>> bottom press (trigger)). >>>>>>> >>>>>>> As I would like to apply the same baseline correction for both (the >>>>>>> fixationcross period) I planned to first define my trials as long trials >>>>>>> including the timewindows of baseline and the stimulus period, applying >>>>>>> filter and baselinecorrection on those long pieces. However, as I do not >>>>>>> wanna do the artifact detection on the whole pieces (but seperately for >>>>>>> baseline and stimulus, to avoid that I have to throw away too many trials) >>>>>>> I would like to redefine my trials then, cutting out only baseline period >>>>>>> and only stimulus period (starting with another trigger >>>>>>> (triggervalue=resp).. >>>>>>> >>>>>>> *Unfortunately I do not understand how I can change the trigger used >>>>>>> with ft redefine trial. * >>>>>>> >>>>>>> Anybody who could give me an example how that is done? >>>>>>> Thanks a million >>>>>>> Katrin >>>>>>> >>>>>>> _______________________________________________ >>>>>>> fieldtrip mailing list >>>>>>> fieldtrip at donders.ru.nl >>>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Max Cantor >>>>>> Research Assistant >>>>>> Computational Neurolinguistics Lab >>>>>> University of Michigan >>>>>> >>>>>> _______________________________________________ >>>>>> fieldtrip mailing list >>>>>> fieldtrip at donders.ru.nl >>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>> >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> Max Cantor >>> Research Assistant >>> Computational Neurolinguistics Lab >>> University of Michigan >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Max Cantor > Research Assistant > Computational Neurolinguistics Lab > University of Michigan > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Wed May 28 12:09:00 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Wed, 28 May 2014 12:09:00 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Dear Max, dear Elmeri! Thanks a million, that was really really helpful! :) Katrin 2014-05-28 12:04 GMT+02:00 Elmeri Syrjänen : > Dear Katrin, > > I have recently done exactly what you are asking for unfortunately I don't > have access to my code right now but basically you can do it manually if > you familiarize yourself with the structure how FieldTrip stores your data. > The idea is to have two trial functions, one where you define only the > baseline, and one without a baseline, I created a variable cfg.trigoffset > where i set the time that you wan't to epoch before the trigger and then > the rest of the trialfun is as normal. > > I then manually in Matlab join the baseline and button press preceding > structures to a new data structure. Make sure that you remove the last > column in data.time and data.trial in the baseline epoch. You may also > wan't to create your own data.sampleinfo with "fake" sample points (1 641, > 642 1282..) because some functions (ft_channelrepair) will use sampleinfo > instead of fsample to calculate your sample rate which will give you head > aches down the road. > > Best Regards > Elmeri Syrjänen > > > On Tue, May 27, 2014 at 11:39 PM, Max Cantor wrote: > >> I'm hesitant to say impossible, but I'm not sure how to do it off-hand. >> Also, there may be some other complications, now that I think I understand >> your situation better. >> >> If you're trying to cut based on the buttonpresses, which are >> inconsistent/unreliable, any large number of trials would make it >> impractical to define/redefine your epoch for each one, especially since >> this process would need to be customized for each subject. It might be >> better to keep it in a larger window, or come up with a few general windows >> to encompass, for instance 'early', 'on target', and 'late' button press >> windows. >> >> For all of the experiments I've worked on in which we've used / are using >> fieldtrip for our data analysis pipeline, we've never used behavioral >> responses for anything other than a control (as in, lack of response or >> incorrect response leads to rejecting the trial), so I don't really know if >> there is a particular systematic way to incorporate behavioral or floating >> triggers like what you seem to be looking to do. >> >> I might suggest, though keep in mind this is entirely speculative, rather >> than trying to create a pinpoint window around the response, that instead >> you use a wide window, and then either by viewing the data, or perhaps >> using independent component analysis, try to pinpoint for each subject when >> the button press may have occurred based on some kind of muscle artifact, >> and then in later timelock/time-frequency/statistical analyses specify that >> time window. Again, that is just me spitballing, but something >> post-processing may be a better solution, if the behavioral response is >> pivotal to the analysis of your experiment and not just for making sure the >> subject was paying attention / understands the prompt, as in the >> experiments I've worked on. >> >> >> On Tue, May 27, 2014 at 5:02 PM, KatrinH Heimann > > wrote: >> >>> Hi! Guys, your help is so much appreciated! >>> So I try to be more clear!: >>> So, yeah, Max, you are right! At the end I would like to use two >>> different triggervalues. >>> >>> If I would use twice ft_definetrial then it would look like this: >>> >>> cfg = []; >>> >>> cfg.dataset = '1.raw'; >>> >>> cfg.trialfun = 'ft_trialfun_general'; >>> >>> cfg.trialdef.eventtype = 'trigger'; >>> >>> cfg.trialdef.eventvalue = 'stim'; % the value of the stimulus trigger for >>> the beginning of baseline >>> >>> cfg.trialdef.prestim = 0.5; %the time of the fixation cross >>> >>> cfg.trialdef.poststim = 1.5; %the time of the baseline (plus 0.5 >>> buffer) >>> >>> cfg = ft_redefinetrial(cfg); >>> >>> >>> This baselinedata I could easily baselinecorrect using 100 ms of the >>> fixationcrossperiod: >>> >>> >>> cfg.channel = 'all'; >>> >>> cfg.preproc.demean = 'yes'; >>> >>> cfg.preproc.baselinewindow = [-0.1 0] >>> >>> cfg.preproc.bpfilter = 'yes'; >>> >>> cfg.preproc.bpfreq = [6 32]; >>> >>> >>> The stimulusdata would be defined using a trigger that corresponds to a >>> button press: >>> >>> >>> cfg = []; >>> >>> cfg.dataset = '1.raw'; >>> >>> cfg.trialfun = 'ft_trialfun_general'; >>> >>> cfg.trialdef.eventtype = 'trigger'; >>> >>> cfg.trialdef.eventvalue = 'resp'; % the value of the stimulus trigger for >>> the beginning of baseline >>> >>> cfg.trialdef.prestim = 0.5; % 0.5 sec before button press >>> >>> cfg.trialdef.poststim = 1.5; % 1.5 sec after button press (time that >>> I wanna analyse) >>> >>> cfg = ft_redefinetrial(cfg); >>> >>> >>> However here I have the problem that I cannot correct with the same >>> baseline than before as the buttonpress is not always at the same time so I >>> don't know when the fixationcrossperiod is located... >>> >>> >>> So I thought I could first "cut" bigger pieces and then redefine trials >>> by cutting again (after the preprocessing), then with different eventvalues >>> ... >>> >>> But you say that is not possible? >>> >>> >>> >>> Thanks a lot for your help!!! >>> >>> >>> Katrin >>> >>> >>> >>> 2014-05-27 21:05 GMT+02:00 Max Cantor : >>> >>> Ya, it would definitely help if we could see your code, but I might have >>>> another idea. >>>> >>>> When you say you have a fixation cross trigger, is this trigger being >>>> recorded from your EEG recording equipment in such a way that it can be >>>> represented as an event value in cfg.trialdef for ft_definetrial? If so, I >>>> think you may be right that it can't be changed through ft_redefinetrial >>>> (at least, as far as I can tell, no mention of this is made in the help >>>> section of the function). That being said, if you run ft_definetrial >>>> separately for both event values that should work. >>>> >>>> That being said, I may still be slightly confused about what you mean >>>> when you say you want to change the trigger. Do you mean you want to create >>>> a new trigger for your data off-line? I think it may be possible to create >>>> custom triggers off-line through fieldtrip, but it's not something I've >>>> tried personally, but if that is what you are trying to do, I could look >>>> into it. >>>> >>>> >>>> On Tue, May 27, 2014 at 2:44 PM, kousik sarathy < >>>> sarathykousik at gmail.com> wrote: >>>> >>>>> Hey Katrin, >>>>> >>>>> It seems to me that Max's suggestion would suffice. But you seem to be >>>>> looking for something else. Could you elaborate a little bit as to what you >>>>> need? >>>>> >>>>> -- >>>>> Regards, >>>>> Kousik Sarathy, S >>>>> >>>>> >>>>> >>>>> On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann < >>>>> katrinheimann at gmail.com> wrote: >>>>> >>>>>> Dear Max, thanks a lot for your prompt answer. Unfortunately this is >>>>>> not what I am looking for (I found an example like this in the tutorial). I >>>>>> would like to change the trigger for one of the two conditions, let it be >>>>>> now the response of the subject, as this is where the stimulus actually >>>>>> starts... Defining two different timewindows is not enough... Can you also >>>>>> help me with that? Thanks a million! Katrin >>>>>> >>>>>> >>>>>> 2014-05-27 18:58 GMT+02:00 Max Cantor : >>>>>> >>>>>> Hi Katrin, >>>>>>> >>>>>>> It may help to see your code, but hopefully this will help. It >>>>>>> should be as simple as taking your epoched data from ft_definetrial and >>>>>>> ft_preprocessing, then creating two configurations for your timewindows and >>>>>>> running ft_redefinetrial. >>>>>>> >>>>>>> For example (from the fieldtrip tutorial, slightly simplified by me >>>>>>> for explanatory purposes): >>>>>>> >>>>>>> *** >>>>>>> >>>>>>> % find the interesting segments of data >>>>>>> >>>>>>> cfg = []; >>>>>>> % empty configuration >>>>>>> cfg.dataset = 'Subject01.ds'; >>>>>>> % name of CTF dataset >>>>>>> cfg.trialdef.eventtype = 'backpanel trigger'; >>>>>>> cfg.trialdef.prestim = 1; >>>>>>> cfg.trialdef.poststim = 2; >>>>>>> cfg.trialdef.eventvalue = 3; >>>>>>> % event value of FIC >>>>>>> cfg = ft_definetrial(cfg); >>>>>>> >>>>>>> % preprocess the data >>>>>>> >>>>>>> cfg.channel = {'MEG'}; >>>>>>> dataFIC = ft_preprocessing(cfg); >>>>>>> >>>>>>> % define time window >>>>>>> >>>>>>> cfg = []; >>>>>>> >>>>>>> cfg.toilim = [-0.5 0]; >>>>>>> dataPre = ft_redefinetrial(cfg, dataFIC); >>>>>>> >>>>>>> cfg.toilim = [0.8 1.3]; >>>>>>> dataPost = ft_redefinetrial(cfg, dataFIC); >>>>>>> >>>>>>> *** >>>>>>> >>>>>>> So if your code resembles this, you are defining in >>>>>>> cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that >>>>>>> encompasses both your baseline period and stimulus period, then for >>>>>>> cfg.toilim in the ft_redefinetrial section you are setting one to your >>>>>>> baseline period and the other to your stimulus period, and outputting them >>>>>>> into separate variables. >>>>>>> >>>>>>> Hopefully this helps. Also, if you haven't done so already, I would >>>>>>> strongly recommend you run through the tutorial, as it may help answer >>>>>>> questions like this in the future (assuming I've properly identified the >>>>>>> issue). >>>>>>> >>>>>>> Good luck, >>>>>>> >>>>>>> Max >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >>>>>>> katrinheimann at gmail.com> wrote: >>>>>>> >>>>>>>> Dear all, >>>>>>>> >>>>>>>> my name is Katrin Heimann, I am phd student at the University of >>>>>>>> Parma. New to Fieldtrip. >>>>>>>> I am doing an EEG analysis, still in the preprocessing phase. >>>>>>>> It is a within trials design. I would like to compare a baseline >>>>>>>> period with an experimental condition (visual stimulus). >>>>>>>> >>>>>>>> I have a trigger after a fixation cross, then a baseline period >>>>>>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a >>>>>>>> bottom press (trigger)). >>>>>>>> >>>>>>>> As I would like to apply the same baseline correction for both >>>>>>>> (the fixationcross period) I planned to first define my trials as long >>>>>>>> trials including the timewindows of baseline and the stimulus period, >>>>>>>> applying filter and baselinecorrection on those long pieces. However, as I >>>>>>>> do not wanna do the artifact detection on the whole pieces (but seperately >>>>>>>> for baseline and stimulus, to avoid that I have to throw away too many >>>>>>>> trials) I would like to redefine my trials then, cutting out only baseline >>>>>>>> period and only stimulus period (starting with another trigger >>>>>>>> (triggervalue=resp).. >>>>>>>> >>>>>>>> *Unfortunately I do not understand how I can change the trigger >>>>>>>> used with ft redefine trial. * >>>>>>>> >>>>>>>> Anybody who could give me an example how that is done? >>>>>>>> Thanks a million >>>>>>>> Katrin >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> fieldtrip mailing list >>>>>>>> fieldtrip at donders.ru.nl >>>>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Max Cantor >>>>>>> Research Assistant >>>>>>> Computational Neurolinguistics Lab >>>>>>> University of Michigan >>>>>>> >>>>>>> _______________________________________________ >>>>>>> fieldtrip mailing list >>>>>>> fieldtrip at donders.ru.nl >>>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> fieldtrip mailing list >>>>>> fieldtrip at donders.ru.nl >>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>> >>>> >>>> >>>> >>>> -- >>>> Max Cantor >>>> Research Assistant >>>> Computational Neurolinguistics Lab >>>> University of Michigan >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Max Cantor >> Research Assistant >> Computational Neurolinguistics Lab >> University of Michigan >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed May 28 12:36:15 2014 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 28 May 2014 12:36:15 +0200 Subject: [FieldTrip] TF transform, data length + padding In-Reply-To: References: Message-ID: Hi Ulrich, one possible explanation for this could be the subtraction of the mean when calling ft_freqanalysis. If you don't specify cfg.polyremoval explicitly, the mean is removed. Of course, changing the time-dimension will change the mean and therefore result in a different value used in the ft_preproc_polyremoval - step. I tried this with a dataset, setting cfg.polyremoval to -1, thereby avoiding the demean results in virtually identical time-freq results for a short (800ms) or long (1000ms) interval. However, setting cfg.polyremoval to 0 (the default) will change the output. Also, setting the padding to 5, as you did in your code, will increase the frequency resolution which again might influence the way the low frequencies contribute to your output. If someone has a more in-depth explanation or if I got this completely wrong, please correct me! Best, Julian ******************** *Dr. Julian Keil* AG Multisensorische Integration Psychiatrische Universitätsklinik der Charité im St. Hedwig-Krankenhaus Große Hamburger Straße 5-11, Raum E 307 10115 Berlin Telefon: +49-30-2311-1879 Fax: +49-30-2311-2209 http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration On Tue, May 27, 2014 at 3:18 PM, Pomper, Ulrich wrote: > Dear community, > I have a question regarding time-frequency transformation. > The data I want to analyse last from -800 to -200 ms before stimulus > onset, I'm using a 400 ms taper. > Importantly, want to make sure that no stimulus-evoked activity leaks into > my prestim analysis. > > I first tried to cut the segment down to -1000 to 0 ms and used (zero) > padding (see figure attached, top row). This would mean that the taper, at > the last samplepoint of interest (-200ms), would include data up to 0ms > Suprisingly, I get quite different looking results when using a longer > data segment (-1200 to 0 ms) (fig. bottom row) without padding. > > Can someone explain to me what is going on here, and which approach would > be more correct? > Either, the padding in the first variant introduces artificial low > frequency activity, or the taper in the second variant uses more than > 400ms, at least for the low frequencies. > Note that the difference between conditions (left coloumn) look almost > identical, so whatever happens, it happens to both conditions very > similarly. > > I hope someone can educate me on that matter. > Cheers, Ulrich > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %% TF transform %% > > cfg = []; > cfg.continuous = 'no'; > cfg.channel = 'all'; > cfg.output = 'pow'; > cfg.method = 'mtmconvol'; > cfg.foi = 2:0.5:35; > cfg.toi = -1:0.01:0; > cfg.taper = 'hanning'; > cfg.tapsmofrq = 2; > cfg.t_ftimwin = 400 > % cfg.pad = 5; > ... > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: poly_vs_nopoly.png Type: image/png Size: 32330 bytes Desc: not available URL: From Ulrich.Pomper at charite.de Wed May 28 12:50:31 2014 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Wed, 28 May 2014 12:50:31 +0200 Subject: [FieldTrip] TF transform, data length + padding In-Reply-To: References: , Message-ID: Hey Julian, Thanks a lot for your help! Both explanations seem quite plausible. I think I will try to avoid the padding and stick with the longer data segments. Cheers, Ulrich ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] On Behalf Of Julian Keil [julian.keil at gmail.com] Sent: Wednesday, May 28, 2014 12:36 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] TF transform, data length + padding Hi Ulrich, one possible explanation for this could be the subtraction of the mean when calling ft_freqanalysis. If you don't specify cfg.polyremoval explicitly, the mean is removed. Of course, changing the time-dimension will change the mean and therefore result in a different value used in the ft_preproc_polyremoval - step. I tried this with a dataset, setting cfg.polyremoval to -1, thereby avoiding the demean results in virtually identical time-freq results for a short (800ms) or long (1000ms) interval. However, setting cfg.polyremoval to 0 (the default) will change the output. Also, setting the padding to 5, as you did in your code, will increase the frequency resolution which again might influence the way the low frequencies contribute to your output. If someone has a more in-depth explanation or if I got this completely wrong, please correct me! Best, Julian ******************** Dr. Julian Keil AG Multisensorische Integration Psychiatrische Universitätsklinik der Charité im St. Hedwig-Krankenhaus Große Hamburger Straße 5-11, Raum E 307 10115 Berlin Telefon: +49-30-2311-1879 Fax: +49-30-2311-2209 http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration On Tue, May 27, 2014 at 3:18 PM, Pomper, Ulrich > wrote: Dear community, I have a question regarding time-frequency transformation. The data I want to analyse last from -800 to -200 ms before stimulus onset, I'm using a 400 ms taper. Importantly, want to make sure that no stimulus-evoked activity leaks into my prestim analysis. I first tried to cut the segment down to -1000 to 0 ms and used (zero) padding (see figure attached, top row). This would mean that the taper, at the last samplepoint of interest (-200ms), would include data up to 0ms Suprisingly, I get quite different looking results when using a longer data segment (-1200 to 0 ms) (fig. bottom row) without padding. Can someone explain to me what is going on here, and which approach would be more correct? Either, the padding in the first variant introduces artificial low frequency activity, or the taper in the second variant uses more than 400ms, at least for the low frequencies. Note that the difference between conditions (left coloumn) look almost identical, so whatever happens, it happens to both conditions very similarly. I hope someone can educate me on that matter. Cheers, Ulrich %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% TF transform %% cfg = []; cfg.continuous = 'no'; cfg.channel = 'all'; cfg.output = 'pow'; cfg.method = 'mtmconvol'; cfg.foi = 2:0.5:35; cfg.toi = -1:0.01:0; cfg.taper = 'hanning'; cfg.tapsmofrq = 2; cfg.t_ftimwin = 400 % cfg.pad = 5; ... _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From katrinheimann at gmail.com Wed May 28 12:59:38 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Wed, 28 May 2014 12:59:38 +0200 Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? Message-ID: Dear all, another question: Is it possible to visualize the Activity power spectrum of the single components after an ICA by using ft_databrowser (or something else). I like this feature from EEG lab as I find it easier to detect artifactual components. Thanks a lot for your help Katrin -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.lozanosoldevilla at fcdonders.ru.nl Wed May 28 14:24:06 2014 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Wed, 28 May 2014 14:24:06 +0200 (CEST) Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? In-Reply-To: Message-ID: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> Hi Katrin, First, to display the independent components: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% cfg = []; cfg.layout = 'CTF151.lay'; % specify the layout file that should be used for plotting cfg.viewmode = 'component' ft_databrowser(cfg, comp) Take a look to the following example script: http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts Second, you'll have to compute the power spectrum for each independent component with ft_freqanalaysis: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% cfg = []; cfg.output = 'pow'; cfg.channel = 'all';%compute the power spectrum in all ICs cfg.method = 'mtmfft'; cfg.taper = 'hanning'; cfg.foi = 2:2:30; freq = ft_freqanalysis(cfg, comp); And you can plot the spectra: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% nsubplots = 25; nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals, type doc subplot Nfigs = ceil(size(comp.topo,1)/nsubplots); tot = Nfigs*nsubplots; rptvect = 1:size(comp.topo,1); rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post'); rptvect = reshape(rptvect,nsubplots,Nfigs)'; for r=1:size(rptvect,1); figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full screen k=0; for j=1:size(rptvect,2); if~(rptvect(r,j)==0); k=k+1; cfg=[]; cfg.channel = rptvect(r,j); subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq); end end end For the IC topos you'll follow the same logic as above but with: figure cfg = []; cfg.component = [1:20]; % specify the component(s) that should be plotted cfg.layout = 'GSN-HydroCel-129.sfp'; cfg.comment = 'no'; ft_topoplotIC(cfg, comp) I hope it helps Diego ----- Original Message ----- > From: "KatrinH Heimann" > To: "FieldTrip discussion list" > Sent: Wednesday, 28 May, 2014 12:59:38 PM > Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of > single components? > Dear all, > another question: > Is it possible to visualize the Activity power spectrum of the single > components after an ICA by using ft_databrowser (or something else). I > like this feature from EEG lab as I find it easier to detect > artifactual components. > Thanks a lot for your help > Katrin > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- PhD Student Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen NL-6525 EN Nijmegen The Netherlands http://www.ru.nl/people/donders/lozano-soldevilla-d/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Wed May 28 15:02:23 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Wed, 28 May 2014 15:02:23 +0200 Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? In-Reply-To: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> References: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Wonderfull! Thanks Diego!!!! Cheers k 2014-05-28 14:24 GMT+02:00 Lozano Soldevilla, D. (Diego) < d.lozanosoldevilla at fcdonders.ru.nl>: > Hi Katrin, > > First, to display the independent components: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > cfg = []; > cfg.layout = 'CTF151.lay'; % specify the layout file that should be used > for plotting > cfg.viewmode = 'component' > ft_databrowser(cfg, comp) > > Take a look to the following example script: > > http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts > > Second, you'll have to compute the power spectrum for each independent > component with ft_freqanalaysis: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'all';%compute the power spectrum in all ICs > cfg.method = 'mtmfft'; > cfg.taper = 'hanning'; > cfg.foi = 2:2:30; > freq = ft_freqanalysis(cfg, comp); > > And you can plot the spectra: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > nsubplots = 25; > nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals, type > doc subplot > > Nfigs = ceil(size(comp.topo,1)/nsubplots); > tot = Nfigs*nsubplots; > > rptvect = 1:size(comp.topo,1); > rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post'); > rptvect = reshape(rptvect,nsubplots,Nfigs)'; > > for r=1:size(rptvect,1); > figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full > screen > k=0; > for j=1:size(rptvect,2); > if~(rptvect(r,j)==0); > k=k+1; > cfg=[]; > cfg.channel = rptvect(r,j); > subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq); > end > end > end > > For the IC topos you'll follow the same logic as above but with: > > figure > cfg = []; > cfg.component = [1:20]; % specify the component(s) that should be > plotted > cfg.layout = 'GSN-HydroCel-129.sfp'; > cfg.comment = 'no'; > ft_topoplotIC(cfg, comp) > > I hope it helps > > Diego > ------------------------------ > > *From: *"KatrinH Heimann" > *To: *"FieldTrip discussion list" > *Sent: *Wednesday, 28 May, 2014 12:59:38 PM > *Subject: *[FieldTrip] ICA - Can I visualize Activity power spectrum of > single components? > > > Dear all, > another question: > Is it possible to visualize the Activity power spectrum of the single > components after an ICA by using ft_databrowser (or something else). I like > this feature from EEG lab as I find it easier to detect artifactual > components. > Thanks a lot for your help > Katrin > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > PhD Student > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > NL-6525 EN Nijmegen > The Netherlands > http://www.ru.nl/people/donders/lozano-soldevilla-d/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Wed May 28 15:54:24 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Wed, 28 May 2014 15:54:24 +0200 Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? In-Reply-To: References: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Diego, can I ask you another advice- this time more conceptually? I am playing with the ICA now and experience, that I get very different components depending on the artifact detection that I do beforehand. So my idea (due to the literature) was, that the ICA works better on already cleaned data. Now, as I want to do a frequency analysis afterwards, I did not want to reject parts of trials. Therefore I deleted a relatively big amount of trials in which I found muscle artifacts/drifts (Say 25% of the whole amount of trials). However, in fact I see that the ICA then does not give me easily to interpret components anymore - actually the results are better (that is easier to interpret which is artifact, which not) if I include all trials. If I only reject parts of the trials it gets even a bit better. So my question is: Shell I a) do the (stricter) artifact detection rather after the ICA or b) perform it on data with parts of trials marked as bad - in which case I also ask: can I then still reject those components in the uncleaned data (saved beforehand) so that I do not get problems with the frequency analysis afterwards...?! Thanks a lot for your help!!! Katrin 2014-05-28 15:02 GMT+02:00 KatrinH Heimann : > Wonderfull! Thanks Diego!!!! > Cheers k > > > 2014-05-28 14:24 GMT+02:00 Lozano Soldevilla, D. (Diego) < > d.lozanosoldevilla at fcdonders.ru.nl>: > > Hi Katrin, >> >> First, to display the independent components: >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> cfg = []; >> cfg.layout = 'CTF151.lay'; % specify the layout file that should be used >> for plotting >> cfg.viewmode = 'component' >> ft_databrowser(cfg, comp) >> >> Take a look to the following example script: >> >> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts >> >> Second, you'll have to compute the power spectrum for each independent >> component with ft_freqanalaysis: >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> cfg = []; >> cfg.output = 'pow'; >> cfg.channel = 'all';%compute the power spectrum in all ICs >> cfg.method = 'mtmfft'; >> cfg.taper = 'hanning'; >> cfg.foi = 2:2:30; >> freq = ft_freqanalysis(cfg, comp); >> >> And you can plot the spectra: >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> nsubplots = 25; >> nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals, >> type doc subplot >> >> Nfigs = ceil(size(comp.topo,1)/nsubplots); >> tot = Nfigs*nsubplots; >> >> rptvect = 1:size(comp.topo,1); >> rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post'); >> rptvect = reshape(rptvect,nsubplots,Nfigs)'; >> >> for r=1:size(rptvect,1); >> figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full >> screen >> k=0; >> for j=1:size(rptvect,2); >> if~(rptvect(r,j)==0); >> k=k+1; >> cfg=[]; >> cfg.channel = rptvect(r,j); >> subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq); >> end >> end >> end >> >> For the IC topos you'll follow the same logic as above but with: >> >> figure >> cfg = []; >> cfg.component = [1:20]; % specify the component(s) that should be >> plotted >> cfg.layout = 'GSN-HydroCel-129.sfp'; >> cfg.comment = 'no'; >> ft_topoplotIC(cfg, comp) >> >> I hope it helps >> >> Diego >> ------------------------------ >> >> *From: *"KatrinH Heimann" >> *To: *"FieldTrip discussion list" >> *Sent: *Wednesday, 28 May, 2014 12:59:38 PM >> *Subject: *[FieldTrip] ICA - Can I visualize Activity power spectrum of >> single components? >> >> >> Dear all, >> another question: >> Is it possible to visualize the Activity power spectrum of the single >> components after an ICA by using ft_databrowser (or something else). I like >> this feature from EEG lab as I find it easier to detect artifactual >> components. >> Thanks a lot for your help >> Katrin >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -- >> PhD Student >> Neuronal Oscillations Group >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> NL-6525 EN Nijmegen >> The Netherlands >> http://www.ru.nl/people/donders/lozano-soldevilla-d/ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Laura.Rueda at faber.kuleuven.be Wed May 28 16:29:08 2014 From: Laura.Rueda at faber.kuleuven.be (Laura Rueda Delgado) Date: Wed, 28 May 2014 14:29:08 +0000 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS Message-ID: Dear Fieldtrip users, I'm following the tutorial of beamformers (Source Analysis: Contrast activity to another interval) to estimate oscillatory sources using DICS. I've checked the surface created after segmentation and the grid generated from the electrode positions and the headmodel. That seems to work ok. However, at the step of source analysis, I get the following error: Error using * Inner matrix dimensions must agree. Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Does anybody have an idea of what I'm doing wrong? Thank you in advance for any help or suggestion! ----------------------------------------------------------------- This is my code: %% 1 - Preparation of MRI- source space % Read MRI mrifile = 'Subject01\Subject01.mri'; mri = ft_read_mri(mrifile); % Reslice to reorient images cfg = []; cfg.dim = [256 256 256]; mri = ft_volumereslice(cfg,mri); % Segment compartments cfg = []; cfg.output = {'brain','skull','scalp'}; segmentedmri = ft_volumesegment(cfg, mri); % Prepare mesh cfg=[]; cfg.tissue={'brain', 'skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); % Prepare headmodel cfg = []; cfg.method ='bemcp'; vol = ft_prepare_headmodel(cfg, bnd); %% 2- Prepare leadfield - Creating grid load elec_aligned2 % Obtained after adjusting electrodes on scalp surface interactively % Three fiducial markers were added to the electrode file, and now they're % removed so that the electrode structure has the same number of channels as the data elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); elec_aligned2.label = elec_aligned2.label(1:128, :); cfg =[]; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.grid.resolution = 10; cfg.grid.unit = 'mm'; [grid] = ft_prepare_leadfield(cfg); %% 3- Join rest and task data % data_rs: resting state data % data4: data during task dataAll = ft_appenddata([], data_rs, data4); cfg = []; cfg.method = 'mtmfft'; cfg.output = 'powandcsd'; cfg.tapsmofrq = 4; cfg.foilim = [18 18]; freqAll = ft_freqanalysis(cfg, dataAll); %---------------------------------- % all seems normal until here %---------------------------------- %% 4- Estimate source of all data cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAll = ft_sourceanalysis(cfg, freqAll); Cheers, Laura Rueda Delgado -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at gmail.com Wed May 28 16:41:54 2014 From: johanna.zumer at gmail.com (Johanna Zumer) Date: Wed, 28 May 2014 15:41:54 +0100 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Hi Laura, Does your data have the same channels as the leadfield (as the electrodes that went in to compute the leadfield)? I often see that error when there is a mismatch of channels in that way. Best, Johanna 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado < Laura.Rueda at faber.kuleuven.be>: > Dear Fieldtrip users, > > > > I’m following the tutorial of beamformers (Source Analysis: Contrast > activity to another interval) > to estimate oscillatory sources using DICS. I’ve checked the surface > created after segmentation and the grid generated from the electrode > positions and the headmodel. That seems to work ok. However, at the step of > source analysis, I get the following error: > > > > Error using * > > Inner matrix dimensions must agree. > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > Does anybody have an idea of what I’m doing wrong? > > Thank you in advance for any help or suggestion! > > > > ----------------------------------------------------------------- > > This is my code: > > %% 1 - Preparation of MRI- source space > > % Read MRI > > mrifile = 'Subject01\Subject01.mri'; > > mri = ft_read_mri(mrifile); > > % Reslice to reorient images > > cfg = []; > > cfg.dim = [256 256 256]; > > mri = ft_volumereslice(cfg,mri); > > % Segment compartments > > cfg = []; > > cfg.output = {'brain','skull','scalp'}; > > segmentedmri = ft_volumesegment(cfg, mri); > > % Prepare mesh > > cfg=[]; > > cfg.tissue={'brain', 'skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > % Prepare headmodel > > cfg = []; > > cfg.method ='bemcp'; > > vol = ft_prepare_headmodel(cfg, bnd); > > %% 2- Prepare leadfield - Creating grid > > load elec_aligned2 % Obtained after adjusting electrodes on scalp surface > interactively > > % Three fiducial markers were added to the electrode file, and now they're > > % removed so that the electrode structure has the same number of channels > as the data > > elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); > > elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); > > elec_aligned2.label = elec_aligned2.label(1:128, :); > > cfg =[]; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.grid.resolution = 10; > > cfg.grid.unit = 'mm'; > > [grid] = ft_prepare_leadfield(cfg); > > %% 3- Join rest and task data > > % data_rs: resting state data > > % data4: data during task > > dataAll = ft_appenddata([], data_rs, data4); > > cfg = []; > > cfg.method = 'mtmfft'; > > cfg.output = 'powandcsd'; > > cfg.tapsmofrq = 4; > > cfg.foilim = [18 18]; > > freqAll = ft_freqanalysis(cfg, dataAll); > > %---------------------------------- > > % all seems normal until here > > %---------------------------------- > > %% 4- Estimate source of all data > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 18; > > cfg.grid = grid; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > sourceAll = ft_sourceanalysis(cfg, freqAll); > > > > > > Cheers, > > > > Laura Rueda Delgado > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Laura.Rueda at faber.kuleuven.be Wed May 28 16:51:27 2014 From: Laura.Rueda at faber.kuleuven.be (Laura Rueda Delgado) Date: Wed, 28 May 2014 14:51:27 +0000 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Dear Johanna, Thank you for your suggestion. On step 2 in the code, I select from the elec structure the channels that are included in the frequency data. So the elec structure used for preparing the leadfield has 128 electrodes, the same as the data (data_rs, data 4, and therefore freqAll). I checked this precisely because I read a previous thread discussing that issue. Best regards, Laura Rueda Delgado From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer Sent: woensdag 28 mei 2014 16:42 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Hi Laura, Does your data have the same channels as the leadfield (as the electrodes that went in to compute the leadfield)? I often see that error when there is a mismatch of channels in that way. Best, Johanna 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado >: Dear Fieldtrip users, I’m following the tutorial of beamformers (Source Analysis: Contrast activity to another interval) to estimate oscillatory sources using DICS. I’ve checked the surface created after segmentation and the grid generated from the electrode positions and the headmodel. That seems to work ok. However, at the step of source analysis, I get the following error: Error using * Inner matrix dimensions must agree. Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Does anybody have an idea of what I’m doing wrong? Thank you in advance for any help or suggestion! ----------------------------------------------------------------- This is my code: %% 1 - Preparation of MRI- source space % Read MRI mrifile = 'Subject01\Subject01.mri'; mri = ft_read_mri(mrifile); % Reslice to reorient images cfg = []; cfg.dim = [256 256 256]; mri = ft_volumereslice(cfg,mri); % Segment compartments cfg = []; cfg.output = {'brain','skull','scalp'}; segmentedmri = ft_volumesegment(cfg, mri); % Prepare mesh cfg=[]; cfg.tissue={'brain', 'skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); % Prepare headmodel cfg = []; cfg.method ='bemcp'; vol = ft_prepare_headmodel(cfg, bnd); %% 2- Prepare leadfield - Creating grid load elec_aligned2 % Obtained after adjusting electrodes on scalp surface interactively % Three fiducial markers were added to the electrode file, and now they're % removed so that the electrode structure has the same number of channels as the data elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); elec_aligned2.label = elec_aligned2.label(1:128, :); cfg =[]; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.grid.resolution = 10; cfg.grid.unit = 'mm'; [grid] = ft_prepare_leadfield(cfg); %% 3- Join rest and task data % data_rs: resting state data % data4: data during task dataAll = ft_appenddata([], data_rs, data4); cfg = []; cfg.method = 'mtmfft'; cfg.output = 'powandcsd'; cfg.tapsmofrq = 4; cfg.foilim = [18 18]; freqAll = ft_freqanalysis(cfg, dataAll); %---------------------------------- % all seems normal until here %---------------------------------- %% 4- Estimate source of all data cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAll = ft_sourceanalysis(cfg, freqAll); Cheers, Laura Rueda Delgado _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcantor at umich.edu Wed May 28 16:24:38 2014 From: mcantor at umich.edu (Max Cantor) Date: Wed, 28 May 2014 10:24:38 -0400 Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? In-Reply-To: References: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: What we usually do before ICA is a rough pass removing the most extremely artifactual trials or channels. For instance, if you see artifacts that are not systematic and are affecting multiple sensors, it may be something like a head scratch that is affecting multiple sensors independently, and so would be turned into multiple ICA components, and so removing these would be beneficial. That being said, anything that might be, for instance, an ECG or EOG artifact, is best not cleaned before ICA, because the whole point of ICA components is to find artifacts that are independent from each other, but dependent to the source (in other words, a systematic artifact as the result of a blink) and remove them without having to throw away the rest of the good data within that trial/channel. In other words, if you're doing a comprehensive artifact rejection before ICA, it makes sense that you aren't necessarily picking up artifactual components, since you might already be removing the data that would be turned into an artifactual component. On Wed, May 28, 2014 at 9:54 AM, KatrinH Heimann wrote: > Diego, can I ask you another advice- this time more conceptually? I am > playing with the ICA now and experience, that I get very different > components depending on the artifact detection that I do beforehand. So my > idea (due to the literature) was, that the ICA works better on already > cleaned data. Now, as I want to do a frequency analysis afterwards, I did > not want to reject parts of trials. Therefore I deleted a relatively big > amount of trials in which I found muscle artifacts/drifts (Say 25% of the > whole amount of trials). However, in fact I see that the ICA then does not > give me easily to interpret components anymore - actually the results are > better (that is easier to interpret which is artifact, which not) if I > include all trials. If I only reject parts of the trials it gets even a bit > better. So my question is: Shell I a) do the (stricter) artifact detection > rather after the ICA or b) perform it on data with parts of trials marked > as bad - in which case I also ask: can I then still reject those components > in the uncleaned data (saved beforehand) so that I do not get problems with > the frequency analysis afterwards...?! > Thanks a lot for your help!!! Katrin > > > 2014-05-28 15:02 GMT+02:00 KatrinH Heimann : > > Wonderfull! Thanks Diego!!!! >> Cheers k >> >> >> 2014-05-28 14:24 GMT+02:00 Lozano Soldevilla, D. (Diego) < >> d.lozanosoldevilla at fcdonders.ru.nl>: >> >> Hi Katrin, >>> >>> First, to display the independent components: >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> cfg = []; >>> cfg.layout = 'CTF151.lay'; % specify the layout file that should be used >>> for plotting >>> cfg.viewmode = 'component' >>> ft_databrowser(cfg, comp) >>> >>> Take a look to the following example script: >>> >>> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts >>> >>> Second, you'll have to compute the power spectrum for each independent >>> component with ft_freqanalaysis: >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> cfg = []; >>> cfg.output = 'pow'; >>> cfg.channel = 'all';%compute the power spectrum in all ICs >>> cfg.method = 'mtmfft'; >>> cfg.taper = 'hanning'; >>> cfg.foi = 2:2:30; >>> freq = ft_freqanalysis(cfg, comp); >>> >>> And you can plot the spectra: >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> nsubplots = 25; >>> nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals, >>> type doc subplot >>> >>> Nfigs = ceil(size(comp.topo,1)/nsubplots); >>> tot = Nfigs*nsubplots; >>> >>> rptvect = 1:size(comp.topo,1); >>> rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post'); >>> rptvect = reshape(rptvect,nsubplots,Nfigs)'; >>> >>> for r=1:size(rptvect,1); >>> figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full >>> screen >>> k=0; >>> for j=1:size(rptvect,2); >>> if~(rptvect(r,j)==0); >>> k=k+1; >>> cfg=[]; >>> cfg.channel = rptvect(r,j); >>> subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq); >>> end >>> end >>> end >>> >>> For the IC topos you'll follow the same logic as above but with: >>> >>> figure >>> cfg = []; >>> cfg.component = [1:20]; % specify the component(s) that should be >>> plotted >>> cfg.layout = 'GSN-HydroCel-129.sfp'; >>> cfg.comment = 'no'; >>> ft_topoplotIC(cfg, comp) >>> >>> I hope it helps >>> >>> Diego >>> ------------------------------ >>> >>> *From: *"KatrinH Heimann" >>> *To: *"FieldTrip discussion list" >>> *Sent: *Wednesday, 28 May, 2014 12:59:38 PM >>> *Subject: *[FieldTrip] ICA - Can I visualize Activity power spectrum of >>> single components? >>> >>> >>> Dear all, >>> another question: >>> Is it possible to visualize the Activity power spectrum of the single >>> components after an ICA by using ft_databrowser (or something else). I like >>> this feature from EEG lab as I find it easier to detect artifactual >>> components. >>> Thanks a lot for your help >>> Katrin >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> -- >>> PhD Student >>> Neuronal Oscillations Group >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognitive Neuroimaging >>> Radboud University Nijmegen >>> NL-6525 EN Nijmegen >>> The Netherlands >>> http://www.ru.nl/people/donders/lozano-soldevilla-d/ >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Research Assistant Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathykousik at gmail.com Wed May 28 17:09:37 2014 From: sarathykousik at gmail.com (kousik sarathy) Date: Wed, 28 May 2014 17:09:37 +0200 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Hey Laura, I too had the same suggestion as Johanna's. Another thing to check would be if the labels that you used for the leadfield estimation are the same as the freq data. I guess FT at some point would also check this to extract the indices. -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 4:51 PM, Laura Rueda Delgado < Laura.Rueda at faber.kuleuven.be> wrote: > Dear Johanna, > > > > Thank you for your suggestion. > > > > On step 2 in the code, I select from the elec structure the channels that > are included in the frequency data. So the elec structure used for > preparing the leadfield has 128 electrodes, the same as the data (data_rs, > data 4, and therefore freqAll). I checked this precisely because I read a > previous thread discussing that issue. > > > > Best regards, > > > > Laura Rueda Delgado > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *Johanna Zumer > *Sent:* woensdag 28 mei 2014 16:42 > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Hi Laura, > > > > Does your data have the same channels as the leadfield (as the electrodes > that went in to compute the leadfield)? I often see that error when there > is a mismatch of channels in that way. > > > > Best, > > Johanna > > > > 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be>: > > Dear Fieldtrip users, > > > > I’m following the tutorial of beamformers (Source Analysis: Contrast > activity to another interval) > to estimate oscillatory sources using DICS. I’ve checked the surface > created after segmentation and the grid generated from the electrode > positions and the headmodel. That seems to work ok. However, at the step of > source analysis, I get the following error: > > > > Error using * > > Inner matrix dimensions must agree. > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > Does anybody have an idea of what I’m doing wrong? > > Thank you in advance for any help or suggestion! > > > > ----------------------------------------------------------------- > > This is my code: > > %% 1 - Preparation of MRI- source space > > % Read MRI > > mrifile = 'Subject01\Subject01.mri'; > > mri = ft_read_mri(mrifile); > > % Reslice to reorient images > > cfg = []; > > cfg.dim = [256 256 256]; > > mri = ft_volumereslice(cfg,mri); > > % Segment compartments > > cfg = []; > > cfg.output = {'brain','skull','scalp'}; > > segmentedmri = ft_volumesegment(cfg, mri); > > % Prepare mesh > > cfg=[]; > > cfg.tissue={'brain', 'skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > % Prepare headmodel > > cfg = []; > > cfg.method ='bemcp'; > > vol = ft_prepare_headmodel(cfg, bnd); > > %% 2- Prepare leadfield - Creating grid > > load elec_aligned2 % Obtained after adjusting electrodes on scalp surface > interactively > > % Three fiducial markers were added to the electrode file, and now they're > > % removed so that the electrode structure has the same number of channels > as the data > > elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); > > elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); > > elec_aligned2.label = elec_aligned2.label(1:128, :); > > cfg =[]; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.grid.resolution = 10; > > cfg.grid.unit = 'mm'; > > [grid] = ft_prepare_leadfield(cfg); > > %% 3- Join rest and task data > > % data_rs: resting state data > > % data4: data during task > > dataAll = ft_appenddata([], data_rs, data4); > > cfg = []; > > cfg.method = 'mtmfft'; > > cfg.output = 'powandcsd'; > > cfg.tapsmofrq = 4; > > cfg.foilim = [18 18]; > > freqAll = ft_freqanalysis(cfg, dataAll); > > %---------------------------------- > > % all seems normal until here > > %---------------------------------- > > %% 4- Estimate source of all data > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 18; > > cfg.grid = grid; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > sourceAll = ft_sourceanalysis(cfg, freqAll); > > > > > > Cheers, > > > > Laura Rueda Delgado > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Laura.Rueda at faber.kuleuven.be Wed May 28 17:31:40 2014 From: Laura.Rueda at faber.kuleuven.be (Laura Rueda Delgado) Date: Wed, 28 May 2014 15:31:40 +0000 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Dear Kousik, I checked the labels and they were the same, except for whether they were in capital letters. So I added the following before ft_sourceanalysis: freqAll.label=cellfun(@upper, freqAll.label, 'UniformOutput', 0); freqAll.labelcmb=cellfun(@upper, freqAll.labelcmb, 'UniformOutput', 0); This way the labels of the elec structure and freqAll are in capital letters. And now I get a different error (although still within the function beamformer_dics): Error using svd Input to SVD must not contain NaN or Inf. Error in beamformer_dics>pinv (line 650) [U,S,V] = svd(A,0); Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); What could it be? Best regards, Laura From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of kousik sarathy Sent: woensdag 28 mei 2014 17:10 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Hey Laura, I too had the same suggestion as Johanna's. Another thing to check would be if the labels that you used for the leadfield estimation are the same as the freq data. I guess FT at some point would also check this to extract the indices. -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 4:51 PM, Laura Rueda Delgado > wrote: Dear Johanna, Thank you for your suggestion. On step 2 in the code, I select from the elec structure the channels that are included in the frequency data. So the elec structure used for preparing the leadfield has 128 electrodes, the same as the data (data_rs, data 4, and therefore freqAll). I checked this precisely because I read a previous thread discussing that issue. Best regards, Laura Rueda Delgado From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer Sent: woensdag 28 mei 2014 16:42 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Hi Laura, Does your data have the same channels as the leadfield (as the electrodes that went in to compute the leadfield)? I often see that error when there is a mismatch of channels in that way. Best, Johanna 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado >: Dear Fieldtrip users, I’m following the tutorial of beamformers (Source Analysis: Contrast activity to another interval) to estimate oscillatory sources using DICS. I’ve checked the surface created after segmentation and the grid generated from the electrode positions and the headmodel. That seems to work ok. However, at the step of source analysis, I get the following error: Error using * Inner matrix dimensions must agree. Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Does anybody have an idea of what I’m doing wrong? Thank you in advance for any help or suggestion! ----------------------------------------------------------------- This is my code: %% 1 - Preparation of MRI- source space % Read MRI mrifile = 'Subject01\Subject01.mri'; mri = ft_read_mri(mrifile); % Reslice to reorient images cfg = []; cfg.dim = [256 256 256]; mri = ft_volumereslice(cfg,mri); % Segment compartments cfg = []; cfg.output = {'brain','skull','scalp'}; segmentedmri = ft_volumesegment(cfg, mri); % Prepare mesh cfg=[]; cfg.tissue={'brain', 'skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); % Prepare headmodel cfg = []; cfg.method ='bemcp'; vol = ft_prepare_headmodel(cfg, bnd); %% 2- Prepare leadfield - Creating grid load elec_aligned2 % Obtained after adjusting electrodes on scalp surface interactively % Three fiducial markers were added to the electrode file, and now they're % removed so that the electrode structure has the same number of channels as the data elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); elec_aligned2.label = elec_aligned2.label(1:128, :); cfg =[]; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.grid.resolution = 10; cfg.grid.unit = 'mm'; [grid] = ft_prepare_leadfield(cfg); %% 3- Join rest and task data % data_rs: resting state data % data4: data during task dataAll = ft_appenddata([], data_rs, data4); cfg = []; cfg.method = 'mtmfft'; cfg.output = 'powandcsd'; cfg.tapsmofrq = 4; cfg.foilim = [18 18]; freqAll = ft_freqanalysis(cfg, dataAll); %---------------------------------- % all seems normal until here %---------------------------------- %% 4- Estimate source of all data cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAll = ft_sourceanalysis(cfg, freqAll); Cheers, Laura Rueda Delgado _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From ayobimpe2004 at hotmail.com Wed May 28 17:36:39 2014 From: ayobimpe2004 at hotmail.com (Azeez Adebimpe) Date: Wed, 28 May 2014 16:36:39 +0100 Subject: [FieldTrip] source resampling Message-ID: Dear all I calculated my leadfield or grid with 8 mm resolution. Please is there anyway after or before source interpolation or before to resample the source to 1 mm resolution. merci! Azeez A. Adebimpe "Knowledge and good manner, the beauty of a man" -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathykousik at gmail.com Wed May 28 17:37:17 2014 From: sarathykousik at gmail.com (kousik sarathy) Date: Wed, 28 May 2014 17:37:17 +0200 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Ah. Interesting. Good that error changes. So that was the problem before. Now, can you check if your Freq matrices contain any NaN's (isnan(freqAll))? It can happen sometimes. -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 5:31 PM, Laura Rueda Delgado < Laura.Rueda at faber.kuleuven.be> wrote: > Dear Kousik, > > > > I checked the labels and they were the same, except for whether they were > in capital letters. So I added the following before ft_sourceanalysis: > > > > freqAll.label=cellfun(@upper, freqAll.label, 'UniformOutput', 0); > > freqAll.labelcmb=cellfun(@upper, freqAll.labelcmb, 'UniformOutput', 0); > > > > This way the labels of the elec structure and freqAll are in capital > letters. > > > > And now I get a different error (although still within the function > beamformer_dics): > > > > Error using svd > > Input to SVD must not contain NaN or Inf. > > > > Error in beamformer_dics>pinv (line 650) > > [U,S,V] = svd(A,0); > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > > > What could it be? > > > > Best regards, > > Laura > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *kousik sarathy > *Sent:* woensdag 28 mei 2014 17:10 > > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Hey Laura, > > > > I too had the same suggestion as Johanna's. > > > > Another thing to check would be if the labels that you used for the > leadfield estimation are the same as the freq data. I guess FT at some > point would also check this to extract the indices. > > > -- > > Regards, > > Kousik Sarathy, S > > > > > > On Wed, May 28, 2014 at 4:51 PM, Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be> wrote: > > Dear Johanna, > > > > Thank you for your suggestion. > > > > On step 2 in the code, I select from the elec structure the channels that > are included in the frequency data. So the elec structure used for > preparing the leadfield has 128 electrodes, the same as the data (data_rs, > data 4, and therefore freqAll). I checked this precisely because I read a > previous thread discussing that issue. > > > > Best regards, > > > > Laura Rueda Delgado > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *Johanna Zumer > *Sent:* woensdag 28 mei 2014 16:42 > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Hi Laura, > > > > Does your data have the same channels as the leadfield (as the electrodes > that went in to compute the leadfield)? I often see that error when there > is a mismatch of channels in that way. > > > > Best, > > Johanna > > > > 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be>: > > Dear Fieldtrip users, > > > > I’m following the tutorial of beamformers (Source Analysis: Contrast > activity to another interval) > to estimate oscillatory sources using DICS. I’ve checked the surface > created after segmentation and the grid generated from the electrode > positions and the headmodel. That seems to work ok. However, at the step of > source analysis, I get the following error: > > > > Error using * > > Inner matrix dimensions must agree. > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > Does anybody have an idea of what I’m doing wrong? > > Thank you in advance for any help or suggestion! > > > > ----------------------------------------------------------------- > > This is my code: > > %% 1 - Preparation of MRI- source space > > % Read MRI > > mrifile = 'Subject01\Subject01.mri'; > > mri = ft_read_mri(mrifile); > > % Reslice to reorient images > > cfg = []; > > cfg.dim = [256 256 256]; > > mri = ft_volumereslice(cfg,mri); > > % Segment compartments > > cfg = []; > > cfg.output = {'brain','skull','scalp'}; > > segmentedmri = ft_volumesegment(cfg, mri); > > % Prepare mesh > > cfg=[]; > > cfg.tissue={'brain', 'skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > % Prepare headmodel > > cfg = []; > > cfg.method ='bemcp'; > > vol = ft_prepare_headmodel(cfg, bnd); > > %% 2- Prepare leadfield - Creating grid > > load elec_aligned2 % Obtained after adjusting electrodes on scalp surface > interactively > > % Three fiducial markers were added to the electrode file, and now they're > > % removed so that the electrode structure has the same number of channels > as the data > > elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); > > elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); > > elec_aligned2.label = elec_aligned2.label(1:128, :); > > cfg =[]; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.grid.resolution = 10; > > cfg.grid.unit = 'mm'; > > [grid] = ft_prepare_leadfield(cfg); > > %% 3- Join rest and task data > > % data_rs: resting state data > > % data4: data during task > > dataAll = ft_appenddata([], data_rs, data4); > > cfg = []; > > cfg.method = 'mtmfft'; > > cfg.output = 'powandcsd'; > > cfg.tapsmofrq = 4; > > cfg.foilim = [18 18]; > > freqAll = ft_freqanalysis(cfg, dataAll); > > %---------------------------------- > > % all seems normal until here > > %---------------------------------- > > %% 4- Estimate source of all data > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 18; > > cfg.grid = grid; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > sourceAll = ft_sourceanalysis(cfg, freqAll); > > > > > > Cheers, > > > > Laura Rueda Delgado > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Wed May 28 17:50:09 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Wed, 28 May 2014 17:50:09 +0200 Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? In-Reply-To: References: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Thanks Max! :) Katrin 2014-05-28 16:24 GMT+02:00 Max Cantor : > What we usually do before ICA is a rough pass removing the most extremely > artifactual trials or channels. For instance, if you see artifacts that are > not systematic and are affecting multiple sensors, it may be something like > a head scratch that is affecting multiple sensors independently, and so > would be turned into multiple ICA components, and so removing these would > be beneficial. That being said, anything that might be, for instance, an > ECG or EOG artifact, is best not cleaned before ICA, because the whole > point of ICA components is to find artifacts that are independent from each > other, but dependent to the source (in other words, a systematic artifact > as the result of a blink) and remove them without having to throw away the > rest of the good data within that trial/channel. In other words, if you're > doing a comprehensive artifact rejection before ICA, it makes sense that > you aren't necessarily picking up artifactual components, since you might > already be removing the data that would be turned into an artifactual > component. > > > On Wed, May 28, 2014 at 9:54 AM, KatrinH Heimann wrote: > >> Diego, can I ask you another advice- this time more conceptually? I am >> playing with the ICA now and experience, that I get very different >> components depending on the artifact detection that I do beforehand. So my >> idea (due to the literature) was, that the ICA works better on already >> cleaned data. Now, as I want to do a frequency analysis afterwards, I did >> not want to reject parts of trials. Therefore I deleted a relatively big >> amount of trials in which I found muscle artifacts/drifts (Say 25% of the >> whole amount of trials). However, in fact I see that the ICA then does not >> give me easily to interpret components anymore - actually the results are >> better (that is easier to interpret which is artifact, which not) if I >> include all trials. If I only reject parts of the trials it gets even a bit >> better. So my question is: Shell I a) do the (stricter) artifact detection >> rather after the ICA or b) perform it on data with parts of trials marked >> as bad - in which case I also ask: can I then still reject those components >> in the uncleaned data (saved beforehand) so that I do not get problems with >> the frequency analysis afterwards...?! >> Thanks a lot for your help!!! Katrin >> >> >> 2014-05-28 15:02 GMT+02:00 KatrinH Heimann : >> >> Wonderfull! Thanks Diego!!!! >>> Cheers k >>> >>> >>> 2014-05-28 14:24 GMT+02:00 Lozano Soldevilla, D. (Diego) < >>> d.lozanosoldevilla at fcdonders.ru.nl>: >>> >>> Hi Katrin, >>>> >>>> First, to display the independent components: >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> cfg = []; >>>> cfg.layout = 'CTF151.lay'; % specify the layout file that should be >>>> used for plotting >>>> cfg.viewmode = 'component' >>>> ft_databrowser(cfg, comp) >>>> >>>> Take a look to the following example script: >>>> >>>> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts >>>> >>>> Second, you'll have to compute the power spectrum for each independent >>>> component with ft_freqanalaysis: >>>> >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> cfg = []; >>>> cfg.output = 'pow'; >>>> cfg.channel = 'all';%compute the power spectrum in all ICs >>>> cfg.method = 'mtmfft'; >>>> cfg.taper = 'hanning'; >>>> cfg.foi = 2:2:30; >>>> freq = ft_freqanalysis(cfg, comp); >>>> >>>> And you can plot the spectra: >>>> >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> nsubplots = 25; >>>> nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals, >>>> type doc subplot >>>> >>>> Nfigs = ceil(size(comp.topo,1)/nsubplots); >>>> tot = Nfigs*nsubplots; >>>> >>>> rptvect = 1:size(comp.topo,1); >>>> rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post'); >>>> rptvect = reshape(rptvect,nsubplots,Nfigs)'; >>>> >>>> for r=1:size(rptvect,1); >>>> figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full >>>> screen >>>> k=0; >>>> for j=1:size(rptvect,2); >>>> if~(rptvect(r,j)==0); >>>> k=k+1; >>>> cfg=[]; >>>> cfg.channel = rptvect(r,j); >>>> subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq); >>>> end >>>> end >>>> end >>>> >>>> For the IC topos you'll follow the same logic as above but with: >>>> >>>> figure >>>> cfg = []; >>>> cfg.component = [1:20]; % specify the component(s) that should be >>>> plotted >>>> cfg.layout = 'GSN-HydroCel-129.sfp'; >>>> cfg.comment = 'no'; >>>> ft_topoplotIC(cfg, comp) >>>> >>>> I hope it helps >>>> >>>> Diego >>>> ------------------------------ >>>> >>>> *From: *"KatrinH Heimann" >>>> *To: *"FieldTrip discussion list" >>>> *Sent: *Wednesday, 28 May, 2014 12:59:38 PM >>>> *Subject: *[FieldTrip] ICA - Can I visualize Activity power spectrum >>>> of single components? >>>> >>>> >>>> Dear all, >>>> another question: >>>> Is it possible to visualize the Activity power spectrum of the single >>>> components after an ICA by using ft_databrowser (or something else). I like >>>> this feature from EEG lab as I find it easier to detect artifactual >>>> components. >>>> Thanks a lot for your help >>>> Katrin >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> >>>> >>>> -- >>>> PhD Student >>>> Neuronal Oscillations Group >>>> Donders Institute for Brain, Cognition and Behaviour >>>> Centre for Cognitive Neuroimaging >>>> Radboud University Nijmegen >>>> NL-6525 EN Nijmegen >>>> The Netherlands >>>> http://www.ru.nl/people/donders/lozano-soldevilla-d/ >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Max Cantor > Research Assistant > Computational Neurolinguistics Lab > University of Michigan > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Laura.Rueda at faber.kuleuven.be Wed May 28 18:01:52 2014 From: Laura.Rueda at faber.kuleuven.be (Laura Rueda Delgado) Date: Wed, 28 May 2014 16:01:52 +0000 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Dear Kousik, I checked for NaN and Inf values in powspctrm and crsspctrm of freqAll. There are none. However, I checked for NaN values in grid.leadfield and it has some. I thought that these were NaN values in the points of the grid outside a brain region, but I might be mistaken. grid = xgrid: [-58 -48 -38 -28 -18 -8 2 12 22 32 42 52 62 72 82 92 102] ygrid: [-61 -51 -41 -31 -21 -11 -1 9 19 29 39 49 59] zgrid: [-13 -3 7 17 27 37 47 57 67 77 87 97 107 117] dim: [17 13 14] pos: [3094x3 double] unit: 'mm' inside: [1x1516 double] outside: [1x1578 double] cfg: [1x1 struct] leadfield: {1x3094 cell} Best regards, Laura Rueda Delgado From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of kousik sarathy Sent: woensdag 28 mei 2014 17:37 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Ah. Interesting. Good that error changes. So that was the problem before. Now, can you check if your Freq matrices contain any NaN's (isnan(freqAll))? It can happen sometimes. -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 5:31 PM, Laura Rueda Delgado > wrote: Dear Kousik, I checked the labels and they were the same, except for whether they were in capital letters. So I added the following before ft_sourceanalysis: freqAll.label=cellfun(@upper, freqAll.label, 'UniformOutput', 0); freqAll.labelcmb=cellfun(@upper, freqAll.labelcmb, 'UniformOutput', 0); This way the labels of the elec structure and freqAll are in capital letters. And now I get a different error (although still within the function beamformer_dics): Error using svd Input to SVD must not contain NaN or Inf. Error in beamformer_dics>pinv (line 650) [U,S,V] = svd(A,0); Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); What could it be? Best regards, Laura From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of kousik sarathy Sent: woensdag 28 mei 2014 17:10 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Hey Laura, I too had the same suggestion as Johanna's. Another thing to check would be if the labels that you used for the leadfield estimation are the same as the freq data. I guess FT at some point would also check this to extract the indices. -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 4:51 PM, Laura Rueda Delgado > wrote: Dear Johanna, Thank you for your suggestion. On step 2 in the code, I select from the elec structure the channels that are included in the frequency data. So the elec structure used for preparing the leadfield has 128 electrodes, the same as the data (data_rs, data 4, and therefore freqAll). I checked this precisely because I read a previous thread discussing that issue. Best regards, Laura Rueda Delgado From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer Sent: woensdag 28 mei 2014 16:42 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Hi Laura, Does your data have the same channels as the leadfield (as the electrodes that went in to compute the leadfield)? I often see that error when there is a mismatch of channels in that way. Best, Johanna 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado >: Dear Fieldtrip users, I’m following the tutorial of beamformers (Source Analysis: Contrast activity to another interval) to estimate oscillatory sources using DICS. I’ve checked the surface created after segmentation and the grid generated from the electrode positions and the headmodel. That seems to work ok. However, at the step of source analysis, I get the following error: Error using * Inner matrix dimensions must agree. Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Does anybody have an idea of what I’m doing wrong? Thank you in advance for any help or suggestion! ----------------------------------------------------------------- This is my code: %% 1 - Preparation of MRI- source space % Read MRI mrifile = 'Subject01\Subject01.mri'; mri = ft_read_mri(mrifile); % Reslice to reorient images cfg = []; cfg.dim = [256 256 256]; mri = ft_volumereslice(cfg,mri); % Segment compartments cfg = []; cfg.output = {'brain','skull','scalp'}; segmentedmri = ft_volumesegment(cfg, mri); % Prepare mesh cfg=[]; cfg.tissue={'brain', 'skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); % Prepare headmodel cfg = []; cfg.method ='bemcp'; vol = ft_prepare_headmodel(cfg, bnd); %% 2- Prepare leadfield - Creating grid load elec_aligned2 % Obtained after adjusting electrodes on scalp surface interactively % Three fiducial markers were added to the electrode file, and now they're % removed so that the electrode structure has the same number of channels as the data elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); elec_aligned2.label = elec_aligned2.label(1:128, :); cfg =[]; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.grid.resolution = 10; cfg.grid.unit = 'mm'; [grid] = ft_prepare_leadfield(cfg); %% 3- Join rest and task data % data_rs: resting state data % data4: data during task dataAll = ft_appenddata([], data_rs, data4); cfg = []; cfg.method = 'mtmfft'; cfg.output = 'powandcsd'; cfg.tapsmofrq = 4; cfg.foilim = [18 18]; freqAll = ft_freqanalysis(cfg, dataAll); %---------------------------------- % all seems normal until here %---------------------------------- %% 4- Estimate source of all data cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAll = ft_sourceanalysis(cfg, freqAll); Cheers, Laura Rueda Delgado _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathykousik at gmail.com Wed May 28 18:09:31 2014 From: sarathykousik at gmail.com (kousik sarathy) Date: Wed, 28 May 2014 18:09:31 +0200 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Oh. Yes. FT puts NaN's into sourcespace points outside the brain. You can constrain FT to only calculate leadfields for sourcespace points inside the brain. I generally do this. I don't know how FT handles those outside the brain source points really. You could give this a try. Check this tutorial/code: http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#forward_solution -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 6:01 PM, Laura Rueda Delgado < Laura.Rueda at faber.kuleuven.be> wrote: > Dear Kousik, > > > > I checked for NaN and Inf values in powspctrm and crsspctrm of freqAll. > There are none. However, I checked for NaN values in grid.leadfield and it > has some. I thought that these were NaN values in the points of the grid > outside a brain region, but I might be mistaken. > > > > > > grid = > > > > xgrid: [-58 -48 -38 -28 -18 -8 2 12 22 32 42 52 62 72 82 92 102] > > ygrid: [-61 -51 -41 -31 -21 -11 -1 9 19 29 39 49 59] > > zgrid: [-13 -3 7 17 27 37 47 57 67 77 87 97 107 117] > > dim: [17 13 14] > > pos: [3094x3 double] > > unit: 'mm' > > inside: [1x1516 double] > > outside: [1x1578 double] > > cfg: [1x1 struct] > > leadfield: {1x3094 cell} > > > > Best regards, > > > > Laura Rueda Delgado > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *kousik sarathy > *Sent:* woensdag 28 mei 2014 17:37 > > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Ah. Interesting. Good that error changes. So that was the problem before. > > > > Now, can you check if your Freq matrices contain any NaN's > (isnan(freqAll))? It can happen sometimes. > > > -- > > Regards, > > Kousik Sarathy, S > > > > > > On Wed, May 28, 2014 at 5:31 PM, Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be> wrote: > > Dear Kousik, > > > > I checked the labels and they were the same, except for whether they were > in capital letters. So I added the following before ft_sourceanalysis: > > > > freqAll.label=cellfun(@upper, freqAll.label, 'UniformOutput', 0); > > freqAll.labelcmb=cellfun(@upper, freqAll.labelcmb, 'UniformOutput', 0); > > > > This way the labels of the elec structure and freqAll are in capital > letters. > > > > And now I get a different error (although still within the function > beamformer_dics): > > > > Error using svd > > Input to SVD must not contain NaN or Inf. > > > > Error in beamformer_dics>pinv (line 650) > > [U,S,V] = svd(A,0); > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > > > What could it be? > > > > Best regards, > > Laura > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *kousik sarathy > *Sent:* woensdag 28 mei 2014 17:10 > > > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Hey Laura, > > > > I too had the same suggestion as Johanna's. > > > > Another thing to check would be if the labels that you used for the > leadfield estimation are the same as the freq data. I guess FT at some > point would also check this to extract the indices. > > > -- > > Regards, > > Kousik Sarathy, S > > > > > > On Wed, May 28, 2014 at 4:51 PM, Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be> wrote: > > Dear Johanna, > > > > Thank you for your suggestion. > > > > On step 2 in the code, I select from the elec structure the channels that > are included in the frequency data. So the elec structure used for > preparing the leadfield has 128 electrodes, the same as the data (data_rs, > data 4, and therefore freqAll). I checked this precisely because I read a > previous thread discussing that issue. > > > > Best regards, > > > > Laura Rueda Delgado > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *Johanna Zumer > *Sent:* woensdag 28 mei 2014 16:42 > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Hi Laura, > > > > Does your data have the same channels as the leadfield (as the electrodes > that went in to compute the leadfield)? I often see that error when there > is a mismatch of channels in that way. > > > > Best, > > Johanna > > > > 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be>: > > Dear Fieldtrip users, > > > > I’m following the tutorial of beamformers (Source Analysis: Contrast > activity to another interval) > to estimate oscillatory sources using DICS. I’ve checked the surface > created after segmentation and the grid generated from the electrode > positions and the headmodel. That seems to work ok. However, at the step of > source analysis, I get the following error: > > > > Error using * > > Inner matrix dimensions must agree. > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > Does anybody have an idea of what I’m doing wrong? > > Thank you in advance for any help or suggestion! > > > > ----------------------------------------------------------------- > > This is my code: > > %% 1 - Preparation of MRI- source space > > % Read MRI > > mrifile = 'Subject01\Subject01.mri'; > > mri = ft_read_mri(mrifile); > > % Reslice to reorient images > > cfg = []; > > cfg.dim = [256 256 256]; > > mri = ft_volumereslice(cfg,mri); > > % Segment compartments > > cfg = []; > > cfg.output = {'brain','skull','scalp'}; > > segmentedmri = ft_volumesegment(cfg, mri); > > % Prepare mesh > > cfg=[]; > > cfg.tissue={'brain', 'skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > % Prepare headmodel > > cfg = []; > > cfg.method ='bemcp'; > > vol = ft_prepare_headmodel(cfg, bnd); > > %% 2- Prepare leadfield - Creating grid > > load elec_aligned2 % Obtained after adjusting electrodes on scalp surface > interactively > > % Three fiducial markers were added to the electrode file, and now they're > > % removed so that the electrode structure has the same number of channels > as the data > > elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); > > elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); > > elec_aligned2.label = elec_aligned2.label(1:128, :); > > cfg =[]; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.grid.resolution = 10; > > cfg.grid.unit = 'mm'; > > [grid] = ft_prepare_leadfield(cfg); > > %% 3- Join rest and task data > > % data_rs: resting state data > > % data4: data during task > > dataAll = ft_appenddata([], data_rs, data4); > > cfg = []; > > cfg.method = 'mtmfft'; > > cfg.output = 'powandcsd'; > > cfg.tapsmofrq = 4; > > cfg.foilim = [18 18]; > > freqAll = ft_freqanalysis(cfg, dataAll); > > %---------------------------------- > > % all seems normal until here > > %---------------------------------- > > %% 4- Estimate source of all data > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 18; > > cfg.grid = grid; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > sourceAll = ft_sourceanalysis(cfg, freqAll); > > > > > > Cheers, > > > > Laura Rueda Delgado > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahjoory86 at gmail.com Wed May 28 23:47:14 2014 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Wed, 28 May 2014 23:47:14 +0200 Subject: [FieldTrip] NaN Values in grid.liedfield Message-ID: Dear all, I want to do EEG source reconstruction. The EEG cap is t 10-20 standard, with 64 channels, but the MRI and electrode positions of subjects are not available. I used Fieldtrip templates for my work. my scripts are as below: cfg = []; cfg.elec=ft_read_sens('standard_1020.elc'); cfg.vol = load('standard_bem.mat'); cfg.channel = epo.clab; [grid] = ft_prepare_leadfield(cfg); But the output for grid.liedfield includes NAN values. I hope someone can give me comments on this matter. Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Thu May 29 03:56:15 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Thu, 29 May 2014 01:56:15 +0000 Subject: [FieldTrip] possible bug with either ft_volumelookup or AAL atlas Message-ID: <1401328562572.43734@flinders.edu.au> Hello fieldtrippers, I just wanted to check if this is a bug or not. When running the following code: atlas = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/aal/ROI_MNI_V4.nii')) It gives you the following: dim: [91 109 91] hdr: [1x1 struct] transform: [4x4 double] unit: 'mm' tissue: [91x109x91 double] tissuelabel: {1x116 cell} coordsys: 'mni' Take note that tissuelabel is 1x116 When running the following code through ft_volumelookup: cfg = []; cfg.atlas = atlas; cfg.inputcoord = 'mni'; cfg.maskparameter = 'inside'; labels = ft_volumelookup( cfg, source); An error occurs: Error using cat Dimensions of matrices being concatenated are not consistent. Error in ft_volumelookup (line 313) labels.name = cat(1, labels.name, atlas.([fn{k},'label'])); If you invert tissuelabel, so that it becomes 116x1, then the code works. For some reason ft_volumelookup doesnt like a 1xY cell. Thank you, Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathykousik at gmail.com Thu May 29 07:29:52 2014 From: sarathykousik at gmail.com (kousik sarathy) Date: Thu, 29 May 2014 07:29:52 +0200 Subject: [FieldTrip] NaN Values in grid.liedfield In-Reply-To: References: Message-ID: Hey Keyvan, When leadfield structure has NaN it generally means the grid points lie outside the brain. Please have a look at this: http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 11:47 PM, Keyvan Mahjoory wrote: > Dear all, > > I want to do EEG source reconstruction. The EEG cap is t 10-20 standard, > with 64 channels, but the MRI and electrode positions of subjects are not > available. I used Fieldtrip templates for my work. my scripts are as below: > > cfg = []; > cfg.elec=ft_read_sens('standard_1020.elc'); > cfg.vol = load('standard_bem.mat'); > cfg.channel = epo.clab; > [grid] = ft_prepare_leadfield(cfg); > > But the output for grid.liedfield includes NAN values. > I hope someone can give me comments on this matter. > > Best, > Keyvan > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu May 29 09:00:40 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 29 May 2014 09:00:40 +0200 Subject: [FieldTrip] possible bug with either ft_volumelookup or AAL atlas In-Reply-To: <1401328562572.43734@flinders.edu.au> References: <1401328562572.43734@flinders.edu.au> Message-ID: Hi Tyler, That sounds like a bug to me. I've filed it on our bugzilla: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2594 Best, Eelke On 29 May 2014 03:56, Tyler Grummett wrote: > Hello fieldtrippers, > > > I just wanted to check if this is a bug or not. > > > When running the following code: atlas = ft_read_atlas( fullfile( > matlabrootpath, 'Matlab/fieldtrip/template/atlas/aal/ROI_MNI_V4.nii')) > > > It gives you the following: > > > dim: [91 109 91] > hdr: [1x1 struct] > transform: [4x4 double] > unit: 'mm' > tissue: [91x109x91 double] > tissuelabel: {1x116 cell} > coordsys: 'mni' > > Take note that tissuelabel is 1x116 > > When running the following code through ft_volumelookup: > > cfg = []; > cfg.atlas = atlas; > cfg.inputcoord = 'mni'; > cfg.maskparameter = 'inside'; > labels = ft_volumelookup( cfg, source); > > An error occurs: > > Error using cat > Dimensions of matrices being concatenated are not consistent. > > Error in ft_volumelookup (line 313) > labels.name = cat(1, labels.name, atlas.([fn{k},'label'])); > > If you invert tissuelabel, so that it becomes 116x1, then the code works. > > For some reason ft_volumelookup doesnt like a 1xY cell. > > Thank you, > > Tyler > > > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From tyler.grummett at flinders.edu.au Thu May 29 09:26:39 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Thu, 29 May 2014 07:26:39 +0000 Subject: [FieldTrip] possible bug with either ft_volumelookup or AAL atlas In-Reply-To: References: <1401328562572.43734@flinders.edu.au>, Message-ID: <1401348385612.16930@flinders.edu.au> Thank you Eelke, I also noticed that with the AFNI atlas, the labels in the file dont match up to the labels that come out of ft_prepare_sourcemodel. when I say label I mean data.( label) I tested it with the AAL atlas and the labels in the file and the data.( label) match up perfectly. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Eelke Spaak Sent: Thursday, 29 May 2014 4:30 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] possible bug with either ft_volumelookup or AAL atlas Hi Tyler, That sounds like a bug to me. I've filed it on our bugzilla: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2594 Best, Eelke On 29 May 2014 03:56, Tyler Grummett wrote: > Hello fieldtrippers, > > > I just wanted to check if this is a bug or not. > > > When running the following code: atlas = ft_read_atlas( fullfile( > matlabrootpath, 'Matlab/fieldtrip/template/atlas/aal/ROI_MNI_V4.nii')) > > > It gives you the following: > > > dim: [91 109 91] > hdr: [1x1 struct] > transform: [4x4 double] > unit: 'mm' > tissue: [91x109x91 double] > tissuelabel: {1x116 cell} > coordsys: 'mni' > > Take note that tissuelabel is 1x116 > > When running the following code through ft_volumelookup: > > cfg = []; > cfg.atlas = atlas; > cfg.inputcoord = 'mni'; > cfg.maskparameter = 'inside'; > labels = ft_volumelookup( cfg, source); > > An error occurs: > > Error using cat > Dimensions of matrices being concatenated are not consistent. > > Error in ft_volumelookup (line 313) > labels.name = cat(1, labels.name, atlas.([fn{k},'label'])); > > If you invert tissuelabel, so that it becomes 116x1, then the code works. > > For some reason ft_volumelookup doesnt like a 1xY cell. > > Thank you, > > Tyler > > > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From katrinheimann at gmail.com Thu May 29 11:55:35 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Thu, 29 May 2014 11:55:35 +0200 Subject: [FieldTrip] which baseline correction to choose for frequency analysis Message-ID: Hey together, another rather conceptual question: I am wondering about the baselinecorrection for the frequencyanalysis. I want to compare two timeperiods of one second each, lying right after each other. In the preprocessing I have baseline corrected them using 100 ms before the first piece (last part of a fixationcross period). Do I use the same part for the frequencyanalysis? Will say, do I run the analysis let's say from -0.5 (0 point is end of fixation cross) to 2.5 s, correcting with [-0.1 0] and then extract the two different conditions by statistical extraction (each 1 second long) ? Or do I run two analysis on (a bit more than) one second each, using the whole trial as baseline? thanks a lot for your advice again! Best Katrin -------------- next part -------------- An HTML attachment was scrubbed... URL: From nickwan at aggiemail.usu.edu Thu May 29 12:12:20 2014 From: nickwan at aggiemail.usu.edu (Nick Wan) Date: Thu, 29 May 2014 04:12:20 -0600 Subject: [FieldTrip] which baseline correction to choose for frequency analysis In-Reply-To: References: Message-ID: The most common event-related ​preprocessing is baseline correction for each event (in your case, 100ms baseline correction unique to each 1000ms epoch) -- at least, in my review of event-related imaging. On Thu, May 29, 2014 at 3:55 AM, KatrinH Heimann wrote: > Hey together, > another rather conceptual question: > I am wondering about the baselinecorrection for the frequencyanalysis. > I want to compare two timeperiods of one second each, lying right after > each other. > In the preprocessing I have baseline corrected them using 100 ms before > the first piece (last part of a fixationcross period). > Do I use the same part for the frequencyanalysis? Will say, do I run the > analysis let's say from -0.5 (0 point is end of fixation cross) to 2.5 s, > correcting with [-0.1 0] and then extract the two different conditions by > statistical extraction (each 1 second long) ? Or do I run two analysis on > (a bit more than) one second each, using the whole trial as baseline? > > thanks a lot for your advice again! Best > Katrin > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Nick Wan Graduate Student Utah State University Psychology Department 2810 Old Main Hill Logan, UT 84322 Office: HSRC 004 Phone: 435-554-8788 Blog: truebra.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Thu May 29 12:20:12 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 29 May 2014 10:20:12 +0000 Subject: [FieldTrip] which baseline correction to choose for frequency analysis In-Reply-To: <23434_1401357818_538705FA_23434_514_1_CACnHcBdHMpYa6PGGz6=c2Cd9FfD1bR3Cgk+OGkTesrgpsR=apA@mail.gmail.com> References: <23434_1401357818_538705FA_23434_514_1_CACnHcBdHMpYa6PGGz6=c2Cd9FfD1bR3Cgk+OGkTesrgpsR=apA@mail.gmail.com> Message-ID: Hi Katrin, it sounds like you will end up using 'depsamplesT' as your statistic (because you compare repeated measures = 2 consecutive time intervals from the same subject or trial) - why do you need to use baseline-correction then? The pairing should already account for differences in baseline power between subjects (or trials). If you do need a baseline correction, I would not choose such a short baseline in the frequency domain, but go for an average over a much longer (.5 to 1 second) interval, particularly if you intend to baseline-correct single trials (because a short baseline is more likely to project noise from the baseline into your interval of interest). Also, keep in mind that ft_freqanalysis computes power across a time window (specified by you in cfg.t_ftimwin), so that power between -.1 and 0 may not only reflect "baseline" power. Best Max ________________________________ Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" im Auftrag von "KatrinH Heimann [katrinheimann at gmail.com] Gesendet: Donnerstag, 29. Mai 2014 11:55 An: FieldTrip discussion list Betreff: [FieldTrip] which baseline correction to choose for frequency analysis Hey together, another rather conceptual question: I am wondering about the baselinecorrection for the frequencyanalysis. I want to compare two timeperiods of one second each, lying right after each other. In the preprocessing I have baseline corrected them using 100 ms before the first piece (last part of a fixationcross period). Do I use the same part for the frequencyanalysis? Will say, do I run the analysis let's say from -0.5 (0 point is end of fixation cross) to 2.5 s, correcting with [-0.1 0] and then extract the two different conditions by statistical extraction (each 1 second long) ? Or do I run two analysis on (a bit more than) one second each, using the whole trial as baseline? thanks a lot for your advice again! Best Katrin From katrinheimann at gmail.com Thu May 29 13:38:53 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Thu, 29 May 2014 13:38:53 +0200 Subject: [FieldTrip] which baseline correction to choose for frequency analysis In-Reply-To: References: <23434_1401357818_538705FA_23434_514_1_CACnHcBdHMpYa6PGGz6=c2Cd9FfD1bR3Cgk+OGkTesrgpsR=apA@mail.gmail.com> Message-ID: Thanks Max! That helped! I will indeed not do the baseline correction! k 2014-05-29 12:20 GMT+02:00 Stenner, Max-Philipp < max-philipp.stenner at med.ovgu.de>: > Hi Katrin, > > it sounds like you will end up using 'depsamplesT' as your statistic > (because you compare repeated measures = 2 consecutive time intervals from > the same subject or trial) - why do you need to use baseline-correction > then? The pairing should already account for differences in baseline power > between subjects (or trials). If you do need a baseline correction, I would > not choose such a short baseline in the frequency domain, but go for an > average over a much longer (.5 to 1 second) interval, particularly if you > intend to baseline-correct single trials (because a short baseline is more > likely to project noise from the baseline into your interval of interest). > Also, keep in mind that ft_freqanalysis computes power across a time window > (specified by you in cfg.t_ftimwin), so that power between -.1 and 0 may > not only reflect "baseline" power. > > Best > > Max > > > > ________________________________ > > Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" > im Auftrag von "KatrinH Heimann [katrinheimann at gmail.com] > Gesendet: Donnerstag, 29. Mai 2014 11:55 > An: FieldTrip discussion list > Betreff: [FieldTrip] which baseline correction to choose for frequency > analysis > > Hey together, > another rather conceptual question: > I am wondering about the baselinecorrection for the frequencyanalysis. > I want to compare two timeperiods of one second each, lying right after > each other. > In the preprocessing I have baseline corrected them using 100 ms before > the first piece (last part of a fixationcross period). > Do I use the same part for the frequencyanalysis? Will say, do I run the > analysis let's say from -0.5 (0 point is end of fixation cross) to 2.5 s, > correcting with [-0.1 0] and then extract the two different conditions by > statistical extraction (each 1 second long) ? Or do I run two analysis on > (a bit more than) one second each, using the whole trial as baseline? > > thanks a lot for your advice again! Best > Katrin > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Fri May 30 04:09:09 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Fri, 30 May 2014 02:09:09 +0000 Subject: [FieldTrip] ft_mvaranalysis Message-ID: <1401415735027.24988@flinders.edu.au> Hello fieldtrippers, Recently when I ran the following code: cfg = []; cfg.order = 5; cfg.toolbox = 'biosig'; mdata = ft_mvaranalysis( cfg, vchan); with this data: vchan = fsample: 500 sampleinfo: [14x2 double] trial: {1x14 cell} time: {1x14 cell} label: {1x116 cell} cfg: [1x1 struct] ?I got this error : Undefined function 'mvar' for input arguments of type 'double'. Error in ft_mvaranalysis (line 385) [ar, rc, pe] = mvar(dat', cfg.order, cfg.mvarmethod); I dont really know what has gone wrong, considering I have ran this code before with 1400 channels. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Fri May 30 04:15:01 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Fri, 30 May 2014 02:15:01 +0000 Subject: [FieldTrip] ft_networkanalysis Message-ID: <1401416086248.33062@flinders.edu.au> Hello fieldtrippers, Really interesting in running ft_networkanalysis and getting the most out of the function. Firstly, what types of analyses are recommended? and in what order... Ive tried looking on the brain connectivity toolbox website, but as it is already incorporated into fieldtrip so I thought I would ask on this forum if there is a recommended flow of processes. I am happy to be told to just look on the website. Also is there a between network comparison? Or is that another thing to just get from the website ( I believe they do it with the 'network based statistic' toolbox). Secondly,? when do you think there will be support for global efficiency, I am mainly interesting in calculating small-worldedness. Kind regards, Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From yingli.ucla at gmail.com Fri May 30 09:14:09 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Fri, 30 May 2014 00:14:09 -0700 Subject: [FieldTrip] Mesh genration error using the template MRI Message-ID: Dear all, Fieldtrip provided a template headmodel “standard_bem.mat" and a template MRI "standard_mri.mat". I tried to use the template MRI to create the BEM head model by myself. But it seems that the scalp mesh generated by myself looks a little weird (attached). I have no idea why the scalp mesh generated by myself looks different from the one provided by the template headmodel. Does anyone know the reason? The code I used is: cfg=[]; cfg.tissue={'brain','skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,seg); Thanks a lot! Ying -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: scalp mesh.fig Type: application/x-matlab-figure Size: 14678 bytes Desc: not available URL: From michelecolombo at live.it Fri May 30 17:19:24 2014 From: michelecolombo at live.it (michele colombo) Date: Fri, 30 May 2014 17:19:24 +0200 Subject: [FieldTrip] how to specify each channel-color in a topoplot Message-ID: Dear all, My goal is to make a double plot: 1) a subplot with a topoplot of channel-values that are color-mapped, 2) a sorted stem-plot where the stem color is mapped to its height., and represent the channel values The outcome should be more easily interpretable than a colorbar, because it would allow to appreciate the whole distribution at a glance, and provide spatial info about the distance between colors. The first step would be to visualize a 1*num_channels vector plotted on the eeg scalp, with the usual topoplot style, and with colors that I define. I compute these values outside of fieldtrip, so I need to re-create the expected fieldtrip structure. Question: how to properly preserve the value-color mapping? all the intuitive options I tried fail with this respect. somehow the colormap given is used as the range of possible color-rgb-values, and subsequently the colors are chosen from this map. Instead, I would want to actually give the channel-by-channel color value to be plotted on the scalp, (interpolating as usual in the space across channels). attached, you can see a failed attempt: the colormap plotted is flattened to a very narrow sub-range of the colomap given. relevant parts of the used code: ---- hh=axes('Position',[.62 .6 .3 .3],'Layer','top'); % overlay on plot % the way i define the colormap. I tried also with a simple: winter(number_of_channels) cfg.colormap= rgbslide(all_chan_stat,'low_color',[0 0 0.75],'low_val',min(all_chan_stat), ... 'zero_color',[0 0.75 0.75],'zero_val',median(all_chan_stat), ... 'high_color',[1 0.9 0],'res',numel(all_chan_stat)); if ~isempty([bads_max bads_min]) cfg.highlight=sort([bads_max bads_min]); % hilight some outliers. this works fine. end cfg.interpolation='v4'; cfg.style='straight'; cfg.maplimits='maxmin'; fieldtrippath='/data1/toolbox/fieldtrip/compat/'; addpath(fieldtrippath); topoplot(cfg,[all_chan_stat']); % all_chan_stat is my 1*num_channels = 257 channels from the EGI system. % the old-deprecated topoplot function seems more easily accessible than the current one, provided I just use fieldtrip to plot, not to compute, the values. sorted=sort(all_chan_stat) for cc= 1: length(channels) stem(cc, sorted(cc), 'Color', cfg.colormap(cc,:), 'MarkerFaceColor', cfg.colormap(cc,:)) ; hold on; end --- Another option would be to first do the topoplot, given a colormap, then to retrieve the color plotted at each channel (but I don't know how), and use these colors to plot the stem --- another attempted option: set(gca,'colororder',cfg.colormap); plot(channels, all_chan_stat) -------------- next part -------------- A non-text attachment was scrubbed... Name: topoplot_and_stem-colors.png Type: image/png Size: 39798 bytes Desc: not available URL: From pgoodin at swin.edu.au Thu May 1 07:30:41 2014 From: pgoodin at swin.edu.au (Peter Goodin) Date: Thu, 1 May 2014 05:30:41 +0000 Subject: [FieldTrip] Multiple source inversion problems for group MNE analysis Message-ID: Hi Fieldtrip list, I'm trying to do group source analysis using MNE but have run into a bit of a snag. After running ft_sourceanalysis (data is 1600ms / 901 data points, source model has been made via SPM (8196 verticies), head model through segmentation of the individual's MRI - all looks to be aligned, similar to the output of SPM (see and plots sensibly using ft_sourcemovie) I've tried running ft_sourceinterpolation using the data on an individual's MRI (freshly read in using ft_read_mri) or the SPM T1 template (also using ft_read_mri). If using the individual's MRI (dimensions = 256 256 176), with or without downsampling, after an hour or so I get an out of memory error and that's that. Running it with the template works fine and is finished ~90 seconds. The results using ft_sourceplot (ortho method) however don't look right (see interp.jpg). Additionally there's no field in the interpolated's cfg about anatomy afterward. So taking another route and just trying to use ft_sourcegrandaverage on the output of ft_sourcelocalisation I'm met with "??? Error using ==> ft_sourcegrandaverage at 111 different grid locations in source reconstructions" I have absolutely no idea what I'm doing wrong and would appreciate any help. An abridged version of the script I'm using for mass conversion to source space is below: sourcemodel = ft_read_headshape(gii_list(i,:)); <-- this is the ...2cortex_8196.surf.gii mesh from spm mri = ft_read_mri([structdir mri_list(i,1:end-2)]); <--- individual participant's raw MRI in nii form. cfg = []; cfg.coordsys = 'spm'; cfg.output = {'brain'}; seg = ft_volumesegment(cfg, mri); cfg = []; cfg.method = 'singleshell'; conductionmodel = ft_prepare_headmodel(cfg, seg); conductionmodel = ft_convert_units(conductionmodel,'cm'); conductionmodel = ft_convert_units(conductionmodel,'mm'); %%Check everything's aligned correctly: figure;hold on; subplot(1,2,1), ft_plot_vol(conductionmodel, 'facecolor', [0 0 1]);alpha 0.5; ft_plot_mesh(sourcemodel, 'edgecolor', [0 1 0]); camlight ft_plot_sens(sens, 'style', 'r*'); subplot(1,2,2), ft_plot_vol(conductionmodel, 'facecolor', [0 0 1]);alpha 0.5; ft_plot_mesh(sourcemodel, 'edgecolor', [0 1 0]); camlight ft_plot_sens(sens, 'style', 'r*'); view([90 0]); view([90 0]) gcf; suptitle([gii_list(i,2:5) ' source model']); saveas(gcf, [gii_list(i,2:6) 'source model.tiff']); close(gcf); assignin('base', [gii_list(i,2:6) 'sourcemodel'], sourcemodel); <--- rename hold variable to participant number assignin('base', [gii_list(i,2:6) 'conductionmodel'], conductionmodel); <--- ditto save([gii_list(i,2:6) 'model'], [gii_list(i,2:6) 'sourcemodel'], [gii_list(i,2:6) 'conductionmodel'], '-v6'); %% CREATE LEADFIELD & LOCALISED DATA load(sens_data_list(i,:)); <--- Load sensor space condition data conds_list = (who('*nback*av')) <--- Create participant specific list datcm = eval(conds_list{1,1}); dat = datcm; dat.grad = ft_convert_units(datcm.grad, 'mm'); %Leadfield goes here <--- Mostly taken from the tutorial cfg = []; cfg.grad = dat.grad; % sensor positions cfg.channel = 'MEG'; % the used channels cfg.grid.pos = sourcemodel.pnt; % source points <---Does this have something to do with the problem? cfg.grid.inside = 1:size(sourcemodel.pnt,1); % all source points are inside of the brain <--- Or this? cfg.vol = conductionmodel; % volume conduction model leadfield = ft_prepare_leadfield(cfg); assignin('base', [conds_list{1,1} '_leadfield'], leadfield); save([gii_list(i,2:6) 'model'], [conds_list{1,1} '_leadfield'], '-v6', '-append'); clear dat; for k = 1:size(conds_list,1); disp('---'); disp(['Creating source data for ' conds_list{k,1}]); disp('---'); datcm = eval(conds_list{k,1}); dat = datcm; dat.grad = ft_convert_units(datcm.grad, 'mm'); %Inversion goes here <--- Mostly taken from the tutorial cfg = []; cfg.method = 'mne'; cfg.grid = leadfield; cfg.vol = conductionmodel; cfg.mne.prewhiten = 'yes'; cfg.mne.lambda = 3; cfg.mne.scalesourcecov = 'yes'; sourcedat = ft_sourceanalysis(cfg,dat); assignin('base', [conds_list{k,1} '_source'], sourcedat); k = k + 1; end %%General saving stuff a = who('*C_av_source'); b = a(1:2:end,1); save([sourcedatadir gii_list(i,2:6) 'condep_conds'], char(b(1,1)), '-v6'); for l = 2:size(b,1); save([sourcedatadir gii_list(i,2:6) 'condep_conds'], char(b(l,1)), '-append', '-v6'); l = l + 1; end save([sourcedatadir gii_list(i,2:6) 'source'], '*_source', '-v6'); Thanks again, Peter __________________________ Peter Goodin, BSc (Hons), Ph.D Candidate. Brain and Psychological Sciences Research Centre (BPsych) Swinburne University, Hawthorn, Vic, 3122 http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149 Monash Alfred Psychiatry Research Centre (MAPrc) Level 4, 607 St Kilda Road, Melbourne 3004 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: interp.jpg Type: image/jpeg Size: 17514 bytes Desc: interp.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: c112_source model.tiff Type: image/tiff Size: 233110 bytes Desc: c112_source model.tiff URL: From pierpaolo12croce at gmail.com Thu May 1 14:56:59 2014 From: pierpaolo12croce at gmail.com (Pierpaolo Croce) Date: Thu, 1 May 2014 14:56:59 +0200 Subject: [FieldTrip] Undefined function 'mtimes' for input arguments of type 'cell'. Message-ID: Undefined function 'mtimes' for input arguments of type 'cell'. I have this error in using "ft_databrowser" like im the tutorial web page. can someone help me? -- PC -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu May 1 15:01:58 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 1 May 2014 15:01:58 +0200 Subject: [FieldTrip] Undefined function 'mtimes' for input arguments of type 'cell'. In-Reply-To: References: Message-ID: Hi Pierpaolo, Could you show us what input data and cfg you are providing for ft_databrowser? Best, Eelke On 1 May 2014 14:56, Pierpaolo Croce wrote: > Undefined function 'mtimes' for input arguments of type 'cell'. > > I have this error in using "ft_databrowser" like im the tutorial web page. > > can someone help me? > > > -- > PC > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From eliasc at live.it Thu May 1 23:54:32 2014 From: eliasc at live.it (Elias P. Casula) Date: Thu, 1 May 2014 23:54:32 +0200 Subject: [FieldTrip] ft_preproc_dftfilter function In-Reply-To: References: Message-ID: Dear all,I found some problems with the ft_preproc_dftfilter function. This function should remove the 50hz noise from the signal. But when I call the function with [filt] = ft_preproc_dftfilter(mymatrixdata, 1024, 50) the 50hz noise is still in the filtered signal. Does anyone else had the same problem?Thanks a lot, Elias -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Fri May 2 08:51:11 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 02 May 2014 08:51:11 +0200 Subject: [FieldTrip] ft_preproc_dftfilter function In-Reply-To: References: Message-ID: <5363405F.3010802@donders.ru.nl> Hi Elias, please see http://fieldtrip.fcdonders.nl/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter that should enlighten you :) Best, Jörn On 5/1/2014 11:54 PM, Elias P. Casula wrote: > > Dear all, > I found some problems with the ft_preproc_dftfilter function. This > function should remove the 50hz noise from the signal. But when I call > the function with > > [filt] = ft_preproc_dftfilter(mymatrixdata, 1024, 50) > > the 50hz noise is still in the filtered signal. Does anyone else had > the same problem? > Thanks a lot, > > Elias > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From eliasc at live.it Fri May 2 09:36:35 2014 From: eliasc at live.it (Elias P. Casula) Date: Fri, 2 May 2014 09:36:35 +0200 Subject: [FieldTrip] ft_preproc_dftfilter function In-Reply-To: <5363405F.3010802@donders.ru.nl> References: , , <5363405F.3010802@donders.ru.nl> Message-ID: Thanks Jorn, Unfortunately in my case the signal remains exactly the same after the dft filter. Maybe there is something that I'm missing in the procedure? When I call the function I just insert my data matrix, the sampling frequency (1024) and the frequency band that I want to filter (50). The function generates a new file but apparently nothing changes. > Date: Fri, 2 May 2014 08:51:11 +0200 > From: jm.horschig at donders.ru.nl > To: fieldtrip at science.ru.nl > Subject: Re: [FieldTrip] ft_preproc_dftfilter function > > Hi Elias, > > please see > http://fieldtrip.fcdonders.nl/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter > that should enlighten you :) > > Best, > Jörn > > On 5/1/2014 11:54 PM, Elias P. Casula wrote: > > > > Dear all, > > I found some problems with the ft_preproc_dftfilter function. This > > function should remove the 50hz noise from the signal. But when I call > > the function with > > > > [filt] = ft_preproc_dftfilter(mymatrixdata, 1024, 50) > > > > the 50hz noise is still in the filtered signal. Does anyone else had > > the same problem? > > Thanks a lot, > > > > Elias > > > > > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Fri May 2 10:27:35 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Fri, 2 May 2014 08:27:35 +0000 Subject: [FieldTrip] clustering of bipolar referenced data Message-ID: Hi all, I would just like to confirm that I am not missing something. I am using cluster-based permutation stats for an intracranial dataset consisting of three bipolar channels. These are derived from four neighbouring contacts on the same electrode (i.e., channel 1 = contact 1 vs. contact 2, channel 2 = contact 2 vs. contact 3, etc.). For clustering in space, I've defined 2 to be a neighbour of 1 (and 3), and vice versa (etc. for the other channels). Since bipolar referencing means looking at differences between contacts, the fact that channels 1 and 2, for example, are partially derived from the same contact (contact 2), should not prevent me from clustering across these two channels when running stats - is that correct? Thanks! Best Max From martine.vanschouwenburg at ucsf.edu Fri May 2 20:16:29 2014 From: martine.vanschouwenburg at ucsf.edu (Martine van Schouwenburg) Date: Fri, 2 May 2014 11:16:29 -0700 Subject: [FieldTrip] ft_databrowser crashes Matlab Message-ID: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> Hi Fieldtrip experts, I am experiencing a problem with the ft_databrowser routine. Matlab crashes when I'm trying to run it, forcing me to end the Matlab session. ('Matlab has encountered an internal problem and needs to close.'). It seems more like a Matlab/Windows related issue when looking at the crash report (see below), but I am posting it here because it also seems to depend on the data that I use as input. When I run the routine on the 'raw' data (after defining the trials) it is working fine, but after I ran ICA and try to use the databrowser to look at the components, it crashes at line 676. This is the part where it calls the subfunction redraw_cb. Does anyone might have a clue what in the component data might cause this problem? Maybe some of you have experienced this before? I also send a request for Tech Support to Matlab. Best, Martine Here is the Matlab crash report if that is of any help: ------------------------------------------------------------------------ Segmentation violation detected at Thu May 01 22:28:30 2014 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Default Encoding: windows-1252 MATLAB Root : C:\Program Files\MATLAB\R2012b MATLAB Version : 8.0.0.783 (R2012b) Operating System: Microsoft Windows 7 Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode Window System : Version 6.1 (Build 7601: Service Pack 1) Fault Count: 1 Abnormal termination: Segmentation violation Register State (from fault): RAX = 00000000000001a4 RBX = 000000007a8425c0 RCX = 00000000000262de RDX = 00000000000001b2 RSP = 0000000004110a50 RBP = 000000000000007e RSI = 000000007a75cab0 RDI = 000000013942b996 R8 = 00000000000262de R9 = 0000000000000230 R10 = 0000000000000000 R11 = 0000000004110b28 R12 = 0000000000f206cd R13 = 0000000077ce4060 R14 = 000000000002635c R15 = 00000000000006c8 RIP = 000000006000d341 EFL = 00010216 CS = 0033 FS = 0053 GS = 002b Stack Trace (from fault): [ 0] 0x000000006000d341 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( RenderEngineBase::~RenderEngineBase+171553 ) [ 1] 0x000000005ff83130 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) [ 2] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) [ 3] 0x000000005fede587 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( renderAnimatedKids+000519 ) [ 4] 0x000000005fee3788 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) [ 5] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) [ 6] 0x000000005ff04729 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( FigureSetVisualAutoMode+001561 ) [ 7] 0x000000005ff0abbd C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( UIJ_CreatePeerWindow+001597 ) [ 8] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) [ 9] 0x0000000060013548 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( RenderEngineBase::~RenderEngineBase+196648 ) [ 10] 0x000000005ff06b87 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( FigureSetVisualAutoMode+010871 ) [ 11] 0x000000005ff06c0d C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( FigureSetVisualAutoMode+011005 ) [ 12] 0x0000000063425006 C:\Program Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( wm_ExposeFcn_Pre_Optional+000374 ) [ 13] 0x0000000064c8c694 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) [ 14] 0x0000000064c8e456 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( UIJ_IsWindowShowing+000438 ) [ 15] 0x0000000064c8f943 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( UIJ_clearWaitForResize+002067 ) [ 16] 0x0000000064c8fa61 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) [ 17] 0x0000000064c707ae C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( UIJ_MarkEventFinished+005838 ) [ 18] 0x0000000064c70800 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( UIJ_MarkEventFinished+005920 ) [ 19] 0x0000000064c892ac C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( uij::JavaDraw2D::paintQuadStrip+001324 ) [ 20] 0x0000000064d4e808 C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( uddSetListenerRecursionWarning+000680 ) [ 21] 0x0000000064d4ee6c C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( UDListenerManagerHost::notifyEvent+000076 ) [ 22] 0x0000000064d4697d C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( UDEventInfo::send+000093 ) [ 23] 0x000000005fb9cedb C:\Program Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( MErrorException::operator=+047675 ) [ 24] 0x00000000055ce0b6 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( UIW_IsUserMessage+000086 ) [ 25] 0x00000000055ce7b9 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( UIW_SetGLIMUserMsg+000153 ) [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( GetMenuBarInfo+000638 ) [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( SystemParametersInfoW+000235 ) [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( IsProcessDPIAware+000465 ) [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( KiUserCallbackDispatcher+000031 ) [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( PeekMessageW+000186 ) [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( GetKeyState+000238 ) [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( PeekMessageA+000087 ) [ 33] 0x00000000055a8f4b C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( UIW_SetCurrentDialog+000731 ) [ 34] 0x00000000055cfbe2 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( ws_FreeSystemFont+000546 ) [ 35] 0x000000000485e6a3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( sysq::removeCommitDatabaseUpdatesHook+002131 ) [ 36] 0x000000000485fe18 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( sysq::removeCommitDatabaseUpdatesHook+008136 ) [ 37] 0x0000000004861a20 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( sysq::addProcessPendingEventsUnitTestHook+000240 ) [ 38] 0x0000000004861ae8 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( sysq::addProcessPendingEventsUnitTestHook+000440 ) [ 39] 0x0000000004861ca3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( sysq::addProcessPendingEventsUnitTestHook+000883 ) [ 40] 0x0000000004861d76 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( sysq::addProcessPendingEventsUnitTestHook+001094 ) [ 41] 0x000000005ff0c4fe C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) [ 42] 0x0000000074e8d17f C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( Mfunction_handle::dispatch+001023 ) [ 43] 0x0000000074e8cf82 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( Mfunction_handle::dispatch+000514 ) [ 44] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) [ 45] 0x000007feef3a5ca4 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( inFunctionHandleInterface::DestroyWorkspace+295012 ) [ 46] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) [ 47] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) [ 48] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) [ 49] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) [ 50] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) [ 51] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) [ 52] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) [ 53] 0x000007feef38210b C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( inFunctionHandleInterface::DestroyWorkspace+148683 ) [ 54] 0x000007feef393edf C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( inFunctionHandleInterface::DestroyWorkspace+221855 ) [ 55] 0x000007feef3b0ae8 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( inFunctionHandleInterface::DestroyWorkspace+339624 ) [ 56] 0x000007feef398d94 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( inFunctionHandleInterface::DestroyWorkspace+242004 ) [ 57] 0x000007feef3a2978 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( inFunctionHandleInterface::DestroyWorkspace+281912 ) [ 58] 0x000007feef3a5a8b C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( inFunctionHandleInterface::DestroyWorkspace+294475 ) [ 59] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) [ 60] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) [ 61] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) [ 62] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) [ 63] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) [ 64] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) [ 65] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) [ 66] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) [ 67] 0x000007feef43318f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( inEachVisibleName+014415 ) [ 68] 0x000007feef3a74ca C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( inFunctionHandleInterface::DestroyWorkspace+301194 ) [ 69] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) [ 70] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) [ 71] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) [ 72] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) [ 73] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) [ 74] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) [ 75] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) [ 76] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) [ 77] 0x000007feef43318f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( inEachVisibleName+014415 ) [ 78] 0x000007feef3a74ca C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( inFunctionHandleInterface::DestroyWorkspace+301194 ) [ 79] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) [ 80] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) [ 81] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) [ 82] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) [ 83] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) [ 84] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) [ 85] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) [ 86] 0x000007feef4451e5 C:\Program 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URL: From mcantor at umich.edu Fri May 2 20:58:06 2014 From: mcantor at umich.edu (Max Cantor) Date: Fri, 2 May 2014 14:58:06 -0400 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: <5363e841.061d2a0a.2297.ffffb0e2SMTPIN_ADDED_BROKEN@mx.google.com> References: <5363e841.061d2a0a.2297.ffffb0e2SMTPIN_ADDED_BROKEN@mx.google.com> Message-ID: Hi Martine, I can't say for sure, but I believe it's because ft_databrowser is only designed to take channel data, not component data. To view component data, you should use ft_componentbrowser. Hope that helps, Max Cantor Research Assistant Computational Neurolinguistics Lab University of Michigan On Fri, May 2, 2014 at 2:16 PM, Martine van Schouwenburg < martine.vanschouwenburg at ucsf.edu> wrote: > Hi Fieldtrip experts, > > > > I am experiencing a problem with the ft_databrowser routine. Matlab > crashes when I’m trying to run it, forcing me to end the Matlab session. > (‘Matlab has encountered an internal problem and needs to close.’). It > seems more like a Matlab/Windows related issue when looking at the crash > report (see below), but I am posting it here because it also seems to > depend on the data that I use as input. When I run the routine on the ‘raw’ > data (after defining the trials) it is working fine, but after I ran ICA > and try to use the databrowser to look at the components, it crashes at > line 676. > > This is the part where it calls the subfunction redraw_cb. Does anyone > might have a clue what in the component data might cause this problem? > Maybe some of you have experienced this before? I also send a request for > Tech Support to Matlab. > > > > Best, Martine > > > > Here is the Matlab crash report if that is of any help: > > > > > > > > ------------------------------------------------------------------------ > > Segmentation violation detected at Thu May 01 22:28:30 2014 > > ------------------------------------------------------------------------ > > > > Configuration: > > Crash Decoding : Disabled > > Default Encoding: windows-1252 > > MATLAB Root : C:\Program Files\MATLAB\R2012b > > MATLAB Version : 8.0.0.783 (R2012b) > > Operating System: Microsoft Windows 7 > > Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD > > Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java > HotSpot(TM) 64-Bit Server VM mixed mode > > Window System : Version 6.1 (Build 7601: Service Pack 1) > > > > Fault Count: 1 > > > > > > Abnormal termination: > > Segmentation violation > > > > Register State (from fault): > > RAX = 00000000000001a4 RBX = 000000007a8425c0 > > RCX = 00000000000262de RDX = 00000000000001b2 > > RSP = 0000000004110a50 RBP = 000000000000007e > > RSI = 000000007a75cab0 RDI = 000000013942b996 > > > > R8 = 00000000000262de R9 = 0000000000000230 > > R10 = 0000000000000000 R11 = 0000000004110b28 > > R12 = 0000000000f206cd R13 = 0000000077ce4060 > > R14 = 000000000002635c R15 = 00000000000006c8 > > > > RIP = 000000006000d341 EFL = 00010216 > > > > CS = 0033 FS = 0053 GS = 002b > > > > Stack Trace (from fault): > > [ 0] 0x000000006000d341 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( > RenderEngineBase::~RenderEngineBase+171553 ) > > [ 1] 0x000000005ff83130 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) > > [ 2] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 3] 0x000000005fede587 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( renderAnimatedKids+000519 ) > > [ 4] 0x000000005fee3788 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) > > [ 5] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 6] 0x000000005ff04729 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( > FigureSetVisualAutoMode+001561 ) > > [ 7] 0x000000005ff0abbd C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( UIJ_CreatePeerWindow+001597 > ) > > [ 8] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 9] 0x0000000060013548 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( > RenderEngineBase::~RenderEngineBase+196648 ) > > [ 10] 0x000000005ff06b87 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( > FigureSetVisualAutoMode+010871 ) > > [ 11] 0x000000005ff06c0d C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( > FigureSetVisualAutoMode+011005 ) > > [ 12] 0x0000000063425006 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( > wm_ExposeFcn_Pre_Optional+000374 ) > > [ 13] 0x0000000064c8c694 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) > > [ 14] 0x0000000064c8e456 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( > UIJ_IsWindowShowing+000438 ) > > [ 15] 0x0000000064c8f943 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( > UIJ_clearWaitForResize+002067 ) > > [ 16] 0x0000000064c8fa61 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) > > [ 17] 0x0000000064c707ae C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( > UIJ_MarkEventFinished+005838 ) > > [ 18] 0x0000000064c70800 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( > UIJ_MarkEventFinished+005920 ) > > [ 19] 0x0000000064c892ac C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( > uij::JavaDraw2D::paintQuadStrip+001324 ) > > [ 20] 0x0000000064d4e808 C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( > uddSetListenerRecursionWarning+000680 ) > > [ 21] 0x0000000064d4ee6c C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( > UDListenerManagerHost::notifyEvent+000076 ) > > [ 22] 0x0000000064d4697d C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( UDEventInfo::send+000093 ) > > [ 23] 0x000000005fb9cedb C:\Program > Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( > MErrorException::operator=+047675 ) > > [ 24] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( UIW_IsUserMessage+000086 ) > > [ 25] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( UIW_SetGLIMUserMsg+000153 ) > > [ 26] 0x00000000774a87fe > C:\Windows\system32\USER32.dll+00165886 ( GetMenuBarInfo+000638 ) > > [ 27] 0x000000007748f5fb > C:\Windows\system32\USER32.dll+00062971 ( SystemParametersInfoW+000235 ) > > [ 28] 0x0000000077494895 > C:\Windows\system32\USER32.dll+00084117 ( IsProcessDPIAware+000465 ) > > [ 29] 0x00000000775d11f5 > C:\Windows\SYSTEM32\ntdll.dll+00332277 ( KiUserCallbackDispatcher+000031 ) > > [ 30] 0x000000007749908a > C:\Windows\system32\USER32.dll+00102538 ( PeekMessageW+000186 ) > > [ 31] 0x00000000774950fe > C:\Windows\system32\USER32.dll+00086270 ( GetKeyState+000238 ) > > [ 32] 0x0000000077493a6f > C:\Windows\system32\USER32.dll+00080495 ( PeekMessageA+000087 ) > > [ 33] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [ 34] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( ws_FreeSystemFont+000546 ) > > [ 35] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [ 36] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [ 37] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [ 38] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [ 39] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [ 40] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [ 41] 0x000000005ff0c4fe C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) > > [ 42] 0x0000000074e8d17f C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( > Mfunction_handle::dispatch+001023 ) > > [ 43] 0x0000000074e8cf82 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( > Mfunction_handle::dispatch+000514 ) > > [ 44] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 45] 0x000007feef3a5ca4 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( > inFunctionHandleInterface::DestroyWorkspace+295012 ) > > [ 46] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 47] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 48] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 49] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 50] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 51] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 52] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 53] 0x000007feef38210b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( > inFunctionHandleInterface::DestroyWorkspace+148683 ) > > [ 54] 0x000007feef393edf C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( > inFunctionHandleInterface::DestroyWorkspace+221855 ) > > [ 55] 0x000007feef3b0ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( > inFunctionHandleInterface::DestroyWorkspace+339624 ) > > [ 56] 0x000007feef398d94 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( > inFunctionHandleInterface::DestroyWorkspace+242004 ) > > [ 57] 0x000007feef3a2978 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( > inFunctionHandleInterface::DestroyWorkspace+281912 ) > > [ 58] 0x000007feef3a5a8b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( > inFunctionHandleInterface::DestroyWorkspace+294475 ) > > [ 59] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 60] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 61] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 62] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 63] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 64] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 65] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 66] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 67] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 68] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 69] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 70] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 71] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 72] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 73] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 74] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 75] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 76] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 77] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 78] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 79] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 80] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 81] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 82] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 83] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 84] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 85] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 86] 0x000007feef4451e5 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( > inValidateLoadedObject+001893 ) > > [ 87] 0x000007feef454595 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( > init_cleaner+015541 ) > > [ 88] 0x000007feef457b75 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( > inSetMaxFrameCount+002261 ) > > [ 89] 0x000007feef457b48 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( > inSetMaxFrameCount+002216 ) > > [ 90] 0x000007feef457b07 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( > inSetMaxFrameCount+002151 ) > > [ 91] 0x000007feef340213 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( > inPathNotification::function_clear_notification+004019 ) > > [ 92] 0x000007feef44aed0 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( > inEvalCmdWithLocalReturn+000416 ) > > [ 93] 0x000007feef44ae2c C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( > inEvalCmdWithLocalReturn+000252 ) > > [ 94] 0x000007feef44ad71 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( > inEvalCmdWithLocalReturn+000065 ) > > [ 95] 0x0000000079fbf90d C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( > mnDebugPrompt+000109 ) > > [ 96] 0x0000000079fc0471 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( mnParser+000593 ) > > [ 97] 0x00000000749a64a4 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( > mcrInstance::mnParser_on_interpreter_thread+000036 ) > > [ 98] 0x000000007498681f C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( > mcr::setInterpreterThreadToCurrent+029887 ) > > [ 99] 0x0000000074986881 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( > mcr::setInterpreterThreadToCurrent+029985 ) > > [100] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( UIW_IsUserMessage+000086 ) > > [101] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( UIW_SetGLIMUserMsg+000153 ) > > [102] 0x00000000774a87fe > C:\Windows\system32\USER32.dll+00165886 ( GetMenuBarInfo+000638 ) > > [103] 0x000000007748f5fb > C:\Windows\system32\USER32.dll+00062971 ( SystemParametersInfoW+000235 ) > > [104] 0x0000000077494895 > C:\Windows\system32\USER32.dll+00084117 ( IsProcessDPIAware+000465 ) > > [105] 0x00000000775d11f5 > C:\Windows\SYSTEM32\ntdll.dll+00332277 ( KiUserCallbackDispatcher+000031 ) > > [106] 0x000000007749908a > C:\Windows\system32\USER32.dll+00102538 ( PeekMessageW+000186 ) > > [107] 0x00000000774950fe > C:\Windows\system32\USER32.dll+00086270 ( GetKeyState+000238 ) > > [108] 0x0000000077493a6f > C:\Windows\system32\USER32.dll+00080495 ( PeekMessageA+000087 ) > > [109] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [110] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( ws_FreeSystemFont+000546 ) > > [111] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [112] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [113] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [114] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [115] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [116] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [117] 0x000000007498837e C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( > mcr::setInterpreterThreadToCurrent+036894 ) > > [118] 0x0000000074988665 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( > mcr::setInterpreterThreadToCurrent+037637 ) > > [119] 0x000000007497b166 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( > DepfunRules::postWarning+003430 ) > > [120] 0x000000013fc78a33 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) > > [121] 0x000000013fc78c97 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) > > [122] 0x000000013fc79163 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) > > [123] 0x00000000773759ed > C:\Windows\system32\kernel32.dll+00088557 ( BaseThreadInitThunk+000013 ) > > [124] 0x00000000775ac541 > C:\Windows\SYSTEM32\ntdll.dll+00181569 ( > RtlUserThreadStart+000033 ) > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri May 2 21:15:00 2014 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 2 May 2014 21:15:00 +0200 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: References: <5363e841.061d2a0a.2297.ffffb0e2SMTPIN_ADDED_BROKEN@mx.google.com> Message-ID: <1B783442-BFEC-4625-AB21-F59A3ABF1011@donders.ru.nl> Dear Martine, Although I don't have a solution right now, the error message indeed suggest a very low level crash of MATLAB. Therefore, I don't think it is likely that it is related to the fact that you are trying to visualize 'component'-data (which in principle should be possible with ft_databrowser). It's more likely that it's a platform dependent issue, likely related to (compiled) mex-files, or a graphics issue. I remember that occasionally in the past people reported crashes specifically with ft_databrowser, but I don't remember the technical details about this. Could I suggest you to create an account on our bugzilla.fcdonders.nl site, and file this as a new bug, with as much information about it as possible? It would even be better to browse around a bit (use the search functionality, and search for ft_databrowser), you may be able to add this issue as a comment to an already existing bug with the same content. Best, JM On May 2, 2014, at 8:58 PM, Max Cantor wrote: > Hi Martine, > > I can't say for sure, but I believe it's because ft_databrowser is only designed to take channel data, not component data. To view component data, you should use ft_componentbrowser. > > Hope that helps, > > Max Cantor > Research Assistant > Computational Neurolinguistics Lab > University of Michigan > > > > On Fri, May 2, 2014 at 2:16 PM, Martine van Schouwenburg wrote: > Hi Fieldtrip experts, > > > > I am experiencing a problem with the ft_databrowser routine. Matlab crashes when I’m trying to run it, forcing me to end the Matlab session. (‘Matlab has encountered an internal problem and needs to close.’). It seems more like a Matlab/Windows related issue when looking at the crash report (see below), but I am posting it here because it also seems to depend on the data that I use as input. When I run the routine on the ‘raw’ data (after defining the trials) it is working fine, but after I ran ICA and try to use the databrowser to look at the components, it crashes at line 676. > > This is the part where it calls the subfunction redraw_cb. Does anyone might have a clue what in the component data might cause this problem? Maybe some of you have experienced this before? I also send a request for Tech Support to Matlab. > > > > Best, Martine > > > > Here is the Matlab crash report if that is of any help: > > > > > > > > ------------------------------------------------------------------------ > > Segmentation violation detected at Thu May 01 22:28:30 2014 > > ------------------------------------------------------------------------ > > > > Configuration: > > Crash Decoding : Disabled > > Default Encoding: windows-1252 > > MATLAB Root : C:\Program Files\MATLAB\R2012b > > MATLAB Version : 8.0.0.783 (R2012b) > > Operating System: Microsoft Windows 7 > > Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD > > Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode > > Window System : Version 6.1 (Build 7601: Service Pack 1) > > > > Fault Count: 1 > > > > > > Abnormal termination: > > Segmentation violation > > > > Register State (from fault): > > RAX = 00000000000001a4 RBX = 000000007a8425c0 > > RCX = 00000000000262de RDX = 00000000000001b2 > > RSP = 0000000004110a50 RBP = 000000000000007e > > RSI = 000000007a75cab0 RDI = 000000013942b996 > > > > R8 = 00000000000262de R9 = 0000000000000230 > > R10 = 0000000000000000 R11 = 0000000004110b28 > > R12 = 0000000000f206cd R13 = 0000000077ce4060 > > R14 = 000000000002635c R15 = 00000000000006c8 > > > > RIP = 000000006000d341 EFL = 00010216 > > > > CS = 0033 FS = 0053 GS = 002b > > > > Stack Trace (from fault): > > [ 0] 0x000000006000d341 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( RenderEngineBase::~RenderEngineBase+171553 ) > > [ 1] 0x000000005ff83130 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) > > [ 2] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 3] 0x000000005fede587 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( renderAnimatedKids+000519 ) > > [ 4] 0x000000005fee3788 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) > > [ 5] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 6] 0x000000005ff04729 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( FigureSetVisualAutoMode+001561 ) > > [ 7] 0x000000005ff0abbd C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( UIJ_CreatePeerWindow+001597 ) > > [ 8] 0x00000000602cc003 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( GO_TransformObject+001571 ) > > [ 9] 0x0000000060013548 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( RenderEngineBase::~RenderEngineBase+196648 ) > > [ 10] 0x000000005ff06b87 C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( FigureSetVisualAutoMode+010871 ) > > [ 11] 0x000000005ff06c0d C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( FigureSetVisualAutoMode+011005 ) > > [ 12] 0x0000000063425006 C:\Program Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( wm_ExposeFcn_Pre_Optional+000374 ) > > [ 13] 0x0000000064c8c694 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) > > [ 14] 0x0000000064c8e456 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( UIJ_IsWindowShowing+000438 ) > > [ 15] 0x0000000064c8f943 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( UIJ_clearWaitForResize+002067 ) > > [ 16] 0x0000000064c8fa61 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) > > [ 17] 0x0000000064c707ae C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( UIJ_MarkEventFinished+005838 ) > > [ 18] 0x0000000064c70800 C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( UIJ_MarkEventFinished+005920 ) > > [ 19] 0x0000000064c892ac C:\Program Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( uij::JavaDraw2D::paintQuadStrip+001324 ) > > [ 20] 0x0000000064d4e808 C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( uddSetListenerRecursionWarning+000680 ) > > [ 21] 0x0000000064d4ee6c C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( UDListenerManagerHost::notifyEvent+000076 ) > > [ 22] 0x0000000064d4697d C:\Program Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( UDEventInfo::send+000093 ) > > [ 23] 0x000000005fb9cedb C:\Program Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( MErrorException::operator=+047675 ) > > [ 24] 0x00000000055ce0b6 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( UIW_IsUserMessage+000086 ) > > [ 25] 0x00000000055ce7b9 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( UIW_SetGLIMUserMsg+000153 ) > > [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( GetMenuBarInfo+000638 ) > > [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( SystemParametersInfoW+000235 ) > > [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( IsProcessDPIAware+000465 ) > > [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( KiUserCallbackDispatcher+000031 ) > > [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( PeekMessageW+000186 ) > > [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( GetKeyState+000238 ) > > [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( PeekMessageA+000087 ) > > [ 33] 0x00000000055a8f4b C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( UIW_SetCurrentDialog+000731 ) > > [ 34] 0x00000000055cfbe2 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( ws_FreeSystemFont+000546 ) > > [ 35] 0x000000000485e6a3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [ 36] 0x000000000485fe18 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [ 37] 0x0000000004861a20 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [ 38] 0x0000000004861ae8 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [ 39] 0x0000000004861ca3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [ 40] 0x0000000004861d76 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [ 41] 0x000000005ff0c4fe C:\Program Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) > > [ 42] 0x0000000074e8d17f C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( Mfunction_handle::dispatch+001023 ) > > [ 43] 0x0000000074e8cf82 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( Mfunction_handle::dispatch+000514 ) > > [ 44] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 45] 0x000007feef3a5ca4 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( inFunctionHandleInterface::DestroyWorkspace+295012 ) > > [ 46] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 47] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 48] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 49] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 50] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 51] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) > > [ 52] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) > > [ 53] 0x000007feef38210b C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( inFunctionHandleInterface::DestroyWorkspace+148683 ) > > [ 54] 0x000007feef393edf C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( inFunctionHandleInterface::DestroyWorkspace+221855 ) > > [ 55] 0x000007feef3b0ae8 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( inFunctionHandleInterface::DestroyWorkspace+339624 ) > > [ 56] 0x000007feef398d94 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( inFunctionHandleInterface::DestroyWorkspace+242004 ) > > [ 57] 0x000007feef3a2978 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( inFunctionHandleInterface::DestroyWorkspace+281912 ) > > [ 58] 0x000007feef3a5a8b C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( inFunctionHandleInterface::DestroyWorkspace+294475 ) > > [ 59] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 60] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 61] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 62] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 63] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 64] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) > > [ 65] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) > > [ 66] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 67] 0x000007feef43318f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( inEachVisibleName+014415 ) > > [ 68] 0x000007feef3a74ca C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 69] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 70] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 71] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 72] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 73] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 74] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) > > [ 75] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) > > [ 76] 0x000007feef3a9482 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 77] 0x000007feef43318f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( inEachVisibleName+014415 ) > > [ 78] 0x000007feef3a74ca C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 79] 0x000007feef38de1f C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 80] 0x000007feef38dd80 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 81] 0x000007feef3b197d C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 82] 0x000007feef3b0271 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 83] 0x000007feef3920e9 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 84] 0x0000000074e8c80d C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( Mfh_file::dispatch_fh+000509 ) > > [ 85] 0x0000000074e8d0d6 C:\Program Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( Mfunction_handle::dispatch+000854 ) > > [ 86] 0x000007feef4451e5 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( inValidateLoadedObject+001893 ) > > [ 87] 0x000007feef454595 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( init_cleaner+015541 ) > > [ 88] 0x000007feef457b75 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( inSetMaxFrameCount+002261 ) > > [ 89] 0x000007feef457b48 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( inSetMaxFrameCount+002216 ) > > [ 90] 0x000007feef457b07 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( inSetMaxFrameCount+002151 ) > > [ 91] 0x000007feef340213 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( inPathNotification::function_clear_notification+004019 ) > > [ 92] 0x000007feef44aed0 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( inEvalCmdWithLocalReturn+000416 ) > > [ 93] 0x000007feef44ae2c C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( inEvalCmdWithLocalReturn+000252 ) > > [ 94] 0x000007feef44ad71 C:\Program Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( inEvalCmdWithLocalReturn+000065 ) > > [ 95] 0x0000000079fbf90d C:\Program Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( mnDebugPrompt+000109 ) > > [ 96] 0x0000000079fc0471 C:\Program Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( mnParser+000593 ) > > [ 97] 0x00000000749a64a4 C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( mcrInstance::mnParser_on_interpreter_thread+000036 ) > > [ 98] 0x000000007498681f C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( mcr::setInterpreterThreadToCurrent+029887 ) > > [ 99] 0x0000000074986881 C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( mcr::setInterpreterThreadToCurrent+029985 ) > > [100] 0x00000000055ce0b6 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( UIW_IsUserMessage+000086 ) > > [101] 0x00000000055ce7b9 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( UIW_SetGLIMUserMsg+000153 ) > > [102] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( GetMenuBarInfo+000638 ) > > [103] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( SystemParametersInfoW+000235 ) > > [104] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( IsProcessDPIAware+000465 ) > > [105] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( KiUserCallbackDispatcher+000031 ) > > [106] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( PeekMessageW+000186 ) > > [107] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( GetKeyState+000238 ) > > [108] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( PeekMessageA+000087 ) > > [109] 0x00000000055a8f4b C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( UIW_SetCurrentDialog+000731 ) > > [110] 0x00000000055cfbe2 C:\Program Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( ws_FreeSystemFont+000546 ) > > [111] 0x000000000485e6a3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [112] 0x000000000485fe18 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [113] 0x0000000004861a20 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [114] 0x0000000004861ae8 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [115] 0x0000000004861ca3 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [116] 0x0000000004861d76 C:\Program Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [117] 0x000000007498837e C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( mcr::setInterpreterThreadToCurrent+036894 ) > > [118] 0x0000000074988665 C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( mcr::setInterpreterThreadToCurrent+037637 ) > > [119] 0x000000007497b166 C:\Program Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( DepfunRules::postWarning+003430 ) > > [120] 0x000000013fc78a33 C:\Program Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) > > [121] 0x000000013fc78c97 C:\Program Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) > > [122] 0x000000013fc79163 C:\Program Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) > > [123] 0x00000000773759ed C:\Windows\system32\kernel32.dll+00088557 ( BaseThreadInitThunk+000013 ) > > [124] 0x00000000775ac541 C:\Windows\SYSTEM32\ntdll.dll+00181569 ( RtlUserThreadStart+000033 ) > > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl 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URL: From kkb268 at nyu.edu Fri May 2 22:41:24 2014 From: kkb268 at nyu.edu (Kristen Berry) Date: Fri, 2 May 2014 16:41:24 -0400 Subject: [FieldTrip] ft_timelockstatistics cluster correction using ECoG data Message-ID: Dear all, I am using an intracranial EEG dataset to compare average high gamma power waveforms between conditions. I want to correct for multiple comparisons across time, but not across number of electrodes. Here is my input code: cfg=[]; cfg.latency = [0.05 .5]; cfg.parameter = 'trial'; cfg.method = 'montecarlo'; cfg.correctm = 'cluster'; cfg.neighbours = []; cfg.numrandomization = 1000; cfg.statistic = 'indepsamplesT'; cfg.channel = ‘all’; cfg.alpha = 0.05; cfg.clusteralpha = 0.05; cfg.tail = 0; stats = ft_timelockstatistics(cfg, data,control); Fieldtrip’s montecarlo reference page ( http://fieldtrip.fcdonders.nl/reference/ft_statistics_montecarlo) says, “If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels.” However, my input code corrects for the number of channels as well. As an example, when cfg.channel = ‘all’ for ft_timelockstatistics, then Elec11 is not significant. However, if the analysis is limited to Elec11 (cfg.channel = 11), then Elec11 has a significant cluster. Is there a mistake in my code that is causing this? Or is there an older version of fieldtrip that doesn’t correct for # of channels, when cfg.neighbours is empty? Thank you for your input! Best regards, Kristen Kristen Berry Research Assistant NYU School of Medicine -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Sat May 3 11:04:42 2014 From: jm.horschig at donders.ru.nl (=?windows-1252?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Sat, 03 May 2014 11:04:42 +0200 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> References: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> Message-ID: <5364B12A.80807@donders.ru.nl> Hi Martine, great to hear that you are using FieldTrip ;) hope you like it. As JM said, it is indeed some low-level problem with Windows 7, Matlab and the databrowser. The only way to escape this is to use another OS... in the past we have not been successful in tracing this down, because it is such a low-level error on only happens on some PCs with Win7, but not on all. There is already a bug on bugzilla for this. Maybe we need to ask Mathworks for support on this ;) @Max: The databrowser is specifically designed to also show components if you set cfg.viewmode = 'components'. The error also has nothing to do with showing components, as it also happens for plotting channel-level data. Best, Jörn On 5/2/2014 8:16 PM, Martine van Schouwenburg wrote: > > Hi Fieldtrip experts, > > I am experiencing a problem with the ft_databrowser routine. Matlab > crashes when I’m trying to run it, forcing me to end the Matlab > session. (‘Matlab has encountered an internal problem and needs to > close.’). It seems more like a Matlab/Windows related issue when > looking at the crash report (see below), but I am posting it here > because it also seems to depend on the data that I use as input. When > I run the routine on the ‘raw’ data (after defining the trials) it is > working fine, but after I ran ICA and try to use the databrowser to > look at the components, it crashes at line 676. > > This is the part where it calls the subfunction redraw_cb. Does anyone > might have a clue what in the component data might cause this problem? > Maybe some of you have experienced this before? I also send a request > for Tech Support to Matlab. > > Best, Martine > > Here is the Matlab crash report if that is of any help: > > ------------------------------------------------------------------------ > > Segmentation violation detected at Thu May 01 22:28:30 2014 > > ------------------------------------------------------------------------ > > Configuration: > > Crash Decoding : Disabled > > Default Encoding: windows-1252 > > MATLAB Root : C:\Program Files\MATLAB\R2012b > > MATLAB Version : 8.0.0.783 (R2012b) > > Operating System: Microsoft Windows 7 > > Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD > > Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java > HotSpot(TM) 64-Bit Server VM mixed mode > > Window System : Version 6.1 (Build 7601: Service Pack 1) > > Fault Count: 1 > > Abnormal termination: > > Segmentation violation > > Register State (from fault): > > RAX = 00000000000001a4 RBX = 000000007a8425c0 > > RCX = 00000000000262de RDX = 00000000000001b2 > > RSP = 0000000004110a50 RBP = 000000000000007e > > RSI = 000000007a75cab0 RDI = 000000013942b996 > > R8 = 00000000000262de R9 = 0000000000000230 > > R10 = 0000000000000000 R11 = 0000000004110b28 > > R12 = 0000000000f206cd R13 = 0000000077ce4060 > > R14 = 000000000002635c R15 = 00000000000006c8 > > RIP = 000000006000d341 EFL = 00010216 > > CS = 0033 FS = 0053 GS = 002b > > Stack Trace (from fault): > > [ 0] 0x000000006000d341 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( > RenderEngineBase::~RenderEngineBase+171553 ) > > [ 1] 0x000000005ff83130 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) > > [ 2] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 3] 0x000000005fede587 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( > renderAnimatedKids+000519 ) > > [ 4] 0x000000005fee3788 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) > > [ 5] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 6] 0x000000005ff04729 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( > FigureSetVisualAutoMode+001561 ) > > [ 7] 0x000000005ff0abbd C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( > UIJ_CreatePeerWindow+001597 ) > > [ 8] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 9] 0x0000000060013548 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( > RenderEngineBase::~RenderEngineBase+196648 ) > > [ 10] 0x000000005ff06b87 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( > FigureSetVisualAutoMode+010871 ) > > [ 11] 0x000000005ff06c0d C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( > FigureSetVisualAutoMode+011005 ) > > [ 12] 0x0000000063425006 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( > wm_ExposeFcn_Pre_Optional+000374 ) > > [ 13] 0x0000000064c8c694 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) > > [ 14] 0x0000000064c8e456 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( > UIJ_IsWindowShowing+000438 ) > > [ 15] 0x0000000064c8f943 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( > UIJ_clearWaitForResize+002067 ) > > [ 16] 0x0000000064c8fa61 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) > > [ 17] 0x0000000064c707ae C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( > UIJ_MarkEventFinished+005838 ) > > [ 18] 0x0000000064c70800 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( > UIJ_MarkEventFinished+005920 ) > > [ 19] 0x0000000064c892ac C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( > uij::JavaDraw2D::paintQuadStrip+001324 ) > > [ 20] 0x0000000064d4e808 C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( > uddSetListenerRecursionWarning+000680 ) > > [ 21] 0x0000000064d4ee6c C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( > UDListenerManagerHost::notifyEvent+000076 ) > > [ 22] 0x0000000064d4697d C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( > UDEventInfo::send+000093 ) > > [ 23] 0x000000005fb9cedb C:\Program > Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( > MErrorException::operator=+047675 ) > > [ 24] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( > UIW_IsUserMessage+000086 ) > > [ 25] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( > UIW_SetGLIMUserMsg+000153 ) > > [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( > GetMenuBarInfo+000638 ) > > [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( > SystemParametersInfoW+000235 ) > > [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( > IsProcessDPIAware+000465 ) > > [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( > KiUserCallbackDispatcher+000031 ) > > [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( > PeekMessageW+000186 ) > > [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( > GetKeyState+000238 ) > > [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( > PeekMessageA+000087 ) > > [ 33] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [ 34] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( > ws_FreeSystemFont+000546 ) > > [ 35] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [ 36] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [ 37] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [ 38] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [ 39] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [ 40] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [ 41] 0x000000005ff0c4fe C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) > > [ 42] 0x0000000074e8d17f C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( > Mfunction_handle::dispatch+001023 ) > > [ 43] 0x0000000074e8cf82 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( > Mfunction_handle::dispatch+000514 ) > > [ 44] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 45] 0x000007feef3a5ca4 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( > inFunctionHandleInterface::DestroyWorkspace+295012 ) > > [ 46] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 47] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 48] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 49] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 50] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 51] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 52] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 53] 0x000007feef38210b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( > inFunctionHandleInterface::DestroyWorkspace+148683 ) > > [ 54] 0x000007feef393edf C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( > inFunctionHandleInterface::DestroyWorkspace+221855 ) > > [ 55] 0x000007feef3b0ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( > inFunctionHandleInterface::DestroyWorkspace+339624 ) > > [ 56] 0x000007feef398d94 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( > inFunctionHandleInterface::DestroyWorkspace+242004 ) > > [ 57] 0x000007feef3a2978 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( > inFunctionHandleInterface::DestroyWorkspace+281912 ) > > [ 58] 0x000007feef3a5a8b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( > inFunctionHandleInterface::DestroyWorkspace+294475 ) > > [ 59] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 60] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 61] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 62] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 63] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 64] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 65] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 66] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 67] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 68] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 69] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 70] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 71] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 72] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 73] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 74] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 75] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 76] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 77] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 78] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 79] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 80] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 81] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 82] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 83] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 84] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 85] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 86] 0x000007feef4451e5 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( > inValidateLoadedObject+001893 ) > > [ 87] 0x000007feef454595 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( > init_cleaner+015541 ) > > [ 88] 0x000007feef457b75 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( > inSetMaxFrameCount+002261 ) > > [ 89] 0x000007feef457b48 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( > inSetMaxFrameCount+002216 ) > > [ 90] 0x000007feef457b07 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( > inSetMaxFrameCount+002151 ) > > [ 91] 0x000007feef340213 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( > inPathNotification::function_clear_notification+004019 ) > > [ 92] 0x000007feef44aed0 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( > inEvalCmdWithLocalReturn+000416 ) > > [ 93] 0x000007feef44ae2c C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( > inEvalCmdWithLocalReturn+000252 ) > > [ 94] 0x000007feef44ad71 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( > inEvalCmdWithLocalReturn+000065 ) > > [ 95] 0x0000000079fbf90d C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( > mnDebugPrompt+000109 ) > > [ 96] 0x0000000079fc0471 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( mnParser+000593 ) > > [ 97] 0x00000000749a64a4 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( > mcrInstance::mnParser_on_interpreter_thread+000036 ) > > [ 98] 0x000000007498681f C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( > mcr::setInterpreterThreadToCurrent+029887 ) > > [ 99] 0x0000000074986881 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( > mcr::setInterpreterThreadToCurrent+029985 ) > > [100] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( > UIW_IsUserMessage+000086 ) > > [101] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( > UIW_SetGLIMUserMsg+000153 ) > > [102] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( > GetMenuBarInfo+000638 ) > > [103] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( > SystemParametersInfoW+000235 ) > > [104] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( > IsProcessDPIAware+000465 ) > > [105] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( > KiUserCallbackDispatcher+000031 ) > > [106] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( > PeekMessageW+000186 ) > > [107] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( > GetKeyState+000238 ) > > [108] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( > PeekMessageA+000087 ) > > [109] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [110] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( > ws_FreeSystemFont+000546 ) > > [111] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [112] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [113] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [114] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [115] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [116] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [117] 0x000000007498837e C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( > mcr::setInterpreterThreadToCurrent+036894 ) > > [118] 0x0000000074988665 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( > mcr::setInterpreterThreadToCurrent+037637 ) > > [119] 0x000000007497b166 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( > DepfunRules::postWarning+003430 ) > > [120] 0x000000013fc78a33 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) > > [121] 0x000000013fc78c97 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) > > [122] 0x000000013fc79163 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) > > [123] 0x00000000773759ed C:\Windows\system32\kernel32.dll+00088557 ( > BaseThreadInitThunk+000013 ) > > [124] 0x00000000775ac541 C:\Windows\SYSTEM32\ntdll.dll+00181569 ( > RtlUserThreadStart+000033 ) > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From martine.vanschouwenburg at ucsf.edu Sat May 3 23:16:43 2014 From: martine.vanschouwenburg at ucsf.edu (Martine van Schouwenburg) Date: Sat, 3 May 2014 14:16:43 -0700 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: <5364B12A.80807@donders.ru.nl> References: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> <5364B12A.80807@donders.ru.nl> Message-ID: <009501cf6714$fbc5e110$f351a330$@vanschouwenburg@ucsf.edu> Hi all, Thank you for all of your quick replies! I have traced the problem down to the ft_plot_topo script, specifically when it calls the 'surf' function. I have been in touch with someone from Mathworks, and I have send him the script and all the variables he needs to run it, and he is looking into the issue. I'll let you know once he gets back to me. Hopefully, with a solution. :) Best, Martine -----Original Message----- From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" Sent: Saturday, May 03, 2014 2:05 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] ft_databrowser crashes Matlab Hi Martine, great to hear that you are using FieldTrip ;) hope you like it. As JM said, it is indeed some low-level problem with Windows 7, Matlab and the databrowser. The only way to escape this is to use another OS... in the past we have not been successful in tracing this down, because it is such a low-level error on only happens on some PCs with Win7, but not on all. There is already a bug on bugzilla for this. Maybe we need to ask Mathworks for support on this ;) @Max: The databrowser is specifically designed to also show components if you set cfg.viewmode = 'components'. The error also has nothing to do with showing components, as it also happens for plotting channel-level data. Best, Jörn On 5/2/2014 8:16 PM, Martine van Schouwenburg wrote: > > Hi Fieldtrip experts, > > I am experiencing a problem with the ft_databrowser routine. Matlab > crashes when I’m trying to run it, forcing me to end the Matlab > session. (‘Matlab has encountered an internal problem and needs to > close.’). It seems more like a Matlab/Windows related issue when > looking at the crash report (see below), but I am posting it here > because it also seems to depend on the data that I use as input. When > I run the routine on the ‘raw’ data (after defining the trials) it is > working fine, but after I ran ICA and try to use the databrowser to > look at the components, it crashes at line 676. > > This is the part where it calls the subfunction redraw_cb. Does anyone > might have a clue what in the component data might cause this problem? > Maybe some of you have experienced this before? I also send a request > for Tech Support to Matlab. > > Best, Martine > > Here is the Matlab crash report if that is of any help: > > ---------------------------------------------------------------------- > -- > > Segmentation violation detected at Thu May 01 22:28:30 2014 > > ---------------------------------------------------------------------- > -- > > Configuration: > > Crash Decoding : Disabled > > Default Encoding: windows-1252 > > MATLAB Root : C:\Program Files\MATLAB\R2012b > > MATLAB Version : 8.0.0.783 (R2012b) > > Operating System: Microsoft Windows 7 > > Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD > > Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java > HotSpot(TM) 64-Bit Server VM mixed mode > > Window System : Version 6.1 (Build 7601: Service Pack 1) > > Fault Count: 1 > > Abnormal termination: > > Segmentation violation > > Register State (from fault): > > RAX = 00000000000001a4 RBX = 000000007a8425c0 > > RCX = 00000000000262de RDX = 00000000000001b2 > > RSP = 0000000004110a50 RBP = 000000000000007e > > RSI = 000000007a75cab0 RDI = 000000013942b996 > > R8 = 00000000000262de R9 = 0000000000000230 > > R10 = 0000000000000000 R11 = 0000000004110b28 > > R12 = 0000000000f206cd R13 = 0000000077ce4060 > > R14 = 000000000002635c R15 = 00000000000006c8 > > RIP = 000000006000d341 EFL = 00010216 > > CS = 0033 FS = 0053 GS = 002b > > Stack Trace (from fault): > > [ 0] 0x000000006000d341 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( > RenderEngineBase::~RenderEngineBase+171553 ) > > [ 1] 0x000000005ff83130 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) > > [ 2] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 3] 0x000000005fede587 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( > renderAnimatedKids+000519 ) > > [ 4] 0x000000005fee3788 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) > > [ 5] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 6] 0x000000005ff04729 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( > FigureSetVisualAutoMode+001561 ) > > [ 7] 0x000000005ff0abbd C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( > UIJ_CreatePeerWindow+001597 ) > > [ 8] 0x00000000602cc003 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( > GO_TransformObject+001571 ) > > [ 9] 0x0000000060013548 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( > RenderEngineBase::~RenderEngineBase+196648 ) > > [ 10] 0x000000005ff06b87 C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( > FigureSetVisualAutoMode+010871 ) > > [ 11] 0x000000005ff06c0d C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( > FigureSetVisualAutoMode+011005 ) > > [ 12] 0x0000000063425006 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( > wm_ExposeFcn_Pre_Optional+000374 ) > > [ 13] 0x0000000064c8c694 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) > > [ 14] 0x0000000064c8e456 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( > UIJ_IsWindowShowing+000438 ) > > [ 15] 0x0000000064c8f943 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( > UIJ_clearWaitForResize+002067 ) > > [ 16] 0x0000000064c8fa61 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) > > [ 17] 0x0000000064c707ae C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( > UIJ_MarkEventFinished+005838 ) > > [ 18] 0x0000000064c70800 C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( > UIJ_MarkEventFinished+005920 ) > > [ 19] 0x0000000064c892ac C:\Program > Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( > uij::JavaDraw2D::paintQuadStrip+001324 ) > > [ 20] 0x0000000064d4e808 C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( > uddSetListenerRecursionWarning+000680 ) > > [ 21] 0x0000000064d4ee6c C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( > UDListenerManagerHost::notifyEvent+000076 ) > > [ 22] 0x0000000064d4697d C:\Program > Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( > UDEventInfo::send+000093 ) > > [ 23] 0x000000005fb9cedb C:\Program > Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( > MErrorException::operator=+047675 ) > > [ 24] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( > UIW_IsUserMessage+000086 ) > > [ 25] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( > UIW_SetGLIMUserMsg+000153 ) > > [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( > GetMenuBarInfo+000638 ) > > [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( > SystemParametersInfoW+000235 ) > > [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( > IsProcessDPIAware+000465 ) > > [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( > KiUserCallbackDispatcher+000031 ) > > [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( > PeekMessageW+000186 ) > > [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( > GetKeyState+000238 ) > > [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( > PeekMessageA+000087 ) > > [ 33] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [ 34] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( > ws_FreeSystemFont+000546 ) > > [ 35] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [ 36] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [ 37] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [ 38] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [ 39] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [ 40] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [ 41] 0x000000005ff0c4fe C:\Program > Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) > > [ 42] 0x0000000074e8d17f C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( > Mfunction_handle::dispatch+001023 ) > > [ 43] 0x0000000074e8cf82 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( > Mfunction_handle::dispatch+000514 ) > > [ 44] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 45] 0x000007feef3a5ca4 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( > inFunctionHandleInterface::DestroyWorkspace+295012 ) > > [ 46] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 47] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 48] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 49] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 50] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 51] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 52] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 53] 0x000007feef38210b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( > inFunctionHandleInterface::DestroyWorkspace+148683 ) > > [ 54] 0x000007feef393edf C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( > inFunctionHandleInterface::DestroyWorkspace+221855 ) > > [ 55] 0x000007feef3b0ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( > inFunctionHandleInterface::DestroyWorkspace+339624 ) > > [ 56] 0x000007feef398d94 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( > inFunctionHandleInterface::DestroyWorkspace+242004 ) > > [ 57] 0x000007feef3a2978 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( > inFunctionHandleInterface::DestroyWorkspace+281912 ) > > [ 58] 0x000007feef3a5a8b C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( > inFunctionHandleInterface::DestroyWorkspace+294475 ) > > [ 59] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 60] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 61] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 62] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 63] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 64] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 65] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 66] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 67] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 68] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 69] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 70] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 71] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 72] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 73] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 74] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 75] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 76] 0x000007feef3a9482 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( > inFunctionHandleInterface::DestroyWorkspace+309314 ) > > [ 77] 0x000007feef43318f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( > inEachVisibleName+014415 ) > > [ 78] 0x000007feef3a74ca C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( > inFunctionHandleInterface::DestroyWorkspace+301194 ) > > [ 79] 0x000007feef38de1f C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( > inFunctionHandleInterface::DestroyWorkspace+197087 ) > > [ 80] 0x000007feef38dd80 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( > inFunctionHandleInterface::DestroyWorkspace+196928 ) > > [ 81] 0x000007feef3b197d C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( > inFunctionHandleInterface::DestroyWorkspace+343357 ) > > [ 82] 0x000007feef3b0271 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( > inFunctionHandleInterface::DestroyWorkspace+337457 ) > > [ 83] 0x000007feef3920e9 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( > inFunctionHandleInterface::DestroyWorkspace+214185 ) > > [ 84] 0x0000000074e8c80d C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( > Mfh_file::dispatch_fh+000509 ) > > [ 85] 0x0000000074e8d0d6 C:\Program > Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( > Mfunction_handle::dispatch+000854 ) > > [ 86] 0x000007feef4451e5 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( > inValidateLoadedObject+001893 ) > > [ 87] 0x000007feef454595 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( > init_cleaner+015541 ) > > [ 88] 0x000007feef457b75 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( > inSetMaxFrameCount+002261 ) > > [ 89] 0x000007feef457b48 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( > inSetMaxFrameCount+002216 ) > > [ 90] 0x000007feef457b07 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( > inSetMaxFrameCount+002151 ) > > [ 91] 0x000007feef340213 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( > inPathNotification::function_clear_notification+004019 ) > > [ 92] 0x000007feef44aed0 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( > inEvalCmdWithLocalReturn+000416 ) > > [ 93] 0x000007feef44ae2c C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( > inEvalCmdWithLocalReturn+000252 ) > > [ 94] 0x000007feef44ad71 C:\Program > Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( > inEvalCmdWithLocalReturn+000065 ) > > [ 95] 0x0000000079fbf90d C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( > mnDebugPrompt+000109 ) > > [ 96] 0x0000000079fc0471 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( mnParser+000593 ) > > [ 97] 0x00000000749a64a4 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( > mcrInstance::mnParser_on_interpreter_thread+000036 ) > > [ 98] 0x000000007498681f C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( > mcr::setInterpreterThreadToCurrent+029887 ) > > [ 99] 0x0000000074986881 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( > mcr::setInterpreterThreadToCurrent+029985 ) > > [100] 0x00000000055ce0b6 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( > UIW_IsUserMessage+000086 ) > > [101] 0x00000000055ce7b9 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( > UIW_SetGLIMUserMsg+000153 ) > > [102] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( > GetMenuBarInfo+000638 ) > > [103] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( > SystemParametersInfoW+000235 ) > > [104] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( > IsProcessDPIAware+000465 ) > > [105] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( > KiUserCallbackDispatcher+000031 ) > > [106] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( > PeekMessageW+000186 ) > > [107] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( > GetKeyState+000238 ) > > [108] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( > PeekMessageA+000087 ) > > [109] 0x00000000055a8f4b C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( > UIW_SetCurrentDialog+000731 ) > > [110] 0x00000000055cfbe2 C:\Program > Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( > ws_FreeSystemFont+000546 ) > > [111] 0x000000000485e6a3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( > sysq::removeCommitDatabaseUpdatesHook+002131 ) > > [112] 0x000000000485fe18 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( > sysq::removeCommitDatabaseUpdatesHook+008136 ) > > [113] 0x0000000004861a20 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( > sysq::addProcessPendingEventsUnitTestHook+000240 ) > > [114] 0x0000000004861ae8 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( > sysq::addProcessPendingEventsUnitTestHook+000440 ) > > [115] 0x0000000004861ca3 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( > sysq::addProcessPendingEventsUnitTestHook+000883 ) > > [116] 0x0000000004861d76 C:\Program > Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( > sysq::addProcessPendingEventsUnitTestHook+001094 ) > > [117] 0x000000007498837e C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( > mcr::setInterpreterThreadToCurrent+036894 ) > > [118] 0x0000000074988665 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( > mcr::setInterpreterThreadToCurrent+037637 ) > > [119] 0x000000007497b166 C:\Program > Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( > DepfunRules::postWarning+003430 ) > > [120] 0x000000013fc78a33 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) > > [121] 0x000000013fc78c97 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) > > [122] 0x000000013fc79163 C:\Program > Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) > > [123] 0x00000000773759ed C:\Windows\system32\kernel32.dll+00088557 ( > BaseThreadInitThunk+000013 ) > > [124] 0x00000000775ac541 C:\Windows\SYSTEM32\ntdll.dll+00181569 ( > RtlUserThreadStart+000033 ) > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From e.maris at psych.ru.nl Sun May 4 12:33:35 2014 From: e.maris at psych.ru.nl (Eric Maris) Date: Sun, 4 May 2014 12:33:35 +0200 (CEST) Subject: [FieldTrip] ft_timelockstatistics cluster correction using ECoG data In-Reply-To: References: Message-ID: <036d01cf6784$4b2602c0$e1720840$@maris@psych.ru.nl> Hi Kristen, If you supply ft_timelockstatistics with data containing multiple channels it will always “correct” (this is not the best word to denote what the method does, but let’s use it anyhow) for the number of channels. By requesting not to do clustering in space you just achieve that a clusters are computed in a different way (ie, assuming that the channels measure functionally independent signals). If you do not want correction for multiple channels, then you must analyze the data per channel, as you did for Elec11. If you have a low number of channels, then you could combine the permutation-based p-value with regular Bonferroni correction (dividing the critical alpha-level by the number of channels). Good luck, Eric Maris From: Kristen Berry [mailto:kkb268 at nyu.edu] Sent: vrijdag 2 mei 2014 22:41 To: fieldtrip at science.ru.nl Subject: [FieldTrip] ft_timelockstatistics cluster correction using ECoG data Dear all, I am using an intracranial EEG dataset to compare average high gamma power waveforms between conditions. I want to correct for multiple comparisons across time, but not across number of electrodes. Here is my input code: cfg=[]; cfg.latency = [0.05 .5]; cfg.parameter = 'trial'; cfg.method = 'montecarlo'; cfg.correctm = 'cluster'; cfg.neighbours = []; cfg.numrandomization = 1000; cfg.statistic = 'indepsamplesT'; cfg.channel = ‘all’; cfg.alpha = 0.05; cfg.clusteralpha = 0.05; cfg.tail = 0; stats = ft_timelockstatistics(cfg, data,control); Fieldtrip’s montecarlo reference page ( http://fieldtrip.fcdonders.nl/reference/ft_statistics_montecarlo) says, “If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels.” However, my input code corrects for the number of channels as well. As an example, when cfg.channel = ‘all’ for ft_timelockstatistics, then Elec11 is not significant. However, if the analysis is limited to Elec11 (cfg.channel = 11), then Elec11 has a significant cluster. Is there a mistake in my code that is causing this? Or is there an older version of fieldtrip that doesn’t correct for # of channels, when cfg.neighbours is empty? Thank you for your input! Best regards, Kristen Kristen Berry Research Assistant NYU School of Medicine -------------- next part -------------- An HTML attachment was scrubbed... URL: From lmelloni at gmail.com Mon May 5 01:10:07 2014 From: lmelloni at gmail.com (Lucia Melloni) Date: Sun, 4 May 2014 19:10:07 -0400 Subject: [FieldTrip] deadline extended for the Neurobiology of Cognition GRC/GRS! Message-ID: Dear colleagues, The deadline for application and abstract submission for the Gordon Research Seminar has been extended to the *15th of May*. Please submit your application and abstract soon!. We are very much looking forward to receiving your contributions and to a vibrant seminar. We have also added a mentorship component which promises to provide us with important tips for a successful transition from postdoc to PI. Looking forward to seeing you at the GRS/GRC! Lucia Melloni. Ayelet A. Landau [image: Gordon Research Conferences] Join us at the 2014 *Gordon Conference* and *Seminar* On *Neurobiology of Cognition* Circuits, Dynamics, Action and Perception We are meeting *July 20-25, 2014 -*New GRC site: *Sunday River Resort* Newry, Maine Click *here*to see the *GRC* program. There is also an associated *GRS* *July 19-20 *for students and postdocs Click *here*to see the *GRS* website. *GRS* application & abstract deadline to be considered for oral presentation- *May 15* *Please use attached **flyer **to help spread the word! * The Neurobiology of Cognition is a recently-inaugurated GRC designed to foster convergence of traditional neuroscience investigations with more recent developments in systems, cellular and molecular neurobiology, in engineering and imaging and in computational sciences. Cognition is construed broadly to embrace empirical findings in a range of species including humans, and there is a strong focus on integration of findings and principles across species and levels of analysis. In the opening Keynote Session, two leading neuroscientists with provide an experimental and computational perspective on the recent initiative, termed Brain Research through Advancing Innovative Neurotechnologies (BRAIN). This initiative, spearheaded by the President and NIH, is aimed at developing innovative methodologies to study how complex systems of neurons interact in time and in space during complex behaviors. Along with recent findings in a few traditional "core" areas, formal sessions will then explore several new themes, including: 1) the neuroanatomy and 2) coordination of cognitive circuits in the brain, 3) motor cognition and brain-computer interfaces, 4) music and language, and 5) learning and plasticity. The program juxtaposes human psychophysical, neuroimaging and electrophysiological studies with parallel investigations in rodents and non-human primates, and with computational approaches that explicate empirical findings and construct robust, detailed models to represent the developing picture and guide future experimentation. The program also underscores novel experimental and theoretical approaches that promise to define fundamental principles that guide and integrate the understanding of cognition at a fundamental level, and to extend these to improved treatment of brain dysfunction. The format of the meeting promotes intensive interactions among investigators and trainees from different perspectives and analytic levels, and in particular, between experimentalists and theorists. There is a linked Gordon Research Seminar for trainees, most of whom also attend the GRC. All that is missing now is your *application* to attend. Click *here*for the *GRC*. Click* here*for the *GRS*. (You must apply to both to attend both.) Best regards, GRC Chair: *Charles E. Schroeder* GRC V. Chair:*Tatiana Pasternak* GRS Chair: *Lucia Melloni* GRS Assoc. Chair: *Ayelet N. Landau* *Apply* now and see why our attendees consistently rate GRCs "the best conference I've attended this year"! [image: Like us on Facebook] [image: Follow us on Twitter] [image: View our profile on LinkedIn] *Forward this email * This email was sent to htobin at grc.org by announcements at grc.org | Instant removal with SafeUnsubscribe™ | Privacy Policy . Gordon Research Conferences | 512 Liberty Lane | West Kingston | RI | 02892 Follow GRC: Facebook | Twitter Call Send SMS Add to Skype You'll need Skype CreditFree via Skype -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue May 6 08:26:21 2014 From: jm.horschig at donders.ru.nl (=?windows-1252?