From megjim1 at GMAIL.COM Sun Apr 5 18:15:44 2009 From: megjim1 at GMAIL.COM (=?GB2312?Q?Jim?=) Date: Sun, 5 Apr 2009 18:15:44 +0200 Subject: help w/ sourceplot Message-ID: Dear all, Could anyone give me a hint how to solve this problem? I tried to played with the mri of subject1 in the tutorial page (http://fieldtrip.fcdonders.nl/tutorial/beamformer). I downloaded the segmented mri from ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/beamformer/segmentedmriF.mat, then did the following: --------------- load segmentedmriF mri = read_fcdc_mri('Subject01.mri'); segmentedmriF.transform = mri.transform; segmentedmriF.anatomy = mri.anatomy; figure cfg = []; sourceplot(cfg,segmentedmriF); %only mri ----------------------- The error message is like this: -------------------- the input is volume data with dimensions [256 256 256] ??? Error using ==> horzcat The following error occurred converting from char to cell: Error using ==> cell Conversion to cell from char is not possible. Error in ==> fieldtrip-20090404\private\parameterselection at 94 if ~issubfield(data, param{i}) && issubfield(data, ['avg.' param{i}]) Error in ==> volumedownsample at 171 cfg.parameter = parameterselection(cfg.parameter, source); Error in ==> sourceplot at 305 data = volumedownsample(tmpcfg, data); ---------------------------- Here is some information about my computer/softwares: MATLAB Version 7.0.0.19920 (R14). Operating System: Microsoft Windows XP Version 5.1 (Build 2600: Service Pack 3) Java VM Version: Java 1.4.2 with Sun Microsystems Inc. Java HotSpot(TM) Client VM And I downloaded the latest 040409 Fieldtrip. Any idea how to solve the issue? Thanks a lot, Jim ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Mon Apr 6 10:43:33 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Mon, 6 Apr 2009 09:43:33 +0100 Subject: help w/ sourceplot In-Reply-To: Message-ID: Dear Jim, Is the "amp;" in line 94 parameterselection really there, or did it pop up during the copy and paste process? I tried to reproduce your problem, but I did not manage. If removing the "amp;" does not solve your case, you could try to debug the code by typing on the command-line: "dbstop if error" and calling sourceplot after that. When it crashes, you have access to the local workspace of the functions (you can toggle between the different functions in the calling hierarchy by the commands dbup and dbdown) so that you can have a look what is going wrong. Usually, matlab is pretty explicit about what it tries to do (but fails) in its error messages. Yours, Jan-Mathijs On Apr 5, 2009, at 5:15 PM, Jim wrote: > if ~issubfield(data, param{i}) && issubfield(data, ['avg.' param > {i}] ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From vinnik at SISSA.IT Tue Apr 7 13:56:04 2009 From: vinnik at SISSA.IT (Katya Vinnik) Date: Tue, 7 Apr 2009 13:56:04 +0200 Subject: plots and stats with biosemi128.lay In-Reply-To: <3d0f9a750903231119o3cf85f4as3f5ab40bcd80af20@mail.gmail.com> Message-ID: Dear FT users, has anyone of you encountered this warning? Duplicate x-y data points detected: using average of the z values. I'm simply plotting my data with cfg.layout      = 'biosemi128.lay'; and it gives me strange plots like the one here: picasaweb.google.com/lh/photo/qmd3BgpeEDegPo4kHdRW0w?feat=directlink basically data from channels B19 and 21 and D22 and 24 are overlayed (circled in red on the pictures). This message appears also with topoplot functions. In the layout file, howether ,positions of this electrodes are different (see below). Do you think it can affect cluster-based multiple comparison correction? For example, if I use cfg.layout      = 'biosemi128.lay'; cfg.correctm = 'cluster';  [stat] = freqstatistics(cfg,x,y) does it calculate it properly? Thank you, Best regards, Katya ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Wed Apr 8 08:59:54 2009 From: megjim1 at GMAIL.COM (=?GB2312?Q?Jim_Li?=) Date: Wed, 8 Apr 2009 08:59:54 +0200 Subject: help w/ sourceplot Message-ID: Dear Jan-Mathijs, You're right: The "amp;" shouldn't be there, it's just a random thing popped up during copying. I followed your recommendation to debug and, when crash happened, I got this: ------------------ K>> param param = {} {} 'anatomy' 'inside' K>> i i = 1 K>> ['avg.' param{i}] ??? Error using ==> horzcat The following error occurred converting from char to cell: Error using ==> cell Conversion to cell from char is not possible. ------------------ Apparently the "{}" is the source of error. Tracing further, I think the following two lines of code in "sourceplot.m" seems to be the source of error since they lead to the two "{}" in the above- mentioned "param": if ~isfield(cfg, 'funparameter'), cfg.funparameter = []; end if ~isfield(cfg, 'maskparameter'), cfg.maskparameter = []; end The "segmentedmriF" I used in "sourceplot(cfg,segmentedmriF)" is like this: ------------ K>> segmentedmriF segmentedmriF = dim: [256 256 256] transform: [4x4 double] gray: [256x256x256 double] white: [256x256x256 double] csf: [256x256x256 double] cfg: [1x1 struct] anatomy: [256x256x256 uint16] ------------------- So, should the 'funparameter' and 'maskparameter' be specified in "segmentedmriF" before running the sourceplot? If so, what should they be? ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Wed Apr 8 15:04:29 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Wed, 8 Apr 2009 15:04:29 +0200 Subject: Need help with BVA files In-Reply-To: Message-ID: Hi Martijn It seems that you are using the trialfun_brainvision.m function to define trials. At least, if I try to replicate your problem it seems that definetrial sets cfg.trialfun to trialfun_brainvision (see line 156). The data format specific trialfuns (like trialfun_brainvision) are not maintained any more because they have been replaced wit a more general way of handling the events and the trial definition. Recent versions of fieldtrip also don't include the trialfun_brainvision any more. Please update your fieldtrip to the latest version and try again. You can use trialfun_general or you can write your own function for the trial definition (see for example http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition) best regards, Robert On 31 Mar 2009, at 15:23, Martijn Barendregt wrote: > I'm trying to process some E.E.G. data that I've exported from > BrainVision > Analyzer. But when I run my script (see below) I don't get any > errors but > the 'time' field in the raw_data struct will be all zeros. Because > of this I > can't do anything with the data. > > What can I do to get the time values in correctly? > > Kinds regards, > > Martijn Barendregt > > My code: > cfg = []; > cfg.datafile = 'somefile.dat'; > cfg.headerfile = 'somefile.vhdr'; > cfg.trialdef.trgfile = 'somefile.vmkr'; > cfg.trialdef.eventtype = 'Stimulus'; > cfg.trialdef.eventvalue = 'M22'; > cfg.traildef.prestim = 3; > cfg.traildef.poststim = 3; > cfg.trialdef.segment = 'no'; > cfg.trialdef.timezero = 'no'; > > [cfg] = definetrial(cfg); > > raw_data = preprocessing(cfg); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Wed Apr 8 15:20:25 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Wed, 8 Apr 2009 15:20:25 +0200 Subject: plots and stats with biosemi128.lay In-Reply-To: <3d0f9a750904070456i59c8d768na2f83e98cb3bf0a3@mail.gmail.com> Message-ID: Dear Katya If I do >> cfg.layout = 'biosemi128.lay' >> layoutplot(cfg) then I get attached figure (which you should be able to reproduce). Looking carefully it seems that D39 is lying on top of another channel. If I then do d = dist(lay.pos') imagesc(d==0) then I see that there are multiple off-diagonal elements in the distance matrix (i.e. a 128x128 matrix containing the distance bwteen all pairs) that are zero. So there are multiple channels overlapping. I don't know why that is and at the moment I don't know where the biosemi layouts were coming from. The only information that I have from the log is revision 1.1 date: 2005/06/15 08:21:08; author: roboos; state: Exp; new layout files, based on excel sheet from biosemi I don't know the details of this excel sheet any more, but probably the excel sheet was already wrong. But to come to