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 06 May 2014 08:26:21 +0200 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: <009501cf6714$fbc5e110$f351a330$@vanschouwenburg@ucsf.edu> References: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> <5364B12A.80807@donders.ru.nl> <009501cf6714$fbc5e110$f351a330$@vanschouwenburg@ucsf.edu> Message-ID: <5368808D.4000803@donders.ru.nl> Hi Martine, that's great, thanks. Looking forward to hearing what they say. @Max: then it seems like Martine's problem really is specific to viewing components, sorry :) Best, Jörn On 5/3/2014 11:16 PM, Martine van Schouwenburg wrote: > Hi all, > > Thank you for all of your quick replies! I have traced the problem down to > the ft_plot_topo script, specifically when it calls the 'surf' function. I > have been in touch with someone from Mathworks, and I have send him the > script and all the variables he needs to run it, and he is looking into the > issue. I'll let you know once he gets back to me. Hopefully, with a > solution. :) > > Best, Martine > > > > > -----Original Message----- > From: fieldtrip-bounces at science.ru.nl > [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" > Sent: Saturday, May 03, 2014 2:05 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] ft_databrowser crashes Matlab > > Hi Martine, > > great to hear that you are using FieldTrip ;) hope you like it. > As JM said, it is indeed some low-level problem with Windows 7, Matlab and > the databrowser. The only way to escape this is to use another OS... > in the past we have not been successful in tracing this down, because it is > such a low-level error on only happens on some PCs with Win7, but not on > all. There is already a bug on bugzilla for this. Maybe we need to ask > Mathworks for support on this ;) > > @Max: The databrowser is specifically designed to also show components if > you set cfg.viewmode = 'components'. The error also has nothing to do with > showing components, as it also happens for plotting channel-level data. > > Best, > Jörn > > On 5/2/2014 8:16 PM, Martine van Schouwenburg wrote: >> Hi Fieldtrip experts, >> >> I am experiencing a problem with the ft_databrowser routine. Matlab >> crashes when I’m trying to run it, forcing me to end the Matlab >> session. (‘Matlab has encountered an internal problem and needs to >> close.’). It seems more like a Matlab/Windows related issue when >> looking at the crash report (see below), but I am posting it here >> because it also seems to depend on the data that I use as input. When >> I run the routine on the ‘raw’ data (after defining the trials) it is >> working fine, but after I ran ICA and try to use the databrowser to >> look at the components, it crashes at line 676. >> >> This is the part where it calls the subfunction redraw_cb. Does anyone >> might have a clue what in the component data might cause this problem? >> Maybe some of you have experienced this before? I also send a request >> for Tech Support to Matlab. >> >> Best, Martine >> >> Here is the Matlab crash report if that is of any help: >> >> ---------------------------------------------------------------------- >> -- >> >> Segmentation violation detected at Thu May 01 22:28:30 2014 >> >> ---------------------------------------------------------------------- >> -- >> >> Configuration: >> >> Crash Decoding : Disabled >> >> Default Encoding: windows-1252 >> >> MATLAB Root : C:\Program Files\MATLAB\R2012b >> >> MATLAB Version : 8.0.0.783 (R2012b) >> >> Operating System: Microsoft Windows 7 >> >> Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD >> >> Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java >> HotSpot(TM) 64-Bit Server VM mixed mode >> >> Window System : Version 6.1 (Build 7601: Service Pack 1) >> >> Fault Count: 1 >> >> Abnormal termination: >> >> Segmentation violation >> >> Register State (from fault): >> >> RAX = 00000000000001a4 RBX = 000000007a8425c0 >> >> RCX = 00000000000262de RDX = 00000000000001b2 >> >> RSP = 0000000004110a50 RBP = 000000000000007e >> >> RSI = 000000007a75cab0 RDI = 000000013942b996 >> >> R8 = 00000000000262de R9 = 0000000000000230 >> >> R10 = 0000000000000000 R11 = 0000000004110b28 >> >> R12 = 0000000000f206cd R13 = 0000000077ce4060 >> >> R14 = 000000000002635c R15 = 00000000000006c8 >> >> RIP = 000000006000d341 EFL = 00010216 >> >> CS = 0033 FS = 0053 GS = 002b >> >> Stack Trace (from fault): >> >> [ 0] 0x000000006000d341 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( >> RenderEngineBase::~RenderEngineBase+171553 ) >> >> [ 1] 0x000000005ff83130 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 ) >> >> [ 2] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 3] 0x000000005fede587 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( >> renderAnimatedKids+000519 ) >> >> [ 4] 0x000000005fee3788 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) >> >> [ 5] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 6] 0x000000005ff04729 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( >> FigureSetVisualAutoMode+001561 ) >> >> [ 7] 0x000000005ff0abbd C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( >> UIJ_CreatePeerWindow+001597 ) >> >> [ 8] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 9] 0x0000000060013548 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( >> RenderEngineBase::~RenderEngineBase+196648 ) >> >> [ 10] 0x000000005ff06b87 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( >> FigureSetVisualAutoMode+010871 ) >> >> [ 11] 0x000000005ff06c0d C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( >> FigureSetVisualAutoMode+011005 ) >> >> [ 12] 0x0000000063425006 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( >> wm_ExposeFcn_Pre_Optional+000374 ) >> >> [ 13] 0x0000000064c8c694 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( GetframeJava+001332 ) >> >> [ 14] 0x0000000064c8e456 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( >> UIJ_IsWindowShowing+000438 ) >> >> [ 15] 0x0000000064c8f943 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( >> UIJ_clearWaitForResize+002067 ) >> >> [ 16] 0x0000000064c8fa61 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( UIJ_ExposeFcn+000145 ) >> >> [ 17] 0x0000000064c707ae C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( >> UIJ_MarkEventFinished+005838 ) >> >> [ 18] 0x0000000064c70800 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( >> UIJ_MarkEventFinished+005920 ) >> >> [ 19] 0x0000000064c892ac C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( >> uij::JavaDraw2D::paintQuadStrip+001324 ) >> >> [ 20] 0x0000000064d4e808 C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( >> uddSetListenerRecursionWarning+000680 ) >> >> [ 21] 0x0000000064d4ee6c C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( >> UDListenerManagerHost::notifyEvent+000076 ) >> >> [ 22] 0x0000000064d4697d C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( >> UDEventInfo::send+000093 ) >> >> [ 23] 0x000000005fb9cedb C:\Program >> Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( >> MErrorException::operator=+047675 ) >> >> [ 24] 0x00000000055ce0b6 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( >> UIW_IsUserMessage+000086 ) >> >> [ 25] 0x00000000055ce7b9 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( >> UIW_SetGLIMUserMsg+000153 ) >> >> [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( >> GetMenuBarInfo+000638 ) >> >> [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( >> SystemParametersInfoW+000235 ) >> >> [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( >> IsProcessDPIAware+000465 ) >> >> [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( >> KiUserCallbackDispatcher+000031 ) >> >> [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( >> PeekMessageW+000186 ) >> >> [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( >> GetKeyState+000238 ) >> >> [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( >> PeekMessageA+000087 ) >> >> [ 33] 0x00000000055a8f4b C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( >> UIW_SetCurrentDialog+000731 ) >> >> [ 34] 0x00000000055cfbe2 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( >> ws_FreeSystemFont+000546 ) >> >> [ 35] 0x000000000485e6a3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( >> sysq::removeCommitDatabaseUpdatesHook+002131 ) >> >> [ 36] 0x000000000485fe18 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( >> sysq::removeCommitDatabaseUpdatesHook+008136 ) >> >> [ 37] 0x0000000004861a20 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( >> sysq::addProcessPendingEventsUnitTestHook+000240 ) >> >> [ 38] 0x0000000004861ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( >> sysq::addProcessPendingEventsUnitTestHook+000440 ) >> >> [ 39] 0x0000000004861ca3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( >> sysq::addProcessPendingEventsUnitTestHook+000883 ) >> >> [ 40] 0x0000000004861d76 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( >> sysq::addProcessPendingEventsUnitTestHook+001094 ) >> >> [ 41] 0x000000005ff0c4fe C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) >> >> [ 42] 0x0000000074e8d17f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( >> Mfunction_handle::dispatch+001023 ) >> >> [ 43] 0x0000000074e8cf82 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( >> Mfunction_handle::dispatch+000514 ) >> >> [ 44] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 45] 0x000007feef3a5ca4 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( >> inFunctionHandleInterface::DestroyWorkspace+295012 ) >> >> [ 46] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 47] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 48] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 49] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 50] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 51] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 52] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 53] 0x000007feef38210b C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( >> inFunctionHandleInterface::DestroyWorkspace+148683 ) >> >> [ 54] 0x000007feef393edf C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( >> inFunctionHandleInterface::DestroyWorkspace+221855 ) >> >> [ 55] 0x000007feef3b0ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( >> inFunctionHandleInterface::DestroyWorkspace+339624 ) >> >> [ 56] 0x000007feef398d94 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( >> inFunctionHandleInterface::DestroyWorkspace+242004 ) >> >> [ 57] 0x000007feef3a2978 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( >> inFunctionHandleInterface::DestroyWorkspace+281912 ) >> >> [ 58] 0x000007feef3a5a8b C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( >> inFunctionHandleInterface::DestroyWorkspace+294475 ) >> >> [ 59] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 60] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 61] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 62] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 63] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 64] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 65] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 66] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 67] 0x000007feef43318f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( >> inEachVisibleName+014415 ) >> >> [ 68] 0x000007feef3a74ca C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( >> inFunctionHandleInterface::DestroyWorkspace+301194 ) >> >> [ 69] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 70] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 71] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 72] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 73] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 74] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 75] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 76] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 77] 0x000007feef43318f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( >> inEachVisibleName+014415 ) >> >> [ 78] 0x000007feef3a74ca C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( >> inFunctionHandleInterface::DestroyWorkspace+301194 ) >> >> [ 79] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 80] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 81] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 82] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 83] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 84] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 85] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 86] 0x000007feef4451e5 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( >> inValidateLoadedObject+001893 ) >> >> [ 87] 0x000007feef454595 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( >> init_cleaner+015541 ) >> >> [ 88] 0x000007feef457b75 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( >> inSetMaxFrameCount+002261 ) >> >> [ 89] 0x000007feef457b48 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( >> inSetMaxFrameCount+002216 ) >> >> [ 90] 0x000007feef457b07 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( >> inSetMaxFrameCount+002151 ) >> >> [ 91] 0x000007feef340213 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( >> inPathNotification::function_clear_notification+004019 ) >> >> [ 92] 0x000007feef44aed0 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( >> inEvalCmdWithLocalReturn+000416 ) >> >> [ 93] 0x000007feef44ae2c C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( >> inEvalCmdWithLocalReturn+000252 ) >> >> [ 94] 0x000007feef44ad71 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( >> inEvalCmdWithLocalReturn+000065 ) >> >> [ 95] 0x0000000079fbf90d C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( >> mnDebugPrompt+000109 ) >> >> [ 96] 0x0000000079fc0471 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( mnParser+000593 ) >> >> [ 97] 0x00000000749a64a4 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( >> mcrInstance::mnParser_on_interpreter_thread+000036 ) >> >> [ 98] 0x000000007498681f C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( >> mcr::setInterpreterThreadToCurrent+029887 ) >> >> [ 99] 0x0000000074986881 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( >> mcr::setInterpreterThreadToCurrent+029985 ) >> >> [100] 0x00000000055ce0b6 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( >> UIW_IsUserMessage+000086 ) >> >> [101] 0x00000000055ce7b9 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( >> UIW_SetGLIMUserMsg+000153 ) >> >> [102] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( >> GetMenuBarInfo+000638 ) >> >> [103] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( >> SystemParametersInfoW+000235 ) >> >> [104] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( >> IsProcessDPIAware+000465 ) >> >> [105] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( >> KiUserCallbackDispatcher+000031 ) >> >> [106] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( >> PeekMessageW+000186 ) >> >> [107] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( >> GetKeyState+000238 ) >> >> [108] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( >> PeekMessageA+000087 ) >> >> [109] 0x00000000055a8f4b C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( >> UIW_SetCurrentDialog+000731 ) >> >> [110] 0x00000000055cfbe2 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( >> ws_FreeSystemFont+000546 ) >> >> [111] 0x000000000485e6a3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( >> sysq::removeCommitDatabaseUpdatesHook+002131 ) >> >> [112] 0x000000000485fe18 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( >> sysq::removeCommitDatabaseUpdatesHook+008136 ) >> >> [113] 0x0000000004861a20 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( >> sysq::addProcessPendingEventsUnitTestHook+000240 ) >> >> [114] 0x0000000004861ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( >> sysq::addProcessPendingEventsUnitTestHook+000440 ) >> >> [115] 0x0000000004861ca3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( >> sysq::addProcessPendingEventsUnitTestHook+000883 ) >> >> [116] 0x0000000004861d76 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( >> sysq::addProcessPendingEventsUnitTestHook+001094 ) >> >> [117] 0x000000007498837e C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( >> mcr::setInterpreterThreadToCurrent+036894 ) >> >> [118] 0x0000000074988665 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( >> mcr::setInterpreterThreadToCurrent+037637 ) >> >> [119] 0x000000007497b166 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( >> DepfunRules::postWarning+003430 ) >> >> [120] 0x000000013fc78a33 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) >> >> [121] 0x000000013fc78c97 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) >> >> [122] 0x000000013fc79163 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) >> >> [123] 0x00000000773759ed C:\Windows\system32\kernel32.dll+00088557 ( >> BaseThreadInitThunk+000013 ) >> >> [124] 0x00000000775ac541 C:\Windows\SYSTEM32\ntdll.dll+00181569 ( >> RtlUserThreadStart+000033 ) >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From Gregor.Volberg at psychologie.uni-regensburg.de Tue May 6 11:03:52 2014 From: Gregor.Volberg at psychologie.uni-regensburg.de (Gregor Volberg) Date: Tue, 06 May 2014 11:03:52 +0200 Subject: [FieldTrip] PhD Job offer in Visual Neuroscience, University of Regensburg (Germany) Message-ID: <5368C198020000570001653B@gwsmtp1.uni-regensburg.de> Dear colleagues, please find below a job offer for a PhD position at the University of Regensburg, Germany. You might send it to interested students if you like. Best regards, Gregor **** The University of Regensburg (Germany), Institute for Psychology, Workgroup Experimental Psychology offers a 65 % position for a three-year PhD project starting in October 2014 (Chair: Prof. Dr. Mark Greenlee; Principal Investigator: PD Dr. G. Volberg). The salary will be according to German TV-L E 13 (65 % position) payment plan. The DFG-funded research project is on the neural basis of grapheme-color synesthesia, a perceptual phenomenon where achromatic letters or numbers produce a simultaneous sensation of color. Methods include electroencephalography (EEG) and functional magnetic resonance imaging (fMRI). Eligible job applicants must hold a masters degree (or comparable) in psychology or neighboring disciplines. They should have an academic background in visual neuroscience, especially in the acquisition and analysis of EEG and/or fMRI data. Programming experience in MatLab is advantageous. Job holders will need to recruit and test synesthetic participants from the local student population. Good skills in German are therefore necessary. We can offer an active research environment, an interesting topic for your PhD thesis, a friendly team and a UNESCO-heritage city located on the Danube River. We are looking forward to receiving your application! The University of Regensburg supports the reconcilability between family and career (see http://www.uni-regensburg.de/chancengleichheit). Physically challenged applicants will be preferred in cases of equivalent qualification. If applicable, please convey extend and type of disability in your résumé. Please note that the university does not refund costs ensuing from job interviews. Please send your application by June 1st, 2014 to PD Dr. Volberg, gregor.volberg at ur.de. The application should hold pertinent information about your academic career. Please send in the application in an electronic form (pdf) and use the subject matter „Application Synesthesia“ in the e-mail. The contact person is PD Dr. Gregor Volberg (office hours, Wednesday 10-12, Tel. +49 941 943 3862; http://www.uni-regensburg.de/psychologie-paedagogik-sport/psychologie-greenlee/team/volberg/index.html). -- PD Dr. rer. nat. Gregor Volberg gregor.volberg at ur.deUniversity of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From martine.vanschouwenburg at ucsf.edu Tue May 6 18:59:06 2014 From: martine.vanschouwenburg at ucsf.edu (Martine van Schouwenburg) Date: Tue, 6 May 2014 09:59:06 -0700 Subject: [FieldTrip] ft_databrowser crashes Matlab In-Reply-To: <5368808D.4000803@donders.ru.nl> References: <004601cf6632$a37b52c0$ea71f840$@vanschouwenburg@ucsf.edu> <5364B12A.80807@donders.ru.nl> <009501cf6714$fbc5e110$f351a330$@vanschouwenburg@ucsf.edu> <5368808D.4000803@donders.ru.nl> Message-ID: <00ff01cf694c$7d847f20$788d7d60$@vanschouwenburg@ucsf.edu> Hi all, Problem is solved! I have had great help from the Mathworks support team and it turns out it was a rendering issue (see below part of the email that I got from Mathworks). Setting the renderer to 'Paintings' did the trick for me, so I have now added this line [set(gcf,'renderer','painters');] to the script, just before it calls the 'surf' function (line 242 of ft_plot_topo). This issue seems to depend strongly on OS, graphics card, software version etc, but if anyone runs into a similar problem you could try to see if changing the renderer works for you too. Best, Martine EMAIL SUPPORT TEAM MATHWORKS: "I have a feeling that the crash might be because of the renderer being chosen by MATLAB to plot the surface plot. MATLAB has three renderers- OpenGL, Painters and Z-Buffer. Each of these renderers has its own merits and limitations. MATLAB chooses the correct renderer based on the type of figure that you are plotting. Here is a documentation page that talks more about the three renderers in MATLAB: http://www.mathworks.com/help/matlab/creating_plots/changing-a-figures-setti ngs.html#f3-102410 Of the three renderers OpenGL has the ability to use the graphics hardware on your system to help render the graphics. This can occasionally cause incompatibilities due to the many different graphics cards out there and also the many different driver versions that exist for each of these cards. So, you can try and switch to the software implementation of OpenGL by executing the following command in the command window: >>opengl software This setting is retained for the current session of MATLAB. If you want MATLAB to remember this setting across settings, then I would suggest that you add this command to your "startup.m". Please use the above command and then run your code to see if the crash still occurs. IF THE ABOVE PROCEDURE DOES NOT WORK: We can try and change the renderer to one of the other two and see if this helps. You can change the renderer by using the "set" command: >> set(gcf,'renderer','painters'); OR >>set(gcf,'renderer','zbuffer'); OR >>set(gcf,'renderer','opengl'); Here "gcf" refers to the currently active figure window. I would suggest that you try changing the renderer just before the "surf" command is executed and see if the crash stops happening when using a particular renderer." -----Original Message----- From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" Sent: Monday, May 05, 2014 11:26 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] ft_databrowser crashes Matlab Hi Martine, that's great, thanks. Looking forward to hearing what they say. @Max: then it seems like Martine's problem really is specific to viewing components, sorry :) Best, Jörn On 5/3/2014 11:16 PM, Martine van Schouwenburg wrote: > Hi all, > > Thank you for all of your quick replies! I have traced the problem > down to the ft_plot_topo script, specifically when it calls the 'surf' > function. I have been in touch with someone from Mathworks, and I have > send him the script and all the variables he needs to run it, and he > is looking into the issue. I'll let you know once he gets back to me. > Hopefully, with a solution. :) > > Best, Martine > > > > > -----Original Message----- > From: fieldtrip-bounces at science.ru.nl > [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" > Sent: Saturday, May 03, 2014 2:05 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] ft_databrowser crashes Matlab > > Hi Martine, > > great to hear that you are using FieldTrip ;) hope you like it. > As JM said, it is indeed some low-level problem with Windows 7, Matlab > and the databrowser. The only way to escape this is to use another OS... > in the past we have not been successful in tracing this down, because > it is such a low-level error on only happens on some PCs with Win7, > but not on all. There is already a bug on bugzilla for this. Maybe we > need to ask Mathworks for support on this ;) > > @Max: The databrowser is specifically designed to also show components > if you set cfg.viewmode = 'components'. The error also has nothing to > do with showing components, as it also happens for plotting channel-level data. > > Best, > Jörn > > On 5/2/2014 8:16 PM, Martine van Schouwenburg wrote: >> Hi Fieldtrip experts, >> >> I am experiencing a problem with the ft_databrowser routine. Matlab >> crashes when I’m trying to run it, forcing me to end the Matlab >> session. (‘Matlab has encountered an internal problem and needs to >> close.’). It seems more like a Matlab/Windows related issue when >> looking at the crash report (see below), but I am posting it here >> because it also seems to depend on the data that I use as input. When >> I run the routine on the ‘raw’ data (after defining the trials) it is >> working fine, but after I ran ICA and try to use the databrowser to >> look at the components, it crashes at line 676. >> >> This is the part where it calls the subfunction redraw_cb. Does >> anyone might have a clue what in the component data might cause this problem? >> Maybe some of you have experienced this before? I also send a request >> for Tech Support to Matlab. >> >> Best, Martine >> >> Here is the Matlab crash report if that is of any help: >> >> --------------------------------------------------------------------- >> - >> -- >> >> Segmentation violation detected at Thu May 01 22:28:30 2014 >> >> --------------------------------------------------------------------- >> - >> -- >> >> Configuration: >> >> Crash Decoding : Disabled >> >> Default Encoding: windows-1252 >> >> MATLAB Root : C:\Program Files\MATLAB\R2012b >> >> MATLAB Version : 8.0.0.783 (R2012b) >> >> Operating System: Microsoft Windows 7 >> >> Processor ID : x86 Family 111 Model 1 Stepping 2, AuthenticAMD >> >> Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java >> HotSpot(TM) 64-Bit Server VM mixed mode >> >> Window System : Version 6.1 (Build 7601: Service Pack 1) >> >> Fault Count: 1 >> >> Abnormal termination: >> >> Segmentation violation >> >> Register State (from fault): >> >> RAX = 00000000000001a4 RBX = 000000007a8425c0 >> >> RCX = 00000000000262de RDX = 00000000000001b2 >> >> RSP = 0000000004110a50 RBP = 000000000000007e >> >> RSI = 000000007a75cab0 RDI = 000000013942b996 >> >> R8 = 00000000000262de R9 = 0000000000000230 >> >> R10 = 0000000000000000 R11 = 0000000004110b28 >> >> R12 = 0000000000f206cd R13 = 0000000077ce4060 >> >> R14 = 000000000002635c R15 = 00000000000006c8 >> >> RIP = 000000006000d341 EFL = 00010216 >> >> CS = 0033 FS = 0053 GS = 002b >> >> Stack Trace (from fault): >> >> [ 0] 0x000000006000d341 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+01364801 ( >> RenderEngineBase::~RenderEngineBase+171553 ) >> >> [ 1] 0x000000005ff83130 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00799024 ( text_to_pixel+005792 >> ) >> >> [ 2] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 3] 0x000000005fede587 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00124295 ( >> renderAnimatedKids+000519 ) >> >> [ 4] 0x000000005fee3788 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00145288 ( getARDonAxis+010488 ) >> >> [ 5] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 6] 0x000000005ff04729 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00280361 ( >> FigureSetVisualAutoMode+001561 ) >> >> [ 7] 0x000000005ff0abbd C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00306109 ( >> UIJ_CreatePeerWindow+001597 ) >> >> [ 8] 0x00000000602cc003 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+04243459 ( >> GO_TransformObject+001571 ) >> >> [ 9] 0x0000000060013548 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+01389896 ( >> RenderEngineBase::~RenderEngineBase+196648 ) >> >> [ 10] 0x000000005ff06b87 C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00289671 ( >> FigureSetVisualAutoMode+010871 ) >> >> [ 11] 0x000000005ff06c0d C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00289805 ( >> FigureSetVisualAutoMode+011005 ) >> >> [ 12] 0x0000000063425006 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwgui.dll+00610310 ( >> wm_ExposeFcn_Pre_Optional+000374 ) >> >> [ 13] 0x0000000064c8c694 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00181908 ( >> GetframeJava+001332 ) >> >> [ 14] 0x0000000064c8e456 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00189526 ( >> UIJ_IsWindowShowing+000438 ) >> >> [ 15] 0x0000000064c8f943 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00194883 ( >> UIJ_clearWaitForResize+002067 ) >> >> [ 16] 0x0000000064c8fa61 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00195169 ( >> UIJ_ExposeFcn+000145 ) >> >> [ 17] 0x0000000064c707ae C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00067502 ( >> UIJ_MarkEventFinished+005838 ) >> >> [ 18] 0x0000000064c70800 C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00067584 ( >> UIJ_MarkEventFinished+005920 ) >> >> [ 19] 0x0000000064c892ac C:\Program >> Files\MATLAB\R2012b\bin\win64\libuij.dll+00168620 ( >> uij::JavaDraw2D::paintQuadStrip+001324 ) >> >> [ 20] 0x0000000064d4e808 C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00190472 ( >> uddSetListenerRecursionWarning+000680 ) >> >> [ 21] 0x0000000064d4ee6c C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00192108 ( >> UDListenerManagerHost::notifyEvent+000076 ) >> >> [ 22] 0x0000000064d4697d C:\Program >> Files\MATLAB\R2012b\bin\win64\udd.dll+00158077 ( >> UDEventInfo::send+000093 ) >> >> [ 23] 0x000000005fb9cedb C:\Program >> Files\MATLAB\R2012b\bin\win64\udd_mi.dll+00052955 ( >> MErrorException::operator=+047675 ) >> >> [ 24] 0x00000000055ce0b6 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( >> UIW_IsUserMessage+000086 ) >> >> [ 25] 0x00000000055ce7b9 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( >> UIW_SetGLIMUserMsg+000153 ) >> >> [ 26] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( >> GetMenuBarInfo+000638 ) >> >> [ 27] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( >> SystemParametersInfoW+000235 ) >> >> [ 28] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( >> IsProcessDPIAware+000465 ) >> >> [ 29] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( >> KiUserCallbackDispatcher+000031 ) >> >> [ 30] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( >> PeekMessageW+000186 ) >> >> [ 31] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( >> GetKeyState+000238 ) >> >> [ 32] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( >> PeekMessageA+000087 ) >> >> [ 33] 0x00000000055a8f4b C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( >> UIW_SetCurrentDialog+000731 ) >> >> [ 34] 0x00000000055cfbe2 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( >> ws_FreeSystemFont+000546 ) >> >> [ 35] 0x000000000485e6a3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( >> sysq::removeCommitDatabaseUpdatesHook+002131 ) >> >> [ 36] 0x000000000485fe18 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( >> sysq::removeCommitDatabaseUpdatesHook+008136 ) >> >> [ 37] 0x0000000004861a20 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( >> sysq::addProcessPendingEventsUnitTestHook+000240 ) >> >> [ 38] 0x0000000004861ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( >> sysq::addProcessPendingEventsUnitTestHook+000440 ) >> >> [ 39] 0x0000000004861ca3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( >> sysq::addProcessPendingEventsUnitTestHook+000883 ) >> >> [ 40] 0x0000000004861d76 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( >> sysq::addProcessPendingEventsUnitTestHook+001094 ) >> >> [ 41] 0x000000005ff0c4fe C:\Program >> Files\MATLAB\R2012b\bin\win64\hg.dll+00312574 ( hgHitTest+001374 ) >> >> [ 42] 0x0000000074e8d17f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053631 ( >> Mfunction_handle::dispatch+001023 ) >> >> [ 43] 0x0000000074e8cf82 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053122 ( >> Mfunction_handle::dispatch+000514 ) >> >> [ 44] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 45] 0x000007feef3a5ca4 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00482468 ( >> inFunctionHandleInterface::DestroyWorkspace+295012 ) >> >> [ 46] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 47] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 48] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 49] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 50] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 51] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 52] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 53] 0x000007feef38210b C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00336139 ( >> inFunctionHandleInterface::DestroyWorkspace+148683 ) >> >> [ 54] 0x000007feef393edf C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00409311 ( >> inFunctionHandleInterface::DestroyWorkspace+221855 ) >> >> [ 55] 0x000007feef3b0ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00527080 ( >> inFunctionHandleInterface::DestroyWorkspace+339624 ) >> >> [ 56] 0x000007feef398d94 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00429460 ( >> inFunctionHandleInterface::DestroyWorkspace+242004 ) >> >> [ 57] 0x000007feef3a2978 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00469368 ( >> inFunctionHandleInterface::DestroyWorkspace+281912 ) >> >> [ 58] 0x000007feef3a5a8b C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00481931 ( >> inFunctionHandleInterface::DestroyWorkspace+294475 ) >> >> [ 59] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 60] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 61] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 62] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 63] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 64] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 65] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 66] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 67] 0x000007feef43318f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( >> inEachVisibleName+014415 ) >> >> [ 68] 0x000007feef3a74ca C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( >> inFunctionHandleInterface::DestroyWorkspace+301194 ) >> >> [ 69] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 70] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 71] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 72] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 73] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 74] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 75] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 76] 0x000007feef3a9482 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00496770 ( >> inFunctionHandleInterface::DestroyWorkspace+309314 ) >> >> [ 77] 0x000007feef43318f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01061263 ( >> inEachVisibleName+014415 ) >> >> [ 78] 0x000007feef3a74ca C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00488650 ( >> inFunctionHandleInterface::DestroyWorkspace+301194 ) >> >> [ 79] 0x000007feef38de1f C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384543 ( >> inFunctionHandleInterface::DestroyWorkspace+197087 ) >> >> [ 80] 0x000007feef38dd80 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00384384 ( >> inFunctionHandleInterface::DestroyWorkspace+196928 ) >> >> [ 81] 0x000007feef3b197d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00530813 ( >> inFunctionHandleInterface::DestroyWorkspace+343357 ) >> >> [ 82] 0x000007feef3b0271 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00524913 ( >> inFunctionHandleInterface::DestroyWorkspace+337457 ) >> >> [ 83] 0x000007feef3920e9 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00401641 ( >> inFunctionHandleInterface::DestroyWorkspace+214185 ) >> >> [ 84] 0x0000000074e8c80d C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00051213 ( >> Mfh_file::dispatch_fh+000509 ) >> >> [ 85] 0x0000000074e8d0d6 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_dispatcher.dll+00053462 ( >> Mfunction_handle::dispatch+000854 ) >> >> [ 86] 0x000007feef4451e5 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01135077 ( >> inValidateLoadedObject+001893 ) >> >> [ 87] 0x000007feef454595 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01197461 ( >> init_cleaner+015541 ) >> >> [ 88] 0x000007feef457b75 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211253 ( >> inSetMaxFrameCount+002261 ) >> >> [ 89] 0x000007feef457b48 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211208 ( >> inSetMaxFrameCount+002216 ) >> >> [ 90] 0x000007feef457b07 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01211143 ( >> inSetMaxFrameCount+002151 ) >> >> [ 91] 0x000007feef340213 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+00066067 ( >> inPathNotification::function_clear_notification+004019 ) >> >> [ 92] 0x000007feef44aed0 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158864 ( >> inEvalCmdWithLocalReturn+000416 ) >> >> [ 93] 0x000007feef44ae2c C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158700 ( >> inEvalCmdWithLocalReturn+000252 ) >> >> [ 94] 0x000007feef44ad71 C:\Program >> Files\MATLAB\R2012b\bin\win64\m_interpreter.dll+01158513 ( >> inEvalCmdWithLocalReturn+000065 ) >> >> [ 95] 0x0000000079fbf90d C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00063757 ( >> mnDebugPrompt+000109 ) >> >> [ 96] 0x0000000079fc0471 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwbridge.dll+00066673 ( >> mnParser+000593 ) >> >> [ 97] 0x00000000749a64a4 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00222372 ( >> mcrInstance::mnParser_on_interpreter_thread+000036 ) >> >> [ 98] 0x000000007498681f C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00092191 ( >> mcr::setInterpreterThreadToCurrent+029887 ) >> >> [ 99] 0x0000000074986881 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00092289 ( >> mcr::setInterpreterThreadToCurrent+029985 ) >> >> [100] 0x00000000055ce0b6 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00385206 ( >> UIW_IsUserMessage+000086 ) >> >> [101] 0x00000000055ce7b9 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00387001 ( >> UIW_SetGLIMUserMsg+000153 ) >> >> [102] 0x00000000774a87fe C:\Windows\system32\USER32.dll+00165886 ( >> GetMenuBarInfo+000638 ) >> >> [103] 0x000000007748f5fb C:\Windows\system32\USER32.dll+00062971 ( >> SystemParametersInfoW+000235 ) >> >> [104] 0x0000000077494895 C:\Windows\system32\USER32.dll+00084117 ( >> IsProcessDPIAware+000465 ) >> >> [105] 0x00000000775d11f5 C:\Windows\SYSTEM32\ntdll.dll+00332277 ( >> KiUserCallbackDispatcher+000031 ) >> >> [106] 0x000000007749908a C:\Windows\system32\USER32.dll+00102538 ( >> PeekMessageW+000186 ) >> >> [107] 0x00000000774950fe C:\Windows\system32\USER32.dll+00086270 ( >> GetKeyState+000238 ) >> >> [108] 0x0000000077493a6f C:\Windows\system32\USER32.dll+00080495 ( >> PeekMessageA+000087 ) >> >> [109] 0x00000000055a8f4b C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00233291 ( >> UIW_SetCurrentDialog+000731 ) >> >> [110] 0x00000000055cfbe2 C:\Program >> Files\MATLAB\R2012b\bin\win64\uiw.dll+00392162 ( >> ws_FreeSystemFont+000546 ) >> >> [111] 0x000000000485e6a3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00779939 ( >> sysq::removeCommitDatabaseUpdatesHook+002131 ) >> >> [112] 0x000000000485fe18 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00785944 ( >> sysq::removeCommitDatabaseUpdatesHook+008136 ) >> >> [113] 0x0000000004861a20 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793120 ( >> sysq::addProcessPendingEventsUnitTestHook+000240 ) >> >> [114] 0x0000000004861ae8 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793320 ( >> sysq::addProcessPendingEventsUnitTestHook+000440 ) >> >> [115] 0x0000000004861ca3 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793763 ( >> sysq::addProcessPendingEventsUnitTestHook+000883 ) >> >> [116] 0x0000000004861d76 C:\Program >> Files\MATLAB\R2012b\bin\win64\libmwservices.dll+00793974 ( >> sysq::addProcessPendingEventsUnitTestHook+001094 ) >> >> [117] 0x000000007498837e C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00099198 ( >> mcr::setInterpreterThreadToCurrent+036894 ) >> >> [118] 0x0000000074988665 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00099941 ( >> mcr::setInterpreterThreadToCurrent+037637 ) >> >> [119] 0x000000007497b166 C:\Program >> Files\MATLAB\R2012b\bin\win64\mcr.dll+00045414 ( >> DepfunRules::postWarning+003430 ) >> >> [120] 0x000000013fc78a33 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035379 ( ???+000000 ) >> >> [121] 0x000000013fc78c97 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00035991 ( ???+000000 ) >> >> [122] 0x000000013fc79163 C:\Program >> Files\MATLAB\R2012b\bin\win64\MATLAB.exe+00037219 ( ???+000000 ) >> >> [123] 0x00000000773759ed C:\Windows\system32\kernel32.dll+00088557 ( >> BaseThreadInitThunk+000013 ) >> >> [124] 0x00000000775ac541 C:\Windows\SYSTEM32\ntdll.dll+00181569 ( >> RtlUserThreadStart+000033 ) >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From ahmeedzeki at yahoo.com Tue May 6 22:41:13 2014 From: ahmeedzeki at yahoo.com (ahmeedzeki at yahoo.com) Date: Tue, 6 May 2014 20:41:13 +0000 Subject: [FieldTrip] =?utf-8?q?Leadfield_Matrix?= Message-ID: <687035.72317.bm@smtp110.mail.bf1.yahoo.com> Dear leadfield Developers and Users: My name is Ahmed Al Hilli, I am a PhD student at Rutgers University. I am working on EEG source localization. I have difficulties in generating the leadfield matrix. I want to generate the leadfield matrix using just a cortex of the brain and I want to use a realistic head model. I’ve generated the cortex sheet using ft_volume_segment function, and also I have the scalp binary mask. My question is what to do next to apply BEM method? Thank you very much Sent from Windows Mail -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.rombetto at cib.na.cnr.it Wed May 7 13:00:50 2014 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Wed, 7 May 2014 13:00:50 +0200 Subject: [FieldTrip] problem occurs when using ft_timelockanalysis Message-ID: <20140507130050.cctyuq8m1w80o4g4@arco.cib.na.cnr.it> Dear fieldtrippers I'm encountering a problem when running ft_timelockanalysis in Matlab. I receive the following message: "A Undefined function 'mxSerialize_cpp' for input arguments of type 'struct' Error in mxSerialize (line 35) argout = mxSerialize_cpp(argin); Error in ft_preamble_provenance (line 67) cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); Error in ft_preamble (line 54) evalin('caller', ['ft_preamble_' cmd]); Error in ft_timelockanalysis (line 95) ft_preamble provenance data" I am using \fieldtrip-20140506 and matlab R2014a - 64 bit Any suggestion is highly appreciated. ------------------------- Dott.ssa Sara Rombetto Istituto di Cibernetica "E. Caianiello" Via Campi Flegrei, 34 80078 Pozzuoli (NA) Italy mob +39 3401689815 tel +39 0818675361 fax +39 0818675128 Lab MEG 0817483511 -------------------------- "I disapprove of what you say, but I will defend to the death your right to say it." [Evelyn Beatrice Hall, The Friends Of Voltaire] ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From yingli.ucla at gmail.com Wed May 7 23:14:22 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Wed, 7 May 2014 14:14:22 -0700 Subject: [FieldTrip] Failed to download the sample data - the links no longer exist Message-ID: Dear all, I am learning to use fieldtrip to do source localization. When I tried to download some sample data, such as 1) The MEG data: ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip 2) The MRI data: ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip . It shows that the links don't exist any more. Are there any other ways for me to download these sample data? Thanks a lot! Ying -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Thu May 8 11:00:29 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 8 May 2014 09:00:29 +0000 Subject: [FieldTrip] (no subject) Message-ID: Dear all, has anyone come across (or used) cluster-based permutation statistics for (human) LFP data obtained from DBS-electrodes? I am looking for a reference and, after a quick search, didn't find any, thanks! Best wishes Max From jm.horschig at donders.ru.nl Thu May 8 13:02:59 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 08 May 2014 13:02:59 +0200 Subject: [FieldTrip] (no subject) In-Reply-To: References: Message-ID: <536B6463.3080504@donders.ru.nl> Hi Max-Philipp, what is it that you want to do specifically? Basically, there is nothing different from doing scalp EEG statistics. Regarding a reference, if you wait for a few more months, then you can cite my paper... once I've written it down ;) Best, Jörn On 5/8/2014 11:00 AM, Stenner, Max-Philipp wrote: > Dear all, > has anyone come across (or used) cluster-based permutation statistics for (human) LFP data obtained from DBS-electrodes? I am looking for a reference and, after a quick search, didn't find any, > thanks! > Best wishes > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From max-philipp.stenner at med.ovgu.de Thu May 8 13:24:47 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 8 May 2014 11:24:47 +0000 Subject: [FieldTrip] (no subject) In-Reply-To: <536B6463.3080504@donders.ru.nl> References: , <536B6463.3080504@donders.ru.nl> Message-ID: Hi Jörn, thanks, you are right, there is no difference to any other montage with a common reference. And thanks for the prospective citation, I'll look out for it, best Max ________________________________________ Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" im Auftrag von ""Jörn M. Horschig" [jm.horschig at donders.ru.nl] Gesendet: Donnerstag, 8. Mai 2014 13:02 An: FieldTrip discussion list Betreff: Re: [FieldTrip] (no subject) Hi Max-Philipp, what is it that you want to do specifically? Basically, there is nothing different from doing scalp EEG statistics. Regarding a reference, if you wait for a few more months, then you can cite my paper... once I've written it down ;) Best, Jörn On 5/8/2014 11:00 AM, Stenner, Max-Philipp wrote: > Dear all, > has anyone come across (or used) cluster-based permutation statistics for (human) LFP data obtained from DBS-electrodes? I am looking for a reference and, after a quick search, didn't find any, > thanks! > Best wishes > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From greg at think-now.com Thu May 8 19:52:17 2014 From: greg at think-now.com (Greg Simpson) Date: Thu, 8 May 2014 10:52:17 -0700 Subject: [FieldTrip] Research Associate Position Available Message-ID: Dear Colleagues - please note our job opening below and spread the word to those that might be interested. Thank you! Greg EEG Research Associate (Data Analysis) Think Now Inc. has a Research Associate opening for an EEG data analyst for 2 NIH-funded studies being conducted with UCLA on the neurophysiological bases of sustained attention, its deficits in ADHD and the effects of computerized brain training. We are seeking candidates with direct hands-on experience in EEG data analysis. MatLab programming skills are required. We prefer strongly self-directed individuals to take on this work. The successful candidate will report directly to Gregory V. Simpson, Ph.D., Chief Scientific Officer of Think Now and will collaborate with Mark Cohen, Ph.D., Agatha Lenartowicz, Ph.D. and the team at UCLA. Think Now is located in San Francisco, so the successful candidate can be located in either San Francisco or Los Angeles. Think Now is creating EEG and mobile-app based solutions for the diagnosis and amelioration of neurological disorders with a focus on attention and its control. Please send your CV and a description of your prior experience with EEG data analysis and MatLab to *jobs at think-now.com *. Gregory V. Simpson, Ph.D. Founder & CSO Think Now, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mossa.luca86 at gmail.com Fri May 9 12:38:05 2014 From: mossa.luca86 at gmail.com (Luca Mossa) Date: Fri, 9 May 2014 12:38:05 +0200 Subject: [FieldTrip] Combine Fieldtrip with BCI2000 Message-ID: Dear community, My name is Luca Mossa and I'm working in a company in Turin (Italy) on BCI experiments. Currently I'm trying to develop some Matlab code to improve the signal processing process. I'm currently trying to use FieldTripBuffer (in matlab) as the Signal Processing module for a mu rhythm application. I have no problems to read the raw signal and states but I have trouble to find a way to sent the processing result back to Bci for the classification. Thanks to Mr. Oostenveld now I know that I must use the ft_write_event function but when I tried to use my code (with ft_write_event function) appears an error: Error using buffer events must be given as struct. Error in ft_write_event buffer('put_evt', event, host, port) Now I think that I must define some parameters, like: event.type=.... event.sample=.... event.offset=.... event.duration=.... event.value=.... but I don't understand which kind of value to insert in these field. Have you some hint? Did you make me some example? Thank you very much. Luca -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Fri May 9 15:20:04 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Fri, 9 May 2014 15:20:04 +0200 Subject: [FieldTrip] Failed to download the sample data - the links no longer exist In-Reply-To: References: Message-ID: Dear Ying, I can download the files with no problems (to an off-campus computer). Are you still having trouble? Best, Eelke On 7 May 2014 23:14, Ying Li wrote: > Dear all, > > I am learning to use fieldtrip to do source localization. When I tried to > download some sample data, such as > 1) The MEG data: ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip > 2) The MRI data: > ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip. > It shows that the links don't exist any more. > > Are there any other ways for me to download these sample data? > > Thanks a lot! > > Ying > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From t.grent-tjong at donders.ru.nl Sun May 11 11:22:14 2014 From: t.grent-tjong at donders.ru.nl (Tineke Grent-'t-Jong) Date: Sun, 11 May 2014 11:22:14 +0200 Subject: [FieldTrip] cfg.parameter definition problem in ft_sourcegrandaverage Message-ID: <30DB2C9C4EC049A4A1128699BF86E778@socrates> Dear all, I tried to grandaverage beamformer source-reconstructions of beta-coherent sources (coherent with a seed-region) this morning and received the following error message: ??? Reference to a non-existent field 'avg.coh' (refering to my specification of cfg.parameter = 'avg.coh', which is where the data truly is) This is strange given the fact that the same procedure worked just fine on comparable data (same analysis, different settings) a few weeks ago. Running the function again with cfg.parameter = 'coh' did initially seem to work, but in hindsight gave the wrong output, likely related to the fact that the field 'coh' was simply ignored (warning during running read: "skipping unknown field 'coh'). Has anyone any idea what the problem is and how to resolve it? Best, Tineke Grent-'t-Jong -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon May 12 09:14:17 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 12 May 2014 09:14:17 +0200 Subject: [FieldTrip] Combine Fieldtrip with BCI2000 In-Reply-To: References: Message-ID: <537074C9.4090303@donders.ru.nl> Hi Luca, nice to hear that you are using the FieldTrip buffer. I guess you saw the relevant pages on our wiki? Like http://fieldtrip.fcdonders.nl/faq/what_is_the_relation_between_events_such_as_triggers_and_trials http://fieldtrip.fcdonders.nl/development/realtime/buffer_protocol?s[]=event http://fieldtrip.fcdonders.nl/example/measuring_the_timing_delay_and_jitter_for_a_real-time_application?s[]=event In general for sending events, you can set all relevant fields to anything you want, so if you want to define: > event.type=.... > event.sample=.... > event.offset=.... > event.duration=.... > event.value=.... The type is a string, and you can set it to whatever you want to distinguish in your code between different types. Sample will be automatically set by the buffer. Offset and duration are, for usual purposes, not necessary in a real-time application (though you could set them to meaningful values). The event.value field is the probably most important field. This is your trigger value, in your case for example the classification outcome. Check out the pages above, especially the last one, I guess it will become clearer then. Also check out the example scripts in the realtime folder. If you have any more questions that don't become obvious from above pages, feel free to ask again here ;) Best, Jörn On 5/9/2014 12:38 PM, Luca Mossa wrote: > Dear community, > > My name is Luca Mossa and I'm working in a company in Turin (Italy) on > BCI experiments. > Currently I'm trying to develop some Matlab code to improve the signal > processing process. > > I'm currently trying to use FieldTripBuffer (in matlab) as the Signal > Processing module for a mu rhythm application. I have no problems to > read the raw signal and states but I have trouble to find a way to > sent the processing result back to Bci for the classification. > > Thanks to Mr. Oostenveld now I know that I must use the ft_write_event > function but when I tried to use my code (with ft_write_event > function) appears an error: > > Error using buffer > events must be given as struct. > > Error in ft_write_event > buffer('put_evt', event, host, port) > > Now I think that I must define some parameters, like: > > event.type=.... > event.sample=.... > event.offset=.... > event.duration=.... > event.value=.... > > but I don't understand which kind of value to insert in these field. > Have you some hint? Did you make me some example? > > Thank you very much. > > Luca > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From j.herring at fcdonders.ru.nl Mon May 12 16:02:01 2014 From: j.herring at fcdonders.ru.nl (Herring, J.D. (Jim)) Date: Mon, 12 May 2014 16:02:01 +0200 (CEST) Subject: [FieldTrip] Brain Stimulation (TMS-tCS-EEG) toolkit course at Donders, Nijmegen - registration is now open Message-ID: <003601cf6dea$bf8df480$3ea9dd80$@herring@fcdonders.ru.nl> On June 24-27, 2014, we will host the “Toolkit of Cognitive Neuroscience: Transcranial Brain Stimulation” at the Donders Institute in Nijmegen. This intensive four-day toolkit course will provide in-depth knowledge on transcranial magnetic stimulation (TMS) and transcranial current stimulation (tDCS/tACS). The course will cover both basic and advanced topics, discussing online and offline approaches of quantification, interference, and modulation of neural activity. We will specifically address multimodal applications of non-invasive brain stimulation, with a special emphasis on concurrent electroencephalography (EEG). The course involves a series of lectures and hands-on training of stimulation application, data acquisition and data analysis. These address fundamental paradigms, such as single-pulse TMS, repetitive TMS, tDCS and tACS, and advanced topics, such as paired-pulse TMS and concurrent TMS-tDCS-EEG, and MEG. Keynote lectures will be announced in the coming months. Please see the attached preliminary program for more details. The participation fee is €200 for (PhD) students and €400 for more senior researchers. This includes coffee/tea, Dutch sandwich lunches, and social events. Because of space limitations the number of participants in the hands-on sessions is limited to 30. Location: Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Kapittelweg 29, 6525 EN Nijmegen Organizers: Ian Cameron (ian.cameron at donders.ru.nl) Dilene van Campen ( a.vancampen at donders.ru.nl) Registration: http://www.ru.nl/donders/toolkit2014 ------------------------------------------------------------------------------------------------------------------------------ Jim Herring, MSc. Neuronal Oscillations Group Centre for Cognitive Neuroimaging Donders Institute for Brain, Cognition and Behaviour Radboud University Nijmegen -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: toolkittms_program2014 (2).pdf Type: application/pdf Size: 336353 bytes Desc: not available URL: From s.rombetto at cib.na.cnr.it Tue May 13 16:15:34 2014 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Tue, 13 May 2014 16:15:34 +0200 Subject: [FieldTrip] problem occurs when using ft_timelockanalysis Message-ID: <20140513161534.pe4l2mabwo8wk40k@arco.cib.na.cnr.it> Any suggestion concerning this problem? it works finewith Matlab 2013 ----- Messaggio inoltrato da s.rombetto at cib.na.cnr.it ----- Data: Wed, 7 May 2014 13:00:50 +0200 Da: s.rombetto at cib.na.cnr.it Rispondi-A:s.rombetto at cib.na.cnr.it Oggetto: problem occurs when using ft_timelockanalysis A: fieldtrip at science.ru.nl Dear fieldtrippers I'm encountering a problem when running ft_timelockanalysis in Matlab. I receive the following message: "A Undefined function 'mxSerialize_cpp' for input arguments of type 'struct' Error in mxSerialize (line 35) argout = mxSerialize_cpp(argin); Error in ft_preamble_provenance (line 67) cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); Error in ft_preamble (line 54) evalin('caller', ['ft_preamble_' cmd]); Error in ft_timelockanalysis (line 95) ft_preamble provenance data" I am using \fieldtrip-20140506 and matlab R2014a - 64 bit Any suggestion is highly appreciated. ------------------------- Dott.ssa Sara Rombetto Istituto di Cibernetica "E. Caianiello" Via Campi Flegrei, 34 80078 Pozzuoli (NA) Italy mob +39 3401689815 tel +39 0818675361 fax +39 0818675128 Lab MEG 0817483511 -------------------------- "I disapprove of what you say, but I will defend to the death your right to say it." [Evelyn Beatrice Hall, The Friends Of Voltaire] ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ----- Fine del messaggio inoltrato ----- ------------------------- Dott.ssa Sara Rombetto Istituto di Cibernetica "E. Caianiello" Via Campi Flegrei, 34 80078 Pozzuoli (NA) Italy mob +39 3401689815 tel +39 0818675361 fax +39 0818675128 Lab MEG 0817483511 -------------------------- "I disapprove of what you say, but I will defend to the death your right to say it." [Evelyn Beatrice Hall, The Friends Of Voltaire] ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From gamaliel.ghu at gmail.com Tue May 13 18:20:03 2014 From: gamaliel.ghu at gmail.com (gamaliel huerta urrea) Date: Tue, 13 May 2014 12:20:03 -0400 Subject: [FieldTrip] questions about ft_prepare_headmodel, error: the compartment nesting cannot be determined Message-ID: hi all fieldtrip my experience is limited, and attempt a head model. I analyze the documents for the user's site, and could reach the head model is presented in the official website successfully. But when trying to do the same from imr own size: 512x512x22, throws me the following errors when trying to run the function ft_headmodel. What could be the problem? because with the Subject01.mri file, the code itself works fine, but with the mri.mat (attached) file not working properly the error is as follows Warning: please specify cfg.method='projectmesh', 'iso2mesh' or 'isosurface' > In ft_prepare_mesh at 116 In ft_prepare_headmodel at 251 In fm_0 at 41 Warning: using 'projectmesh' as default > In ft_prepare_mesh at 117 In ft_prepare_headmodel at 251 In fm_0 at 41 making mesh for scalp tissue making mesh for brain tissue making mesh for skull tissue converting seg creating probabilistic representation for scalp creating probabilistic representation for brain creating probabilistic representation for skull triangulating the outer boundary of compartment 1 (scalp) with 3000 vertices triangulating the outer boundary of compartment 2 (brain) with 3000 vertices triangulating the outer boundary of compartment 3 (skull) with 3000 vertices the call to "ft_prepare_mesh" took 6 seconds Error using surface_nesting (line 26) the compartment nesting cannot be determined Error in ft_headmodel_bemcp (line 66) order = surface_nesting(vol.bnd, 'insidefirst'); Error in ft_prepare_headmodel (line 257) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in fm_0 (line 41) vol = ft_prepare_headmodel(cfg, segmentedmri); the used code is: %% load MRI data mri = ft_read_mri('IM-0001-0001.dcm'); disp(mri)%muestra informacion de mri data cfg = []; cfg.output = {'brain','skull','scalp'};%escoge las superficies segmentedmri = ft_volumesegment(cfg, mri);%Realiza la segmentacion save segmentedmri segmentedmri disp(segmentedmri) %% Mesh cfg=[]; cfg.tissue={'brain','skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); save bnd bnd disp(bnd(1)) %% Head Model cfg = []; cfg.method ='bemcp';% el tipo de modelo se puede cambiar vol = ft_prepare_headmodel(cfg, segmentedmri); save vol vol disp(vol) -- regards -- *Gamaliel Huerta* *Ingeniería Civil Biomédica* *Universidad de Valparaíso* -------------- next part -------------- An HTML attachment was scrubbed... URL: From gamaliel.ghu at gmail.com Wed May 14 08:24:32 2014 From: gamaliel.ghu at gmail.com (gamaliel huerta urrea) Date: Wed, 14 May 2014 02:24:32 -0400 Subject: [FieldTrip] questions about ft_prepare_headmodel, error: the compartment nesting cannot be determined Message-ID: hi all fieldtrip my experience is limited, and attempt a head model. I analyze the documents for the user's site, and could reach the head model is presented in the official website successfully. But when trying to do the same from imr own size: 512x512x22, throws me the following errors when trying to run the function ft_headmodel. What could be the problem? because with the Subject01.mri file, the code itself works fine, but with the mri.mat (attached) file not working properly the error is as follows Warning: please specify cfg.method='projectmesh', 'iso2mesh' or 'isosurface' > In ft_prepare_mesh at 116 In ft_prepare_headmodel at 251 In fm_0 at 41 Warning: using 'projectmesh' as default > In ft_prepare_mesh at 117 In ft_prepare_headmodel at 251 In fm_0 at 41 making mesh for scalp tissue making mesh for brain tissue making mesh for skull tissue converting seg creating probabilistic representation for scalp creating probabilistic representation for brain creating probabilistic representation for skull triangulating the outer boundary of compartment 1 (scalp) with 3000 vertices triangulating the outer boundary of compartment 2 (brain) with 3000 vertices triangulating the outer boundary of compartment 3 (skull) with 3000 vertices the call to "ft_prepare_mesh" took 6 seconds Error using surface_nesting (line 26) the compartment nesting cannot be determined Error in ft_headmodel_bemcp (line 66) order = surface_nesting(vol.bnd, 'insidefirst'); Error in ft_prepare_headmodel (line 257) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in fm_0 (line 41) vol = ft_prepare_headmodel(cfg, segmentedmri); the used code is: %% load MRI data mri = ft_read_mri('IM-0001-0001.dcm'); disp(mri)%muestra informacion de mri data cfg = []; cfg.output = {'brain','skull','scalp'};%escoge las superficies segmentedmri = ft_volumesegment(cfg, mri);%Realiza la segmentacion save segmentedmri segmentedmri disp(segmentedmri) %% Mesh cfg=[]; cfg.tissue={'brain','skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); save bnd bnd disp(bnd(1)) %% Head Model cfg = []; cfg.method ='bemcp';% el tipo de modelo se puede cambiar vol = ft_prepare_headmodel(cfg, segmentedmri); save vol vol disp(vol) -- *Gamaliel Huerta* *Ingeniería Civil Biomédica* *Universidad de Valparaíso* -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Wed May 14 10:35:03 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 14 May 2014 10:35:03 +0200 Subject: [FieldTrip] problem occurs when using ft_timelockanalysis In-Reply-To: <20140513161534.pe4l2mabwo8wk40k@arco.cib.na.cnr.it> References: <20140513161534.pe4l2mabwo8wk40k@arco.cib.na.cnr.it> Message-ID: <53732AB7.6020203@donders.ru.nl> Hi Sara, I guess you are not using a mac. What you describe concerns bug 2452 on our Bugzilla page: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2452 which pertains to some undocumented change in Matlab. Therefore it is necessary to use a different mxserialize function that from matlab 2014a onwards than before. This is a c++ function, which requires to be compiled for each platform independently. In FieldTrip, this file exists e.g. in fileio/private but only for MacOS 64-bit platforms. Apparently, we still need to compile it for MacOS 32bit, Windows and Linux platforms. I guess we should do that quite soon ;) I'll bring it up in today's FT meeting so that hopefully from tomorrow onwards it should work. btw, for you it will help to go to the FieldTrip/src directory in Matlab and type >> mex mxSerialize_cpp.cpp Then Matlab will mex (~compile) the file for you. You can then copy that file to your matlab code directory and everything should work out fine for you. I'll keep you updated on this. Best, Jörn On 5/13/2014 4:15 PM, s.rombetto at cib.na.cnr.it wrote: > Any suggestion concerning this problem? > > it works finewith Matlab 2013 > > > > ----- Messaggio inoltrato da s.rombetto at cib.na.cnr.it ----- > Data: Wed, 7 May 2014 13:00:50 +0200 > Da: s.rombetto at cib.na.cnr.it > Rispondi-A:s.rombetto at cib.na.cnr.it > Oggetto: problem occurs when using ft_timelockanalysis > A: fieldtrip at science.ru.nl > > Dear fieldtrippers > > I'm encountering a problem when running ft_timelockanalysis in Matlab. > I receive the following message: > > "A Undefined function 'mxSerialize_cpp' for input arguments of type > 'struct' > > Error in mxSerialize (line 35) > argout = mxSerialize_cpp(argin); > > Error in ft_preamble_provenance (line 67) > cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); > > Error in ft_preamble (line 54) > evalin('caller', ['ft_preamble_' cmd]); > > Error in ft_timelockanalysis (line 95) > ft_preamble provenance data" > > > I am using \fieldtrip-20140506 and matlab R2014a - 64 bit > > Any suggestion is highly appreciated. > ------------------------- > Dott.ssa Sara Rombetto > Istituto di Cibernetica > "E. Caianiello" > Via Campi Flegrei, 34 > 80078 Pozzuoli (NA) > Italy > mob +39 3401689815 > tel +39 0818675361 > fax +39 0818675128 > Lab MEG 0817483511 > -------------------------- > "I disapprove of what you say, but I will defend to the death your > right to say > it." [Evelyn Beatrice Hall, The Friends Of Voltaire] > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > ----- Fine del messaggio inoltrato ----- > > > ------------------------- > Dott.ssa Sara Rombetto > Istituto di Cibernetica > "E. Caianiello" > Via Campi Flegrei, 34 > 80078 Pozzuoli (NA) > Italy > mob +39 3401689815 > tel +39 0818675361 > fax +39 0818675128 > Lab MEG 0817483511 > -------------------------- > "I disapprove of what you say, but I will defend to the death your > right to say > it." [Evelyn Beatrice Hall, The Friends Of Voltaire] > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From max-philipp.stenner at med.ovgu.de Wed May 14 16:25:44 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Wed, 14 May 2014 14:25:44 +0000 Subject: [FieldTrip] (no subject) Message-ID: Dear fieldtrippers, I was planning to use cluster-based permutation statistics for group-level inference on the difference between two conditions (depsamplesT) for a fairly small number of subjects (as few as 5). However, this would mean a total of only 2^5=32 possible permutations (=discrete values for the non-parametric null distribution), and therefore a maximum "p-value-resolution" of only 1/32=.0313. Does this mean that group-level permutation statistics are not appropriate for small sample sizes? How do people correct for MC in these cases (using fieldtrip)? (I am specifically interested in group-level analyses, not primarily in within-subject/across-trials testing). Thanks in advance, best Max From r.oostenveld at donders.ru.nl Wed May 14 18:10:09 2014 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 14 May 2014 18:10:09 +0200 Subject: [FieldTrip] postdoc position at NatMEG, Karolinska Institute, Stockholm, Sweden Message-ID: <4B9B1EED-6A34-4E46-95B8-F8F30B155399@donders.ru.nl> Post doc, Stockholm, Sweden The Department of Clinical Neuroscience at Karolinska Institutet offers a 2 year post doc position giving the researcher an unique mix of inspiring interactions with researchers from a wide range of research areas and a freedom to pursuit one's own qualified research questions. NatMEG – the national facility for magnetoencephalography (MEG) As of September 2013 Karolinska Institutet hosts a superbly equipped MEG lab. The NatMEG lab is a national facility open for researchers from all across Sweden. Due to it being a national facility, a wide array of projects is currently ongoing or under initiation at NatMEG. We are covering areas such as next generation SQUIDS, computational modelling, epilepsy work-ups and cognitive neuroscience in the areas of memory, language, attention, perception, pain, music, decision making, emotion, autism, schizophrenia, Parkinson's and Alzheimer's disease and more. We currently have 1 post doc and 3 guest professors that supports and initiates research at NatMEG and we are now recruiting another postdoc researcher to the lab. Please visit http://www.natmeg.se for more information. Duties Your duties as a postdoc will consist of: • The postdocs own qualified research with MEG and/or simultaneous MEG & EEG. • Research at the national infrastructure for magnetoencephalography (NatMEG), including some general operation. • Scientific support to users at NatMEG, regarding methods, experimental design and analysis. • Development of routines, experimental design and analysis with MEG and EEG. Entry requirements An ideal candidate has extensive MEG experience and is experienced in psychophysiology measurements. The person has strong skills in FieldTrip, MNE or other MEG analysis tools as well as in MatLab and/or Python. We are looking for candidates with a research interest within the cognitive neuroscience domain, that master academic English, is independent and service minded. A person is eligible for a position as postdoctoral research fellow if he or she has obtained a PhD no more than seven years before the last date of employment as postdoc. Application process Read more about the application process at https://ki.mynetworkglobal.com/en/what:job/jobID:35553/. Applications are to be submitted in the recruitment system NetRecruiter. Application deadline 2014-06-15 Contact information Daniel Lundqvist, Project manager daniel.lundqvist at ki.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.rombetto at cib.na.cnr.it Thu May 15 10:29:35 2014 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Thu, 15 May 2014 10:29:35 +0200 Subject: [FieldTrip] problem occurs when using ft_timelockanalysis In-Reply-To: <53732AB7.6020203@donders.ru.nl> References: <20140513161534.pe4l2mabwo8wk40k@arco.cib.na.cnr.it> <53732AB7.6020203@donders.ru.nl> Message-ID: <20140515102935.krkki9plw4gw40k0@arco.cib.na.cnr.it> dear Jörn thanks for your answer. You were right, I am using a win 64 pc. With your trick it works now :) Sara > Hi Sara, > > I guess you are not using a mac. What you describe concerns bug 2452 on > our Bugzilla page: > http://bugzilla.fcdonders.nl/show_bug.cgi?id=2452 > which pertains to some undocumented change in Matlab. Therefore it is > necessary to use a different mxserialize function that from matlab > 2014a onwards than before. This is a c++ function, which requires to > be compiled for each platform independently. In FieldTrip, this file > exists e.g. in fileio/private but only for MacOS 64-bit platforms. > Apparently, we still need to compile it for MacOS 32bit, Windows and > Linux platforms. I guess we should do that quite soon ;) I'll bring it > up in today's FT meeting so that hopefully from tomorrow onwards it > should work. > > btw, for you it will help to go to the FieldTrip/src directory in > Matlab and type >>> mex mxSerialize_cpp.cpp > > Then Matlab will mex (~compile) the file for you. You can then copy > that file to your matlab code directory and everything should work out > fine for you. I'll keep you updated on this. > > Best, > Jörn > > On 5/13/2014 4:15 PM, s.rombetto at cib.na.cnr.it wrote: >> Any suggestion concerning this problem? >> >> it works finewith Matlab 2013 >> >> >> >> ----- Messaggio inoltrato da s.rombetto at cib.na.cnr.it ----- >> Data: Wed, 7 May 2014 13:00:50 +0200 >> Da: s.rombetto at cib.na.cnr.it >> Rispondi-A:s.rombetto at cib.na.cnr.it >> Oggetto: problem occurs when using ft_timelockanalysis >> A: fieldtrip at science.ru.nl >> >> Dear fieldtrippers >> >> I'm encountering a problem when running ft_timelockanalysis in Matlab. >> I receive the following message: >> >> "A Undefined function 'mxSerialize_cpp' for input arguments of type 'struct' >> >> Error in mxSerialize (line 35) >> argout = mxSerialize_cpp(argin); >> >> Error in ft_preamble_provenance (line 67) >> cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); >> >> Error in ft_preamble (line 54) >> evalin('caller', ['ft_preamble_' cmd]); >> >> Error in ft_timelockanalysis (line 95) >> ft_preamble provenance data" >> >> >> I am using \fieldtrip-20140506 and matlab R2014a - 64 bit >> >> Any suggestion is highly appreciated. >> ------------------------- >> Dott.ssa Sara Rombetto >> Istituto di Cibernetica >> "E. Caianiello" >> Via Campi Flegrei, 34 >> 80078 Pozzuoli (NA) >> Italy >> mob +39 3401689815 >> tel +39 0818675361 >> fax +39 0818675128 >> Lab MEG 0817483511 >> -------------------------- >> "I disapprove of what you say, but I will defend to the death your >> right to say >> it." [Evelyn Beatrice Hall, The Friends Of Voltaire] >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> >> ----- Fine del messaggio inoltrato ----- >> >> >> ------------------------- >> Dott.ssa Sara Rombetto >> Istituto di Cibernetica >> "E. Caianiello" >> Via Campi Flegrei, 34 >> 80078 Pozzuoli (NA) >> Italy >> mob +39 3401689815 >> tel +39 0818675361 >> fax +39 0818675128 >> Lab MEG 0817483511 >> -------------------------- >> "I disapprove of what you say, but I will defend to the death your >> right to say >> it." [Evelyn Beatrice Hall, The Friends Of Voltaire] >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ------------------------- Dott.ssa Sara Rombetto Istituto di Cibernetica "E. Caianiello" Via Campi Flegrei, 34 80078 Pozzuoli (NA) Italy mob +39 3401689815 tel +39 0818675361 fax +39 0818675128 Lab MEG 0817483511 -------------------------- "I disapprove of what you say, but I will defend to the death your right to say it." [Evelyn Beatrice Hall, The Friends Of Voltaire] ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From max-philipp.stenner at med.ovgu.de Thu May 15 17:09:18 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 15 May 2014 15:09:18 +0000 Subject: [FieldTrip] within-subject partition for between-subject stats Message-ID: Dear fieldtrippers, I have a question regarding permutation statistics in a mixed design with only very few subjects (5 subjects, 2 conditions/subject; this follows up on my email yesterday). Since the number of unique permutations of *trial-averaged* data is limited (2^5=32), would it make sense (is it statistically sound) to re-compute trial-averages for each subject after randomly partitioning trials *within* each of the five subjects for a large number of iterations first (since there are >>5 trials/subject the number of unique permutations is much larger than for trial-averaged data) and then re-compute cluster-statistics (e.g. maxsum) for each of these sets of re-computed trial-averages to obtain a null-distribution? Thanks very much in advance, best Max ________________________________________ Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" im Auftrag von "Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de] Gesendet: Mittwoch, 14. Mai 2014 16:25 An: FieldTrip discussion list Betreff: [FieldTrip] (no subject) Dear fieldtrippers, I was planning to use cluster-based permutation statistics for group-level inference on the difference between two conditions (depsamplesT) for a fairly small number of subjects (as few as 5). However, this would mean a total of only 2^5=32 possible permutations (=discrete values for the non-parametric null distribution), and therefore a maximum "p-value-resolution" of only 1/32=.0313. Does this mean that group-level permutation statistics are not appropriate for small sample sizes? How do people correct for MC in these cases (using fieldtrip)? (I am specifically interested in group-level analyses, not primarily in within-subject/across-trials testing). Thanks in advance, best Max _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From laura.marzetti at gmail.com Thu May 15 18:44:26 2014 From: laura.marzetti at gmail.com (Laura Marzetti) Date: Thu, 15 May 2014 18:44:26 +0200 Subject: [FieldTrip] regularized depth weighting for MNE Message-ID: Dear all, I was wondering if the leadfield depth weighting option implemented by the configuration setting cfg.normalize = 'column' or cfg.normalize = 'yes' in input to ft_prepareleadfield, also supports a way to regularize such depth weighting in order to not artificially boost low-gain locations such as the head center in MEG. Thanks, Laura -- Laura Marzetti, PhD Istituto di Tecnologie Avanzate Biomediche Università di Chieti "G. D'Annunzio" Via dei Vestini - Campus Universitario 66013 Chieti - ITALY phone: 0039-0871-3556944 fax: 0039-0871-3556930 From yingli.ucla at gmail.com Sun May 18 00:23:29 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Sat, 17 May 2014 15:23:29 -0700 Subject: [FieldTrip] EEG source reconstruction using fieldtrip (MRI not available) Message-ID: Dear all, Fieldtrip provides a great tool of using MRI to do MEG source reconstruction (http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate). Now I want to do EEG source reconstruction. The EEG cap we used is the standard 10-10 system, but the MRI of the subject is not available. I'm thinking to use another person's MRI instead (i.e. the MNI template). Does fieldtrip provide some tools to match the electrode location and the head model from another person? In addition, since MEG sensor positions are always defined relative to the fiducial coils, so we don't need to transform it into CTF coordinate system any more. When doing EEG source reconstruction, is there any extra steps needed? (i.e. transform the EEG sensor to some certain coordinate system, etc.) Thanks a lot! Best, Ying -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at gmail.com Sun May 18 10:35:34 2014 From: johanna.zumer at gmail.com (Johanna Zumer) Date: Sun, 18 May 2014 09:35:34 +0100 Subject: [FieldTrip] EEG source reconstruction using fieldtrip (MRI not available) In-Reply-To: References: Message-ID: Dear Ying, Yes, that is possible (although in an ideal world, one does have the subject's real MRI). You might gain some help from http://fieldtrip.fcdonders.nl/example/align_eeg_electrode_positions_to_bem_headmodel or http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg (which also then links you to http://fieldtrip.fcdonders.nl/template/headmodel) for the case of using the MNI brain). Best, Johanna 2014-05-17 23:23 GMT+01:00 Ying Li : > Dear all, > > Fieldtrip provides a great tool of using MRI to do MEG source > reconstruction (http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate). > Now I want to do EEG source reconstruction. The EEG cap we used is the > standard 10-10 system, but the MRI of the subject is not available. I'm > thinking to use another person's MRI instead (i.e. the MNI template). Does > fieldtrip provide some tools to match the electrode location and the head > model from another person? > > In addition, since MEG sensor positions are always defined relative to the > fiducial coils, so we don't need to transform it into CTF coordinate system > any more. When doing EEG source reconstruction, is there any extra steps > needed? (i.e. transform the EEG sensor to some certain coordinate system, > etc.) Thanks a lot! > > Best, > > Ying > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From anne.urai at gmail.com Sun May 18 19:41:05 2014 From: anne.urai at gmail.com (anne.urai at gmail.com) Date: Sun, 18 May 2014 19:41:05 +0200 Subject: [FieldTrip] efficiently handling multiple events within a trial Message-ID: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> Hi Fieldtrippers, I have a design in which every trial has several events of interest (two stimuli with a maintenance period in between, response and feedback) - all of which I’d like to analyse at some point. I started by drafting my pipeline separately for stimulus-, response- and feedback-locked trial definitions, but this leads me to do the artefact rejection and ICA multiple times for each subject. I would prefer to reject whole trials and not use any of the events in there, rather than eg. use the response for some and the stimulus for others. I was wondering if you have any advice on how to best store multiple events in one trial (which would be, say, 12 seconds long, and have 4 different evens in it, at times that would also need to be stored). Would it work better to (1) make one big trialfun and store the onset and offset of each of those events in the trl matrix, or (2) have several trl matrices for each event and redefine the trials based on this trl matrix after I applied some other analyses? For example, it would be nice to run ft_freqanalysis once on the whole trial, and then redefine which part of the trial I’m interested in for plotting. Thanks for your thoughts on this! Best, --- Anne E. Urai, MSc PhD student | Institut für Neurophysiologie und Pathophysiologie Universitätsklinikum Hamburg-Eppendorf Martinistrasse 52, 20246 Hamburg, Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From yingli.ucla at gmail.com Mon May 19 08:16:43 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Sun, 18 May 2014 23:16:43 -0700 Subject: [FieldTrip] EEG source reconstruction using fieldtrip (MRI not available) In-Reply-To: References: Message-ID: Hi Johanna, That is exactly what I want! Appreciate your help so much! : ) Best, Ying On Sun, May 18, 2014 at 1:35 AM, Johanna Zumer wrote: > Dear Ying, > > Yes, that is possible (although in an ideal world, one does have the > subject's real MRI). > > You might gain some help from > http://fieldtrip.fcdonders.nl/example/align_eeg_electrode_positions_to_bem_headmodel > or http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg (which also > then links you to http://fieldtrip.fcdonders.nl/template/headmodel) for > the case of using the MNI brain). > > Best, > Johanna > > > > 2014-05-17 23:23 GMT+01:00 Ying Li : > >> Dear all, >> >> Fieldtrip provides a great tool of using MRI to do MEG source >> reconstruction ( >> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate). Now I want >> to do EEG source reconstruction. The EEG cap we used is the standard 10-10 >> system, but the MRI of the subject is not available. I'm thinking to use >> another person's MRI instead (i.e. the MNI template). Does fieldtrip >> provide some tools to match the electrode location and the head model from >> another person? >> >> In addition, since MEG sensor positions are always defined relative to >> the fiducial coils, so we don't need to transform it into CTF coordinate >> system any more. When doing EEG source reconstruction, is there any extra >> steps needed? (i.e. transform the EEG sensor to some certain coordinate >> system, etc.) Thanks a lot! >> >> Best, >> >> Ying >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Mon May 19 09:20:26 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 19 May 2014 09:20:26 +0200 Subject: [FieldTrip] efficiently handling multiple events within a trial In-Reply-To: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> References: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> Message-ID: Hi Anne, What I usually do is segment my data initially such that a "trial" in the data structure really corresponds to a logical trial in the experiment. So, in your case, it would contain the data for both stimuli and the maintenance period. I assume you are writing your own trialfun for this (if not, see http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition). In your trialfun, you can specify arbitrary metadata for every trial by adding extra columns to the output trl-matrix. The 4th and higher columns in the trl matrix will end up in data.trialinfo in the output data. This trialinfo field is kept throughout your analysis pipeline, as long as the data still contains trials. You could, for instance, store the time index of the response as the 4th column of your trl, the time index of the feedback onset as the 5th, etc. I always make sure that at least a condition identifier and a reaction time (if applicable) appear the trialinfo field. Once this information is present in data.trialinfo, you can use ft_selectdata and ft_redefinetrial to select the appropriate trials and (if necessary) shift the time axis, respectively. Hope that helps, Best, Eelke On 18 May 2014 19:41, wrote: > Hi Fieldtrippers, > > I have a design in which every trial has several events of interest (two > stimuli with a maintenance period in between, response and feedback) - all > of which I’d like to analyse at some point. I started by drafting my > pipeline separately for stimulus-, response- and feedback-locked trial > definitions, but this leads me to do the artefact rejection and ICA multiple > times for each subject. I would prefer to reject whole trials and not use > any of the events in there, rather than eg. use the response for some and > the stimulus for others. > > I was wondering if you have any advice on how to best store multiple events > in one trial (which would be, say, 12 seconds long, and have 4 different > evens in it, at times that would also need to be stored). Would it work > better to (1) make one big trialfun and store the onset and offset of each > of those events in the trl matrix, or (2) have several trl matrices for each > event and redefine the trials based on this trl matrix after I applied some > other analyses? For example, it would be nice to run ft_freqanalysis once on > the whole trial, and then redefine which part of the trial I’m interested in > for plotting. > > Thanks for your thoughts on this! > > Best, > > --- > Anne E. Urai, MSc > PhD student | Institut für Neurophysiologie und Pathophysiologie > Universitätsklinikum Hamburg-Eppendorf > Martinistrasse 52, 20246 Hamburg, Germany > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From anne.urai at gmail.com Mon May 19 10:24:08 2014 From: anne.urai at gmail.com (Anne Urai) Date: Mon, 19 May 2014 10:24:08 +0200 Subject: [FieldTrip] efficiently handling multiple events within a trial In-Reply-To: References: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> Message-ID: I've been writing my own trialfun but so far I've gotten by with a separate one for eg. stimulus- and response locked, which seems rather inefficient indeed. Thanks for the suggestion of using ft_selectdata, didn't know that one yet! Anne Anne Urai On 19 May 2014 09:20, Eelke Spaak wrote: > Hi Anne, > > What I usually do is segment my data initially such that a "trial" in > the data structure really corresponds to a logical trial in the > experiment. So, in your case, it would contain the data for both > stimuli and the maintenance period. > > I assume you are writing your own trialfun for this (if not, see > > http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition > ). > In your trialfun, you can specify arbitrary metadata for every trial > by adding extra columns to the output trl-matrix. The 4th and higher > columns in the trl matrix will end up in data.trialinfo in the output > data. This trialinfo field is kept throughout your analysis pipeline, > as long as the data still contains trials. You could, for instance, > store the time index of the response as the 4th column of your trl, > the time index of the feedback onset as the 5th, etc. I always make > sure that at least a condition identifier and a reaction time (if > applicable) appear the trialinfo field. > > Once this information is present in data.trialinfo, you can use > ft_selectdata and ft_redefinetrial to select the appropriate trials > and (if necessary) shift the time axis, respectively. > > Hope that helps, > Best, > Eelke > > On 18 May 2014 19:41, wrote: > > Hi Fieldtrippers, > > > > I have a design in which every trial has several events of interest (two > > stimuli with a maintenance period in between, response and feedback) - > all > > of which I’d like to analyse at some point. I started by drafting my > > pipeline separately for stimulus-, response- and feedback-locked trial > > definitions, but this leads me to do the artefact rejection and ICA > multiple > > times for each subject. I would prefer to reject whole trials and not use > > any of the events in there, rather than eg. use the response for some and > > the stimulus for others. > > > > I was wondering if you have any advice on how to best store multiple > events > > in one trial (which would be, say, 12 seconds long, and have 4 different > > evens in it, at times that would also need to be stored). Would it work > > better to (1) make one big trialfun and store the onset and offset of > each > > of those events in the trl matrix, or (2) have several trl matrices for > each > > event and redefine the trials based on this trl matrix after I applied > some > > other analyses? For example, it would be nice to run ft_freqanalysis > once on > > the whole trial, and then redefine which part of the trial I’m > interested in > > for plotting. > > > > Thanks for your thoughts on this! > > > > Best, > > > > --- > > Anne E. Urai, MSc > > PhD student | Institut für Neurophysiologie und Pathophysiologie > > Universitätsklinikum Hamburg-Eppendorf > > Martinistrasse 52, 20246 Hamburg, Germany > > > > > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.piai.research at gmail.com Mon May 19 23:14:30 2014 From: v.piai.research at gmail.com (Vitoria Piai) Date: Mon, 19 May 2014 14:14:30 -0700 Subject: [FieldTrip] Error: Undefined function 'mxSerialize_cpp' In-Reply-To: References: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> Message-ID: <537A7436.3080307@gmail.com> Hello everyone, I'm getting a low-level error (below) when running ft_singleplotER to plot FFTs. I recently changed to Matlab2014a so I'm guessing that's why I'm getting the error (different FT versions give same error for as far back in time as I could come). Does anyone know a way around this issue? Thanks a lot, Vitoria Undefined function 'mxSerialize_cpp' for input arguments of type 'struct'. Error in mxSerialize (line 35) argout = mxSerialize_cpp(argin); Error in ft_preamble_provenance (line 67) cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); Error in ft_preamble (line 54) evalin('caller', ['ft_preamble_' cmd]); Error in ft_singleplotER (line 109) ft_preamble provenance varargin From jan.schoffelen at donders.ru.nl Tue May 20 11:57:59 2014 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 20 May 2014 11:57:59 +0200 Subject: [FieldTrip] Error: Undefined function 'mxSerialize_cpp' In-Reply-To: <537A7436.3080307@gmail.com> References: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> <537A7436.3080307@gmail.com> Message-ID: Hi Vitoria, Sara Rombetto asked the same question last week (or the week before) ;-), and Jörn provided an adequate answer. See below, with credits to Jörn... +++++++++++++++++++++++++++++++++++++++++++++++++++++++ Hi Sara, I guess you are not using a mac. What you describe concerns bug 2452 on our Bugzilla page: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2452 which pertains to some undocumented change in Matlab. Therefore it is necessary to use a different mxserialize function that from matlab 2014a onwards than before. This is a c++ function, which requires to be compiled for each platform independently. In FieldTrip, this file exists e.g. in fileio/private but only for MacOS 64-bit platforms. Apparently, we still need to compile it for MacOS 32bit, Windows and Linux platforms. I guess we should do that quite soon ;) I'll bring it up in today's FT meeting so that hopefully from tomorrow onwards it should work. btw, for you it will help to go to the FieldTrip/src directory in Matlab and type >> mex mxSerialize_cpp.cpp Then Matlab will mex (~compile) the file for you. You can then copy that file to your matlab code directory and everything should work out fine for you. I'll keep you updated on this. Best, Jörn +++++++++++++++++++++++++++++++++++++++++++++++++++++++ Best, JM On May 19, 2014, at 11:14 PM, Vitoria Piai wrote: > Hello everyone, > > I'm getting a low-level error (below) when running ft_singleplotER to plot FFTs. > I recently changed to Matlab2014a so I'm guessing that's why I'm getting the error (different FT versions give same error for as far back in time as I could come). Does anyone know a way around this issue? > Thanks a lot, Vitoria > > Undefined function 'mxSerialize_cpp' for input arguments of type 'struct'. > > Error in mxSerialize (line 35) > argout = mxSerialize_cpp(argin); > > Error in ft_preamble_provenance (line 67) > cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); > > Error in ft_preamble (line 54) > evalin('caller', ['ft_preamble_' cmd]); > > Error in ft_singleplotER (line 109) > ft_preamble provenance varargin > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue May 20 11:58:11 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 20 May 2014 11:58:11 +0200 Subject: [FieldTrip] Error: Undefined function 'mxSerialize_cpp' In-Reply-To: <537A7436.3080307@gmail.com> References: <1CA31478-2340-4DE6-9D10-9C3E0773C5FD@gmail.com> <537A7436.3080307@gmail.com> Message-ID: <537B2733.20802@donders.ru.nl> Hi Vitoria, hope you're enjoying Berkeley ;) I assume the same error will occur for more people in a bit. We'll discuss it in the next FT meeting tomorrow. In the meanwhile, check this out (I responded to Sara last week, who got the same error): > I guess you are not using a mac. What you describe concerns bug 2452 > on our Bugzilla page: > http://bugzilla.fcdonders.nl/show_bug.cgi?id=2452 > which pertains to some undocumented change in Matlab. Therefore it is > necessary to use a different mxserialize function that from matlab > 2014a onwards than before. This is a c++ function, which requires to > be compiled for each platform independently. In FieldTrip, this file > exists e.g. in fileio/private but only for MacOS 64-bit platforms. > Apparently, we still need to compile it for MacOS 32bit, Windows and > Linux platforms. I guess we should do that quite soon I'll bring it up > in today's FT meeting so that hopefully from tomorrow onwards it > should work. > > btw, for you it will help to go to the FieldTrip/src directory in > Matlab and type > >> mex mxSerialize_cpp.cpp > > Then Matlab will mex (~compile) the file for you. You can then copy > that file to your matlab code directory and everything should work out > fine for you. I'll keep you updated on this. > Best, Jörn On 5/19/2014 11:14 PM, Vitoria Piai wrote: > Hello everyone, > > I'm getting a low-level error (below) when running ft_singleplotER to > plot FFTs. > I recently changed to Matlab2014a so I'm guessing that's why I'm > getting the error (different FT versions give same error for as far > back in time as I could come). Does anyone know a way around this issue? > Thanks a lot, Vitoria > > Undefined function 'mxSerialize_cpp' for input arguments of type > 'struct'. > > Error in mxSerialize (line 35) > argout = mxSerialize_cpp(argin); > > Error in ft_preamble_provenance (line 67) > cfg.callinfo.inputhash{iargin} = CalcMD5(mxSerialize(tmparg)); > > Error in ft_preamble (line 54) > evalin('caller', ['ft_preamble_' cmd]); > > Error in ft_singleplotER (line 109) > ft_preamble provenance varargin > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From yingli.ucla at gmail.com Thu May 22 10:26:45 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Thu, 22 May 2014 01:26:45 -0700 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface Message-ID: Dear all, I tried to use fieldtrip to generate a source space and calculate lead field matrix. I found that the dipoles in the source space has x, y, z orientations. Is it possible to generate a source model where the dipole is perpendicular to the cortex surface? Actually this can be very helpful, since it will reduce the unknown variables and make the inverse problem easier to solve. Also, there are some inverse algorithms which require the dipole to be perpendicular to the cortex surface. Thanks a lot!!! Best, Ying -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu May 22 10:56:24 2014 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 22 May 2014 10:56:24 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: References: Message-ID: <537DBBB8.600@donders.ru.nl> Hi Ying, when computing the leadfields you can set the option cfg.reducerank, which 'nulls' the dimension(s) which explain(s) the least variance (this is not quite true, but figuratively speaking). I think this is what comes closest to what you are looking for. There is no way to explicitly set desired orientations to zero apart from modifying the leadfield structure yourself. But that should be easily achievable, right? Best, Jörn On 5/22/2014 10:26 AM, Ying Li wrote: > Dear all, > > I tried to use fieldtrip to generate a source space and calculate lead > field matrix. I found that the dipoles in the source space has x, y, z > orientations. Is it possible to generate a source model where the > dipole is perpendicular to the cortex surface? > > Actually this can be very helpful, since it will reduce the unknown > variables and make the inverse problem easier to solve. Also, there > are some inverse algorithms which require the dipole to be > perpendicular to the cortex surface. > > Thanks a lot!!! > > Best, > > Ying > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From eelke.spaak at donders.ru.nl Thu May 22 11:04:04 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 22 May 2014 11:04:04 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: <537DBBB8.600@donders.ru.nl> References: <537DBBB8.600@donders.ru.nl> Message-ID: Hi Ying, In addition to this, of course first you would need a model of the cortical surface for your subjects. See http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to obtain such a model (using FreeSurfer) and getting it into FieldTrip. Best, Eelke On 22 May 2014 10:56, "Jörn M. Horschig" wrote: > Hi Ying, > > when computing the leadfields you can set the option cfg.reducerank, which > 'nulls' the dimension(s) which explain(s) the least variance (this is not > quite true, but figuratively speaking). I think this is what comes closest > to what you are looking for. There is no way to explicitly set desired > orientations to zero apart from modifying the leadfield structure yourself. > But that should be easily achievable, right? > > Best, > Jörn > > > On 5/22/2014 10:26 AM, Ying Li wrote: >> >> Dear all, >> >> I tried to use fieldtrip to generate a source space and calculate lead >> field matrix. I found that the dipoles in the source space has x, y, z >> orientations. Is it possible to generate a source model where the dipole is >> perpendicular to the cortex surface? >> >> Actually this can be very helpful, since it will reduce the unknown >> variables and make the inverse problem easier to solve. Also, there are some >> inverse algorithms which require the dipole to be perpendicular to the >> cortex surface. >> >> Thanks a lot!!! >> >> Best, >> >> Ying >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Thu May 22 11:47:03 2014 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 22 May 2014 11:47:03 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: References: <537DBBB8.600@donders.ru.nl> Message-ID: <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> Hi Ying, Yes, it's possible to constrain the dipole orientation. If you have a cortical sheet based source model that contains a triangulation that describes the topology, it's in principle possible to compute the orientation perpendicular to the sheet (this can e.g. be done by the 'normals' function which I believe should be in ~/fieldtrip/private). Subsequently, for each vertex in the cortical sheet you can multiply the leadfield matrix with this vector to get a single column leadfield vector per vertex that describes the sensor topography of a dipolar source with orientation perpendicular to the cortex. Best, Jan-Mathijs On May 22, 2014, at 11:04 AM, Eelke Spaak wrote: > Hi Ying, > > In addition to this, of course first you would need a model of the > cortical surface for your subjects. See > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to > obtain such a model (using FreeSurfer) and getting it into FieldTrip. > > Best, > Eelke > > On 22 May 2014 10:56, "Jörn M. Horschig" wrote: >> Hi Ying, >> >> when computing the leadfields you can set the option cfg.reducerank, which >> 'nulls' the dimension(s) which explain(s) the least variance (this is not >> quite true, but figuratively speaking). I think this is what comes closest >> to what you are looking for. There is no way to explicitly set desired >> orientations to zero apart from modifying the leadfield structure yourself. >> But that should be easily achievable, right? >> >> Best, >> Jörn >> >> >> On 5/22/2014 10:26 AM, Ying Li wrote: >>> >>> Dear all, >>> >>> I tried to use fieldtrip to generate a source space and calculate lead >>> field matrix. I found that the dipoles in the source space has x, y, z >>> orientations. Is it possible to generate a source model where the dipole is >>> perpendicular to the cortex surface? >>> >>> Actually this can be very helpful, since it will reduce the unknown >>> variables and make the inverse problem easier to solve. Also, there are some >>> inverse algorithms which require the dipole to be perpendicular to the >>> cortex surface. >>> >>> Thanks a lot!!! >>> >>> Best, >>> >>> Ying >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Jörn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> FieldTrip Development Team >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu May 22 13:25:58 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 22 May 2014 13:25:58 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> References: <537DBBB8.600@donders.ru.nl> <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> Message-ID: Hi Ying & JM & the rest of the list, I've never worked with cortex-constrained source reconstructions before, but one question came to mind: doesn't it make more sense to constrain the dipole orientations to *orthogonal* to the cortex, rather than perpendicular? Given that currents along the aligned dendrites of L5 pyramidal cells are (afaik) likely the most important origin of the MEG signal, and those dendrites are oriented approximately orthogonal to the cortical surface, isn't that what you would expect? Best, Eelke On 22 May 2014 11:47, jan-mathijs schoffelen wrote: > Hi Ying, > > Yes, it's possible to constrain the dipole orientation. If you have a > cortical sheet based source model that contains a triangulation that > describes the topology, it's in principle possible to compute the > orientation perpendicular to the sheet (this can e.g. be done by the > 'normals' function which I believe should be in ~/fieldtrip/private). > Subsequently, for each vertex in the cortical sheet you can multiply the > leadfield matrix with this vector to get a single column leadfield vector > per vertex that describes the sensor topography of a dipolar source with > orientation perpendicular to the cortex. > > Best, > Jan-Mathijs > > On May 22, 2014, at 11:04 AM, Eelke Spaak wrote: > > Hi Ying, > > In addition to this, of course first you would need a model of the > cortical surface for your subjects. See > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to > obtain such a model (using FreeSurfer) and getting it into FieldTrip. > > Best, > Eelke > > On 22 May 2014 10:56, "Jörn M. Horschig" wrote: > > Hi Ying, > > > when computing the leadfields you can set the option cfg.reducerank, which > > 'nulls' the dimension(s) which explain(s) the least variance (this is not > > quite true, but figuratively speaking). I think this is what comes closest > > to what you are looking for. There is no way to explicitly set desired > > orientations to zero apart from modifying the leadfield structure yourself. > > But that should be easily achievable, right? > > > Best, > > Jörn > > > > On 5/22/2014 10:26 AM, Ying Li wrote: > > > Dear all, > > > I tried to use fieldtrip to generate a source space and calculate lead > > field matrix. I found that the dipoles in the source space has x, y, z > > orientations. Is it possible to generate a source model where the dipole is > > perpendicular to the cortex surface? > > > Actually this can be very helpful, since it will reduce the unknown > > variables and make the inverse problem easier to solve. Also, there are some > > inverse algorithms which require the dipole to be perpendicular to the > > cortex surface. > > > Thanks a lot!!! > > > Best, > > > Ying > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > > Jörn M. Horschig > > PhD Student > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Neuronal Oscillations Group > > FieldTrip Development Team > > > P.O. Box 9101 > > NL-6500 HB Nijmegen > > The Netherlands > > > Contact: > > E-Mail: jm.horschig at donders.ru.nl > > Tel: +31-(0)24-36-68493 > > Web: http://www.ru.nl/donders > > > Visiting address: > > Trigon, room 2.30 > > Kapittelweg 29 > > NL-6525 EN Nijmegen > > The Netherlands > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > http://www.hettaligebrein.nl > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Thu May 22 13:42:11 2014 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 22 May 2014 13:42:11 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: References: <537DBBB8.600@donders.ru.nl> <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> Message-ID: <09B16AC6-4417-448C-8B82-1399CEFC062F@donders.ru.nl> Eelke, You're absolutely right one should take the orientation that is othogonal! In my dictionary this is exactly what the word perpendicular means ;-)... JM On May 22, 2014, at 1:25 PM, Eelke Spaak wrote: > Hi Ying & JM & the rest of the list, > > I've never worked with cortex-constrained source reconstructions > before, but one question came to mind: doesn't it make more sense to > constrain the dipole orientations to *orthogonal* to the cortex, > rather than perpendicular? Given that currents along the aligned > dendrites of L5 pyramidal cells are (afaik) likely the most important > origin of the MEG signal, and those dendrites are oriented > approximately orthogonal to the cortical surface, isn't that what you > would expect? > > Best, > Eelke > > On 22 May 2014 11:47, jan-mathijs schoffelen > wrote: >> Hi Ying, >> >> Yes, it's possible to constrain the dipole orientation. If you have a >> cortical sheet based source model that contains a triangulation that >> describes the topology, it's in principle possible to compute the >> orientation perpendicular to the sheet (this can e.g. be done by the >> 'normals' function which I believe should be in ~/fieldtrip/private). >> Subsequently, for each vertex in the cortical sheet you can multiply the >> leadfield matrix with this vector to get a single column leadfield vector >> per vertex that describes the sensor topography of a dipolar source with >> orientation perpendicular to the cortex. >> >> Best, >> Jan-Mathijs >> >> On May 22, 2014, at 11:04 AM, Eelke Spaak wrote: >> >> Hi Ying, >> >> In addition to this, of course first you would need a model of the >> cortical surface for your subjects. See >> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to >> obtain such a model (using FreeSurfer) and getting it into FieldTrip. >> >> Best, >> Eelke >> >> On 22 May 2014 10:56, "Jörn M. Horschig" wrote: >> >> Hi Ying, >> >> >> when computing the leadfields you can set the option cfg.reducerank, which >> >> 'nulls' the dimension(s) which explain(s) the least variance (this is not >> >> quite true, but figuratively speaking). I think this is what comes closest >> >> to what you are looking for. There is no way to explicitly set desired >> >> orientations to zero apart from modifying the leadfield structure yourself. >> >> But that should be easily achievable, right? >> >> >> Best, >> >> Jörn >> >> >> >> On 5/22/2014 10:26 AM, Ying Li wrote: >> >> >> Dear all, >> >> >> I tried to use fieldtrip to generate a source space and calculate lead >> >> field matrix. I found that the dipoles in the source space has x, y, z >> >> orientations. Is it possible to generate a source model where the dipole is >> >> perpendicular to the cortex surface? >> >> >> Actually this can be very helpful, since it will reduce the unknown >> >> variables and make the inverse problem easier to solve. Also, there are some >> >> inverse algorithms which require the dipole to be perpendicular to the >> >> cortex surface. >> >> >> Thanks a lot!!! >> >> >> Best, >> >> >> Ying >> >> >> >> _______________________________________________ >> >> fieldtrip mailing list >> >> fieldtrip at donders.ru.nl >> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -- >> >> Jörn M. Horschig >> >> PhD Student >> >> Donders Institute for Brain, Cognition and Behaviour >> >> Centre for Cognitive Neuroimaging >> >> Radboud University Nijmegen >> >> Neuronal Oscillations Group >> >> FieldTrip Development Team >> >> >> P.O. Box 9101 >> >> NL-6500 HB Nijmegen >> >> The Netherlands >> >> >> Contact: >> >> E-Mail: jm.horschig at donders.ru.nl >> >> Tel: +31-(0)24-36-68493 >> >> Web: http://www.ru.nl/donders >> >> >> Visiting address: >> >> Trigon, room 2.30 >> >> Kapittelweg 29 >> >> NL-6525 EN Nijmegen >> >> The Netherlands >> >> >> _______________________________________________ >> >> fieldtrip mailing list >> >> fieldtrip at donders.ru.nl >> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> http://www.hettaligebrein.nl >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu May 22 13:47:14 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 22 May 2014 13:47:14 +0200 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: <09B16AC6-4417-448C-8B82-1399CEFC062F@donders.ru.nl> References: <537DBBB8.600@donders.ru.nl> <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> <09B16AC6-4417-448C-8B82-1399CEFC062F@donders.ru.nl> Message-ID: Haha never mind, I was totally confused. "Perpendicular" and "parallel" both start with a p... On 22 May 2014 13:42, jan-mathijs schoffelen wrote: > Eelke, > > You're absolutely right one should take the orientation that is othogonal! > In my dictionary this is exactly what the word perpendicular means ;-)... > > JM > > On May 22, 2014, at 1:25 PM, Eelke Spaak wrote: > > Hi Ying & JM & the rest of the list, > > I've never worked with cortex-constrained source reconstructions > before, but one question came to mind: doesn't it make more sense to > constrain the dipole orientations to *orthogonal* to the cortex, > rather than perpendicular? Given that currents along the aligned > dendrites of L5 pyramidal cells are (afaik) likely the most important > origin of the MEG signal, and those dendrites are oriented > approximately orthogonal to the cortical surface, isn't that what you > would expect? > > Best, > Eelke > > On 22 May 2014 11:47, jan-mathijs schoffelen > wrote: > > Hi Ying, > > > Yes, it's possible to constrain the dipole orientation. If you have a > > cortical sheet based source model that contains a triangulation that > > describes the topology, it's in principle possible to compute the > > orientation perpendicular to the sheet (this can e.g. be done by the > > 'normals' function which I believe should be in ~/fieldtrip/private). > > Subsequently, for each vertex in the cortical sheet you can multiply the > > leadfield matrix with this vector to get a single column leadfield vector > > per vertex that describes the sensor topography of a dipolar source with > > orientation perpendicular to the cortex. > > > Best, > > Jan-Mathijs > > > On May 22, 2014, at 11:04 AM, Eelke Spaak wrote: > > > Hi Ying, > > > In addition to this, of course first you would need a model of the > > cortical surface for your subjects. See > > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to > > obtain such a model (using FreeSurfer) and getting it into FieldTrip. > > > Best, > > Eelke > > > On 22 May 2014 10:56, "Jörn M. Horschig" wrote: > > > Hi Ying, > > > > when computing the leadfields you can set the option cfg.reducerank, which > > > 'nulls' the dimension(s) which explain(s) the least variance (this is not > > > quite true, but figuratively speaking). I think this is what comes closest > > > to what you are looking for. There is no way to explicitly set desired > > > orientations to zero apart from modifying the leadfield structure yourself. > > > But that should be easily achievable, right? > > > > Best, > > > Jörn > > > > > On 5/22/2014 10:26 AM, Ying Li wrote: > > > > Dear all, > > > > I tried to use fieldtrip to generate a source space and calculate lead > > > field matrix. I found that the dipoles in the source space has x, y, z > > > orientations. Is it possible to generate a source model where the dipole is > > > perpendicular to the cortex surface? > > > > Actually this can be very helpful, since it will reduce the unknown > > > variables and make the inverse problem easier to solve. Also, there are some > > > inverse algorithms which require the dipole to be perpendicular to the > > > cortex surface. > > > > Thanks a lot!!! > > > > Best, > > > > Ying > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > > > Jörn M. Horschig > > > PhD Student > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Neuronal Oscillations Group > > > FieldTrip Development Team > > > > P.O. Box 9101 > > > NL-6500 HB Nijmegen > > > The Netherlands > > > > Contact: > > > E-Mail: jm.horschig at donders.ru.nl > > > Tel: +31-(0)24-36-68493 > > > Web: http://www.ru.nl/donders > > > > Visiting address: > > > Trigon, room 2.30 > > > Kapittelweg 29 > > > NL-6525 EN Nijmegen > > > The Netherlands > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > Jan-Mathijs Schoffelen, MD PhD > > > Donders Institute for Brain, Cognition and Behaviour, > > Centre for Cognitive Neuroimaging, > > Radboud University Nijmegen, The Netherlands > > > Max Planck Institute for Psycholinguistics, > > Nijmegen, The Netherlands > > > J.Schoffelen at donders.ru.nl > > Telephone: +31-24-3614793 > > > http://www.hettaligebrein.nl > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > http://www.hettaligebrein.nl > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From tyler.grummett at flinders.edu.au Fri May 23 04:10:10 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Fri, 23 May 2014 02:10:10 +0000 Subject: [FieldTrip] layout file from beamformer Message-ID: <1400811002490.44354@flinders.edu.au> Hello fieldtrippers, I am trying to create a layout file that has the positions of the beamformer sources. The output of my beamformer analysis was 1400 channels and I am trying to create a layout file with certain position which correspond to certain sources. For example, if I wanted to plot 30 sources and all I had were the x y z position. I am hoping that this made sense, I cant quite work out what I should be asking for. I have worked out how to plot the power of the sources, but ft_topoplotIC is asking for a layout file (after I ran an ICA over it), which I cant work out how to make. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From yingli.ucla at gmail.com Fri May 23 04:18:48 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Thu, 22 May 2014 19:18:48 -0700 Subject: [FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface In-Reply-To: References: <537DBBB8.600@donders.ru.nl> <36907BC5-B278-4D42-8037-88B2CB45EEBC@donders.ru.nl> <09B16AC6-4417-448C-8B82-1399CEFC062F@donders.ru.nl> Message-ID: Dear all, Thanks so much for all of your enthusiastic replies. I'll give a try to your suggestions. Best wishes, Ying On Thu, May 22, 2014 at 4:47 AM, Eelke Spaak wrote: > Haha never mind, I was totally confused. "Perpendicular" and > "parallel" both start with a p... > > On 22 May 2014 13:42, jan-mathijs schoffelen > wrote: > > Eelke, > > > > You're absolutely right one should take the orientation that is > othogonal! > > In my dictionary this is exactly what the word perpendicular means ;-)... > > > > JM > > > > On May 22, 2014, at 1:25 PM, Eelke Spaak wrote: > > > > Hi Ying & JM & the rest of the list, > > > > I've never worked with cortex-constrained source reconstructions > > before, but one question came to mind: doesn't it make more sense to > > constrain the dipole orientations to *orthogonal* to the cortex, > > rather than perpendicular? Given that currents along the aligned > > dendrites of L5 pyramidal cells are (afaik) likely the most important > > origin of the MEG signal, and those dendrites are oriented > > approximately orthogonal to the cortical surface, isn't that what you > > would expect? > > > > Best, > > Eelke > > > > On 22 May 2014 11:47, jan-mathijs schoffelen > > wrote: > > > > Hi Ying, > > > > > > Yes, it's possible to constrain the dipole orientation. If you have a > > > > cortical sheet based source model that contains a triangulation that > > > > describes the topology, it's in principle possible to compute the > > > > orientation perpendicular to the sheet (this can e.g. be done by the > > > > 'normals' function which I believe should be in ~/fieldtrip/private). > > > > Subsequently, for each vertex in the cortical sheet you can multiply the > > > > leadfield matrix with this vector to get a single column leadfield vector > > > > per vertex that describes the sensor topography of a dipolar source with > > > > orientation perpendicular to the cortex. > > > > > > Best, > > > > Jan-Mathijs > > > > > > On May 22, 2014, at 11:04 AM, Eelke Spaak wrote: > > > > > > Hi Ying, > > > > > > In addition to this, of course first you would need a model of the > > > > cortical surface for your subjects. See > > > > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to > > > > obtain such a model (using FreeSurfer) and getting it into FieldTrip. > > > > > > Best, > > > > Eelke > > > > > > On 22 May 2014 10:56, "Jörn M. Horschig" > wrote: > > > > > > Hi Ying, > > > > > > > > when computing the leadfields you can set the option cfg.reducerank, > which > > > > > > 'nulls' the dimension(s) which explain(s) the least variance (this is not > > > > > > quite true, but figuratively speaking). I think this is what comes > closest > > > > > > to what you are looking for. There is no way to explicitly set desired > > > > > > orientations to zero apart from modifying the leadfield structure > yourself. > > > > > > But that should be easily achievable, right? > > > > > > > > Best, > > > > > > Jörn > > > > > > > > > > On 5/22/2014 10:26 AM, Ying Li wrote: > > > > > > > > Dear all, > > > > > > > > I tried to use fieldtrip to generate a source space and calculate lead > > > > > > field matrix. I found that the dipoles in the source space has x, y, z > > > > > > orientations. Is it possible to generate a source model where the dipole > is > > > > > > perpendicular to the cortex surface? > > > > > > > > Actually this can be very helpful, since it will reduce the unknown > > > > > > variables and make the inverse problem easier to solve. Also, there are > some > > > > > > inverse algorithms which require the dipole to be perpendicular to the > > > > > > cortex surface. > > > > > > > > Thanks a lot!!! > > > > > > > > Best, > > > > > > > > Ying > > > > > > > > > > _______________________________________________ > > > > > > fieldtrip mailing list > > > > > > fieldtrip at donders.ru.nl > > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > -- > > > > > > Jörn M. Horschig > > > > > > PhD Student > > > > > > Donders Institute for Brain, Cognition and Behaviour > > > > > > Centre for Cognitive Neuroimaging > > > > > > Radboud University Nijmegen > > > > > > Neuronal Oscillations Group > > > > > > FieldTrip Development Team > > > > > > > > P.O. Box 9101 > > > > > > NL-6500 HB Nijmegen > > > > > > The Netherlands > > > > > > > > Contact: > > > > > > E-Mail: jm.horschig at donders.ru.nl > > > > > > Tel: +31-(0)24-36-68493 > > > > > > Web: http://www.ru.nl/donders > > > > > > > > Visiting address: > > > > > > Trigon, room 2.30 > > > > > > Kapittelweg 29 > > > > > > NL-6525 EN Nijmegen > > > > > > The Netherlands > > > > > > > > _______________________________________________ > > > > > > fieldtrip mailing list > > > > > > fieldtrip at donders.ru.nl > > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > Jan-Mathijs Schoffelen, MD PhD > > > > > > Donders Institute for Brain, Cognition and Behaviour, > > > > Centre for Cognitive Neuroimaging, > > > > Radboud University Nijmegen, The Netherlands > > > > > > Max Planck Institute for Psycholinguistics, > > > > Nijmegen, The Netherlands > > > > > > J.Schoffelen at donders.ru.nl > > > > Telephone: +31-24-3614793 > > > > > > http://www.hettaligebrein.nl > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > Jan-Mathijs Schoffelen, MD PhD > > > > Donders Institute for Brain, Cognition and Behaviour, > > Centre for Cognitive Neuroimaging, > > Radboud University Nijmegen, The Netherlands > > > > Max Planck Institute for Psycholinguistics, > > Nijmegen, The Netherlands > > > > J.Schoffelen at donders.ru.nl > > Telephone: +31-24-3614793 > > > > http://www.hettaligebrein.nl > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Fri May 23 09:01:45 2014 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 23 May 2014 09:01:45 +0200 Subject: [FieldTrip] layout file from beamformer In-Reply-To: <1400811002490.44354@flinders.edu.au> References: <1400811002490.44354@flinders.edu.au> Message-ID: <53A25C84-5000-471D-A96B-A1EEF293ACAD@gmail.com> Dear Tyler, I recently had a similar problem. I solved this by plotting the x,y,z-coordinates of all dipoles within the BEM-Model and assign a color value depending on the power value to the dipole markers. In short: use ft_triplot to plot the mesh of the BEM. Then select the .pos-field of the dipoles inside your volume and plot them with plot3. In the plot3-step, you can assign each dipole a 'Color'-property based on your power or stats value. Alternatively, you can use ft_prepare_layout to get a planar projection of your sources, but at least in my case it did not look too good. Hope that helps, if you want to, I can send you an example of what the plots look like. Best, Julian Am 23.05.2014 um 04:10 schrieb Tyler Grummett: > Hello fieldtrippers, > > I am trying to create a layout file that has the positions of the beamformer sources. > > The output of my beamformer analysis was 1400 channels and I am trying to create a layout file with certain position which correspond to certain sources. > > For example, if I wanted to plot 30 sources and all I had were the x y z position. > > I am hoping that this made sense, I cant quite work out what I should be asking for. I have worked out how to plot the power of the sources, but > ft_topoplotIC is asking for a layout file (after I ran an ICA over it), which I cant work out how to make. > > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Fri May 23 10:04:12 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Fri, 23 May 2014 08:04:12 +0000 Subject: [FieldTrip] layout file from beamformer In-Reply-To: <53A25C84-5000-471D-A96B-A1EEF293ACAD@gmail.com> References: <1400811002490.44354@flinders.edu.au>, <53A25C84-5000-471D-A96B-A1EEF293ACAD@gmail.com> Message-ID: <13054238-2E21-4214-851F-F6481F0860B0@flinders.edu.au> Hey Julian, That sounds good, it would be awesome if you could give me an example. Also though, what are the steps of using ft_prepare_layout with beamformer data. I am away it gives you permissions, but how do you enter that into ft_prepare_layout. This is only for using in trentool, otherwise I would be using your method Tyler On 23 May 2014, at 4:40 pm, "Julian Keil" > wrote: Dear Tyler, I recently had a similar problem. I solved this by plotting the x,y,z-coordinates of all dipoles within the BEM-Model and assign a color value depending on the power value to the dipole markers. In short: use ft_triplot to plot the mesh of the BEM. Then select the .pos-field of the dipoles inside your volume and plot them with plot3. In the plot3-step, you can assign each dipole a 'Color'-property based on your power or stats value. Alternatively, you can use ft_prepare_layout to get a planar projection of your sources, but at least in my case it did not look too good. Hope that helps, if you want to, I can send you an example of what the plots look like. Best, Julian Am 23.05.2014 um 04:10 schrieb Tyler Grummett: Hello fieldtrippers, I am trying to create a layout file that has the positions of the beamformer sources. The output of my beamformer analysis was 1400 channels and I am trying to create a layout file with certain position which correspond to certain sources. For example, if I wanted to plot 30 sources and all I had were the x y z position. I am hoping that this made sense, I cant quite work out what I should be asking for. I have worked out how to plot the power of the sources, but ft_topoplotIC is asking for a layout file (after I ran an ICA over it), which I cant work out how to make. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.herring at fcdonders.ru.nl Fri May 23 10:42:58 2014 From: j.herring at fcdonders.ru.nl (Herring, J.D. (Jim)) Date: Fri, 23 May 2014 10:42:58 +0200 (CEST) Subject: [FieldTrip] layout file from beamformer In-Reply-To: <13054238-2E21-4214-851F-F6481F0860B0@flinders.edu.au> References: <1400811002490.44354@flinders.edu.au>, <53A25C84-5000-471D-A96B-A1EEF293ACAD@gmail.com> <13054238-2E21-4214-851F-F6481F0860B0@flinders.edu.au> Message-ID: <010201cf7663$002490f0$006db2d0$@herring@fcdonders.ru.nl> Hi Tyler, What would you like to plot? It seems like you want to plot the spatial weights of independent components after running ICA on your source data. Ft_topoplotIC plots data on a 2D-layout of your sensors/electrodes, I do not think you want this. It seems to me you should have a look at ft_sourceplot and add a field to your source data structure that, for each IC, represents the weights per gridpoint. Then you should be able to plot the IC weights in 3D (with anatomy if you wish). Best, Jim From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Tyler Grummett Sent: vrijdag 23 mei 2014 10:04 To: FieldTrip discussion list Subject: Re: [FieldTrip] layout file from beamformer Hey Julian, That sounds good, it would be awesome if you could give me an example. Also though, what are the steps of using ft_prepare_layout with beamformer data. I am away it gives you permissions, but how do you enter that into ft_prepare_layout. This is only for using in trentool, otherwise I would be using your method Tyler On 23 May 2014, at 4:40 pm, "Julian Keil" wrote: Dear Tyler, I recently had a similar problem. I solved this by plotting the x,y,z-coordinates of all dipoles within the BEM-Model and assign a color value depending on the power value to the dipole markers. In short: use ft_triplot to plot the mesh of the BEM. Then select the .pos-field of the dipoles inside your volume and plot them with plot3. In the plot3-step, you can assign each dipole a 'Color'-property based on your power or stats value. Alternatively, you can use ft_prepare_layout to get a planar projection of your sources, but at least in my case it did not look too good. Hope that helps, if you want to, I can send you an example of what the plots look like. Best, Julian Am 23.05.2014 um 04:10 schrieb Tyler Grummett: Hello fieldtrippers, I am trying to create a layout file that has the positions of the beamformer sources. The output of my beamformer analysis was 1400 channels and I am trying to create a layout file with certain position which correspond to certain sources. For example, if I wanted to plot 30 sources and all I had were the x y z position. I am hoping that this made sense, I cant quite work out what I should be asking for. I have worked out how to plot the power of the sources, but ft_topoplotIC is asking for a layout file (after I ran an ICA over it), which I cant work out how to make. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Fri May 23 10:45:20 2014 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 23 May 2014 10:45:20 +0200 Subject: [FieldTrip] layout file from beamformer In-Reply-To: <13054238-2E21-4214-851F-F6481F0860B0@flinders.edu.au> References: <1400811002490.44354@flinders.edu.au> <53A25C84-5000-471D-A96B-A1EEF293ACAD@gmail.com> <13054238-2E21-4214-851F-F6481F0860B0@flinders.edu.au> Message-ID: Hi Tyler, I attached 2 plots for you, one with evoked ERF activity, and one of the same activity but masked for the maximum. As you can see, you get information about the activity for each dipole as well as the location within the volume. As for the layout, here's how it works for me: % Sourcedummy in this case is a source structure containing the grid .pos % and .inside field elec = []; elec.elecpos = sourcedummy.pos(sourcedummy.inside,:); elec.chanpos = sourcedummy.pos(sourcedummy.inside,:); tmp = num2cell(sourcedummy.inside); elec.label = cellfun(@num2str,tmp,'UniformOutput',0); cfg = []; cfg.elec = elec; cfg.projection = 'polar'; example_lay = ft_prepare_layout(cfg); cfg=[]; cfg.layout = example_lay; ft_layoutplot(cfg); Please be careful with the 2D-projection of 3D-data. I'm not sure how accurate the projection is and some grid points might overlap. Good Luck, Julian On Fri, May 23, 2014 at 10:04 AM, Tyler Grummett < tyler.grummett at flinders.edu.au> wrote: > Hey Julian, > > That sounds good, it would be awesome if you could give me an example. > > Also though, what are the steps of using ft_prepare_layout with > beamformer data. I am away it gives you permissions, but how do you enter > that into ft_prepare_layout. > > This is only for using in trentool, otherwise I would be using your > method > > Tyler > > > On 23 May 2014, at 4:40 pm, "Julian Keil" wrote: > > Dear Tyler, > > I recently had a similar problem. > > I solved this by plotting the x,y,z-coordinates of all dipoles within > the BEM-Model and assign a color value depending on the power value to the > dipole markers. > > In short: use ft_triplot to plot the mesh of the BEM. Then select the > .pos-field of the dipoles inside your volume and plot them with plot3. > In the plot3-step, you can assign each dipole a 'Color'-property based on > your power or stats value. > > Alternatively, you can use ft_prepare_layout to get a planar projection > of your sources, but at least in my case it did not look too good. > > Hope that helps, if you want to, I can send you an example of what the > plots look like. > > Best, > > Julian > > Am 23.05.2014 um 04:10 schrieb Tyler Grummett: > > Hello fieldtrippers, > > I am trying to create a layout file that has the positions of the > beamformer sources. > > The output of my beamformer analysis was 1400 channels and I am trying > to create a layout file with certain position which correspond to certain > sources. > > For example, if I wanted to plot 30 sources and all I had were the x y z > position. > > I am hoping that this made sense, I cant quite work out what I should be > asking for. I have worked out how to plot the power of the sources, but > ft_topoplotIC is asking for a layout file (after I ran an ICA over it), > which I cant work out how to make. > > Tyler > > ************************* > > *Tyler Grummett ( BBSc, BSc(Hons I))* > *PhD Candidate* > *Brain Signals Laboratory* > *Flinders University* > *Rm 5A301* > *Ext 66124* > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: wirebrain_example_mask.png Type: image/png Size: 37668 bytes Desc: not available URL: From s.hassel at aston.ac.uk Fri May 23 13:06:23 2014 From: s.hassel at aston.ac.uk (Hassel, Stefanie) Date: Fri, 23 May 2014 11:06:23 +0000 Subject: [FieldTrip] PhD Studentship at Aston University, Birmingham, UK Message-ID: <282D53FEFCF0B44EA5D1E7977E0C32E61FACE2E5@exch-mb-g50-02.campus.aston.ac.uk> Dear all, Please see below for information on a PhD Studentship available in the School of Life & Health Sciences at Aston University, Birmingham, UK Using Response Inhibition and Reward Responsiveness to Investigate Risk for Psychopathology Dr Stefanie Hassel and Prof. Klaus Kessler Biological predisposition towards psychopathology as well as environmental events may influence whether and when symptoms surface among individuals, who are at an increased risk for psychopathology. Individuals differ in their degree of responsiveness to cues of reward or cues of threat, in goal-seeking behaviours and/or anxiety. A high degree of responsiveness to cues of reward or threat may play an additional role in placing individuals at risk for psychopathologies, especially mood disorders. For instance, high reward responsiveness on a specific behavioural task, individual characteristics like impulsivity or extreme appraisals of social approval as well as family history of psychopathology may all aid in predicting future diagnoses. This project will address the underlying mechanisms that control fluctuations in mood and behaviour, specific sensitivities which may determine the strength of a person's emotional reaction to reward or threat and investigate potential relationships between sensitivity levels to cues of reward and threat and sub-threshold symptoms of (hypo)mania and depression in individuals at increased risk for a mood disorder (or other psychopathology), compared to undergraduate students classified as not at risk. Multi-modal experimental methods will be used to examine these issues, such as behavioural task-based and questionnaire measures, as well as structural and functional neuroimaging (Magnetic Resonance Imaging (MRI), Diffusion Tensor Imaging, functional MRI and Magnetoencephalography). Outcomes from this research may be used to help inform early identification of risk factors for general psychopathology and mood disorders (depression and bipolar disorder) in particular. The high quality of research in Aston's School of Life and Health Sciences was confirmed in the last Research Assessment Exercise (RAE): research in Allied Health Professions and Studies ranked 3rd out of 63 UK Higher Education Institutions. Additional information about research in the School can be found at http://www1.aston.ac.uk/lhs/research/ Financial Support: The studentship comprises of a tax-free stipend of £13,863 p.a. and payment of Home/EU tuition fees only. The studentship is available for three years, subject to satisfactory progress review at the end of the first year with an anticipated Registration date of 1st October 2014. Application Requirements: * Eligible Applicants should hold at least a Bachelor (Hons.) Degree of either First Class/Upper Second Class or hold a Master's Degree in Psychology or related discipline. A demonstrable interest in affective neuroscience and/or clinical psychology is a requirement. (Supervisors are based at Aston University, and draw on expertise with experimental and neuroimaging research with healthy and clinical populations). * EU Applicants will need to demonstrate adequate proficiency in English Language skills, with a minimum overall score of 101 (Internet Based) (with a minimum score in each section of: R: 23, W: 26, L: 23 and S: 22) in TOEFL or IELTS with minimum marks of 6.5 in each section and an overall band of 7.0. * Informal enquiries should be addressed to the Project Supervisor, Dr Stefanie Hassel (E-mail:s.hassel at aston.ac.uk). Closing Date: Monday 09 June 2014 Reference: R140127 To apply please complete the on-line application form athttps://map.aston.ac.uk/urd/sits.urd/run/siw_ipp_lgn.login?process=siw_ipp_app&&code1=LHS029PR&code2=0014 Email details to a friend --- --- --- Stefanie Hassel, PhD Department of Psychology School of Life and Health Sciences Aston University Birmingham B4 7ET Email: s.hassel at aston.ac.uk Phone: 0121 204 4003 Students can make an appointment with me by following this link: https://wass.aston.ac.uk/pages/login.page.php Adjunct Assistant Professor: Dept. of Psychiatry, Faculty of Medicine, University of Calgary, Calgary, AB, Canada Adjunct Instructor: Western Psychiatric Institute and Clinic, University of Pittsburgh, Pittsburgh, PA, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: From diezmartini at gmail.com Mon May 26 02:30:57 2014 From: diezmartini at gmail.com (Ana Laura Diez Martini) Date: Mon, 26 May 2014 12:30:57 +1200 Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW Message-ID: Hi all! This is the .BDF file of one of my EEG subjects. For my last experiment I used a Biosemi system and now I'm using an EGI system which gives me .RAW files. I exported the .RAW file with EEGlab to .BDF format and I tried using the scripts I use to analise the data of my previous experiment but I realised that it was not reading the events: cfg = []; cfg.dataset = ' (location)'; cfg.trialdef.eventtype = '?'; definetrial(cfg); Warning: no trialfun was specified, using trialfun_general > In definetrial at 79 evaluating trialfunction 'trialfun_general' no events were found in the datafile no trials have been defined yet, see DEFINETRIAL for further help found 0 events created 0 trials EEGlab does read them. Any idea of what could be wrong? Thank you all!! -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Mon May 26 08:59:13 2014 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Mon, 26 May 2014 08:59:13 +0200 Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW In-Reply-To: References: Message-ID: Hi Ana Laura, Have you tried importing the .RAW file directly? That is, by specifying cfg.dataset = 'XXX.raw'? Best regards, Arjen 2014-05-26 2:30 GMT+02:00 Ana Laura Diez Martini : > Hi all! > > This is the .BDF file > of one of > my EEG subjects. For my last experiment I used a Biosemi system and now I'm > using an EGI system which gives me .RAW files. I exported the .RAW file > with EEGlab to .BDF format and I tried using the scripts I use to analise > the data of my previous experiment but I realised that it was not reading > the events: > > cfg = []; > cfg.dataset = ' (location)'; > cfg.trialdef.eventtype = '?'; > definetrial(cfg); > Warning: no trialfun was specified, using trialfun_general > > In definetrial at 79 > evaluating trialfunction 'trialfun_general' > no events were found in the datafile > no trials have been defined yet, see DEFINETRIAL for further help > found 0 events > created 0 trials > > EEGlab does read them. Any idea of what could be wrong? > > Thank you all!! > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Mon May 26 09:03:09 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 26 May 2014 09:03:09 +0200 Subject: [FieldTrip] Fwd: summer school on stress & cognition Message-ID: Forwarding on behalf of a colleague. ---------- Forwarded message ---------- From: Vogel, S. (Susanne) Date: 23 May 2014 11:38 Subject: fieldtrip and MEG mailing lists To: Eelke Spaak Dear colleague, Each year, the Donders Institute for Brain, Cognition and Behaviour organizes a highly prestigious international summer school in cognitive neuroscience, bringing together world-leading scientists and outstanding MSc students, PhD students, and postdocs. The topic of this year's summer school is STRESS & COGNITION: FROM BASIC MECHANISMS TO PSYCHOPATHOLOGY. The event will take place in the week of August 11-15, 2014, on the campus of Radboud University in Nijmegen. With a list of highly renowned international experts in the interdisciplinary field of stress and cognition, we are convinced that our summer school will be of great interest to your research group and/or department. In addition to lectures, we will organize group discussions, a poster session for students to get feedback on their work, lab tours at the Donders' research facilities, and a range of social activities. There is optional accommodation available on campus. Currently, the application procedure is in full swing. We are proud to inform you that thus far we have accepted students from 17 different countries: Belgium, Brazil, Bulgaria, Chili, China, Denmark, Germany, Greece, Italy, Korea, Netherlands, Poland, Romania, Russia, Scotland, Spain, and the United States. Please note that we are rapidly approaching the maximum number of participants. Registration will close on JUNE 15, 2014. More information can be found on our website: HTTP://WWW.RU.NL/DONDERS/SUMMERSCHOOL We would like to ask you to kindly bring this to the attention of MSc students, PhD students, and postdocs who might be interested. With warm regards, Benno Roozendaal Erno Hermans (Organizers) From d.lozanosoldevilla at fcdonders.ru.nl Mon May 26 10:58:01 2014 From: d.lozanosoldevilla at fcdonders.ru.nl (Diego Lozano Soldevilla) Date: Mon, 26 May 2014 10:58:01 +0200 Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW In-Reply-To: References: Message-ID: Hi Ana, Fieldtrip does not read events in BDF format. Take a look to our wiki: http://fieldtrip.fcdonders.nl/getting_started/egi - *EDF+* (.edf) All channels, including PIB channels, are read in correctly, including channel labels. However, the events, which are stored on the annotation channel, are written in a way by Net Station that is not compatible with the edf+ reading implementation in FieldTrip. So, events do not come out properly. Also discontinuous epochs are “glued” together as one “continuous” data stream. As Arjen suggested, with *.RAW you shouldn't have any problem. event = ft_read_event('*.RAW') If you encounter it, please let us know. best, Diego On 26 May 2014 08:59, Arjen Stolk wrote: > Hi Ana Laura, > > Have you tried importing the .RAW file directly? That is, by specifying > cfg.dataset = 'XXX.raw'? > > Best regards, > Arjen > > > 2014-05-26 2:30 GMT+02:00 Ana Laura Diez Martini : > >> Hi all! >> >> This is the .BDF file >> of one of >> my EEG subjects. For my last experiment I used a Biosemi system and now I'm >> using an EGI system which gives me .RAW files. I exported the .RAW file >> with EEGlab to .BDF format and I tried using the scripts I use to analise >> the data of my previous experiment but I realised that it was not reading >> the events: >> >> cfg = []; >> cfg.dataset = ' (location)'; >> cfg.trialdef.eventtype = '?'; >> definetrial(cfg); >> Warning: no trialfun was specified, using trialfun_general >> > In definetrial at 79 >> evaluating trialfunction 'trialfun_general' >> no events were found in the datafile >> no trials have been defined yet, see DEFINETRIAL for further help >> found 0 events >> created 0 trials >> >> EEGlab does read them. Any idea of what could be wrong? >> >> Thank you all!! >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dr.chungki.lee at gmail.com Mon May 26 11:18:34 2014 From: dr.chungki.lee at gmail.com (Chungki Lee) Date: Mon, 26 May 2014 18:18:34 +0900 Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW In-Reply-To: References: Message-ID: Dear all Fieldtrip can read events in BDF format ! Hear simple examples example #1 %% cfg = []; cfg.dataset = '~~~ '; % your filename with file extension; cfg.trialdef.eventtype = 'STATUS'; % Status notation maybe Biosemi's tigger name cfg.trialdef.eventvalue = 1; % your event value cfg.trialdef.prestim = 4; % before stimulation (sec), only use positive value cfg.trialdef.poststim = 8; % after stimulation (sec) , only use positive value cfg = ft_definetrial(cfg); cfg.method = 'trial'; data = ft_preprocessing(cfg); %% example #2 %% % if you executed these command lines cfg = []; cfg.dataset = '~~~ '; % your filename with file extension; cfg.trialdef.eventtype = '?'; % Status notation maybe Biosemi's tigger name cfg = ft_definetrial(cfg); % result example #2 the following events were found in the datafile event type: 'CM_in_range' with event values: event type: 'Epoch' with event values: event type: 'STATUS' with event values: 1 2 3 4 255 <----------- "this indicate your file configuration for trigger information" no trials have been defined yet, see FT_DEFINETRIAL for further help found 255 events created 0 trials the call to "ft_definetrial" took 8 seconds have fun~!! 2014-05-26 17:58 GMT+09:00 Diego Lozano Soldevilla < d.lozanosoldevilla at fcdonders.ru.nl>: > Hi Ana, > > Fieldtrip does not read events in BDF format. Take a look to our wiki: > > http://fieldtrip.fcdonders.nl/getting_started/egi > > > - *EDF+* (.edf) All channels, including PIB channels, are read in > correctly, including channel labels. However, the events, which are stored > on the annotation channel, are written in a way by Net Station that is not > compatible with the edf+ reading implementation in FieldTrip. So, events do > not come out properly. Also discontinuous epochs are “glued” together as > one “continuous” data stream. > > As Arjen suggested, with *.RAW you shouldn't have any problem. > > event = ft_read_event('*.RAW') > > If you encounter it, please let us know. > > best, > > Diego > > > On 26 May 2014 08:59, Arjen Stolk wrote: > >> Hi Ana Laura, >> >> Have you tried importing the .RAW file directly? That is, by specifying >> cfg.dataset = 'XXX.raw'? >> >> Best regards, >> Arjen >> >> >> 2014-05-26 2:30 GMT+02:00 Ana Laura Diez Martini : >> >>> Hi all! >>> >>> This is the .BDF file >>> of one of >>> my EEG subjects. For my last experiment I used a Biosemi system and now I'm >>> using an EGI system which gives me .RAW files. I exported the .RAW file >>> with EEGlab to .BDF format and I tried using the scripts I use to analise >>> the data of my previous experiment but I realised that it was not reading >>> the events: >>> >>> cfg = []; >>> cfg.dataset = ' (location)'; >>> cfg.trialdef.eventtype = '?'; >>> definetrial(cfg); >>> Warning: no trialfun was specified, using trialfun_general >>> > In definetrial at 79 >>> evaluating trialfunction 'trialfun_general' >>> no events were found in the datafile >>> no trials have been defined yet, see DEFINETRIAL for further help >>> found 0 events >>> created 0 trials >>> >>> EEGlab does read them. Any idea of what could be wrong? >>> >>> Thank you all!! >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ---------------------------------------------------------------- Chungki Lee, Ph.D. Post-doc Biomedical Research Institute Korea Institute of Science and Technology E-mail: chungki at kist.re.kr Tel:+82-2-958-5636, C.P: +82-10-5223-7309 ---------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.lozanosoldevilla at fcdonders.ru.nl Mon May 26 11:44:13 2014 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Mon, 26 May 2014 11:44:13 +0200 (CEST) Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW In-Reply-To: Message-ID: <222446912.7087267.1401097453356.JavaMail.root@sculptor.zimbra.ru.nl> Dear Ana, Sorry for my file extension confusion: edf instead of bdf. However, I don't know a way to read events coded in BDF format exported by NETSTATION. I encounter this problem in the past but I had no problems with RAW file format Dear Chungki , Fieldtrip can read events in *.bdf but from BIOSEMI eeg system but Ana was refering to a different eeg system that has the same fileformat extension. best, Diego ----- Original Message ----- > From: "Chungki Lee" > To: "FieldTrip discussion list" > Sent: Monday, 26 May, 2014 11:18:34 AM > Subject: Re: [FieldTrip] Cannot read the events of a .BDF file > exported from an EGI .RAW > Dear all > Fieldtrip can read events in BDF format ! > Hear simple examples > example #1 > %% > cfg = []; > cfg.dataset = '~~~ '; % your filename with file extension; > cfg.trialdef.eventtype = 'STATUS'; % Status notation maybe Biosemi's > tigger name > cfg.trialdef.eventvalue = 1; % your event value > cfg.trialdef.prestim = 4; % before stimulation (sec), only use > positive value > cfg.trialdef.poststim = 8; % after stimulation (sec) , only use > positive value > cfg = ft_definetrial(cfg); > cfg.method = 'trial'; > data = ft_preprocessing(cfg); > %% > example #2 > %% > % if you executed these command lines > cfg = []; > cfg.dataset = '~~~ '; % your filename with file extension; > cfg.trialdef.eventtype = '?'; % Status notation maybe Biosemi's tigger > name > cfg = ft_definetrial(cfg); > % result example #2 > the following events were found in the datafile > event type: 'CM_in_range' with event values: > event type: 'Epoch' with event values: > event type: 'STATUS' with event values: 1 2 3 4 255 <----------- "this > indicate your file configuration for trigger information" > no trials have been defined yet, see FT_DEFINETRIAL for further help > found 255 events > created 0 trials > the call to "ft_definetrial" took 8 seconds > have fun~!! > 2014-05-26 17:58 GMT+09:00 Diego Lozano Soldevilla < > d.lozanosoldevilla at fcdonders.ru.nl > : > > Hi Ana, > > Fieldtrip does not read events in BDF format. Take a look to our > > wiki: > > http://fieldtrip.fcdonders.nl/getting_started/egi > > • > > EDF+ (.edf) All channels, including PIB channels, are read in > > correctly, including channel labels. However, the events, which are > > stored on the annotation channel, are written in a way by Net > > Station > > that is not compatible with the edf+ reading implementation in > > FieldTrip. So, events do not come out properly. Also discontinuous > > epochs are “glued” together as one “continuous” data stream. > > As Arjen suggested, with *.RAW you shouldn't have any problem. > > event = ft_read_event('*.RAW') > > If you encounter it, please let us know. > > best, > > Diego > > On 26 May 2014 08:59, Arjen Stolk < a.stolk8 at gmail.com > wrote: > > > Hi Ana Laura, > > > Have you tried importing the .RAW file directly? That is, by > > > specifying cfg.dataset = 'XXX.raw'? > > > Best regards, > > > Arjen > > > 2014-05-26 2:30 GMT+02:00 Ana Laura Diez Martini < > > > diezmartini at gmail.com > : > > > > Hi all! > > > > This is the .BDF file of one of my EEG subjects. For my last > > > > experiment I used a Biosemi system and now I'm using an EGI > > > > system > > > > which gives me .RAW files. I exported the .RAW file with EEGlab > > > > to > > > > .BDF format and I tried using the scripts I use to analise the > > > > data > > > > of > > > > my previous experiment but I realised that it was not reading > > > > the > > > > events: > > > > cfg = []; > > > > cfg.dataset = ' (location)'; > > > > cfg.trialdef.eventtype = '?'; > > > > definetrial(cfg); > > > > Warning: no trialfun was specified, using trialfun_general > > > > > In definetrial at 79 > > > > evaluating trialfunction 'trialfun_general' > > > > no events were found in the datafile > > > > no trials have been defined yet, see DEFINETRIAL for further > > > > help > > > > found 0 events > > > > created 0 trials > > > > EEGlab does read them. Any idea of what could be wrong? > > > > Thank you all!! > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- > ---------------------------------------------------------------- > Chungki Lee, Ph.D. > Post-doc > Biomedical Research Institute > Korea Institute of Science and Technology > E-mail: chungki at kist.re.kr > Tel:+82-2-958-5636, C.P: +82-10-5223-7309 > ---------------------------------------------------------------- > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- PhD Student Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen NL-6525 EN Nijmegen The Netherlands http://www.ru.nl/people/donders/lozano-soldevilla-d/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahjoory86 at gmail.com Mon May 26 13:42:51 2014 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Mon, 26 May 2014 13:42:51 +0200 Subject: [FieldTrip] Template for Electrode Positions Message-ID: Dear all, I want to do EEG source reconstruction. The EEG cap we used is the standard 10-20 system with 64 channels, but the MRI and electrode positions of subjects are not available. I'm thinking of using Fieldtrip templates. For head model I used: load standard_bem.mat cfg.vol=vol; But for Electrode positions I checked all options at this link: http://fieldtrip.fcdonders.nl/template/electrode the only option with 64 channel is GSN-HydroCel-64_1.0.sfp. It includes labels in this format: E1 E2 E3... So, How can I use it for my work? Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From i.e.j.de.vries at student.vu.nl Mon May 26 14:20:44 2014 From: i.e.j.de.vries at student.vu.nl (Vries, I.E.J. de) Date: Mon, 26 May 2014 12:20:44 +0000 Subject: [FieldTrip] Template for Electrode Positions In-Reply-To: References: Message-ID: <19DD7427D34B7E47B33093FB4C3CFDD2010950FF81@PEXMB001B.vu.local> Hi Keyvan, I also used a 64 channel EEG cap and used the Fieldtrip template standard_1020.elc. Although this template has more electrodes, Fieldtrip automatically only uses the electrodes from that template that are also present in your data (it checks the labels, so make sure your electrode labels agree with the ones in the template when it comes to upper/lower case). The 64 electrodes that I used in my experiment are all present in the standard_1020.elc template and they are on the same position as in my cap. Good luck! Ingmar ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Keyvan Mahjoory [mahjoory86 at gmail.com] Sent: 26 May 2014 13:42 To: FieldTrip discussion list Subject: [FieldTrip] Template for Electrode Positions Dear all, I want to do EEG source reconstruction. The EEG cap we used is the standard 10-20 system with 64 channels, but the MRI and electrode positions of subjects are not available. I'm thinking of using Fieldtrip templates. For head model I used: load standard_bem.mat cfg.vol=vol; But for Electrode positions I checked all options at this link: http://fieldtrip.fcdonders.nl/template/electrode the only option with 64 channel is GSN-HydroCel-64_1.0.sfp. It includes labels in this format: E1 E2 E3... So, How can I use it for my work? Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.herring at fcdonders.ru.nl Mon May 26 14:22:10 2014 From: j.herring at fcdonders.ru.nl (Herring, J.D. (Jim)) Date: Mon, 26 May 2014 14:22:10 +0200 (CEST) Subject: [FieldTrip] Template for Electrode Positions In-Reply-To: References: Message-ID: <005c01cf78dd$1d9519d0$58bf4d70$@herring@fcdonders.ru.nl> Dear Keyvan, As is stated on http://fieldtrip.fcdonders.nl/template/electrode, Fieldtrip also has electrode positions for the standard 10-20 system, namely: standard_1020.elc. To read in the sensor positions you would have to do something like: Filename = 'c:\fieldtrip\template\electrode\standard_1020.elc'; sens = ft_read_sens(filename); Best, Jim From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Keyvan Mahjoory Sent: maandag 26 mei 2014 13:43 To: FieldTrip discussion list Subject: [FieldTrip] Template for Electrode Positions Dear all, I want to do EEG source reconstruction. The EEG cap we used is the standard 10-20 system with 64 channels, but the MRI and electrode positions of subjects are not available. I'm thinking of using Fieldtrip templates. For head model I used: load standard_bem.mat cfg.vol=vol; But for Electrode positions I checked all options at this link: http://fieldtrip.fcdonders.nl/template/electrode the only option with 64 channel is GSN-HydroCel-64_1.0.sfp. It includes labels in this format: E1 E2 E3... So, How can I use it for my work? Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From frsantos at fpce.up.pt Mon May 26 18:08:41 2014 From: frsantos at fpce.up.pt (Fernando Ferreira-Santos) Date: Mon, 26 May 2014 16:08:41 +0000 Subject: [FieldTrip] Porto III CAN: 3rd Cognitive and Affective Neurophysiology Summer School Message-ID: <2BAB036A9BAEA44984A131DFCE44610801099FB3BD@SRVMBX01.fpceup.psi.up.pt> Dear colleagues, The Laboratory of Neuropsychopsysiology of the University of Porto (http://www.fpce.up.pt/labpsi/) is pleased to announce the 3rd edition of the International Cognitive and Affective Neurophysiology Summer School: Acquisition, processing and analysis of EEG signal. This summer school is focused on the application of Electroencephalography (EEG) and Event Related Potential (ERP) techniques to the study of cognitive and affective processes. The course will be fully taught in English and is aimed at an introductory level, so no previous experience with EEG or ERP is required. This event will take place from 8-13 of September in the lovely city of Porto, recently elected as the Best European Destination of 2014 (http://www.europeanbestdestinations.org/top/europe-best-destinations-2014/#PORTO). In last year’s edition the course was fully booked and, as such, we recommend early registration (course places are attributed by order of registration). For additional details and instructions on how to register, please consult our website (http://www.fpce.up.pt/labpsi/summerschool/). Please feel free to pass this information along to students or researchers that may be potentially interested. Thanks you and best wishes, -- Fernando Ferreira-Santos, PhD Laboratory of Neuropsychophysiology Faculty of Psychology and Education Sciences University of Porto Rua Alfredo Allen, 4200-135 Porto (Portugal) Tel.: +351 226079700 (ext. 301) Email: frsantos at fpce.up.pt http://www.fpce.up.pt/labpsi/ -- Fernando Ferreira-Santos, PhD Laboratory of Neuropsychophysiology Faculty of Psychology and Education Sciences University of Porto Rua Alfredo Allen, 4200-135 Porto (Portugal) Tel.: +351 226079700 (ext. 301) Email: frsantos at fpce.up.pt http://www.fpce.up.pt/labpsi/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahjoory86 at gmail.com Mon May 26 18:14:17 2014 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Mon, 26 May 2014 18:14:17 +0200 Subject: [FieldTrip] Error in source analysis Message-ID: Dear All, Here is my scripts for source analysis, when I run it, I face with error mentioned below, load 'standard_bem.mat' cfg = []; cfg.method = 'dics'; cfg.frequency = 10; cfg.grid = grid; cfg.elec=ft_read_sens('standard_1020.elc'); cfg.vol = vol; sourcePost_nocon = ft_sourceanalysis(cfg,freq); ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> beamformer_dics>pinv at 650 [U,S,V] = svd(A,0); Error in ==> beamformer_dics at 339 filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ==> ft_sourceanalysis at 567 dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Thank you in advance, Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From diezmartini at gmail.com Tue May 27 00:25:39 2014 From: diezmartini at gmail.com (Ana Laura Diez Martini) Date: Tue, 27 May 2014 10:25:39 +1200 Subject: [FieldTrip] Cannot read the events of a .BDF file exported from an EGI .RAW In-Reply-To: <222446912.7087267.1401097453356.JavaMail.root@sculptor.zimbra.ru.nl> References: <222446912.7087267.1401097453356.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Thank you Arjen, Diego and Chungki Lee! I tried with the .RAW and it reads the event. The problem is that my triggers have the following format "11,12,13,14,15,21,22...." . Netstation instead of saving them as they are, returns them in this way: say my trigger is 12, I get "DIN4" and "DIN8". or 11 is DIN1 + DIN8 + DIN2. so I had to convert them into my original triggers. After that I can either save the set (I tried this but it didn't work) or export it to bdf. When I open the exported file in EEGlab, it reads the events correctly, but fieldtrip doesn't. Any ideas? Thanks!! On Mon, May 26, 2014 at 9:44 PM, Lozano Soldevilla, D. (Diego) < d.lozanosoldevilla at fcdonders.ru.nl> wrote: > Dear Ana, > > Sorry for my file extension confusion: edf instead of bdf. However, I > don't know a way to read events coded in BDF format exported by NETSTATION. > I encounter this problem in the past but I had no problems with RAW file > format > > Dear Chungki, > > Fieldtrip can read events in *.bdf but from BIOSEMI eeg system but Ana was > refering to a different eeg system that has the same fileformat extension. > > best, > > Diego > > ------------------------------ > > *From: *"Chungki Lee" > *To: *"FieldTrip discussion list" > *Sent: *Monday, 26 May, 2014 11:18:34 AM > *Subject: *Re: [FieldTrip] Cannot read the events of a .BDF file exported > from an EGI .RAW > > > Dear all > > Fieldtrip can read events in BDF format ! > > Hear simple examples > > example #1 > %% > cfg = []; > cfg.dataset = '~~~ '; % your filename with file extension; > cfg.trialdef.eventtype = 'STATUS'; % Status notation maybe Biosemi's > tigger name > cfg.trialdef.eventvalue = 1; % your event value > cfg.trialdef.prestim = 4; % before stimulation (sec), only use > positive value > cfg.trialdef.poststim = 8; % after stimulation (sec) , only use > positive value > cfg = ft_definetrial(cfg); > cfg.method = 'trial'; > data = ft_preprocessing(cfg); > %% > > example #2 > %% > % if you executed these command lines > cfg = []; > cfg.dataset = '~~~ '; % your filename with file extension; > cfg.trialdef.eventtype = '?'; % Status notation maybe Biosemi's > tigger name > cfg = ft_definetrial(cfg); > > % result example #2 > the following events were found in the datafile > event type: 'CM_in_range' with event values: > event type: 'Epoch' with event values: > event type: 'STATUS' with event values: 1 2 3 4 255 <----------- > "this indicate your file configuration for trigger information" > no trials have been defined yet, see FT_DEFINETRIAL for further help > found 255 events > created 0 trials > the call to "ft_definetrial" took 8 seconds > > have fun~!! > > > > 2014-05-26 17:58 GMT+09:00 Diego Lozano Soldevilla < > d.lozanosoldevilla at fcdonders.ru.nl>: > >> Hi Ana, >> >> Fieldtrip does not read events in BDF format. Take a look to our wiki: >> >> http://fieldtrip.fcdonders.nl/getting_started/egi >> >> >> - *EDF+* (.edf) All channels, including PIB channels, are read in >> correctly, including channel labels. However, the events, which are stored >> on the annotation channel, are written in a way by Net Station that is not >> compatible with the edf+ reading implementation in FieldTrip. So, events do >> not come out properly. Also discontinuous epochs are “glued” together as >> one “continuous” data stream. >> >> As Arjen suggested, with *.RAW you shouldn't have any problem. >> >> event = ft_read_event('*.RAW') >> >> If you encounter it, please let us know. >> >> best, >> >> Diego >> >> >> On 26 May 2014 08:59, Arjen Stolk wrote: >> >>> Hi Ana Laura, >>> >>> Have you tried importing the .RAW file directly? That is, by specifying >>> cfg.dataset = 'XXX.raw'? >>> >>> Best regards, >>> Arjen >>> >>> >>> 2014-05-26 2:30 GMT+02:00 Ana Laura Diez Martini >>> : >>> >>>> Hi all! >>>> >>>> This is the .BDF file >>>> of one >>>> of my EEG subjects. For my last experiment I used a Biosemi system and now >>>> I'm using an EGI system which gives me .RAW files. I exported the .RAW file >>>> with EEGlab to .BDF format and I tried using the scripts I use to analise >>>> the data of my previous experiment but I realised that it was not reading >>>> the events: >>>> >>>> cfg = []; >>>> cfg.dataset = ' (location)'; >>>> cfg.trialdef.eventtype = '?'; >>>> definetrial(cfg); >>>> Warning: no trialfun was specified, using trialfun_general >>>> > In definetrial at 79 >>>> evaluating trialfunction 'trialfun_general' >>>> no events were found in the datafile >>>> no trials have been defined yet, see DEFINETRIAL for further help >>>> found 0 events >>>> created 0 trials >>>> >>>> EEGlab does read them. Any idea of what could be wrong? >>>> >>>> Thank you all!! >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > ---------------------------------------------------------------- > Chungki Lee, Ph.D. > Post-doc > Biomedical Research Institute > Korea Institute of Science and Technology > E-mail: chungki at kist.re.kr > Tel:+82-2-958-5636, C.P: +82-10-5223-7309 > ---------------------------------------------------------------- > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > PhD Student > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > NL-6525 EN Nijmegen > The Netherlands > http://www.ru.nl/people/donders/lozano-soldevilla-d/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Tue May 27 07:44:49 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Tue, 27 May 2014 05:44:49 +0000 Subject: [FieldTrip] granger causality on beamformer data Message-ID: <1401169475061.32086@flinders.edu.au> ?Hello fieldtrippers, I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. Or should you do a PCA reduction of some description beforehand. I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. Im open to all suggestions. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ulrich.Pomper at charite.de Tue May 27 15:18:57 2014 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Tue, 27 May 2014 15:18:57 +0200 Subject: [FieldTrip] TF transform, data length + padding Message-ID: Dear community, I have a question regarding time-frequency transformation. The data I want to analyse last from -800 to -200 ms before stimulus onset, I'm using a 400 ms taper. Importantly, want to make sure that no stimulus-evoked activity leaks into my prestim analysis. I first tried to cut the segment down to -1000 to 0 ms and used (zero) padding (see figure attached, top row). This would mean that the taper, at the last samplepoint of interest (-200ms), would include data up to 0ms Suprisingly, I get quite different looking results when using a longer data segment (-1200 to 0 ms) (fig. bottom row) without padding. Can someone explain to me what is going on here, and which approach would be more correct? Either, the padding in the first variant introduces artificial low frequency activity, or the taper in the second variant uses more than 400ms, at least for the low frequencies. Note that the difference between conditions (left coloumn) look almost identical, so whatever happens, it happens to both conditions very similarly. I hope someone can educate me on that matter. Cheers, Ulrich %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% TF transform %% cfg = []; cfg.continuous = 'no'; cfg.channel = 'all'; cfg.output = 'pow'; cfg.method = 'mtmconvol'; cfg.foi = 2:0.5:35; cfg.toi = -1:0.01:0; cfg.taper = 'hanning'; cfg.tapsmofrq = 2; cfg.t_ftimwin = 400 % cfg.pad = 5; ... -------------- next part -------------- A non-text attachment was scrubbed... Name: Bild5.png Type: image/png Size: 128717 bytes Desc: Bild5.png URL: From litvak.vladimir at gmail.com Tue May 27 15:29:33 2014 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Tue, 27 May 2014 14:29:33 +0100 Subject: [FieldTrip] Head model for a phantom Message-ID: Dear all, I need to to do source reconstruction of activity generated with current dipole phantom in CTF MEG. The HPI coils were at the front and sides as they would be for a subject. I was thinking I could just make a single sphere vol with origin set at [0 0 0] as that would coincide with the center of the phantom in this case. The radius shouldn't matter anyway if we are not fitting it to anything, right? Please let me know if you think this is the right approach. Thanks, Vladimir -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcgoiv0 at wfu.edu Tue May 27 16:18:28 2014 From: mcgoiv0 at wfu.edu (McGowin, Inna) Date: Tue, 27 May 2014 10:18:28 -0400 Subject: [FieldTrip] Head model for a phantom In-Reply-To: References: Message-ID: Hello Vladimir, According to the CTF MEG tech support to apply DipFit or SAM to the Current Dipole phantom recordings you need to change (0,0,4) sphere center to (0,0,0) and multiple spheres to a single sphere model for SAM.Thus you are correct. To view the results of SAM any MRI can be used. Cheers, Inna On Tue, May 27, 2014 at 9:29 AM, Vladimir Litvak wrote: > Dear all, > > I need to to do source reconstruction of activity generated with current > dipole phantom in CTF MEG. The HPI coils were at the front and sides as > they would be for a subject. I was thinking I could just make a single > sphere vol with origin set at [0 0 0] as that would coincide with the > center of the phantom in this case. The radius shouldn't matter anyway if > we are not fitting it to anything, right? > > Please let me know if you think this is the right approach. > > Thanks, > > Vladimir > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Tue May 27 18:10:24 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Tue, 27 May 2014 18:10:24 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? Message-ID: Dear all, my name is Katrin Heimann, I am phd student at the University of Parma. New to Fieldtrip. I am doing an EEG analysis, still in the preprocessing phase. It is a within trials design. I would like to compare a baseline period with an experimental condition (visual stimulus). I have a trigger after a fixation cross, then a baseline period (approx 1 sec) , then the period of my stimulus (1 sec- starting with a bottom press (trigger)). As I would like to apply the same baseline correction for both (the fixationcross period) I planned to first define my trials as long trials including the timewindows of baseline and the stimulus period, applying filter and baselinecorrection on those long pieces. However, as I do not wanna do the artifact detection on the whole pieces (but seperately for baseline and stimulus, to avoid that I have to throw away too many trials) I would like to redefine my trials then, cutting out only baseline period and only stimulus period (starting with another trigger (triggervalue=resp).. *Unfortunately I do not understand how I can change the trigger used with ft redefine trial. * Anybody who could give me an example how that is done? Thanks a million Katrin -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Tue May 27 18:25:18 2014 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 27 May 2014 18:25:18 +0200 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: <1401169475061.32086@flinders.edu.au> References: <1401169475061.32086@flinders.edu.au> Message-ID: Hi Tyler, I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 connections, so I hope you have a fast computer. As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website: http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). I hope that helps, if you have specific questions, feel free to ask. Best, Julian On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett < tyler.grummett at flinders.edu.au> wrote: > ​Hello fieldtrippers, > > > I was just wondering whether it would be sensible to do granger > causality on all 1400 virtual channels, as calculated using beamformer. > > > Or should you do a PCA reduction of some description beforehand. > > > I was also wondering how to create regions of interest. Some of my > colleagues think that we should use some kind of spatial ICA technique. > > > Im open to all suggestions. > > > Tyler > > > ************************* > > *Tyler Grummett ( BBSc, BSc(Hons I))* > *PhD Candidate* > *Brain Signals Laboratory* > *Flinders University* > *Rm 5A301* > *Ext 66124* > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcantor at umich.edu Tue May 27 18:58:32 2014 From: mcantor at umich.edu (Max Cantor) Date: Tue, 27 May 2014 12:58:32 -0400 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Hi Katrin, It may help to see your code, but hopefully this will help. It should be as simple as taking your epoched data from ft_definetrial and ft_preprocessing, then creating two configurations for your timewindows and running ft_redefinetrial. For example (from the fieldtrip tutorial, slightly simplified by me for explanatory purposes): *** % find the interesting segments of data cfg = []; % empty configuration cfg.dataset = 'Subject01.ds'; % name of CTF dataset cfg.trialdef.eventtype = 'backpanel trigger'; cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 2; cfg.trialdef.eventvalue = 3; % event value of FIC cfg = ft_definetrial(cfg); % preprocess the data cfg.channel = {'MEG'}; dataFIC = ft_preprocessing(cfg); % define time window cfg = []; cfg.toilim = [-0.5 0]; dataPre = ft_redefinetrial(cfg, dataFIC); cfg.toilim = [0.8 1.3]; dataPost = ft_redefinetrial(cfg, dataFIC); *** So if your code resembles this, you are defining in cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that encompasses both your baseline period and stimulus period, then for cfg.toilim in the ft_redefinetrial section you are setting one to your baseline period and the other to your stimulus period, and outputting them into separate variables. Hopefully this helps. Also, if you haven't done so already, I would strongly recommend you run through the tutorial, as it may help answer questions like this in the future (assuming I've properly identified the issue). Good luck, Max On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann wrote: > Dear all, > > my name is Katrin Heimann, I am phd student at the University of Parma. > New to Fieldtrip. > I am doing an EEG analysis, still in the preprocessing phase. > It is a within trials design. I would like to compare a baseline period > with an experimental condition (visual stimulus). > > I have a trigger after a fixation cross, then a baseline period (approx 1 > sec) , then the period of my stimulus (1 sec- starting with a bottom press > (trigger)). > > As I would like to apply the same baseline correction for both (the > fixationcross period) I planned to first define my trials as long trials > including the timewindows of baseline and the stimulus period, applying > filter and baselinecorrection on those long pieces. However, as I do not > wanna do the artifact detection on the whole pieces (but seperately for > baseline and stimulus, to avoid that I have to throw away too many trials) > I would like to redefine my trials then, cutting out only baseline period > and only stimulus period (starting with another trigger > (triggervalue=resp).. > > *Unfortunately I do not understand how I can change the trigger used with > ft redefine trial. * > > Anybody who could give me an example how that is done? > Thanks a million > Katrin > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Research Assistant Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Tue May 27 20:30:14 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Tue, 27 May 2014 20:30:14 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Dear Max, thanks a lot for your prompt answer. Unfortunately this is not what I am looking for (I found an example like this in the tutorial). I would like to change the trigger for one of the two conditions, let it be now the response of the subject, as this is where the stimulus actually starts... Defining two different timewindows is not enough... Can you also help me with that? Thanks a million! Katrin 2014-05-27 18:58 GMT+02:00 Max Cantor : > Hi Katrin, > > It may help to see your code, but hopefully this will help. It should be > as simple as taking your epoched data from ft_definetrial and > ft_preprocessing, then creating two configurations for your timewindows and > running ft_redefinetrial. > > For example (from the fieldtrip tutorial, slightly simplified by me for > explanatory purposes): > > *** > > % find the interesting segments of data > > cfg = []; > % empty configuration > cfg.dataset = 'Subject01.ds'; > % name of CTF dataset > cfg.trialdef.eventtype = 'backpanel trigger'; > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 2; > cfg.trialdef.eventvalue = 3; > % event value of FIC > cfg = ft_definetrial(cfg); > > % preprocess the data > > cfg.channel = {'MEG'}; > dataFIC = ft_preprocessing(cfg); > > % define time window > > cfg = []; > > cfg.toilim = [-0.5 0]; > dataPre = ft_redefinetrial(cfg, dataFIC); > > cfg.toilim = [0.8 1.3]; > dataPost = ft_redefinetrial(cfg, dataFIC); > > *** > > So if your code resembles this, you are defining in cfg.trialdef.prestim > and cfg.trialdef.poststim a timewindow that encompasses both your baseline > period and stimulus period, then for cfg.toilim in the ft_redefinetrial > section you are setting one to your baseline period and the other to your > stimulus period, and outputting them into separate variables. > > Hopefully this helps. Also, if you haven't done so already, I would > strongly recommend you run through the tutorial, as it may help answer > questions like this in the future (assuming I've properly identified the > issue). > > Good luck, > > Max > > > > > On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann > wrote: > >> Dear all, >> >> my name is Katrin Heimann, I am phd student at the University of Parma. >> New to Fieldtrip. >> I am doing an EEG analysis, still in the preprocessing phase. >> It is a within trials design. I would like to compare a baseline period >> with an experimental condition (visual stimulus). >> >> I have a trigger after a fixation cross, then a baseline period (approx >> 1 sec) , then the period of my stimulus (1 sec- starting with a bottom >> press (trigger)). >> >> As I would like to apply the same baseline correction for both (the >> fixationcross period) I planned to first define my trials as long trials >> including the timewindows of baseline and the stimulus period, applying >> filter and baselinecorrection on those long pieces. However, as I do not >> wanna do the artifact detection on the whole pieces (but seperately for >> baseline and stimulus, to avoid that I have to throw away too many trials) >> I would like to redefine my trials then, cutting out only baseline period >> and only stimulus period (starting with another trigger >> (triggervalue=resp).. >> >> *Unfortunately I do not understand how I can change the trigger used with >> ft redefine trial. * >> >> Anybody who could give me an example how that is done? >> Thanks a million >> Katrin >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Max Cantor > Research Assistant > Computational Neurolinguistics Lab > University of Michigan > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathykousik at gmail.com Tue May 27 20:44:15 2014 From: sarathykousik at gmail.com (kousik sarathy) Date: Tue, 27 May 2014 20:44:15 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Hey Katrin, It seems to me that Max's suggestion would suffice. But you seem to be looking for something else. Could you elaborate a little bit as to what you need? -- Regards, Kousik Sarathy, S On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann wrote: > Dear Max, thanks a lot for your prompt answer. Unfortunately this is not > what I am looking for (I found an example like this in the tutorial). I > would like to change the trigger for one of the two conditions, let it be > now the response of the subject, as this is where the stimulus actually > starts... Defining two different timewindows is not enough... Can you also > help me with that? Thanks a million! Katrin > > > 2014-05-27 18:58 GMT+02:00 Max Cantor : > > Hi Katrin, >> >> It may help to see your code, but hopefully this will help. It should be >> as simple as taking your epoched data from ft_definetrial and >> ft_preprocessing, then creating two configurations for your timewindows and >> running ft_redefinetrial. >> >> For example (from the fieldtrip tutorial, slightly simplified by me for >> explanatory purposes): >> >> *** >> >> % find the interesting segments of data >> >> cfg = []; >> % empty configuration >> cfg.dataset = 'Subject01.ds'; >> % name of CTF dataset >> cfg.trialdef.eventtype = 'backpanel trigger'; >> cfg.trialdef.prestim = 1; >> cfg.trialdef.poststim = 2; >> cfg.trialdef.eventvalue = 3; >> % event value of FIC >> cfg = ft_definetrial(cfg); >> >> % preprocess the data >> >> cfg.channel = {'MEG'}; >> dataFIC = ft_preprocessing(cfg); >> >> % define time window >> >> cfg = []; >> >> cfg.toilim = [-0.5 0]; >> dataPre = ft_redefinetrial(cfg, dataFIC); >> >> cfg.toilim = [0.8 1.3]; >> dataPost = ft_redefinetrial(cfg, dataFIC); >> >> *** >> >> So if your code resembles this, you are defining in cfg.trialdef.prestim >> and cfg.trialdef.poststim a timewindow that encompasses both your baseline >> period and stimulus period, then for cfg.toilim in the ft_redefinetrial >> section you are setting one to your baseline period and the other to your >> stimulus period, and outputting them into separate variables. >> >> Hopefully this helps. Also, if you haven't done so already, I would >> strongly recommend you run through the tutorial, as it may help answer >> questions like this in the future (assuming I've properly identified the >> issue). >> >> Good luck, >> >> Max >> >> >> >> >> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >> katrinheimann at gmail.com> wrote: >> >>> Dear all, >>> >>> my name is Katrin Heimann, I am phd student at the University of Parma. >>> New to Fieldtrip. >>> I am doing an EEG analysis, still in the preprocessing phase. >>> It is a within trials design. I would like to compare a baseline period >>> with an experimental condition (visual stimulus). >>> >>> I have a trigger after a fixation cross, then a baseline period (approx >>> 1 sec) , then the period of my stimulus (1 sec- starting with a bottom >>> press (trigger)). >>> >>> As I would like to apply the same baseline correction for both (the >>> fixationcross period) I planned to first define my trials as long trials >>> including the timewindows of baseline and the stimulus period, applying >>> filter and baselinecorrection on those long pieces. However, as I do not >>> wanna do the artifact detection on the whole pieces (but seperately for >>> baseline and stimulus, to avoid that I have to throw away too many trials) >>> I would like to redefine my trials then, cutting out only baseline period >>> and only stimulus period (starting with another trigger >>> (triggervalue=resp).. >>> >>> *Unfortunately I do not understand how I can change the trigger used >>> with ft redefine trial. * >>> >>> Anybody who could give me an example how that is done? >>> Thanks a million >>> Katrin >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Max Cantor >> Research Assistant >> Computational Neurolinguistics Lab >> University of Michigan >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcantor at umich.edu Tue May 27 21:05:17 2014 From: mcantor at umich.edu (Max Cantor) Date: Tue, 27 May 2014 15:05:17 -0400 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Ya, it would definitely help if we could see your code, but I might have another idea. When you say you have a fixation cross trigger, is this trigger being recorded from your EEG recording equipment in such a way that it can be represented as an event value in cfg.trialdef for ft_definetrial? If so, I think you may be right that it can't be changed through ft_redefinetrial (at least, as far as I can tell, no mention of this is made in the help section of the function). That being said, if you run ft_definetrial separately for both event values that should work. That being said, I may still be slightly confused about what you mean when you say you want to change the trigger. Do you mean you want to create a new trigger for your data off-line? I think it may be possible to create custom triggers off-line through fieldtrip, but it's not something I've tried personally, but if that is what you are trying to do, I could look into it. On Tue, May 27, 2014 at 2:44 PM, kousik sarathy wrote: > Hey Katrin, > > It seems to me that Max's suggestion would suffice. But you seem to be > looking for something else. Could you elaborate a little bit as to what you > need? > > -- > Regards, > Kousik Sarathy, S > > > > On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann wrote: > >> Dear Max, thanks a lot for your prompt answer. Unfortunately this is not >> what I am looking for (I found an example like this in the tutorial). I >> would like to change the trigger for one of the two conditions, let it be >> now the response of the subject, as this is where the stimulus actually >> starts... Defining two different timewindows is not enough... Can you also >> help me with that? Thanks a million! Katrin >> >> >> 2014-05-27 18:58 GMT+02:00 Max Cantor : >> >> Hi Katrin, >>> >>> It may help to see your code, but hopefully this will help. It should be >>> as simple as taking your epoched data from ft_definetrial and >>> ft_preprocessing, then creating two configurations for your timewindows and >>> running ft_redefinetrial. >>> >>> For example (from the fieldtrip tutorial, slightly simplified by me for >>> explanatory purposes): >>> >>> *** >>> >>> % find the interesting segments of data >>> >>> cfg = []; >>> % empty configuration >>> cfg.dataset = 'Subject01.ds'; >>> % name of CTF dataset >>> cfg.trialdef.eventtype = 'backpanel trigger'; >>> cfg.trialdef.prestim = 1; >>> cfg.trialdef.poststim = 2; >>> cfg.trialdef.eventvalue = 3; >>> % event value of FIC >>> cfg = ft_definetrial(cfg); >>> >>> % preprocess the data >>> >>> cfg.channel = {'MEG'}; >>> dataFIC = ft_preprocessing(cfg); >>> >>> % define time window >>> >>> cfg = []; >>> >>> cfg.toilim = [-0.5 0]; >>> dataPre = ft_redefinetrial(cfg, dataFIC); >>> >>> cfg.toilim = [0.8 1.3]; >>> dataPost = ft_redefinetrial(cfg, dataFIC); >>> >>> *** >>> >>> So if your code resembles this, you are defining in cfg.trialdef.prestim >>> and cfg.trialdef.poststim a timewindow that encompasses both your baseline >>> period and stimulus period, then for cfg.toilim in the ft_redefinetrial >>> section you are setting one to your baseline period and the other to your >>> stimulus period, and outputting them into separate variables. >>> >>> Hopefully this helps. Also, if you haven't done so already, I would >>> strongly recommend you run through the tutorial, as it may help answer >>> questions like this in the future (assuming I've properly identified the >>> issue). >>> >>> Good luck, >>> >>> Max >>> >>> >>> >>> >>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >>> katrinheimann at gmail.com> wrote: >>> >>>> Dear all, >>>> >>>> my name is Katrin Heimann, I am phd student at the University of Parma. >>>> New to Fieldtrip. >>>> I am doing an EEG analysis, still in the preprocessing phase. >>>> It is a within trials design. I would like to compare a baseline period >>>> with an experimental condition (visual stimulus). >>>> >>>> I have a trigger after a fixation cross, then a baseline period >>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a >>>> bottom press (trigger)). >>>> >>>> As I would like to apply the same baseline correction for both (the >>>> fixationcross period) I planned to first define my trials as long trials >>>> including the timewindows of baseline and the stimulus period, applying >>>> filter and baselinecorrection on those long pieces. However, as I do not >>>> wanna do the artifact detection on the whole pieces (but seperately for >>>> baseline and stimulus, to avoid that I have to throw away too many trials) >>>> I would like to redefine my trials then, cutting out only baseline period >>>> and only stimulus period (starting with another trigger >>>> (triggervalue=resp).. >>>> >>>> *Unfortunately I do not understand how I can change the trigger used >>>> with ft redefine trial. * >>>> >>>> Anybody who could give me an example how that is done? >>>> Thanks a million >>>> Katrin >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> Max Cantor >>> Research Assistant >>> Computational Neurolinguistics Lab >>> University of Michigan >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Research Assistant Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Tue May 27 23:02:41 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Tue, 27 May 2014 23:02:41 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Hi! Guys, your help is so much appreciated! So I try to be more clear!: So, yeah, Max, you are right! At the end I would like to use two different triggervalues. If I would use twice ft_definetrial then it would look like this: cfg = []; cfg.dataset = '1.raw'; cfg.trialfun = 'ft_trialfun_general'; cfg.trialdef.eventtype = 'trigger'; cfg.trialdef.eventvalue = 'stim'; % the value of the stimulus trigger for the beginning of baseline cfg.trialdef.prestim = 0.5; %the time of the fixation cross cfg.trialdef.poststim = 1.5; %the time of the baseline (plus 0.5 buffer) cfg = ft_redefinetrial(cfg); This baselinedata I could easily baselinecorrect using 100 ms of the fixationcrossperiod: cfg.channel = 'all'; cfg.preproc.demean = 'yes'; cfg.preproc.baselinewindow = [-0.1 0] cfg.preproc.bpfilter = 'yes'; cfg.preproc.bpfreq = [6 32]; The stimulusdata would be defined using a trigger that corresponds to a button press: cfg = []; cfg.dataset = '1.raw'; cfg.trialfun = 'ft_trialfun_general'; cfg.trialdef.eventtype = 'trigger'; cfg.trialdef.eventvalue = 'resp'; % the value of the stimulus trigger for the beginning of baseline cfg.trialdef.prestim = 0.5; % 0.5 sec before button press cfg.trialdef.poststim = 1.5; % 1.5 sec after button press (time that I wanna analyse) cfg = ft_redefinetrial(cfg); However here I have the problem that I cannot correct with the same baseline than before as the buttonpress is not always at the same time so I don't know when the fixationcrossperiod is located... So I thought I could first "cut" bigger pieces and then redefine trials by cutting again (after the preprocessing), then with different eventvalues ... But you say that is not possible? Thanks a lot for your help!!! Katrin 2014-05-27 21:05 GMT+02:00 Max Cantor : > Ya, it would definitely help if we could see your code, but I might have > another idea. > > When you say you have a fixation cross trigger, is this trigger being > recorded from your EEG recording equipment in such a way that it can be > represented as an event value in cfg.trialdef for ft_definetrial? If so, I > think you may be right that it can't be changed through ft_redefinetrial > (at least, as far as I can tell, no mention of this is made in the help > section of the function). That being said, if you run ft_definetrial > separately for both event values that should work. > > That being said, I may still be slightly confused about what you mean when > you say you want to change the trigger. Do you mean you want to create a > new trigger for your data off-line? I think it may be possible to create > custom triggers off-line through fieldtrip, but it's not something I've > tried personally, but if that is what you are trying to do, I could look > into it. > > > On Tue, May 27, 2014 at 2:44 PM, kousik sarathy wrote: > >> Hey Katrin, >> >> It seems to me that Max's suggestion would suffice. But you seem to be >> looking for something else. Could you elaborate a little bit as to what you >> need? >> >> -- >> Regards, >> Kousik Sarathy, S >> >> >> >> On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann > > wrote: >> >>> Dear Max, thanks a lot for your prompt answer. Unfortunately this is not >>> what I am looking for (I found an example like this in the tutorial). I >>> would like to change the trigger for one of the two conditions, let it be >>> now the response of the subject, as this is where the stimulus actually >>> starts... Defining two different timewindows is not enough... Can you also >>> help me with that? Thanks a million! Katrin >>> >>> >>> 2014-05-27 18:58 GMT+02:00 Max Cantor : >>> >>> Hi Katrin, >>>> >>>> It may help to see your code, but hopefully this will help. It should >>>> be as simple as taking your epoched data from ft_definetrial and >>>> ft_preprocessing, then creating two configurations for your timewindows and >>>> running ft_redefinetrial. >>>> >>>> For example (from the fieldtrip tutorial, slightly simplified by me for >>>> explanatory purposes): >>>> >>>> *** >>>> >>>> % find the interesting segments of data >>>> >>>> cfg = []; >>>> % empty configuration >>>> cfg.dataset = 'Subject01.ds'; >>>> % name of CTF dataset >>>> cfg.trialdef.eventtype = 'backpanel trigger'; >>>> cfg.trialdef.prestim = 1; >>>> cfg.trialdef.poststim = 2; >>>> cfg.trialdef.eventvalue = 3; >>>> % event value of FIC >>>> cfg = ft_definetrial(cfg); >>>> >>>> % preprocess the data >>>> >>>> cfg.channel = {'MEG'}; >>>> dataFIC = ft_preprocessing(cfg); >>>> >>>> % define time window >>>> >>>> cfg = []; >>>> >>>> cfg.toilim = [-0.5 0]; >>>> dataPre = ft_redefinetrial(cfg, dataFIC); >>>> >>>> cfg.toilim = [0.8 1.3]; >>>> dataPost = ft_redefinetrial(cfg, dataFIC); >>>> >>>> *** >>>> >>>> So if your code resembles this, you are defining in >>>> cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that >>>> encompasses both your baseline period and stimulus period, then for >>>> cfg.toilim in the ft_redefinetrial section you are setting one to your >>>> baseline period and the other to your stimulus period, and outputting them >>>> into separate variables. >>>> >>>> Hopefully this helps. Also, if you haven't done so already, I would >>>> strongly recommend you run through the tutorial, as it may help answer >>>> questions like this in the future (assuming I've properly identified the >>>> issue). >>>> >>>> Good luck, >>>> >>>> Max >>>> >>>> >>>> >>>> >>>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >>>> katrinheimann at gmail.com> wrote: >>>> >>>>> Dear all, >>>>> >>>>> my name is Katrin Heimann, I am phd student at the University of >>>>> Parma. New to Fieldtrip. >>>>> I am doing an EEG analysis, still in the preprocessing phase. >>>>> It is a within trials design. I would like to compare a baseline >>>>> period with an experimental condition (visual stimulus). >>>>> >>>>> I have a trigger after a fixation cross, then a baseline period >>>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a >>>>> bottom press (trigger)). >>>>> >>>>> As I would like to apply the same baseline correction for both (the >>>>> fixationcross period) I planned to first define my trials as long trials >>>>> including the timewindows of baseline and the stimulus period, applying >>>>> filter and baselinecorrection on those long pieces. However, as I do not >>>>> wanna do the artifact detection on the whole pieces (but seperately for >>>>> baseline and stimulus, to avoid that I have to throw away too many trials) >>>>> I would like to redefine my trials then, cutting out only baseline period >>>>> and only stimulus period (starting with another trigger >>>>> (triggervalue=resp).. >>>>> >>>>> *Unfortunately I do not understand how I can change the trigger used >>>>> with ft redefine trial. * >>>>> >>>>> Anybody who could give me an example how that is done? >>>>> Thanks a million >>>>> Katrin >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>> >>>> >>>> >>>> >>>> -- >>>> Max Cantor >>>> Research Assistant >>>> Computational Neurolinguistics Lab >>>> University of Michigan >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Max Cantor > Research Assistant > Computational Neurolinguistics Lab > University of Michigan > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcantor at umich.edu Tue May 27 23:39:31 2014 From: mcantor at umich.edu (Max Cantor) Date: Tue, 27 May 2014 17:39:31 -0400 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: I'm hesitant to say impossible, but I'm not sure how to do it off-hand. Also, there may be some other complications, now that I think I understand your situation better. If you're trying to cut based on the buttonpresses, which are inconsistent/unreliable, any large number of trials would make it impractical to define/redefine your epoch for each one, especially since this process would need to be customized for each subject. It might be better to keep it in a larger window, or come up with a few general windows to encompass, for instance 'early', 'on target', and 'late' button press windows. For all of the experiments I've worked on in which we've used / are using fieldtrip for our data analysis pipeline, we've never used behavioral responses for anything other than a control (as in, lack of response or incorrect response leads to rejecting the trial), so I don't really know if there is a particular systematic way to incorporate behavioral or floating triggers like what you seem to be looking to do. I might suggest, though keep in mind this is entirely speculative, rather than trying to create a pinpoint window around the response, that instead you use a wide window, and then either by viewing the data, or perhaps using independent component analysis, try to pinpoint for each subject when the button press may have occurred based on some kind of muscle artifact, and then in later timelock/time-frequency/statistical analyses specify that time window. Again, that is just me spitballing, but something post-processing may be a better solution, if the behavioral response is pivotal to the analysis of your experiment and not just for making sure the subject was paying attention / understands the prompt, as in the experiments I've worked on. On Tue, May 27, 2014 at 5:02 PM, KatrinH Heimann wrote: > Hi! Guys, your help is so much appreciated! > So I try to be more clear!: > So, yeah, Max, you are right! At the end I would like to use two different > triggervalues. > > If I would use twice ft_definetrial then it would look like this: > > cfg = []; > > cfg.dataset = '1.raw'; > > cfg.trialfun = 'ft_trialfun_general'; > > cfg.trialdef.eventtype = 'trigger'; > > cfg.trialdef.eventvalue = 'stim'; % the value of the stimulus trigger for > the beginning of baseline > > cfg.trialdef.prestim = 0.5; %the time of the fixation cross > > cfg.trialdef.poststim = 1.5; %the time of the baseline (plus 0.5 buffer) > > cfg = ft_redefinetrial(cfg); > > > This baselinedata I could easily baselinecorrect using 100 ms of the > fixationcrossperiod: > > > cfg.channel = 'all'; > > cfg.preproc.demean = 'yes'; > > cfg.preproc.baselinewindow = [-0.1 0] > > cfg.preproc.bpfilter = 'yes'; > > cfg.preproc.bpfreq = [6 32]; > > > The stimulusdata would be defined using a trigger that corresponds to a > button press: > > > cfg = []; > > cfg.dataset = '1.raw'; > > cfg.trialfun = 'ft_trialfun_general'; > > cfg.trialdef.eventtype = 'trigger'; > > cfg.trialdef.eventvalue = 'resp'; % the value of the stimulus trigger for > the beginning of baseline > > cfg.trialdef.prestim = 0.5; % 0.5 sec before button press > > cfg.trialdef.poststim = 1.5; % 1.5 sec after button press (time that I > wanna analyse) > > cfg = ft_redefinetrial(cfg); > > > However here I have the problem that I cannot correct with the same > baseline than before as the buttonpress is not always at the same time so I > don't know when the fixationcrossperiod is located... > > > So I thought I could first "cut" bigger pieces and then redefine trials by > cutting again (after the preprocessing), then with different eventvalues > ... > > But you say that is not possible? > > > > Thanks a lot for your help!!! > > > Katrin > > > > 2014-05-27 21:05 GMT+02:00 Max Cantor : > > Ya, it would definitely help if we could see your code, but I might have >> another idea. >> >> When you say you have a fixation cross trigger, is this trigger being >> recorded from your EEG recording equipment in such a way that it can be >> represented as an event value in cfg.trialdef for ft_definetrial? If so, I >> think you may be right that it can't be changed through ft_redefinetrial >> (at least, as far as I can tell, no mention of this is made in the help >> section of the function). That being said, if you run ft_definetrial >> separately for both event values that should work. >> >> That being said, I may still be slightly confused about what you mean >> when you say you want to change the trigger. Do you mean you want to create >> a new trigger for your data off-line? I think it may be possible to create >> custom triggers off-line through fieldtrip, but it's not something I've >> tried personally, but if that is what you are trying to do, I could look >> into it. >> >> >> On Tue, May 27, 2014 at 2:44 PM, kousik sarathy wrote: >> >>> Hey Katrin, >>> >>> It seems to me that Max's suggestion would suffice. But you seem to be >>> looking for something else. Could you elaborate a little bit as to what you >>> need? >>> >>> -- >>> Regards, >>> Kousik Sarathy, S >>> >>> >>> >>> On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann < >>> katrinheimann at gmail.com> wrote: >>> >>>> Dear Max, thanks a lot for your prompt answer. Unfortunately this is >>>> not what I am looking for (I found an example like this in the tutorial). I >>>> would like to change the trigger for one of the two conditions, let it be >>>> now the response of the subject, as this is where the stimulus actually >>>> starts... Defining two different timewindows is not enough... Can you also >>>> help me with that? Thanks a million! Katrin >>>> >>>> >>>> 2014-05-27 18:58 GMT+02:00 Max Cantor : >>>> >>>> Hi Katrin, >>>>> >>>>> It may help to see your code, but hopefully this will help. It should >>>>> be as simple as taking your epoched data from ft_definetrial and >>>>> ft_preprocessing, then creating two configurations for your timewindows and >>>>> running ft_redefinetrial. >>>>> >>>>> For example (from the fieldtrip tutorial, slightly simplified by me >>>>> for explanatory purposes): >>>>> >>>>> *** >>>>> >>>>> % find the interesting segments of data >>>>> >>>>> cfg = []; >>>>> % empty configuration >>>>> cfg.dataset = 'Subject01.ds'; >>>>> % name of CTF dataset >>>>> cfg.trialdef.eventtype = 'backpanel trigger'; >>>>> cfg.trialdef.prestim = 1; >>>>> cfg.trialdef.poststim = 2; >>>>> cfg.trialdef.eventvalue = 3; >>>>> % event value of FIC >>>>> cfg = ft_definetrial(cfg); >>>>> >>>>> % preprocess the data >>>>> >>>>> cfg.channel = {'MEG'}; >>>>> dataFIC = ft_preprocessing(cfg); >>>>> >>>>> % define time window >>>>> >>>>> cfg = []; >>>>> >>>>> cfg.toilim = [-0.5 0]; >>>>> dataPre = ft_redefinetrial(cfg, dataFIC); >>>>> >>>>> cfg.toilim = [0.8 1.3]; >>>>> dataPost = ft_redefinetrial(cfg, dataFIC); >>>>> >>>>> *** >>>>> >>>>> So if your code resembles this, you are defining in >>>>> cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that >>>>> encompasses both your baseline period and stimulus period, then for >>>>> cfg.toilim in the ft_redefinetrial section you are setting one to your >>>>> baseline period and the other to your stimulus period, and outputting them >>>>> into separate variables. >>>>> >>>>> Hopefully this helps. Also, if you haven't done so already, I would >>>>> strongly recommend you run through the tutorial, as it may help answer >>>>> questions like this in the future (assuming I've properly identified the >>>>> issue). >>>>> >>>>> Good luck, >>>>> >>>>> Max >>>>> >>>>> >>>>> >>>>> >>>>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >>>>> katrinheimann at gmail.com> wrote: >>>>> >>>>>> Dear all, >>>>>> >>>>>> my name is Katrin Heimann, I am phd student at the University of >>>>>> Parma. New to Fieldtrip. >>>>>> I am doing an EEG analysis, still in the preprocessing phase. >>>>>> It is a within trials design. I would like to compare a baseline >>>>>> period with an experimental condition (visual stimulus). >>>>>> >>>>>> I have a trigger after a fixation cross, then a baseline period >>>>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a >>>>>> bottom press (trigger)). >>>>>> >>>>>> As I would like to apply the same baseline correction for both (the >>>>>> fixationcross period) I planned to first define my trials as long trials >>>>>> including the timewindows of baseline and the stimulus period, applying >>>>>> filter and baselinecorrection on those long pieces. However, as I do not >>>>>> wanna do the artifact detection on the whole pieces (but seperately for >>>>>> baseline and stimulus, to avoid that I have to throw away too many trials) >>>>>> I would like to redefine my trials then, cutting out only baseline period >>>>>> and only stimulus period (starting with another trigger >>>>>> (triggervalue=resp).. >>>>>> >>>>>> *Unfortunately I do not understand how I can change the trigger used >>>>>> with ft redefine trial. * >>>>>> >>>>>> Anybody who could give me an example how that is done? >>>>>> Thanks a million >>>>>> Katrin >>>>>> >>>>>> _______________________________________________ >>>>>> fieldtrip mailing list >>>>>> fieldtrip at donders.ru.nl >>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Max Cantor >>>>> Research Assistant >>>>> Computational Neurolinguistics Lab >>>>> University of Michigan >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>> >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Max Cantor >> Research Assistant >> Computational Neurolinguistics Lab >> University of Michigan >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Research Assistant Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Wed May 28 03:06:47 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Wed, 28 May 2014 01:06:47 +0000 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: References: <1401169475061.32086@flinders.edu.au>, Message-ID: <1401239195251.79033@flinders.edu.au> ?Hey Julian, Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense. Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it? Regards, Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil Sent: Wednesday, 28 May 2014 1:55 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data Hi Tyler, I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 connections, so I hope you have a fast computer. As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website: http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). I hope that helps, if you have specific questions, feel free to ask. Best, Julian On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett > wrote: ?Hello fieldtrippers, I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. Or should you do a PCA reduction of some description beforehand. I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. Im open to all suggestions. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Wed May 28 05:56:58 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Wed, 28 May 2014 03:56:58 +0000 Subject: [FieldTrip] ft_networkanalysis over many subjects, between groups etc Message-ID: <1401249406137.6651@flinders.edu.au> ?Hello fieldtrippers, I was just wondering how to run the ft_networkanalysis function with input of many subjects. Would you run the analysis over each subject individually or can you combine subjects/groups of subjects. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Wed May 28 08:23:42 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Wed, 28 May 2014 06:23:42 +0000 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: <1401239195251.79033@flinders.edu.au> References: <1401169475061.32086@flinders.edu.au>, , <1401239195251.79033@flinders.edu.au> Message-ID: <1401258209971.36904@flinders.edu.au> Hello Julian, I think I got a few steps further into what I am trying to do, except I dont know whether I have done the correct thing or not, could you check it? % interpolate sources mri = ft_read_mri('Subject01.mri'); mri = ft_volumereslice([], mri); % read in atlas from fieldtrip template afni = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/afni/TTatlas+tlrc.HEAD')); % construct grid that lies only in grey matter cfg = []; cfg.mri = mri; cfg.grid.warpmni = 'yes'; cfg.grid = afni; grid = ft_prepare_sourcemodel( cfg); % Source Analysis: without contrasting condition cfg = []; cfg.channel = 'EEG'; cfg.method = 'lcmv'; cfg.grid = grid; cfg.vol = vol; cfg.keepfilter = 'yes'; source = ft_sourceanalysis( cfg, timelock); ? Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Tyler Grummett Sent: Wednesday, 28 May 2014 10:36 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data ?Hey Julian, Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense. Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it? Regards, Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil Sent: Wednesday, 28 May 2014 1:55 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data Hi Tyler, I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 connections, so I hope you have a fast computer. As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website: http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). I hope that helps, if you have specific questions, feel free to ask. Best, Julian On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett > wrote: ?Hello fieldtrippers, I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. Or should you do a PCA reduction of some description beforehand. I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. Im open to all suggestions. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed May 28 09:04:01 2014 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 28 May 2014 09:04:01 +0200 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: <1401239195251.79033@flinders.edu.au> References: <1401169475061.32086@flinders.edu.au>, <1401239195251.79033@flinders.edu.au> Message-ID: <8AB768DB-56A0-4081-9A58-44286BB0F9BB@gmail.com> Hi Tyler, if you follow the link, you get to the "Volumes of Interest" Data base. You can browse through the volumes by then clicking on "Alphabetic index" (http://neuro.imm.dtu.dk/services/jerne/ninf/voi/index-alphabetic.html) If you then click on a volume (e.g. "amygdala" http://neuro.imm.dtu.dk/services/jerne/ninf/voi/amygdala.html) you get to a definition of that VOI. Here, you can now download .hdr and .img files. These are ANALYZE volumes with 1s for all voxels inside a VOI and 0s outside. You can read these with ft_read_mri and normalize to the MNI brain. tl;dr You don't need any functions, just the .hdr and .img files defining the volumes Best, Julian Am 28.05.2014 um 03:06 schrieb Tyler Grummett: > ​Hey Julian, > > Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense. > > Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it? > > Regards, > > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil > Sent: Wednesday, 28 May 2014 1:55 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] granger causality on beamformer data > > Hi Tyler, > > I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 > connections, so I hope you have a fast computer. > > As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website:http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html > > The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. > > In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). > > I hope that helps, if you have specific questions, feel free to ask. > > Best, > > Julian > > > On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett wrote: > ​Hello fieldtrippers, > > I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. > > Or should you do a PCA reduction of some description beforehand. > > I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. > > Im open to all suggestions. > > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Wed May 28 09:05:52 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Wed, 28 May 2014 07:05:52 +0000 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: <1401258209971.36904@flinders.edu.au> References: <1401169475061.32086@flinders.edu.au>, , <1401239195251.79033@flinders.edu.au>,<1401258209971.36904@flinders.edu.au> Message-ID: <1401260739200.88415@flinders.edu.au> I then do the following: % look up which virtual channels correspond to particular areas % of the brain cfg = []; cfg.atlas = afni; cfg.inputcoord = 'mni'; cfg.maskparameter = 'inside'; labels = ft_volumelookup( cfg, source); % how many sources found in grey matter [tmp ind] = sort(labels.count,1,'descend'); sel = find(tmp); for j = 1:length(sel) found_areas{j,1} = [num2str(labels.count(ind(j))) ': ' labels.name{ind(j)}]; end​ However I dont know how to find out what sources are the 'found_areas', after that I dont know how to cluster the source in a particular area. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Tyler Grummett Sent: Wednesday, 28 May 2014 3:53 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data Hello Julian, I think I got a few steps further into what I am trying to do, except I dont know whether I have done the correct thing or not, could you check it? % interpolate sources mri = ft_read_mri('Subject01.mri'); mri = ft_volumereslice([], mri); % read in atlas from fieldtrip template afni = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/afni/TTatlas+tlrc.HEAD')); % construct grid that lies only in grey matter cfg = []; cfg.mri = mri; cfg.grid.warpmni = 'yes'; cfg.grid = afni; grid = ft_prepare_sourcemodel( cfg); % Source Analysis: without contrasting condition cfg = []; cfg.channel = 'EEG'; cfg.method = 'lcmv'; cfg.grid = grid; cfg.vol = vol; cfg.keepfilter = 'yes'; source = ft_sourceanalysis( cfg, timelock); ​ Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Tyler Grummett Sent: Wednesday, 28 May 2014 10:36 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data ​Hey Julian, Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense. Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it? Regards, Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil Sent: Wednesday, 28 May 2014 1:55 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] granger causality on beamformer data Hi Tyler, I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 connections, so I hope you have a fast computer. As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website: http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). I hope that helps, if you have specific questions, feel free to ask. Best, Julian On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett > wrote: ​Hello fieldtrippers, I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. Or should you do a PCA reduction of some description beforehand. I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. Im open to all suggestions. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Wed May 28 10:00:49 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Wed, 28 May 2014 08:00:49 +0000 Subject: [FieldTrip] ft_volumelookup source reconstruction (?) Message-ID: <1401264036357.85337@flinders.edu.au> Hello fieldtrippers, I would like to know if it is possible to determine the sources that correspond to a brain region as found by ft_volumelookup. I have used the following code: % interpolate sources mri = ft_read_mri('Subject01.mri'); mri = ft_volumereslice([], mri); % read in atlas from fieldtrip template afni = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/afni/TTatlas+tlrc.HEAD')); % construct grid that lies only in grey matter cfg = []; cfg.mri = mri; cfg.grid.warpmni = 'yes'; cfg.grid = afni; grid = ft_prepare_sourcemodel( cfg);? % Source Analysis: without contrasting condition cfg = []; cfg.channel = 'EEG'; cfg.method = 'lcmv'; cfg.grid = grid; cfg.grid.outside = []; cfg.vol = vol; cfg.keepfilter = 'yes'; source = ft_sourceanalysis( cfg, timelock); source.pos = source.pos( source.inside( :), :); % look up which virtual channels correspond to particular areas % of the brain cfg = []; cfg.atlas = afni; cfg.inputcoord = 'mni'; cfg.maskparameter = 'inside'; labels = ft_volumelookup( cfg, source); It gives me a set of labels, but I dont know what sources are located in the brain regions found. I would like to somehow combine the sources in these brain regions, so that I am left with one source per brain region. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed May 28 10:13:03 2014 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 28 May 2014 10:13:03 +0200 Subject: [FieldTrip] granger causality on beamformer data In-Reply-To: <1401260739200.88415@flinders.edu.au> References: <1401169475061.32086@flinders.edu.au>, , <1401239195251.79033@flinders.edu.au>, <1401258209971.36904@flinders.edu.au> <1401260739200.88415@flinders.edu.au> Message-ID: Hi Tyler, sorry if my description was a bit brief, so here's a bit more information. You need: 1) Virtual Electrodes (you have your 1400 electrodes, so I assume you got that far) and the .pos field with the XYZ-coordinates of the virtual electrodes. 2) A grid with a grid point for each voxel of the MNI brain (That's what you do using ft_prepare_sourcemodel) 3) A "inside" definition for your VOI (That's what you do with ft_volumelookup). Now, given that your steps 1-3 all are in the same coordinate system, you can simply use pythagoras (s = sqrt((X2-X1)^2 + (Y2-Y1)^2 + (Z2-Z1)^2) to find the minimum distance between each virtual channels of step 1 and all grid points of step 2. From the min (find the minimum distance) step, you can get the index of closest virtual channel to each grid point. You then apply this index to the output of ft_volumelookup and you have the virtual electrodes inside your ROI. Best, Julian Am 28.05.2014 um 09:05 schrieb Tyler Grummett: > I then do the following: > > % look up which virtual channels correspond to particular areas > % of the brain > cfg = []; > cfg.atlas = afni; > cfg.inputcoord = 'mni'; > cfg.maskparameter = 'inside'; > labels = ft_volumelookup( cfg, source); > > % how many sources found in grey matter > [tmp ind] = sort(labels.count,1,'descend'); > sel = find(tmp); > for j = 1:length(sel) > found_areas{j,1} = [num2str(labels.count(ind(j))) ': ' labels.name{ind(j)}]; > end​ > > However I dont know how to find out what sources are the 'found_areas', after that I dont know how to cluster the source in a particular area. > > Tyler > > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > From: fieldtrip-bounces at science.ru.nl on behalf of Tyler Grummett > Sent: Wednesday, 28 May 2014 3:53 PM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] granger causality on beamformer data > > Hello Julian, > > I think I got a few steps further into what I am trying to do, except I dont know whether I have done the correct thing or not, could you check it? > > % interpolate sources > mri = ft_read_mri('Subject01.mri'); > mri = ft_volumereslice([], mri); > > % read in atlas from fieldtrip template > afni = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/afni/TTatlas+tlrc.HEAD')); > > % construct grid that lies only in grey matter > cfg = []; > cfg.mri = mri; > cfg.grid.warpmni = 'yes'; > cfg.grid = afni; > grid = ft_prepare_sourcemodel( cfg); > > % Source Analysis: without contrasting condition > cfg = []; > cfg.channel = 'EEG'; > cfg.method = 'lcmv'; > cfg.grid = grid; > cfg.vol = vol; > cfg.keepfilter = 'yes'; > source = ft_sourceanalysis( cfg, timelock); > ​ > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > From: fieldtrip-bounces at science.ru.nl on behalf of Tyler Grummett > Sent: Wednesday, 28 May 2014 10:36 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] granger causality on beamformer data > > ​Hey Julian, > > Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense. > > Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it? > > Regards, > > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil > Sent: Wednesday, 28 May 2014 1:55 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] granger causality on beamformer data > > Hi Tyler, > > I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400 > connections, so I hope you have a fast computer. > > As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website:http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html > > The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI. > > In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI). > > I hope that helps, if you have specific questions, feel free to ask. > > Best, > > Julian > > > On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett wrote: > ​Hello fieldtrippers, > > I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer. > > Or should you do a PCA reduction of some description beforehand. > > I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique. > > Im open to all suggestions. > > Tyler > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From elmeri.syrjanen at gmail.com Wed May 28 12:04:33 2014 From: elmeri.syrjanen at gmail.com (=?UTF-8?Q?Elmeri_Syrj=C3=A4nen?=) Date: Wed, 28 May 2014 12:04:33 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Dear Katrin, I have recently done exactly what you are asking for unfortunately I don't have access to my code right now but basically you can do it manually if you familiarize yourself with the structure how FieldTrip stores your data. The idea is to have two trial functions, one where you define only the baseline, and one without a baseline, I created a variable cfg.trigoffset where i set the time that you wan't to epoch before the trigger and then the rest of the trialfun is as normal. I then manually in Matlab join the baseline and button press preceding structures to a new data structure. Make sure that you remove the last column in data.time and data.trial in the baseline epoch. You may also wan't to create your own data.sampleinfo with "fake" sample points (1 641, 642 1282..) because some functions (ft_channelrepair) will use sampleinfo instead of fsample to calculate your sample rate which will give you head aches down the road. Best Regards Elmeri Syrjänen On Tue, May 27, 2014 at 11:39 PM, Max Cantor wrote: > I'm hesitant to say impossible, but I'm not sure how to do it off-hand. > Also, there may be some other complications, now that I think I understand > your situation better. > > If you're trying to cut based on the buttonpresses, which are > inconsistent/unreliable, any large number of trials would make it > impractical to define/redefine your epoch for each one, especially since > this process would need to be customized for each subject. It might be > better to keep it in a larger window, or come up with a few general windows > to encompass, for instance 'early', 'on target', and 'late' button press > windows. > > For all of the experiments I've worked on in which we've used / are using > fieldtrip for our data analysis pipeline, we've never used behavioral > responses for anything other than a control (as in, lack of response or > incorrect response leads to rejecting the trial), so I don't really know if > there is a particular systematic way to incorporate behavioral or floating > triggers like what you seem to be looking to do. > > I might suggest, though keep in mind this is entirely speculative, rather > than trying to create a pinpoint window around the response, that instead > you use a wide window, and then either by viewing the data, or perhaps > using independent component analysis, try to pinpoint for each subject when > the button press may have occurred based on some kind of muscle artifact, > and then in later timelock/time-frequency/statistical analyses specify that > time window. Again, that is just me spitballing, but something > post-processing may be a better solution, if the behavioral response is > pivotal to the analysis of your experiment and not just for making sure the > subject was paying attention / understands the prompt, as in the > experiments I've worked on. > > > On Tue, May 27, 2014 at 5:02 PM, KatrinH Heimann wrote: > >> Hi! Guys, your help is so much appreciated! >> So I try to be more clear!: >> So, yeah, Max, you are right! At the end I would like to use two >> different triggervalues. >> >> If I would use twice ft_definetrial then it would look like this: >> >> cfg = []; >> >> cfg.dataset = '1.raw'; >> >> cfg.trialfun = 'ft_trialfun_general'; >> >> cfg.trialdef.eventtype = 'trigger'; >> >> cfg.trialdef.eventvalue = 'stim'; % the value of the stimulus trigger for >> the beginning of baseline >> >> cfg.trialdef.prestim = 0.5; %the time of the fixation cross >> >> cfg.trialdef.poststim = 1.5; %the time of the baseline (plus 0.5 >> buffer) >> >> cfg = ft_redefinetrial(cfg); >> >> >> This baselinedata I could easily baselinecorrect using 100 ms of the >> fixationcrossperiod: >> >> >> cfg.channel = 'all'; >> >> cfg.preproc.demean = 'yes'; >> >> cfg.preproc.baselinewindow = [-0.1 0] >> >> cfg.preproc.bpfilter = 'yes'; >> >> cfg.preproc.bpfreq = [6 32]; >> >> >> The stimulusdata would be defined using a trigger that corresponds to a >> button press: >> >> >> cfg = []; >> >> cfg.dataset = '1.raw'; >> >> cfg.trialfun = 'ft_trialfun_general'; >> >> cfg.trialdef.eventtype = 'trigger'; >> >> cfg.trialdef.eventvalue = 'resp'; % the value of the stimulus trigger for >> the beginning of baseline >> >> cfg.trialdef.prestim = 0.5; % 0.5 sec before button press >> >> cfg.trialdef.poststim = 1.5; % 1.5 sec after button press (time that I >> wanna analyse) >> >> cfg = ft_redefinetrial(cfg); >> >> >> However here I have the problem that I cannot correct with the same >> baseline than before as the buttonpress is not always at the same time so I >> don't know when the fixationcrossperiod is located... >> >> >> So I thought I could first "cut" bigger pieces and then redefine trials >> by cutting again (after the preprocessing), then with different eventvalues >> ... >> >> But you say that is not possible? >> >> >> >> Thanks a lot for your help!!! >> >> >> Katrin >> >> >> >> 2014-05-27 21:05 GMT+02:00 Max Cantor : >> >> Ya, it would definitely help if we could see your code, but I might have >>> another idea. >>> >>> When you say you have a fixation cross trigger, is this trigger being >>> recorded from your EEG recording equipment in such a way that it can be >>> represented as an event value in cfg.trialdef for ft_definetrial? If so, I >>> think you may be right that it can't be changed through ft_redefinetrial >>> (at least, as far as I can tell, no mention of this is made in the help >>> section of the function). That being said, if you run ft_definetrial >>> separately for both event values that should work. >>> >>> That being said, I may still be slightly confused about what you mean >>> when you say you want to change the trigger. Do you mean you want to create >>> a new trigger for your data off-line? I think it may be possible to create >>> custom triggers off-line through fieldtrip, but it's not something I've >>> tried personally, but if that is what you are trying to do, I could look >>> into it. >>> >>> >>> On Tue, May 27, 2014 at 2:44 PM, kousik sarathy >> > wrote: >>> >>>> Hey Katrin, >>>> >>>> It seems to me that Max's suggestion would suffice. But you seem to be >>>> looking for something else. Could you elaborate a little bit as to what you >>>> need? >>>> >>>> -- >>>> Regards, >>>> Kousik Sarathy, S >>>> >>>> >>>> >>>> On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann < >>>> katrinheimann at gmail.com> wrote: >>>> >>>>> Dear Max, thanks a lot for your prompt answer. Unfortunately this is >>>>> not what I am looking for (I found an example like this in the tutorial). I >>>>> would like to change the trigger for one of the two conditions, let it be >>>>> now the response of the subject, as this is where the stimulus actually >>>>> starts... Defining two different timewindows is not enough... Can you also >>>>> help me with that? Thanks a million! Katrin >>>>> >>>>> >>>>> 2014-05-27 18:58 GMT+02:00 Max Cantor : >>>>> >>>>> Hi Katrin, >>>>>> >>>>>> It may help to see your code, but hopefully this will help. It should >>>>>> be as simple as taking your epoched data from ft_definetrial and >>>>>> ft_preprocessing, then creating two configurations for your timewindows and >>>>>> running ft_redefinetrial. >>>>>> >>>>>> For example (from the fieldtrip tutorial, slightly simplified by me >>>>>> for explanatory purposes): >>>>>> >>>>>> *** >>>>>> >>>>>> % find the interesting segments of data >>>>>> >>>>>> cfg = []; >>>>>> % empty configuration >>>>>> cfg.dataset = 'Subject01.ds'; >>>>>> % name of CTF dataset >>>>>> cfg.trialdef.eventtype = 'backpanel trigger'; >>>>>> cfg.trialdef.prestim = 1; >>>>>> cfg.trialdef.poststim = 2; >>>>>> cfg.trialdef.eventvalue = 3; >>>>>> % event value of FIC >>>>>> cfg = ft_definetrial(cfg); >>>>>> >>>>>> % preprocess the data >>>>>> >>>>>> cfg.channel = {'MEG'}; >>>>>> dataFIC = ft_preprocessing(cfg); >>>>>> >>>>>> % define time window >>>>>> >>>>>> cfg = []; >>>>>> >>>>>> cfg.toilim = [-0.5 0]; >>>>>> dataPre = ft_redefinetrial(cfg, dataFIC); >>>>>> >>>>>> cfg.toilim = [0.8 1.3]; >>>>>> dataPost = ft_redefinetrial(cfg, dataFIC); >>>>>> >>>>>> *** >>>>>> >>>>>> So if your code resembles this, you are defining in >>>>>> cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that >>>>>> encompasses both your baseline period and stimulus period, then for >>>>>> cfg.toilim in the ft_redefinetrial section you are setting one to your >>>>>> baseline period and the other to your stimulus period, and outputting them >>>>>> into separate variables. >>>>>> >>>>>> Hopefully this helps. Also, if you haven't done so already, I would >>>>>> strongly recommend you run through the tutorial, as it may help answer >>>>>> questions like this in the future (assuming I've properly identified the >>>>>> issue). >>>>>> >>>>>> Good luck, >>>>>> >>>>>> Max >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >>>>>> katrinheimann at gmail.com> wrote: >>>>>> >>>>>>> Dear all, >>>>>>> >>>>>>> my name is Katrin Heimann, I am phd student at the University of >>>>>>> Parma. New to Fieldtrip. >>>>>>> I am doing an EEG analysis, still in the preprocessing phase. >>>>>>> It is a within trials design. I would like to compare a baseline >>>>>>> period with an experimental condition (visual stimulus). >>>>>>> >>>>>>> I have a trigger after a fixation cross, then a baseline period >>>>>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a >>>>>>> bottom press (trigger)). >>>>>>> >>>>>>> As I would like to apply the same baseline correction for both (the >>>>>>> fixationcross period) I planned to first define my trials as long trials >>>>>>> including the timewindows of baseline and the stimulus period, applying >>>>>>> filter and baselinecorrection on those long pieces. However, as I do not >>>>>>> wanna do the artifact detection on the whole pieces (but seperately for >>>>>>> baseline and stimulus, to avoid that I have to throw away too many trials) >>>>>>> I would like to redefine my trials then, cutting out only baseline period >>>>>>> and only stimulus period (starting with another trigger >>>>>>> (triggervalue=resp).. >>>>>>> >>>>>>> *Unfortunately I do not understand how I can change the trigger used >>>>>>> with ft redefine trial. * >>>>>>> >>>>>>> Anybody who could give me an example how that is done? >>>>>>> Thanks a million >>>>>>> Katrin >>>>>>> >>>>>>> _______________________________________________ >>>>>>> fieldtrip mailing list >>>>>>> fieldtrip at donders.ru.nl >>>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Max Cantor >>>>>> Research Assistant >>>>>> Computational Neurolinguistics Lab >>>>>> University of Michigan >>>>>> >>>>>> _______________________________________________ >>>>>> fieldtrip mailing list >>>>>> fieldtrip at donders.ru.nl >>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>> >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> Max Cantor >>> Research Assistant >>> Computational Neurolinguistics Lab >>> University of Michigan >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Max Cantor > Research Assistant > Computational Neurolinguistics Lab > University of Michigan > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Wed May 28 12:09:00 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Wed, 28 May 2014 12:09:00 +0200 Subject: [FieldTrip] ft redefine trials: how to change trigger? In-Reply-To: References: Message-ID: Dear Max, dear Elmeri! Thanks a million, that was really really helpful! :) Katrin 2014-05-28 12:04 GMT+02:00 Elmeri Syrjänen : > Dear Katrin, > > I have recently done exactly what you are asking for unfortunately I don't > have access to my code right now but basically you can do it manually if > you familiarize yourself with the structure how FieldTrip stores your data. > The idea is to have two trial functions, one where you define only the > baseline, and one without a baseline, I created a variable cfg.trigoffset > where i set the time that you wan't to epoch before the trigger and then > the rest of the trialfun is as normal. > > I then manually in Matlab join the baseline and button press preceding > structures to a new data structure. Make sure that you remove the last > column in data.time and data.trial in the baseline epoch. You may also > wan't to create your own data.sampleinfo with "fake" sample points (1 641, > 642 1282..) because some functions (ft_channelrepair) will use sampleinfo > instead of fsample to calculate your sample rate which will give you head > aches down the road. > > Best Regards > Elmeri Syrjänen > > > On Tue, May 27, 2014 at 11:39 PM, Max Cantor wrote: > >> I'm hesitant to say impossible, but I'm not sure how to do it off-hand. >> Also, there may be some other complications, now that I think I understand >> your situation better. >> >> If you're trying to cut based on the buttonpresses, which are >> inconsistent/unreliable, any large number of trials would make it >> impractical to define/redefine your epoch for each one, especially since >> this process would need to be customized for each subject. It might be >> better to keep it in a larger window, or come up with a few general windows >> to encompass, for instance 'early', 'on target', and 'late' button press >> windows. >> >> For all of the experiments I've worked on in which we've used / are using >> fieldtrip for our data analysis pipeline, we've never used behavioral >> responses for anything other than a control (as in, lack of response or >> incorrect response leads to rejecting the trial), so I don't really know if >> there is a particular systematic way to incorporate behavioral or floating >> triggers like what you seem to be looking to do. >> >> I might suggest, though keep in mind this is entirely speculative, rather >> than trying to create a pinpoint window around the response, that instead >> you use a wide window, and then either by viewing the data, or perhaps >> using independent component analysis, try to pinpoint for each subject when >> the button press may have occurred based on some kind of muscle artifact, >> and then in later timelock/time-frequency/statistical analyses specify that >> time window. Again, that is just me spitballing, but something >> post-processing may be a better solution, if the behavioral response is >> pivotal to the analysis of your experiment and not just for making sure the >> subject was paying attention / understands the prompt, as in the >> experiments I've worked on. >> >> >> On Tue, May 27, 2014 at 5:02 PM, KatrinH Heimann > > wrote: >> >>> Hi! Guys, your help is so much appreciated! >>> So I try to be more clear!: >>> So, yeah, Max, you are right! At the end I would like to use two >>> different triggervalues. >>> >>> If I would use twice ft_definetrial then it would look like this: >>> >>> cfg = []; >>> >>> cfg.dataset = '1.raw'; >>> >>> cfg.trialfun = 'ft_trialfun_general'; >>> >>> cfg.trialdef.eventtype = 'trigger'; >>> >>> cfg.trialdef.eventvalue = 'stim'; % the value of the stimulus trigger for >>> the beginning of baseline >>> >>> cfg.trialdef.prestim = 0.5; %the time of the fixation cross >>> >>> cfg.trialdef.poststim = 1.5; %the time of the baseline (plus 0.5 >>> buffer) >>> >>> cfg = ft_redefinetrial(cfg); >>> >>> >>> This baselinedata I could easily baselinecorrect using 100 ms of the >>> fixationcrossperiod: >>> >>> >>> cfg.channel = 'all'; >>> >>> cfg.preproc.demean = 'yes'; >>> >>> cfg.preproc.baselinewindow = [-0.1 0] >>> >>> cfg.preproc.bpfilter = 'yes'; >>> >>> cfg.preproc.bpfreq = [6 32]; >>> >>> >>> The stimulusdata would be defined using a trigger that corresponds to a >>> button press: >>> >>> >>> cfg = []; >>> >>> cfg.dataset = '1.raw'; >>> >>> cfg.trialfun = 'ft_trialfun_general'; >>> >>> cfg.trialdef.eventtype = 'trigger'; >>> >>> cfg.trialdef.eventvalue = 'resp'; % the value of the stimulus trigger for >>> the beginning of baseline >>> >>> cfg.trialdef.prestim = 0.5; % 0.5 sec before button press >>> >>> cfg.trialdef.poststim = 1.5; % 1.5 sec after button press (time that >>> I wanna analyse) >>> >>> cfg = ft_redefinetrial(cfg); >>> >>> >>> However here I have the problem that I cannot correct with the same >>> baseline than before as the buttonpress is not always at the same time so I >>> don't know when the fixationcrossperiod is located... >>> >>> >>> So I thought I could first "cut" bigger pieces and then redefine trials >>> by cutting again (after the preprocessing), then with different eventvalues >>> ... >>> >>> But you say that is not possible? >>> >>> >>> >>> Thanks a lot for your help!!! >>> >>> >>> Katrin >>> >>> >>> >>> 2014-05-27 21:05 GMT+02:00 Max Cantor : >>> >>> Ya, it would definitely help if we could see your code, but I might have >>>> another idea. >>>> >>>> When you say you have a fixation cross trigger, is this trigger being >>>> recorded from your EEG recording equipment in such a way that it can be >>>> represented as an event value in cfg.trialdef for ft_definetrial? If so, I >>>> think you may be right that it can't be changed through ft_redefinetrial >>>> (at least, as far as I can tell, no mention of this is made in the help >>>> section of the function). That being said, if you run ft_definetrial >>>> separately for both event values that should work. >>>> >>>> That being said, I may still be slightly confused about what you mean >>>> when you say you want to change the trigger. Do you mean you want to create >>>> a new trigger for your data off-line? I think it may be possible to create >>>> custom triggers off-line through fieldtrip, but it's not something I've >>>> tried personally, but if that is what you are trying to do, I could look >>>> into it. >>>> >>>> >>>> On Tue, May 27, 2014 at 2:44 PM, kousik sarathy < >>>> sarathykousik at gmail.com> wrote: >>>> >>>>> Hey Katrin, >>>>> >>>>> It seems to me that Max's suggestion would suffice. But you seem to be >>>>> looking for something else. Could you elaborate a little bit as to what you >>>>> need? >>>>> >>>>> -- >>>>> Regards, >>>>> Kousik Sarathy, S >>>>> >>>>> >>>>> >>>>> On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann < >>>>> katrinheimann at gmail.com> wrote: >>>>> >>>>>> Dear Max, thanks a lot for your prompt answer. Unfortunately this is >>>>>> not what I am looking for (I found an example like this in the tutorial). I >>>>>> would like to change the trigger for one of the two conditions, let it be >>>>>> now the response of the subject, as this is where the stimulus actually >>>>>> starts... Defining two different timewindows is not enough... Can you also >>>>>> help me with that? Thanks a million! Katrin >>>>>> >>>>>> >>>>>> 2014-05-27 18:58 GMT+02:00 Max Cantor : >>>>>> >>>>>> Hi Katrin, >>>>>>> >>>>>>> It may help to see your code, but hopefully this will help. It >>>>>>> should be as simple as taking your epoched data from ft_definetrial and >>>>>>> ft_preprocessing, then creating two configurations for your timewindows and >>>>>>> running ft_redefinetrial. >>>>>>> >>>>>>> For example (from the fieldtrip tutorial, slightly simplified by me >>>>>>> for explanatory purposes): >>>>>>> >>>>>>> *** >>>>>>> >>>>>>> % find the interesting segments of data >>>>>>> >>>>>>> cfg = []; >>>>>>> % empty configuration >>>>>>> cfg.dataset = 'Subject01.ds'; >>>>>>> % name of CTF dataset >>>>>>> cfg.trialdef.eventtype = 'backpanel trigger'; >>>>>>> cfg.trialdef.prestim = 1; >>>>>>> cfg.trialdef.poststim = 2; >>>>>>> cfg.trialdef.eventvalue = 3; >>>>>>> % event value of FIC >>>>>>> cfg = ft_definetrial(cfg); >>>>>>> >>>>>>> % preprocess the data >>>>>>> >>>>>>> cfg.channel = {'MEG'}; >>>>>>> dataFIC = ft_preprocessing(cfg); >>>>>>> >>>>>>> % define time window >>>>>>> >>>>>>> cfg = []; >>>>>>> >>>>>>> cfg.toilim = [-0.5 0]; >>>>>>> dataPre = ft_redefinetrial(cfg, dataFIC); >>>>>>> >>>>>>> cfg.toilim = [0.8 1.3]; >>>>>>> dataPost = ft_redefinetrial(cfg, dataFIC); >>>>>>> >>>>>>> *** >>>>>>> >>>>>>> So if your code resembles this, you are defining in >>>>>>> cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that >>>>>>> encompasses both your baseline period and stimulus period, then for >>>>>>> cfg.toilim in the ft_redefinetrial section you are setting one to your >>>>>>> baseline period and the other to your stimulus period, and outputting them >>>>>>> into separate variables. >>>>>>> >>>>>>> Hopefully this helps. Also, if you haven't done so already, I would >>>>>>> strongly recommend you run through the tutorial, as it may help answer >>>>>>> questions like this in the future (assuming I've properly identified the >>>>>>> issue). >>>>>>> >>>>>>> Good luck, >>>>>>> >>>>>>> Max >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann < >>>>>>> katrinheimann at gmail.com> wrote: >>>>>>> >>>>>>>> Dear all, >>>>>>>> >>>>>>>> my name is Katrin Heimann, I am phd student at the University of >>>>>>>> Parma. New to Fieldtrip. >>>>>>>> I am doing an EEG analysis, still in the preprocessing phase. >>>>>>>> It is a within trials design. I would like to compare a baseline >>>>>>>> period with an experimental condition (visual stimulus). >>>>>>>> >>>>>>>> I have a trigger after a fixation cross, then a baseline period >>>>>>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a >>>>>>>> bottom press (trigger)). >>>>>>>> >>>>>>>> As I would like to apply the same baseline correction for both >>>>>>>> (the fixationcross period) I planned to first define my trials as long >>>>>>>> trials including the timewindows of baseline and the stimulus period, >>>>>>>> applying filter and baselinecorrection on those long pieces. However, as I >>>>>>>> do not wanna do the artifact detection on the whole pieces (but seperately >>>>>>>> for baseline and stimulus, to avoid that I have to throw away too many >>>>>>>> trials) I would like to redefine my trials then, cutting out only baseline >>>>>>>> period and only stimulus period (starting with another trigger >>>>>>>> (triggervalue=resp).. >>>>>>>> >>>>>>>> *Unfortunately I do not understand how I can change the trigger >>>>>>>> used with ft redefine trial. * >>>>>>>> >>>>>>>> Anybody who could give me an example how that is done? >>>>>>>> Thanks a million >>>>>>>> Katrin >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> fieldtrip mailing list >>>>>>>> fieldtrip at donders.ru.nl >>>>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Max Cantor >>>>>>> Research Assistant >>>>>>> Computational Neurolinguistics Lab >>>>>>> University of Michigan >>>>>>> >>>>>>> _______________________________________________ >>>>>>> fieldtrip mailing list >>>>>>> fieldtrip at donders.ru.nl >>>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> fieldtrip mailing list >>>>>> fieldtrip at donders.ru.nl >>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>> >>>> >>>> >>>> >>>> -- >>>> Max Cantor >>>> Research Assistant >>>> Computational Neurolinguistics Lab >>>> University of Michigan >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Max Cantor >> Research Assistant >> Computational Neurolinguistics Lab >> University of Michigan >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed May 28 12:36:15 2014 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 28 May 2014 12:36:15 +0200 Subject: [FieldTrip] TF transform, data length + padding In-Reply-To: References: Message-ID: Hi Ulrich, one possible explanation for this could be the subtraction of the mean when calling ft_freqanalysis. If you don't specify cfg.polyremoval explicitly, the mean is removed. Of course, changing the time-dimension will change the mean and therefore result in a different value used in the ft_preproc_polyremoval - step. I tried this with a dataset, setting cfg.polyremoval to -1, thereby avoiding the demean results in virtually identical time-freq results for a short (800ms) or long (1000ms) interval. However, setting cfg.polyremoval to 0 (the default) will change the output. Also, setting the padding to 5, as you did in your code, will increase the frequency resolution which again might influence the way the low frequencies contribute to your output. If someone has a more in-depth explanation or if I got this completely wrong, please correct me! Best, Julian ******************** *Dr. Julian Keil* AG Multisensorische Integration Psychiatrische Universitätsklinik der Charité im St. Hedwig-Krankenhaus Große Hamburger Straße 5-11, Raum E 307 10115 Berlin Telefon: +49-30-2311-1879 Fax: +49-30-2311-2209 http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration On Tue, May 27, 2014 at 3:18 PM, Pomper, Ulrich wrote: > Dear community, > I have a question regarding time-frequency transformation. > The data I want to analyse last from -800 to -200 ms before stimulus > onset, I'm using a 400 ms taper. > Importantly, want to make sure that no stimulus-evoked activity leaks into > my prestim analysis. > > I first tried to cut the segment down to -1000 to 0 ms and used (zero) > padding (see figure attached, top row). This would mean that the taper, at > the last samplepoint of interest (-200ms), would include data up to 0ms > Suprisingly, I get quite different looking results when using a longer > data segment (-1200 to 0 ms) (fig. bottom row) without padding. > > Can someone explain to me what is going on here, and which approach would > be more correct? > Either, the padding in the first variant introduces artificial low > frequency activity, or the taper in the second variant uses more than > 400ms, at least for the low frequencies. > Note that the difference between conditions (left coloumn) look almost > identical, so whatever happens, it happens to both conditions very > similarly. > > I hope someone can educate me on that matter. > Cheers, Ulrich > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %% TF transform %% > > cfg = []; > cfg.continuous = 'no'; > cfg.channel = 'all'; > cfg.output = 'pow'; > cfg.method = 'mtmconvol'; > cfg.foi = 2:0.5:35; > cfg.toi = -1:0.01:0; > cfg.taper = 'hanning'; > cfg.tapsmofrq = 2; > cfg.t_ftimwin = 400 > % cfg.pad = 5; > ... > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: poly_vs_nopoly.png Type: image/png Size: 32330 bytes Desc: not available URL: From Ulrich.Pomper at charite.de Wed May 28 12:50:31 2014 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Wed, 28 May 2014 12:50:31 +0200 Subject: [FieldTrip] TF transform, data length + padding In-Reply-To: References: , Message-ID: Hey Julian, Thanks a lot for your help! Both explanations seem quite plausible. I think I will try to avoid the padding and stick with the longer data segments. Cheers, Ulrich ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] On Behalf Of Julian Keil [julian.keil at gmail.com] Sent: Wednesday, May 28, 2014 12:36 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] TF transform, data length + padding Hi Ulrich, one possible explanation for this could be the subtraction of the mean when calling ft_freqanalysis. If you don't specify cfg.polyremoval explicitly, the mean is removed. Of course, changing the time-dimension will change the mean and therefore result in a different value used in the ft_preproc_polyremoval - step. I tried this with a dataset, setting cfg.polyremoval to -1, thereby avoiding the demean results in virtually identical time-freq results for a short (800ms) or long (1000ms) interval. However, setting cfg.polyremoval to 0 (the default) will change the output. Also, setting the padding to 5, as you did in your code, will increase the frequency resolution which again might influence the way the low frequencies contribute to your output. If someone has a more in-depth explanation or if I got this completely wrong, please correct me! Best, Julian ******************** Dr. Julian Keil AG Multisensorische Integration Psychiatrische Universitätsklinik der Charité im St. Hedwig-Krankenhaus Große Hamburger Straße 5-11, Raum E 307 10115 Berlin Telefon: +49-30-2311-1879 Fax: +49-30-2311-2209 http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration On Tue, May 27, 2014 at 3:18 PM, Pomper, Ulrich > wrote: Dear community, I have a question regarding time-frequency transformation. The data I want to analyse last from -800 to -200 ms before stimulus onset, I'm using a 400 ms taper. Importantly, want to make sure that no stimulus-evoked activity leaks into my prestim analysis. I first tried to cut the segment down to -1000 to 0 ms and used (zero) padding (see figure attached, top row). This would mean that the taper, at the last samplepoint of interest (-200ms), would include data up to 0ms Suprisingly, I get quite different looking results when using a longer data segment (-1200 to 0 ms) (fig. bottom row) without padding. Can someone explain to me what is going on here, and which approach would be more correct? Either, the padding in the first variant introduces artificial low frequency activity, or the taper in the second variant uses more than 400ms, at least for the low frequencies. Note that the difference between conditions (left coloumn) look almost identical, so whatever happens, it happens to both conditions very similarly. I hope someone can educate me on that matter. Cheers, Ulrich %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% TF transform %% cfg = []; cfg.continuous = 'no'; cfg.channel = 'all'; cfg.output = 'pow'; cfg.method = 'mtmconvol'; cfg.foi = 2:0.5:35; cfg.toi = -1:0.01:0; cfg.taper = 'hanning'; cfg.tapsmofrq = 2; cfg.t_ftimwin = 400 % cfg.pad = 5; ... _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From katrinheimann at gmail.com Wed May 28 12:59:38 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Wed, 28 May 2014 12:59:38 +0200 Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? Message-ID: Dear all, another question: Is it possible to visualize the Activity power spectrum of the single components after an ICA by using ft_databrowser (or something else). I like this feature from EEG lab as I find it easier to detect artifactual components. Thanks a lot for your help Katrin -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.lozanosoldevilla at fcdonders.ru.nl Wed May 28 14:24:06 2014 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Wed, 28 May 2014 14:24:06 +0200 (CEST) Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? In-Reply-To: Message-ID: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> Hi Katrin, First, to display the independent components: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% cfg = []; cfg.layout = 'CTF151.lay'; % specify the layout file that should be used for plotting cfg.viewmode = 'component' ft_databrowser(cfg, comp) Take a look to the following example script: http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts Second, you'll have to compute the power spectrum for each independent component with ft_freqanalaysis: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% cfg = []; cfg.output = 'pow'; cfg.channel = 'all';%compute the power spectrum in all ICs cfg.method = 'mtmfft'; cfg.taper = 'hanning'; cfg.foi = 2:2:30; freq = ft_freqanalysis(cfg, comp); And you can plot the spectra: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% nsubplots = 25; nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals, type doc subplot Nfigs = ceil(size(comp.topo,1)/nsubplots); tot = Nfigs*nsubplots; rptvect = 1:size(comp.topo,1); rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post'); rptvect = reshape(rptvect,nsubplots,Nfigs)'; for r=1:size(rptvect,1); figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full screen k=0; for j=1:size(rptvect,2); if~(rptvect(r,j)==0); k=k+1; cfg=[]; cfg.channel = rptvect(r,j); subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq); end end end For the IC topos you'll follow the same logic as above but with: figure cfg = []; cfg.component = [1:20]; % specify the component(s) that should be plotted cfg.layout = 'GSN-HydroCel-129.sfp'; cfg.comment = 'no'; ft_topoplotIC(cfg, comp) I hope it helps Diego ----- Original Message ----- > From: "KatrinH Heimann" > To: "FieldTrip discussion list" > Sent: Wednesday, 28 May, 2014 12:59:38 PM > Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of > single components? > Dear all, > another question: > Is it possible to visualize the Activity power spectrum of the single > components after an ICA by using ft_databrowser (or something else). I > like this feature from EEG lab as I find it easier to detect > artifactual components. > Thanks a lot for your help > Katrin > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- PhD Student Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen NL-6525 EN Nijmegen The Netherlands http://www.ru.nl/people/donders/lozano-soldevilla-d/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Wed May 28 15:02:23 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Wed, 28 May 2014 15:02:23 +0200 Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? In-Reply-To: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> References: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Wonderfull! Thanks Diego!!!! Cheers k 2014-05-28 14:24 GMT+02:00 Lozano Soldevilla, D. (Diego) < d.lozanosoldevilla at fcdonders.ru.nl>: > Hi Katrin, > > First, to display the independent components: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > cfg = []; > cfg.layout = 'CTF151.lay'; % specify the layout file that should be used > for plotting > cfg.viewmode = 'component' > ft_databrowser(cfg, comp) > > Take a look to the following example script: > > http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts > > Second, you'll have to compute the power spectrum for each independent > component with ft_freqanalaysis: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'all';%compute the power spectrum in all ICs > cfg.method = 'mtmfft'; > cfg.taper = 'hanning'; > cfg.foi = 2:2:30; > freq = ft_freqanalysis(cfg, comp); > > And you can plot the spectra: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > nsubplots = 25; > nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals, type > doc subplot > > Nfigs = ceil(size(comp.topo,1)/nsubplots); > tot = Nfigs*nsubplots; > > rptvect = 1:size(comp.topo,1); > rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post'); > rptvect = reshape(rptvect,nsubplots,Nfigs)'; > > for r=1:size(rptvect,1); > figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full > screen > k=0; > for j=1:size(rptvect,2); > if~(rptvect(r,j)==0); > k=k+1; > cfg=[]; > cfg.channel = rptvect(r,j); > subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq); > end > end > end > > For the IC topos you'll follow the same logic as above but with: > > figure > cfg = []; > cfg.component = [1:20]; % specify the component(s) that should be > plotted > cfg.layout = 'GSN-HydroCel-129.sfp'; > cfg.comment = 'no'; > ft_topoplotIC(cfg, comp) > > I hope it helps > > Diego > ------------------------------ > > *From: *"KatrinH Heimann" > *To: *"FieldTrip discussion list" > *Sent: *Wednesday, 28 May, 2014 12:59:38 PM > *Subject: *[FieldTrip] ICA - Can I visualize Activity power spectrum of > single components? > > > Dear all, > another question: > Is it possible to visualize the Activity power spectrum of the single > components after an ICA by using ft_databrowser (or something else). I like > this feature from EEG lab as I find it easier to detect artifactual > components. > Thanks a lot for your help > Katrin > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > PhD Student > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > NL-6525 EN Nijmegen > The Netherlands > http://www.ru.nl/people/donders/lozano-soldevilla-d/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Wed May 28 15:54:24 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Wed, 28 May 2014 15:54:24 +0200 Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? In-Reply-To: References: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Diego, can I ask you another advice- this time more conceptually? I am playing with the ICA now and experience, that I get very different components depending on the artifact detection that I do beforehand. So my idea (due to the literature) was, that the ICA works better on already cleaned data. Now, as I want to do a frequency analysis afterwards, I did not want to reject parts of trials. Therefore I deleted a relatively big amount of trials in which I found muscle artifacts/drifts (Say 25% of the whole amount of trials). However, in fact I see that the ICA then does not give me easily to interpret components anymore - actually the results are better (that is easier to interpret which is artifact, which not) if I include all trials. If I only reject parts of the trials it gets even a bit better. So my question is: Shell I a) do the (stricter) artifact detection rather after the ICA or b) perform it on data with parts of trials marked as bad - in which case I also ask: can I then still reject those components in the uncleaned data (saved beforehand) so that I do not get problems with the frequency analysis afterwards...?! Thanks a lot for your help!!! Katrin 2014-05-28 15:02 GMT+02:00 KatrinH Heimann : > Wonderfull! Thanks Diego!!!! > Cheers k > > > 2014-05-28 14:24 GMT+02:00 Lozano Soldevilla, D. (Diego) < > d.lozanosoldevilla at fcdonders.ru.nl>: > > Hi Katrin, >> >> First, to display the independent components: >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> cfg = []; >> cfg.layout = 'CTF151.lay'; % specify the layout file that should be used >> for plotting >> cfg.viewmode = 'component' >> ft_databrowser(cfg, comp) >> >> Take a look to the following example script: >> >> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts >> >> Second, you'll have to compute the power spectrum for each independent >> component with ft_freqanalaysis: >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> cfg = []; >> cfg.output = 'pow'; >> cfg.channel = 'all';%compute the power spectrum in all ICs >> cfg.method = 'mtmfft'; >> cfg.taper = 'hanning'; >> cfg.foi = 2:2:30; >> freq = ft_freqanalysis(cfg, comp); >> >> And you can plot the spectra: >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> nsubplots = 25; >> nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals, >> type doc subplot >> >> Nfigs = ceil(size(comp.topo,1)/nsubplots); >> tot = Nfigs*nsubplots; >> >> rptvect = 1:size(comp.topo,1); >> rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post'); >> rptvect = reshape(rptvect,nsubplots,Nfigs)'; >> >> for r=1:size(rptvect,1); >> figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full >> screen >> k=0; >> for j=1:size(rptvect,2); >> if~(rptvect(r,j)==0); >> k=k+1; >> cfg=[]; >> cfg.channel = rptvect(r,j); >> subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq); >> end >> end >> end >> >> For the IC topos you'll follow the same logic as above but with: >> >> figure >> cfg = []; >> cfg.component = [1:20]; % specify the component(s) that should be >> plotted >> cfg.layout = 'GSN-HydroCel-129.sfp'; >> cfg.comment = 'no'; >> ft_topoplotIC(cfg, comp) >> >> I hope it helps >> >> Diego >> ------------------------------ >> >> *From: *"KatrinH Heimann" >> *To: *"FieldTrip discussion list" >> *Sent: *Wednesday, 28 May, 2014 12:59:38 PM >> *Subject: *[FieldTrip] ICA - Can I visualize Activity power spectrum of >> single components? >> >> >> Dear all, >> another question: >> Is it possible to visualize the Activity power spectrum of the single >> components after an ICA by using ft_databrowser (or something else). I like >> this feature from EEG lab as I find it easier to detect artifactual >> components. >> Thanks a lot for your help >> Katrin >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -- >> PhD Student >> Neuronal Oscillations Group >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> NL-6525 EN Nijmegen >> The Netherlands >> http://www.ru.nl/people/donders/lozano-soldevilla-d/ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Laura.Rueda at faber.kuleuven.be Wed May 28 16:29:08 2014 From: Laura.Rueda at faber.kuleuven.be (Laura Rueda Delgado) Date: Wed, 28 May 2014 14:29:08 +0000 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS Message-ID: Dear Fieldtrip users, I'm following the tutorial of beamformers (Source Analysis: Contrast activity to another interval) to estimate oscillatory sources using DICS. I've checked the surface created after segmentation and the grid generated from the electrode positions and the headmodel. That seems to work ok. However, at the step of source analysis, I get the following error: Error using * Inner matrix dimensions must agree. Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Does anybody have an idea of what I'm doing wrong? Thank you in advance for any help or suggestion! ----------------------------------------------------------------- This is my code: %% 1 - Preparation of MRI- source space % Read MRI mrifile = 'Subject01\Subject01.mri'; mri = ft_read_mri(mrifile); % Reslice to reorient images cfg = []; cfg.dim = [256 256 256]; mri = ft_volumereslice(cfg,mri); % Segment compartments cfg = []; cfg.output = {'brain','skull','scalp'}; segmentedmri = ft_volumesegment(cfg, mri); % Prepare mesh cfg=[]; cfg.tissue={'brain', 'skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); % Prepare headmodel cfg = []; cfg.method ='bemcp'; vol = ft_prepare_headmodel(cfg, bnd); %% 2- Prepare leadfield - Creating grid load elec_aligned2 % Obtained after adjusting electrodes on scalp surface interactively % Three fiducial markers were added to the electrode file, and now they're % removed so that the electrode structure has the same number of channels as the data elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); elec_aligned2.label = elec_aligned2.label(1:128, :); cfg =[]; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.grid.resolution = 10; cfg.grid.unit = 'mm'; [grid] = ft_prepare_leadfield(cfg); %% 3- Join rest and task data % data_rs: resting state data % data4: data during task dataAll = ft_appenddata([], data_rs, data4); cfg = []; cfg.method = 'mtmfft'; cfg.output = 'powandcsd'; cfg.tapsmofrq = 4; cfg.foilim = [18 18]; freqAll = ft_freqanalysis(cfg, dataAll); %---------------------------------- % all seems normal until here %---------------------------------- %% 4- Estimate source of all data cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAll = ft_sourceanalysis(cfg, freqAll); Cheers, Laura Rueda Delgado -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at gmail.com Wed May 28 16:41:54 2014 From: johanna.zumer at gmail.com (Johanna Zumer) Date: Wed, 28 May 2014 15:41:54 +0100 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Hi Laura, Does your data have the same channels as the leadfield (as the electrodes that went in to compute the leadfield)? I often see that error when there is a mismatch of channels in that way. Best, Johanna 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado < Laura.Rueda at faber.kuleuven.be>: > Dear Fieldtrip users, > > > > I’m following the tutorial of beamformers (Source Analysis: Contrast > activity to another interval) > to estimate oscillatory sources using DICS. I’ve checked the surface > created after segmentation and the grid generated from the electrode > positions and the headmodel. That seems to work ok. However, at the step of > source analysis, I get the following error: > > > > Error using * > > Inner matrix dimensions must agree. > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > Does anybody have an idea of what I’m doing wrong? > > Thank you in advance for any help or suggestion! > > > > ----------------------------------------------------------------- > > This is my code: > > %% 1 - Preparation of MRI- source space > > % Read MRI > > mrifile = 'Subject01\Subject01.mri'; > > mri = ft_read_mri(mrifile); > > % Reslice to reorient images > > cfg = []; > > cfg.dim = [256 256 256]; > > mri = ft_volumereslice(cfg,mri); > > % Segment compartments > > cfg = []; > > cfg.output = {'brain','skull','scalp'}; > > segmentedmri = ft_volumesegment(cfg, mri); > > % Prepare mesh > > cfg=[]; > > cfg.tissue={'brain', 'skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > % Prepare headmodel > > cfg = []; > > cfg.method ='bemcp'; > > vol = ft_prepare_headmodel(cfg, bnd); > > %% 2- Prepare leadfield - Creating grid > > load elec_aligned2 % Obtained after adjusting electrodes on scalp surface > interactively > > % Three fiducial markers were added to the electrode file, and now they're > > % removed so that the electrode structure has the same number of channels > as the data > > elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); > > elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); > > elec_aligned2.label = elec_aligned2.label(1:128, :); > > cfg =[]; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.grid.resolution = 10; > > cfg.grid.unit = 'mm'; > > [grid] = ft_prepare_leadfield(cfg); > > %% 3- Join rest and task data > > % data_rs: resting state data > > % data4: data during task > > dataAll = ft_appenddata([], data_rs, data4); > > cfg = []; > > cfg.method = 'mtmfft'; > > cfg.output = 'powandcsd'; > > cfg.tapsmofrq = 4; > > cfg.foilim = [18 18]; > > freqAll = ft_freqanalysis(cfg, dataAll); > > %---------------------------------- > > % all seems normal until here > > %---------------------------------- > > %% 4- Estimate source of all data > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 18; > > cfg.grid = grid; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > sourceAll = ft_sourceanalysis(cfg, freqAll); > > > > > > Cheers, > > > > Laura Rueda Delgado > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Laura.Rueda at faber.kuleuven.be Wed May 28 16:51:27 2014 From: Laura.Rueda at faber.kuleuven.be (Laura Rueda Delgado) Date: Wed, 28 May 2014 14:51:27 +0000 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Dear Johanna, Thank you for your suggestion. On step 2 in the code, I select from the elec structure the channels that are included in the frequency data. So the elec structure used for preparing the leadfield has 128 electrodes, the same as the data (data_rs, data 4, and therefore freqAll). I checked this precisely because I read a previous thread discussing that issue. Best regards, Laura Rueda Delgado From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer Sent: woensdag 28 mei 2014 16:42 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Hi Laura, Does your data have the same channels as the leadfield (as the electrodes that went in to compute the leadfield)? I often see that error when there is a mismatch of channels in that way. Best, Johanna 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado >: Dear Fieldtrip users, I’m following the tutorial of beamformers (Source Analysis: Contrast activity to another interval) to estimate oscillatory sources using DICS. I’ve checked the surface created after segmentation and the grid generated from the electrode positions and the headmodel. That seems to work ok. However, at the step of source analysis, I get the following error: Error using * Inner matrix dimensions must agree. Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Does anybody have an idea of what I’m doing wrong? Thank you in advance for any help or suggestion! ----------------------------------------------------------------- This is my code: %% 1 - Preparation of MRI- source space % Read MRI mrifile = 'Subject01\Subject01.mri'; mri = ft_read_mri(mrifile); % Reslice to reorient images cfg = []; cfg.dim = [256 256 256]; mri = ft_volumereslice(cfg,mri); % Segment compartments cfg = []; cfg.output = {'brain','skull','scalp'}; segmentedmri = ft_volumesegment(cfg, mri); % Prepare mesh cfg=[]; cfg.tissue={'brain', 'skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); % Prepare headmodel cfg = []; cfg.method ='bemcp'; vol = ft_prepare_headmodel(cfg, bnd); %% 2- Prepare leadfield - Creating grid load elec_aligned2 % Obtained after adjusting electrodes on scalp surface interactively % Three fiducial markers were added to the electrode file, and now they're % removed so that the electrode structure has the same number of channels as the data elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); elec_aligned2.label = elec_aligned2.label(1:128, :); cfg =[]; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.grid.resolution = 10; cfg.grid.unit = 'mm'; [grid] = ft_prepare_leadfield(cfg); %% 3- Join rest and task data % data_rs: resting state data % data4: data during task dataAll = ft_appenddata([], data_rs, data4); cfg = []; cfg.method = 'mtmfft'; cfg.output = 'powandcsd'; cfg.tapsmofrq = 4; cfg.foilim = [18 18]; freqAll = ft_freqanalysis(cfg, dataAll); %---------------------------------- % all seems normal until here %---------------------------------- %% 4- Estimate source of all data cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAll = ft_sourceanalysis(cfg, freqAll); Cheers, Laura Rueda Delgado _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcantor at umich.edu Wed May 28 16:24:38 2014 From: mcantor at umich.edu (Max Cantor) Date: Wed, 28 May 2014 10:24:38 -0400 Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? In-Reply-To: References: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: What we usually do before ICA is a rough pass removing the most extremely artifactual trials or channels. For instance, if you see artifacts that are not systematic and are affecting multiple sensors, it may be something like a head scratch that is affecting multiple sensors independently, and so would be turned into multiple ICA components, and so removing these would be beneficial. That being said, anything that might be, for instance, an ECG or EOG artifact, is best not cleaned before ICA, because the whole point of ICA components is to find artifacts that are independent from each other, but dependent to the source (in other words, a systematic artifact as the result of a blink) and remove them without having to throw away the rest of the good data within that trial/channel. In other words, if you're doing a comprehensive artifact rejection before ICA, it makes sense that you aren't necessarily picking up artifactual components, since you might already be removing the data that would be turned into an artifactual component. On Wed, May 28, 2014 at 9:54 AM, KatrinH Heimann wrote: > Diego, can I ask you another advice- this time more conceptually? I am > playing with the ICA now and experience, that I get very different > components depending on the artifact detection that I do beforehand. So my > idea (due to the literature) was, that the ICA works better on already > cleaned data. Now, as I want to do a frequency analysis afterwards, I did > not want to reject parts of trials. Therefore I deleted a relatively big > amount of trials in which I found muscle artifacts/drifts (Say 25% of the > whole amount of trials). However, in fact I see that the ICA then does not > give me easily to interpret components anymore - actually the results are > better (that is easier to interpret which is artifact, which not) if I > include all trials. If I only reject parts of the trials it gets even a bit > better. So my question is: Shell I a) do the (stricter) artifact detection > rather after the ICA or b) perform it on data with parts of trials marked > as bad - in which case I also ask: can I then still reject those components > in the uncleaned data (saved beforehand) so that I do not get problems with > the frequency analysis afterwards...?! > Thanks a lot for your help!!! Katrin > > > 2014-05-28 15:02 GMT+02:00 KatrinH Heimann : > > Wonderfull! Thanks Diego!!!! >> Cheers k >> >> >> 2014-05-28 14:24 GMT+02:00 Lozano Soldevilla, D. (Diego) < >> d.lozanosoldevilla at fcdonders.ru.nl>: >> >> Hi Katrin, >>> >>> First, to display the independent components: >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> cfg = []; >>> cfg.layout = 'CTF151.lay'; % specify the layout file that should be used >>> for plotting >>> cfg.viewmode = 'component' >>> ft_databrowser(cfg, comp) >>> >>> Take a look to the following example script: >>> >>> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts >>> >>> Second, you'll have to compute the power spectrum for each independent >>> component with ft_freqanalaysis: >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> cfg = []; >>> cfg.output = 'pow'; >>> cfg.channel = 'all';%compute the power spectrum in all ICs >>> cfg.method = 'mtmfft'; >>> cfg.taper = 'hanning'; >>> cfg.foi = 2:2:30; >>> freq = ft_freqanalysis(cfg, comp); >>> >>> And you can plot the spectra: >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> nsubplots = 25; >>> nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals, >>> type doc subplot >>> >>> Nfigs = ceil(size(comp.topo,1)/nsubplots); >>> tot = Nfigs*nsubplots; >>> >>> rptvect = 1:size(comp.topo,1); >>> rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post'); >>> rptvect = reshape(rptvect,nsubplots,Nfigs)'; >>> >>> for r=1:size(rptvect,1); >>> figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full >>> screen >>> k=0; >>> for j=1:size(rptvect,2); >>> if~(rptvect(r,j)==0); >>> k=k+1; >>> cfg=[]; >>> cfg.channel = rptvect(r,j); >>> subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq); >>> end >>> end >>> end >>> >>> For the IC topos you'll follow the same logic as above but with: >>> >>> figure >>> cfg = []; >>> cfg.component = [1:20]; % specify the component(s) that should be >>> plotted >>> cfg.layout = 'GSN-HydroCel-129.sfp'; >>> cfg.comment = 'no'; >>> ft_topoplotIC(cfg, comp) >>> >>> I hope it helps >>> >>> Diego >>> ------------------------------ >>> >>> *From: *"KatrinH Heimann" >>> *To: *"FieldTrip discussion list" >>> *Sent: *Wednesday, 28 May, 2014 12:59:38 PM >>> *Subject: *[FieldTrip] ICA - Can I visualize Activity power spectrum of >>> single components? >>> >>> >>> Dear all, >>> another question: >>> Is it possible to visualize the Activity power spectrum of the single >>> components after an ICA by using ft_databrowser (or something else). I like >>> this feature from EEG lab as I find it easier to detect artifactual >>> components. >>> Thanks a lot for your help >>> Katrin >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> -- >>> PhD Student >>> Neuronal Oscillations Group >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognitive Neuroimaging >>> Radboud University Nijmegen >>> NL-6525 EN Nijmegen >>> The Netherlands >>> http://www.ru.nl/people/donders/lozano-soldevilla-d/ >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Research Assistant Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathykousik at gmail.com Wed May 28 17:09:37 2014 From: sarathykousik at gmail.com (kousik sarathy) Date: Wed, 28 May 2014 17:09:37 +0200 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Hey Laura, I too had the same suggestion as Johanna's. Another thing to check would be if the labels that you used for the leadfield estimation are the same as the freq data. I guess FT at some point would also check this to extract the indices. -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 4:51 PM, Laura Rueda Delgado < Laura.Rueda at faber.kuleuven.be> wrote: > Dear Johanna, > > > > Thank you for your suggestion. > > > > On step 2 in the code, I select from the elec structure the channels that > are included in the frequency data. So the elec structure used for > preparing the leadfield has 128 electrodes, the same as the data (data_rs, > data 4, and therefore freqAll). I checked this precisely because I read a > previous thread discussing that issue. > > > > Best regards, > > > > Laura Rueda Delgado > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *Johanna Zumer > *Sent:* woensdag 28 mei 2014 16:42 > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Hi Laura, > > > > Does your data have the same channels as the leadfield (as the electrodes > that went in to compute the leadfield)? I often see that error when there > is a mismatch of channels in that way. > > > > Best, > > Johanna > > > > 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be>: > > Dear Fieldtrip users, > > > > I’m following the tutorial of beamformers (Source Analysis: Contrast > activity to another interval) > to estimate oscillatory sources using DICS. I’ve checked the surface > created after segmentation and the grid generated from the electrode > positions and the headmodel. That seems to work ok. However, at the step of > source analysis, I get the following error: > > > > Error using * > > Inner matrix dimensions must agree. > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > Does anybody have an idea of what I’m doing wrong? > > Thank you in advance for any help or suggestion! > > > > ----------------------------------------------------------------- > > This is my code: > > %% 1 - Preparation of MRI- source space > > % Read MRI > > mrifile = 'Subject01\Subject01.mri'; > > mri = ft_read_mri(mrifile); > > % Reslice to reorient images > > cfg = []; > > cfg.dim = [256 256 256]; > > mri = ft_volumereslice(cfg,mri); > > % Segment compartments > > cfg = []; > > cfg.output = {'brain','skull','scalp'}; > > segmentedmri = ft_volumesegment(cfg, mri); > > % Prepare mesh > > cfg=[]; > > cfg.tissue={'brain', 'skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > % Prepare headmodel > > cfg = []; > > cfg.method ='bemcp'; > > vol = ft_prepare_headmodel(cfg, bnd); > > %% 2- Prepare leadfield - Creating grid > > load elec_aligned2 % Obtained after adjusting electrodes on scalp surface > interactively > > % Three fiducial markers were added to the electrode file, and now they're > > % removed so that the electrode structure has the same number of channels > as the data > > elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); > > elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); > > elec_aligned2.label = elec_aligned2.label(1:128, :); > > cfg =[]; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.grid.resolution = 10; > > cfg.grid.unit = 'mm'; > > [grid] = ft_prepare_leadfield(cfg); > > %% 3- Join rest and task data > > % data_rs: resting state data > > % data4: data during task > > dataAll = ft_appenddata([], data_rs, data4); > > cfg = []; > > cfg.method = 'mtmfft'; > > cfg.output = 'powandcsd'; > > cfg.tapsmofrq = 4; > > cfg.foilim = [18 18]; > > freqAll = ft_freqanalysis(cfg, dataAll); > > %---------------------------------- > > % all seems normal until here > > %---------------------------------- > > %% 4- Estimate source of all data > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 18; > > cfg.grid = grid; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > sourceAll = ft_sourceanalysis(cfg, freqAll); > > > > > > Cheers, > > > > Laura Rueda Delgado > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Laura.Rueda at faber.kuleuven.be Wed May 28 17:31:40 2014 From: Laura.Rueda at faber.kuleuven.be (Laura Rueda Delgado) Date: Wed, 28 May 2014 15:31:40 +0000 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Dear Kousik, I checked the labels and they were the same, except for whether they were in capital letters. So I added the following before ft_sourceanalysis: freqAll.label=cellfun(@upper, freqAll.label, 'UniformOutput', 0); freqAll.labelcmb=cellfun(@upper, freqAll.labelcmb, 'UniformOutput', 0); This way the labels of the elec structure and freqAll are in capital letters. And now I get a different error (although still within the function beamformer_dics): Error using svd Input to SVD must not contain NaN or Inf. Error in beamformer_dics>pinv (line 650) [U,S,V] = svd(A,0); Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); What could it be? Best regards, Laura From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of kousik sarathy Sent: woensdag 28 mei 2014 17:10 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Hey Laura, I too had the same suggestion as Johanna's. Another thing to check would be if the labels that you used for the leadfield estimation are the same as the freq data. I guess FT at some point would also check this to extract the indices. -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 4:51 PM, Laura Rueda Delgado > wrote: Dear Johanna, Thank you for your suggestion. On step 2 in the code, I select from the elec structure the channels that are included in the frequency data. So the elec structure used for preparing the leadfield has 128 electrodes, the same as the data (data_rs, data 4, and therefore freqAll). I checked this precisely because I read a previous thread discussing that issue. Best regards, Laura Rueda Delgado From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer Sent: woensdag 28 mei 2014 16:42 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Hi Laura, Does your data have the same channels as the leadfield (as the electrodes that went in to compute the leadfield)? I often see that error when there is a mismatch of channels in that way. Best, Johanna 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado >: Dear Fieldtrip users, I’m following the tutorial of beamformers (Source Analysis: Contrast activity to another interval) to estimate oscillatory sources using DICS. I’ve checked the surface created after segmentation and the grid generated from the electrode positions and the headmodel. That seems to work ok. However, at the step of source analysis, I get the following error: Error using * Inner matrix dimensions must agree. Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Does anybody have an idea of what I’m doing wrong? Thank you in advance for any help or suggestion! ----------------------------------------------------------------- This is my code: %% 1 - Preparation of MRI- source space % Read MRI mrifile = 'Subject01\Subject01.mri'; mri = ft_read_mri(mrifile); % Reslice to reorient images cfg = []; cfg.dim = [256 256 256]; mri = ft_volumereslice(cfg,mri); % Segment compartments cfg = []; cfg.output = {'brain','skull','scalp'}; segmentedmri = ft_volumesegment(cfg, mri); % Prepare mesh cfg=[]; cfg.tissue={'brain', 'skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); % Prepare headmodel cfg = []; cfg.method ='bemcp'; vol = ft_prepare_headmodel(cfg, bnd); %% 2- Prepare leadfield - Creating grid load elec_aligned2 % Obtained after adjusting electrodes on scalp surface interactively % Three fiducial markers were added to the electrode file, and now they're % removed so that the electrode structure has the same number of channels as the data elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); elec_aligned2.label = elec_aligned2.label(1:128, :); cfg =[]; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.grid.resolution = 10; cfg.grid.unit = 'mm'; [grid] = ft_prepare_leadfield(cfg); %% 3- Join rest and task data % data_rs: resting state data % data4: data during task dataAll = ft_appenddata([], data_rs, data4); cfg = []; cfg.method = 'mtmfft'; cfg.output = 'powandcsd'; cfg.tapsmofrq = 4; cfg.foilim = [18 18]; freqAll = ft_freqanalysis(cfg, dataAll); %---------------------------------- % all seems normal until here %---------------------------------- %% 4- Estimate source of all data cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAll = ft_sourceanalysis(cfg, freqAll); Cheers, Laura Rueda Delgado _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From ayobimpe2004 at hotmail.com Wed May 28 17:36:39 2014 From: ayobimpe2004 at hotmail.com (Azeez Adebimpe) Date: Wed, 28 May 2014 16:36:39 +0100 Subject: [FieldTrip] source resampling Message-ID: Dear all I calculated my leadfield or grid with 8 mm resolution. Please is there anyway after or before source interpolation or before to resample the source to 1 mm resolution. merci! Azeez A. Adebimpe "Knowledge and good manner, the beauty of a man" -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathykousik at gmail.com Wed May 28 17:37:17 2014 From: sarathykousik at gmail.com (kousik sarathy) Date: Wed, 28 May 2014 17:37:17 +0200 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Ah. Interesting. Good that error changes. So that was the problem before. Now, can you check if your Freq matrices contain any NaN's (isnan(freqAll))? It can happen sometimes. -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 5:31 PM, Laura Rueda Delgado < Laura.Rueda at faber.kuleuven.be> wrote: > Dear Kousik, > > > > I checked the labels and they were the same, except for whether they were > in capital letters. So I added the following before ft_sourceanalysis: > > > > freqAll.label=cellfun(@upper, freqAll.label, 'UniformOutput', 0); > > freqAll.labelcmb=cellfun(@upper, freqAll.labelcmb, 'UniformOutput', 0); > > > > This way the labels of the elec structure and freqAll are in capital > letters. > > > > And now I get a different error (although still within the function > beamformer_dics): > > > > Error using svd > > Input to SVD must not contain NaN or Inf. > > > > Error in beamformer_dics>pinv (line 650) > > [U,S,V] = svd(A,0); > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > > > What could it be? > > > > Best regards, > > Laura > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *kousik sarathy > *Sent:* woensdag 28 mei 2014 17:10 > > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Hey Laura, > > > > I too had the same suggestion as Johanna's. > > > > Another thing to check would be if the labels that you used for the > leadfield estimation are the same as the freq data. I guess FT at some > point would also check this to extract the indices. > > > -- > > Regards, > > Kousik Sarathy, S > > > > > > On Wed, May 28, 2014 at 4:51 PM, Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be> wrote: > > Dear Johanna, > > > > Thank you for your suggestion. > > > > On step 2 in the code, I select from the elec structure the channels that > are included in the frequency data. So the elec structure used for > preparing the leadfield has 128 electrodes, the same as the data (data_rs, > data 4, and therefore freqAll). I checked this precisely because I read a > previous thread discussing that issue. > > > > Best regards, > > > > Laura Rueda Delgado > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *Johanna Zumer > *Sent:* woensdag 28 mei 2014 16:42 > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Hi Laura, > > > > Does your data have the same channels as the leadfield (as the electrodes > that went in to compute the leadfield)? I often see that error when there > is a mismatch of channels in that way. > > > > Best, > > Johanna > > > > 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be>: > > Dear Fieldtrip users, > > > > I’m following the tutorial of beamformers (Source Analysis: Contrast > activity to another interval) > to estimate oscillatory sources using DICS. I’ve checked the surface > created after segmentation and the grid generated from the electrode > positions and the headmodel. That seems to work ok. However, at the step of > source analysis, I get the following error: > > > > Error using * > > Inner matrix dimensions must agree. > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > Does anybody have an idea of what I’m doing wrong? > > Thank you in advance for any help or suggestion! > > > > ----------------------------------------------------------------- > > This is my code: > > %% 1 - Preparation of MRI- source space > > % Read MRI > > mrifile = 'Subject01\Subject01.mri'; > > mri = ft_read_mri(mrifile); > > % Reslice to reorient images > > cfg = []; > > cfg.dim = [256 256 256]; > > mri = ft_volumereslice(cfg,mri); > > % Segment compartments > > cfg = []; > > cfg.output = {'brain','skull','scalp'}; > > segmentedmri = ft_volumesegment(cfg, mri); > > % Prepare mesh > > cfg=[]; > > cfg.tissue={'brain', 'skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > % Prepare headmodel > > cfg = []; > > cfg.method ='bemcp'; > > vol = ft_prepare_headmodel(cfg, bnd); > > %% 2- Prepare leadfield - Creating grid > > load elec_aligned2 % Obtained after adjusting electrodes on scalp surface > interactively > > % Three fiducial markers were added to the electrode file, and now they're > > % removed so that the electrode structure has the same number of channels > as the data > > elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); > > elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); > > elec_aligned2.label = elec_aligned2.label(1:128, :); > > cfg =[]; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.grid.resolution = 10; > > cfg.grid.unit = 'mm'; > > [grid] = ft_prepare_leadfield(cfg); > > %% 3- Join rest and task data > > % data_rs: resting state data > > % data4: data during task > > dataAll = ft_appenddata([], data_rs, data4); > > cfg = []; > > cfg.method = 'mtmfft'; > > cfg.output = 'powandcsd'; > > cfg.tapsmofrq = 4; > > cfg.foilim = [18 18]; > > freqAll = ft_freqanalysis(cfg, dataAll); > > %---------------------------------- > > % all seems normal until here > > %---------------------------------- > > %% 4- Estimate source of all data > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 18; > > cfg.grid = grid; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > sourceAll = ft_sourceanalysis(cfg, freqAll); > > > > > > Cheers, > > > > Laura Rueda Delgado > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From katrinheimann at gmail.com Wed May 28 17:50:09 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Wed, 28 May 2014 17:50:09 +0200 Subject: [FieldTrip] ICA - Can I visualize Activity power spectrum of single components? In-Reply-To: References: <1071348354.7145235.1401279846796.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Thanks Max! :) Katrin 2014-05-28 16:24 GMT+02:00 Max Cantor : > What we usually do before ICA is a rough pass removing the most extremely > artifactual trials or channels. For instance, if you see artifacts that are > not systematic and are affecting multiple sensors, it may be something like > a head scratch that is affecting multiple sensors independently, and so > would be turned into multiple ICA components, and so removing these would > be beneficial. That being said, anything that might be, for instance, an > ECG or EOG artifact, is best not cleaned before ICA, because the whole > point of ICA components is to find artifacts that are independent from each > other, but dependent to the source (in other words, a systematic artifact > as the result of a blink) and remove them without having to throw away the > rest of the good data within that trial/channel. In other words, if you're > doing a comprehensive artifact rejection before ICA, it makes sense that > you aren't necessarily picking up artifactual components, since you might > already be removing the data that would be turned into an artifactual > component. > > > On Wed, May 28, 2014 at 9:54 AM, KatrinH Heimann wrote: > >> Diego, can I ask you another advice- this time more conceptually? I am >> playing with the ICA now and experience, that I get very different >> components depending on the artifact detection that I do beforehand. So my >> idea (due to the literature) was, that the ICA works better on already >> cleaned data. Now, as I want to do a frequency analysis afterwards, I did >> not want to reject parts of trials. Therefore I deleted a relatively big >> amount of trials in which I found muscle artifacts/drifts (Say 25% of the >> whole amount of trials). However, in fact I see that the ICA then does not >> give me easily to interpret components anymore - actually the results are >> better (that is easier to interpret which is artifact, which not) if I >> include all trials. If I only reject parts of the trials it gets even a bit >> better. So my question is: Shell I a) do the (stricter) artifact detection >> rather after the ICA or b) perform it on data with parts of trials marked >> as bad - in which case I also ask: can I then still reject those components >> in the uncleaned data (saved beforehand) so that I do not get problems with >> the frequency analysis afterwards...?! >> Thanks a lot for your help!!! Katrin >> >> >> 2014-05-28 15:02 GMT+02:00 KatrinH Heimann : >> >> Wonderfull! Thanks Diego!!!! >>> Cheers k >>> >>> >>> 2014-05-28 14:24 GMT+02:00 Lozano Soldevilla, D. (Diego) < >>> d.lozanosoldevilla at fcdonders.ru.nl>: >>> >>> Hi Katrin, >>>> >>>> First, to display the independent components: >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> cfg = []; >>>> cfg.layout = 'CTF151.lay'; % specify the layout file that should be >>>> used for plotting >>>> cfg.viewmode = 'component' >>>> ft_databrowser(cfg, comp) >>>> >>>> Take a look to the following example script: >>>> >>>> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts >>>> >>>> Second, you'll have to compute the power spectrum for each independent >>>> component with ft_freqanalaysis: >>>> >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> cfg = []; >>>> cfg.output = 'pow'; >>>> cfg.channel = 'all';%compute the power spectrum in all ICs >>>> cfg.method = 'mtmfft'; >>>> cfg.taper = 'hanning'; >>>> cfg.foi = 2:2:30; >>>> freq = ft_freqanalysis(cfg, comp); >>>> >>>> And you can plot the spectra: >>>> >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> nsubplots = 25; >>>> nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals, >>>> type doc subplot >>>> >>>> Nfigs = ceil(size(comp.topo,1)/nsubplots); >>>> tot = Nfigs*nsubplots; >>>> >>>> rptvect = 1:size(comp.topo,1); >>>> rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post'); >>>> rptvect = reshape(rptvect,nsubplots,Nfigs)'; >>>> >>>> for r=1:size(rptvect,1); >>>> figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full >>>> screen >>>> k=0; >>>> for j=1:size(rptvect,2); >>>> if~(rptvect(r,j)==0); >>>> k=k+1; >>>> cfg=[]; >>>> cfg.channel = rptvect(r,j); >>>> subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq); >>>> end >>>> end >>>> end >>>> >>>> For the IC topos you'll follow the same logic as above but with: >>>> >>>> figure >>>> cfg = []; >>>> cfg.component = [1:20]; % specify the component(s) that should be >>>> plotted >>>> cfg.layout = 'GSN-HydroCel-129.sfp'; >>>> cfg.comment = 'no'; >>>> ft_topoplotIC(cfg, comp) >>>> >>>> I hope it helps >>>> >>>> Diego >>>> ------------------------------ >>>> >>>> *From: *"KatrinH Heimann" >>>> *To: *"FieldTrip discussion list" >>>> *Sent: *Wednesday, 28 May, 2014 12:59:38 PM >>>> *Subject: *[FieldTrip] ICA - Can I visualize Activity power spectrum >>>> of single components? >>>> >>>> >>>> Dear all, >>>> another question: >>>> Is it possible to visualize the Activity power spectrum of the single >>>> components after an ICA by using ft_databrowser (or something else). I like >>>> this feature from EEG lab as I find it easier to detect artifactual >>>> components. >>>> Thanks a lot for your help >>>> Katrin >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> >>>> >>>> -- >>>> PhD Student >>>> Neuronal Oscillations Group >>>> Donders Institute for Brain, Cognition and Behaviour >>>> Centre for Cognitive Neuroimaging >>>> Radboud University Nijmegen >>>> NL-6525 EN Nijmegen >>>> The Netherlands >>>> http://www.ru.nl/people/donders/lozano-soldevilla-d/ >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Max Cantor > Research Assistant > Computational Neurolinguistics Lab > University of Michigan > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Laura.Rueda at faber.kuleuven.be Wed May 28 18:01:52 2014 From: Laura.Rueda at faber.kuleuven.be (Laura Rueda Delgado) Date: Wed, 28 May 2014 16:01:52 +0000 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Dear Kousik, I checked for NaN and Inf values in powspctrm and crsspctrm of freqAll. There are none. However, I checked for NaN values in grid.leadfield and it has some. I thought that these were NaN values in the points of the grid outside a brain region, but I might be mistaken. grid = xgrid: [-58 -48 -38 -28 -18 -8 2 12 22 32 42 52 62 72 82 92 102] ygrid: [-61 -51 -41 -31 -21 -11 -1 9 19 29 39 49 59] zgrid: [-13 -3 7 17 27 37 47 57 67 77 87 97 107 117] dim: [17 13 14] pos: [3094x3 double] unit: 'mm' inside: [1x1516 double] outside: [1x1578 double] cfg: [1x1 struct] leadfield: {1x3094 cell} Best regards, Laura Rueda Delgado From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of kousik sarathy Sent: woensdag 28 mei 2014 17:37 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Ah. Interesting. Good that error changes. So that was the problem before. Now, can you check if your Freq matrices contain any NaN's (isnan(freqAll))? It can happen sometimes. -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 5:31 PM, Laura Rueda Delgado > wrote: Dear Kousik, I checked the labels and they were the same, except for whether they were in capital letters. So I added the following before ft_sourceanalysis: freqAll.label=cellfun(@upper, freqAll.label, 'UniformOutput', 0); freqAll.labelcmb=cellfun(@upper, freqAll.labelcmb, 'UniformOutput', 0); This way the labels of the elec structure and freqAll are in capital letters. And now I get a different error (although still within the function beamformer_dics): Error using svd Input to SVD must not contain NaN or Inf. Error in beamformer_dics>pinv (line 650) [U,S,V] = svd(A,0); Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); What could it be? Best regards, Laura From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of kousik sarathy Sent: woensdag 28 mei 2014 17:10 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Hey Laura, I too had the same suggestion as Johanna's. Another thing to check would be if the labels that you used for the leadfield estimation are the same as the freq data. I guess FT at some point would also check this to extract the indices. -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 4:51 PM, Laura Rueda Delgado > wrote: Dear Johanna, Thank you for your suggestion. On step 2 in the code, I select from the elec structure the channels that are included in the frequency data. So the elec structure used for preparing the leadfield has 128 electrodes, the same as the data (data_rs, data 4, and therefore freqAll). I checked this precisely because I read a previous thread discussing that issue. Best regards, Laura Rueda Delgado From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer Sent: woensdag 28 mei 2014 16:42 To: FieldTrip discussion list Subject: Re: [FieldTrip] Error in ft_sourceanalysis: DICS Hi Laura, Does your data have the same channels as the leadfield (as the electrodes that went in to compute the leadfield)? I often see that error when there is a mismatch of channels in that way. Best, Johanna 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado >: Dear Fieldtrip users, I’m following the tutorial of beamformers (Source Analysis: Contrast activity to another interval) to estimate oscillatory sources using DICS. I’ve checked the surface created after segmentation and the grid generated from the electrode positions and the headmodel. That seems to work ok. However, at the step of source analysis, I get the following error: Error using * Inner matrix dimensions must agree. Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 567) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Does anybody have an idea of what I’m doing wrong? Thank you in advance for any help or suggestion! ----------------------------------------------------------------- This is my code: %% 1 - Preparation of MRI- source space % Read MRI mrifile = 'Subject01\Subject01.mri'; mri = ft_read_mri(mrifile); % Reslice to reorient images cfg = []; cfg.dim = [256 256 256]; mri = ft_volumereslice(cfg,mri); % Segment compartments cfg = []; cfg.output = {'brain','skull','scalp'}; segmentedmri = ft_volumesegment(cfg, mri); % Prepare mesh cfg=[]; cfg.tissue={'brain', 'skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); % Prepare headmodel cfg = []; cfg.method ='bemcp'; vol = ft_prepare_headmodel(cfg, bnd); %% 2- Prepare leadfield - Creating grid load elec_aligned2 % Obtained after adjusting electrodes on scalp surface interactively % Three fiducial markers were added to the electrode file, and now they're % removed so that the electrode structure has the same number of channels as the data elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); elec_aligned2.label = elec_aligned2.label(1:128, :); cfg =[]; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.grid.resolution = 10; cfg.grid.unit = 'mm'; [grid] = ft_prepare_leadfield(cfg); %% 3- Join rest and task data % data_rs: resting state data % data4: data during task dataAll = ft_appenddata([], data_rs, data4); cfg = []; cfg.method = 'mtmfft'; cfg.output = 'powandcsd'; cfg.tapsmofrq = 4; cfg.foilim = [18 18]; freqAll = ft_freqanalysis(cfg, dataAll); %---------------------------------- % all seems normal until here %---------------------------------- %% 4- Estimate source of all data cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.vol = vol; cfg.elec = elec_aligned2; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAll = ft_sourceanalysis(cfg, freqAll); Cheers, Laura Rueda Delgado _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathykousik at gmail.com Wed May 28 18:09:31 2014 From: sarathykousik at gmail.com (kousik sarathy) Date: Wed, 28 May 2014 18:09:31 +0200 Subject: [FieldTrip] Error in ft_sourceanalysis: DICS In-Reply-To: References: Message-ID: Oh. Yes. FT puts NaN's into sourcespace points outside the brain. You can constrain FT to only calculate leadfields for sourcespace points inside the brain. I generally do this. I don't know how FT handles those outside the brain source points really. You could give this a try. Check this tutorial/code: http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#forward_solution -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 6:01 PM, Laura Rueda Delgado < Laura.Rueda at faber.kuleuven.be> wrote: > Dear Kousik, > > > > I checked for NaN and Inf values in powspctrm and crsspctrm of freqAll. > There are none. However, I checked for NaN values in grid.leadfield and it > has some. I thought that these were NaN values in the points of the grid > outside a brain region, but I might be mistaken. > > > > > > grid = > > > > xgrid: [-58 -48 -38 -28 -18 -8 2 12 22 32 42 52 62 72 82 92 102] > > ygrid: [-61 -51 -41 -31 -21 -11 -1 9 19 29 39 49 59] > > zgrid: [-13 -3 7 17 27 37 47 57 67 77 87 97 107 117] > > dim: [17 13 14] > > pos: [3094x3 double] > > unit: 'mm' > > inside: [1x1516 double] > > outside: [1x1578 double] > > cfg: [1x1 struct] > > leadfield: {1x3094 cell} > > > > Best regards, > > > > Laura Rueda Delgado > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *kousik sarathy > *Sent:* woensdag 28 mei 2014 17:37 > > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Ah. Interesting. Good that error changes. So that was the problem before. > > > > Now, can you check if your Freq matrices contain any NaN's > (isnan(freqAll))? It can happen sometimes. > > > -- > > Regards, > > Kousik Sarathy, S > > > > > > On Wed, May 28, 2014 at 5:31 PM, Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be> wrote: > > Dear Kousik, > > > > I checked the labels and they were the same, except for whether they were > in capital letters. So I added the following before ft_sourceanalysis: > > > > freqAll.label=cellfun(@upper, freqAll.label, 'UniformOutput', 0); > > freqAll.labelcmb=cellfun(@upper, freqAll.labelcmb, 'UniformOutput', 0); > > > > This way the labels of the elec structure and freqAll are in capital > letters. > > > > And now I get a different error (although still within the function > beamformer_dics): > > > > Error using svd > > Input to SVD must not contain NaN or Inf. > > > > Error in beamformer_dics>pinv (line 650) > > [U,S,V] = svd(A,0); > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > > > What could it be? > > > > Best regards, > > Laura > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *kousik sarathy > *Sent:* woensdag 28 mei 2014 17:10 > > > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Hey Laura, > > > > I too had the same suggestion as Johanna's. > > > > Another thing to check would be if the labels that you used for the > leadfield estimation are the same as the freq data. I guess FT at some > point would also check this to extract the indices. > > > -- > > Regards, > > Kousik Sarathy, S > > > > > > On Wed, May 28, 2014 at 4:51 PM, Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be> wrote: > > Dear Johanna, > > > > Thank you for your suggestion. > > > > On step 2 in the code, I select from the elec structure the channels that > are included in the frequency data. So the elec structure used for > preparing the leadfield has 128 electrodes, the same as the data (data_rs, > data 4, and therefore freqAll). I checked this precisely because I read a > previous thread discussing that issue. > > > > Best regards, > > > > Laura Rueda Delgado > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *Johanna Zumer > *Sent:* woensdag 28 mei 2014 16:42 > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Error in ft_sourceanalysis: DICS > > > > Hi Laura, > > > > Does your data have the same channels as the leadfield (as the electrodes > that went in to compute the leadfield)? I often see that error when there > is a mismatch of channels in that way. > > > > Best, > > Johanna > > > > 2014-05-28 15:29 GMT+01:00 Laura Rueda Delgado < > Laura.Rueda at faber.kuleuven.be>: > > Dear Fieldtrip users, > > > > I’m following the tutorial of beamformers (Source Analysis: Contrast > activity to another interval) > to estimate oscillatory sources using DICS. I’ve checked the surface > created after segmentation and the grid generated from the electrode > positions and the headmodel. That seems to work ok. However, at the step of > source analysis, I get the following error: > > > > Error using * > > Inner matrix dimensions must agree. > > > > Error in beamformer_dics (line 339) > > filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross > eqn. 3, use PINV/SVD to cover rank > > deficient leadfield > > > > Error in ft_sourceanalysis (line 567) > > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), > optarg{:}); > > > > Does anybody have an idea of what I’m doing wrong? > > Thank you in advance for any help or suggestion! > > > > ----------------------------------------------------------------- > > This is my code: > > %% 1 - Preparation of MRI- source space > > % Read MRI > > mrifile = 'Subject01\Subject01.mri'; > > mri = ft_read_mri(mrifile); > > % Reslice to reorient images > > cfg = []; > > cfg.dim = [256 256 256]; > > mri = ft_volumereslice(cfg,mri); > > % Segment compartments > > cfg = []; > > cfg.output = {'brain','skull','scalp'}; > > segmentedmri = ft_volumesegment(cfg, mri); > > % Prepare mesh > > cfg=[]; > > cfg.tissue={'brain', 'skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > % Prepare headmodel > > cfg = []; > > cfg.method ='bemcp'; > > vol = ft_prepare_headmodel(cfg, bnd); > > %% 2- Prepare leadfield - Creating grid > > load elec_aligned2 % Obtained after adjusting electrodes on scalp surface > interactively > > % Three fiducial markers were added to the electrode file, and now they're > > % removed so that the electrode structure has the same number of channels > as the data > > elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :); > > elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :); > > elec_aligned2.label = elec_aligned2.label(1:128, :); > > cfg =[]; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.grid.resolution = 10; > > cfg.grid.unit = 'mm'; > > [grid] = ft_prepare_leadfield(cfg); > > %% 3- Join rest and task data > > % data_rs: resting state data > > % data4: data during task > > dataAll = ft_appenddata([], data_rs, data4); > > cfg = []; > > cfg.method = 'mtmfft'; > > cfg.output = 'powandcsd'; > > cfg.tapsmofrq = 4; > > cfg.foilim = [18 18]; > > freqAll = ft_freqanalysis(cfg, dataAll); > > %---------------------------------- > > % all seems normal until here > > %---------------------------------- > > %% 4- Estimate source of all data > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 18; > > cfg.grid = grid; > > cfg.vol = vol; > > cfg.elec = elec_aligned2; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > sourceAll = ft_sourceanalysis(cfg, freqAll); > > > > > > Cheers, > > > > Laura Rueda Delgado > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahjoory86 at gmail.com Wed May 28 23:47:14 2014 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Wed, 28 May 2014 23:47:14 +0200 Subject: [FieldTrip] NaN Values in grid.liedfield Message-ID: Dear all, I want to do EEG source reconstruction. The EEG cap is t 10-20 standard, with 64 channels, but the MRI and electrode positions of subjects are not available. I used Fieldtrip templates for my work. my scripts are as below: cfg = []; cfg.elec=ft_read_sens('standard_1020.elc'); cfg.vol = load('standard_bem.mat'); cfg.channel = epo.clab; [grid] = ft_prepare_leadfield(cfg); But the output for grid.liedfield includes NAN values. I hope someone can give me comments on this matter. Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Thu May 29 03:56:15 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Thu, 29 May 2014 01:56:15 +0000 Subject: [FieldTrip] possible bug with either ft_volumelookup or AAL atlas Message-ID: <1401328562572.43734@flinders.edu.au> Hello fieldtrippers, I just wanted to check if this is a bug or not. When running the following code: atlas = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/aal/ROI_MNI_V4.nii')) It gives you the following: dim: [91 109 91] hdr: [1x1 struct] transform: [4x4 double] unit: 'mm' tissue: [91x109x91 double] tissuelabel: {1x116 cell} coordsys: 'mni' Take note that tissuelabel is 1x116 When running the following code through ft_volumelookup: cfg = []; cfg.atlas = atlas; cfg.inputcoord = 'mni'; cfg.maskparameter = 'inside'; labels = ft_volumelookup( cfg, source); An error occurs: Error using cat Dimensions of matrices being concatenated are not consistent. Error in ft_volumelookup (line 313) labels.name = cat(1, labels.name, atlas.([fn{k},'label'])); If you invert tissuelabel, so that it becomes 116x1, then the code works. For some reason ft_volumelookup doesnt like a 1xY cell. Thank you, Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathykousik at gmail.com Thu May 29 07:29:52 2014 From: sarathykousik at gmail.com (kousik sarathy) Date: Thu, 29 May 2014 07:29:52 +0200 Subject: [FieldTrip] NaN Values in grid.liedfield In-Reply-To: References: Message-ID: Hey Keyvan, When leadfield structure has NaN it generally means the grid points lie outside the brain. Please have a look at this: http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg -- Regards, Kousik Sarathy, S On Wed, May 28, 2014 at 11:47 PM, Keyvan Mahjoory wrote: > Dear all, > > I want to do EEG source reconstruction. The EEG cap is t 10-20 standard, > with 64 channels, but the MRI and electrode positions of subjects are not > available. I used Fieldtrip templates for my work. my scripts are as below: > > cfg = []; > cfg.elec=ft_read_sens('standard_1020.elc'); > cfg.vol = load('standard_bem.mat'); > cfg.channel = epo.clab; > [grid] = ft_prepare_leadfield(cfg); > > But the output for grid.liedfield includes NAN values. > I hope someone can give me comments on this matter. > > Best, > Keyvan > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu May 29 09:00:40 2014 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 29 May 2014 09:00:40 +0200 Subject: [FieldTrip] possible bug with either ft_volumelookup or AAL atlas In-Reply-To: <1401328562572.43734@flinders.edu.au> References: <1401328562572.43734@flinders.edu.au> Message-ID: Hi Tyler, That sounds like a bug to me. I've filed it on our bugzilla: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2594 Best, Eelke On 29 May 2014 03:56, Tyler Grummett wrote: > Hello fieldtrippers, > > > I just wanted to check if this is a bug or not. > > > When running the following code: atlas = ft_read_atlas( fullfile( > matlabrootpath, 'Matlab/fieldtrip/template/atlas/aal/ROI_MNI_V4.nii')) > > > It gives you the following: > > > dim: [91 109 91] > hdr: [1x1 struct] > transform: [4x4 double] > unit: 'mm' > tissue: [91x109x91 double] > tissuelabel: {1x116 cell} > coordsys: 'mni' > > Take note that tissuelabel is 1x116 > > When running the following code through ft_volumelookup: > > cfg = []; > cfg.atlas = atlas; > cfg.inputcoord = 'mni'; > cfg.maskparameter = 'inside'; > labels = ft_volumelookup( cfg, source); > > An error occurs: > > Error using cat > Dimensions of matrices being concatenated are not consistent. > > Error in ft_volumelookup (line 313) > labels.name = cat(1, labels.name, atlas.([fn{k},'label'])); > > If you invert tissuelabel, so that it becomes 116x1, then the code works. > > For some reason ft_volumelookup doesnt like a 1xY cell. > > Thank you, > > Tyler > > > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From tyler.grummett at flinders.edu.au Thu May 29 09:26:39 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Thu, 29 May 2014 07:26:39 +0000 Subject: [FieldTrip] possible bug with either ft_volumelookup or AAL atlas In-Reply-To: References: <1401328562572.43734@flinders.edu.au>, Message-ID: <1401348385612.16930@flinders.edu.au> Thank you Eelke, I also noticed that with the AFNI atlas, the labels in the file dont match up to the labels that come out of ft_prepare_sourcemodel. when I say label I mean data.( label) I tested it with the AAL atlas and the labels in the file and the data.( label) match up perfectly. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 ________________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Eelke Spaak Sent: Thursday, 29 May 2014 4:30 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] possible bug with either ft_volumelookup or AAL atlas Hi Tyler, That sounds like a bug to me. I've filed it on our bugzilla: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2594 Best, Eelke On 29 May 2014 03:56, Tyler Grummett wrote: > Hello fieldtrippers, > > > I just wanted to check if this is a bug or not. > > > When running the following code: atlas = ft_read_atlas( fullfile( > matlabrootpath, 'Matlab/fieldtrip/template/atlas/aal/ROI_MNI_V4.nii')) > > > It gives you the following: > > > dim: [91 109 91] > hdr: [1x1 struct] > transform: [4x4 double] > unit: 'mm' > tissue: [91x109x91 double] > tissuelabel: {1x116 cell} > coordsys: 'mni' > > Take note that tissuelabel is 1x116 > > When running the following code through ft_volumelookup: > > cfg = []; > cfg.atlas = atlas; > cfg.inputcoord = 'mni'; > cfg.maskparameter = 'inside'; > labels = ft_volumelookup( cfg, source); > > An error occurs: > > Error using cat > Dimensions of matrices being concatenated are not consistent. > > Error in ft_volumelookup (line 313) > labels.name = cat(1, labels.name, atlas.([fn{k},'label'])); > > If you invert tissuelabel, so that it becomes 116x1, then the code works. > > For some reason ft_volumelookup doesnt like a 1xY cell. > > Thank you, > > Tyler > > > > ************************* > > Tyler Grummett ( BBSc, BSc(Hons I)) > PhD Candidate > Brain Signals Laboratory > Flinders University > Rm 5A301 > Ext 66124 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From katrinheimann at gmail.com Thu May 29 11:55:35 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Thu, 29 May 2014 11:55:35 +0200 Subject: [FieldTrip] which baseline correction to choose for frequency analysis Message-ID: Hey together, another rather conceptual question: I am wondering about the baselinecorrection for the frequencyanalysis. I want to compare two timeperiods of one second each, lying right after each other. In the preprocessing I have baseline corrected them using 100 ms before the first piece (last part of a fixationcross period). Do I use the same part for the frequencyanalysis? Will say, do I run the analysis let's say from -0.5 (0 point is end of fixation cross) to 2.5 s, correcting with [-0.1 0] and then extract the two different conditions by statistical extraction (each 1 second long) ? Or do I run two analysis on (a bit more than) one second each, using the whole trial as baseline? thanks a lot for your advice again! Best Katrin -------------- next part -------------- An HTML attachment was scrubbed... URL: From nickwan at aggiemail.usu.edu Thu May 29 12:12:20 2014 From: nickwan at aggiemail.usu.edu (Nick Wan) Date: Thu, 29 May 2014 04:12:20 -0600 Subject: [FieldTrip] which baseline correction to choose for frequency analysis In-Reply-To: References: Message-ID: The most common event-related ​preprocessing is baseline correction for each event (in your case, 100ms baseline correction unique to each 1000ms epoch) -- at least, in my review of event-related imaging. On Thu, May 29, 2014 at 3:55 AM, KatrinH Heimann wrote: > Hey together, > another rather conceptual question: > I am wondering about the baselinecorrection for the frequencyanalysis. > I want to compare two timeperiods of one second each, lying right after > each other. > In the preprocessing I have baseline corrected them using 100 ms before > the first piece (last part of a fixationcross period). > Do I use the same part for the frequencyanalysis? Will say, do I run the > analysis let's say from -0.5 (0 point is end of fixation cross) to 2.5 s, > correcting with [-0.1 0] and then extract the two different conditions by > statistical extraction (each 1 second long) ? Or do I run two analysis on > (a bit more than) one second each, using the whole trial as baseline? > > thanks a lot for your advice again! Best > Katrin > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Nick Wan Graduate Student Utah State University Psychology Department 2810 Old Main Hill Logan, UT 84322 Office: HSRC 004 Phone: 435-554-8788 Blog: truebra.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Thu May 29 12:20:12 2014 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 29 May 2014 10:20:12 +0000 Subject: [FieldTrip] which baseline correction to choose for frequency analysis In-Reply-To: <23434_1401357818_538705FA_23434_514_1_CACnHcBdHMpYa6PGGz6=c2Cd9FfD1bR3Cgk+OGkTesrgpsR=apA@mail.gmail.com> References: <23434_1401357818_538705FA_23434_514_1_CACnHcBdHMpYa6PGGz6=c2Cd9FfD1bR3Cgk+OGkTesrgpsR=apA@mail.gmail.com> Message-ID: Hi Katrin, it sounds like you will end up using 'depsamplesT' as your statistic (because you compare repeated measures = 2 consecutive time intervals from the same subject or trial) - why do you need to use baseline-correction then? The pairing should already account for differences in baseline power between subjects (or trials). If you do need a baseline correction, I would not choose such a short baseline in the frequency domain, but go for an average over a much longer (.5 to 1 second) interval, particularly if you intend to baseline-correct single trials (because a short baseline is more likely to project noise from the baseline into your interval of interest). Also, keep in mind that ft_freqanalysis computes power across a time window (specified by you in cfg.t_ftimwin), so that power between -.1 and 0 may not only reflect "baseline" power. Best Max ________________________________ Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" im Auftrag von "KatrinH Heimann [katrinheimann at gmail.com] Gesendet: Donnerstag, 29. Mai 2014 11:55 An: FieldTrip discussion list Betreff: [FieldTrip] which baseline correction to choose for frequency analysis Hey together, another rather conceptual question: I am wondering about the baselinecorrection for the frequencyanalysis. I want to compare two timeperiods of one second each, lying right after each other. In the preprocessing I have baseline corrected them using 100 ms before the first piece (last part of a fixationcross period). Do I use the same part for the frequencyanalysis? Will say, do I run the analysis let's say from -0.5 (0 point is end of fixation cross) to 2.5 s, correcting with [-0.1 0] and then extract the two different conditions by statistical extraction (each 1 second long) ? Or do I run two analysis on (a bit more than) one second each, using the whole trial as baseline? thanks a lot for your advice again! Best Katrin From katrinheimann at gmail.com Thu May 29 13:38:53 2014 From: katrinheimann at gmail.com (KatrinH Heimann) Date: Thu, 29 May 2014 13:38:53 +0200 Subject: [FieldTrip] which baseline correction to choose for frequency analysis In-Reply-To: References: <23434_1401357818_538705FA_23434_514_1_CACnHcBdHMpYa6PGGz6=c2Cd9FfD1bR3Cgk+OGkTesrgpsR=apA@mail.gmail.com> Message-ID: Thanks Max! That helped! I will indeed not do the baseline correction! k 2014-05-29 12:20 GMT+02:00 Stenner, Max-Philipp < max-philipp.stenner at med.ovgu.de>: > Hi Katrin, > > it sounds like you will end up using 'depsamplesT' as your statistic > (because you compare repeated measures = 2 consecutive time intervals from > the same subject or trial) - why do you need to use baseline-correction > then? The pairing should already account for differences in baseline power > between subjects (or trials). If you do need a baseline correction, I would > not choose such a short baseline in the frequency domain, but go for an > average over a much longer (.5 to 1 second) interval, particularly if you > intend to baseline-correct single trials (because a short baseline is more > likely to project noise from the baseline into your interval of interest). > Also, keep in mind that ft_freqanalysis computes power across a time window > (specified by you in cfg.t_ftimwin), so that power between -.1 and 0 may > not only reflect "baseline" power. > > Best > > Max > > > > ________________________________ > > Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" > im Auftrag von "KatrinH Heimann [katrinheimann at gmail.com] > Gesendet: Donnerstag, 29. Mai 2014 11:55 > An: FieldTrip discussion list > Betreff: [FieldTrip] which baseline correction to choose for frequency > analysis > > Hey together, > another rather conceptual question: > I am wondering about the baselinecorrection for the frequencyanalysis. > I want to compare two timeperiods of one second each, lying right after > each other. > In the preprocessing I have baseline corrected them using 100 ms before > the first piece (last part of a fixationcross period). > Do I use the same part for the frequencyanalysis? Will say, do I run the > analysis let's say from -0.5 (0 point is end of fixation cross) to 2.5 s, > correcting with [-0.1 0] and then extract the two different conditions by > statistical extraction (each 1 second long) ? Or do I run two analysis on > (a bit more than) one second each, using the whole trial as baseline? > > thanks a lot for your advice again! Best > Katrin > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Fri May 30 04:09:09 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Fri, 30 May 2014 02:09:09 +0000 Subject: [FieldTrip] ft_mvaranalysis Message-ID: <1401415735027.24988@flinders.edu.au> Hello fieldtrippers, Recently when I ran the following code: cfg = []; cfg.order = 5; cfg.toolbox = 'biosig'; mdata = ft_mvaranalysis( cfg, vchan); with this data: vchan = fsample: 500 sampleinfo: [14x2 double] trial: {1x14 cell} time: {1x14 cell} label: {1x116 cell} cfg: [1x1 struct] ?I got this error : Undefined function 'mvar' for input arguments of type 'double'. Error in ft_mvaranalysis (line 385) [ar, rc, pe] = mvar(dat', cfg.order, cfg.mvarmethod); I dont really know what has gone wrong, considering I have ran this code before with 1400 channels. Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.grummett at flinders.edu.au Fri May 30 04:15:01 2014 From: tyler.grummett at flinders.edu.au (Tyler Grummett) Date: Fri, 30 May 2014 02:15:01 +0000 Subject: [FieldTrip] ft_networkanalysis Message-ID: <1401416086248.33062@flinders.edu.au> Hello fieldtrippers, Really interesting in running ft_networkanalysis and getting the most out of the function. Firstly, what types of analyses are recommended? and in what order... Ive tried looking on the brain connectivity toolbox website, but as it is already incorporated into fieldtrip so I thought I would ask on this forum if there is a recommended flow of processes. I am happy to be told to just look on the website. Also is there a between network comparison? Or is that another thing to just get from the website ( I believe they do it with the 'network based statistic' toolbox). Secondly,? when do you think there will be support for global efficiency, I am mainly interesting in calculating small-worldedness. Kind regards, Tyler ************************* Tyler Grummett ( BBSc, BSc(Hons I)) PhD Candidate Brain Signals Laboratory Flinders University Rm 5A301 Ext 66124 -------------- next part -------------- An HTML attachment was scrubbed... URL: From yingli.ucla at gmail.com Fri May 30 09:14:09 2014 From: yingli.ucla at gmail.com (Ying Li) Date: Fri, 30 May 2014 00:14:09 -0700 Subject: [FieldTrip] Mesh genration error using the template MRI Message-ID: Dear all, Fieldtrip provided a template headmodel “standard_bem.mat" and a template MRI "standard_mri.mat". I tried to use the template MRI to create the BEM head model by myself. But it seems that the scalp mesh generated by myself looks a little weird (attached). I have no idea why the scalp mesh generated by myself looks different from the one provided by the template headmodel. Does anyone know the reason? The code I used is: cfg=[]; cfg.tissue={'brain','skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,seg); Thanks a lot! Ying -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: scalp mesh.fig Type: application/x-matlab-figure Size: 14678 bytes Desc: not available URL: From michelecolombo at live.it Fri May 30 17:19:24 2014 From: michelecolombo at live.it (michele colombo) Date: Fri, 30 May 2014 17:19:24 +0200 Subject: [FieldTrip] how to specify each channel-color in a topoplot Message-ID: Dear all, My goal is to make a double plot: 1) a subplot with a topoplot of channel-values that are color-mapped, 2) a sorted stem-plot where the stem color is mapped to its height., and represent the channel values The outcome should be more easily interpretable than a colorbar, because it would allow to appreciate the whole distribution at a glance, and provide spatial info about the distance between colors. The first step would be to visualize a 1*num_channels vector plotted on the eeg scalp, with the usual topoplot style, and with colors that I define. I compute these values outside of fieldtrip, so I need to re-create the expected fieldtrip structure. Question: how to properly preserve the value-color mapping? all the intuitive options I tried fail with this respect. somehow the colormap given is used as the range of possible color-rgb-values, and subsequently the colors are chosen from this map. Instead, I would want to actually give the channel-by-channel color value to be plotted on the scalp, (interpolating as usual in the space across channels). attached, you can see a failed attempt: the colormap plotted is flattened to a very narrow sub-range of the colomap given. relevant parts of the used code: ---- hh=axes('Position',[.62 .6 .3 .3],'Layer','top'); % overlay on plot % the way i define the colormap. I tried also with a simple: winter(number_of_channels) cfg.colormap= rgbslide(all_chan_stat,'low_color',[0 0 0.75],'low_val',min(all_chan_stat), ... 'zero_color',[0 0.75 0.75],'zero_val',median(all_chan_stat), ... 'high_color',[1 0.9 0],'res',numel(all_chan_stat)); if ~isempty([bads_max bads_min]) cfg.highlight=sort([bads_max bads_min]); % hilight some outliers. this works fine. end cfg.interpolation='v4'; cfg.style='straight'; cfg.maplimits='maxmin'; fieldtrippath='/data1/toolbox/fieldtrip/compat/'; addpath(fieldtrippath); topoplot(cfg,[all_chan_stat']); % all_chan_stat is my 1*num_channels = 257 channels from the EGI system. % the old-deprecated topoplot function seems more easily accessible than the current one, provided I just use fieldtrip to plot, not to compute, the values. sorted=sort(all_chan_stat) for cc= 1: length(channels) stem(cc, sorted(cc), 'Color', cfg.colormap(cc,:), 'MarkerFaceColor', cfg.colormap(cc,:)) ; hold on; end --- Another option would be to first do the topoplot, given a colormap, then to retrieve the color plotted at each channel (but I don't know how), and use these colors to plot the stem --- another attempted option: set(gca,'colororder',cfg.colormap); plot(channels, all_chan_stat) -------------- next part -------------- A non-text attachment was scrubbed... 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