your prime question: does it affect clustering? Yes it will. You are using the layout to define neighbours. If the layout is flawed, the neighbour definition might also be flawed. Please use the neighbourselection function to make a neighbour definition explicitely and check the neighbours by looking at the output of the neighbourselection function. best regards, Robert PS it would be nice if you could provide a better layout for the biosemi128 cap ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 1.png Type: image/png Size: 37404 bytes Desc: not available URL: -------------- next part -------------- On 7 Apr 2009, at 13:56, Katya Vinnik wrote: > Dear FT users, > > has anyone of you encountered this warning? > Duplicate x-y data points detected: using average of the z values. > > I'm simply plotting my data with cfg.layout = > 'biosemi128.lay'; > > and it gives me strange plots like the one here: > picasaweb.google.com/lh/photo/qmd3BgpeEDegPo4kHdRW0w?feat=directlink > > basically data from channels B19 and 21 and D22 and 24 are overlayed > (circled in red on the pictures). > This message appears also with topoplot functions. In the layout file, > howether ,positions of this electrodes are different (see below). > > Do you think it can affect cluster-based multiple comparison > correction? > > For example, if I use > > cfg.layout = 'biosemi128.lay'; > cfg.correctm = 'cluster'; > [stat] = freqstatistics(cfg,x,y) > > does it calculate it properly? > > Thank you, > Best regards, > Katya > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From lulswinnik at GMAIL.COM Wed Apr 8 17:19:19 2009 From: lulswinnik at GMAIL.COM (Katya Vinnik) Date: Wed, 8 Apr 2009 17:19:19 +0200 Subject: plots and stats with biosemi128.lay In-Reply-To: Message-ID: Thank you, Robert! Regards, Katya 2009/4/8 Robert Oostenveld : > Dear Katya > > If I do >>> cfg.layout = 'biosemi128.lay' >>> layoutplot(cfg) > > then I get attached figure (which you should be able to reproduce). Looking > carefully it seems that D39 is lying on top of another channel. > > If I then do > d = dist(lay.pos') > imagesc(d==0) > > then I see that there are multiple off-diagonal elements in the distance > matrix (i.e. a 128x128 matrix containing the distance bwteen all pairs) that > are zero.  So there are multiple channels overlapping. I don't know why that > is and at the moment I don't know where the biosemi layouts were coming > from. The only information that I have from the log is >  revision 1.1 >  date: 2005/06/15 08:21:08;  author: roboos;  state: Exp; >  new layout files, based on excel sheet from biosemi > > I don't know the details of this excel sheet any more, but probably the > excel sheet was already wrong. > > But to come to your prime question: does it affect clustering? Yes it will. > You are using the layout to define neighbours. If the layout is flawed, the > neighbour definition might also be flawed. Please use the neighbourselection > function to make a neighbour definition explicitely and check the neighbours > by looking at the output of the neighbourselection function. > > > best regards, > Robert > > PS it would be nice if you could provide a better layout for the biosemi128 > cap > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > > > > On 7 Apr 2009, at 13:56, Katya Vinnik wrote: > >> Dear FT users, >> >> has anyone of you encountered this warning? >> Duplicate x-y data points detected: using average of the z values. >> >> I'm simply plotting my data with       cfg.layout      = 'biosemi128.lay'; >> >> and it gives me strange plots  like the one here: >> picasaweb.google.com/lh/photo/qmd3BgpeEDegPo4kHdRW0w?feat=directlink >> >> basically data from channels B19 and 21 and D22 and 24 are overlayed >> (circled in red on the pictures). >> This message appears also with topoplot functions. In the layout file, >> howether ,positions of this electrodes are different (see below). >> >> Do you think it can affect cluster-based multiple comparison correction? >> >> For example, if I use >> >> cfg.layout      = 'biosemi128.lay'; >> cfg.correctm = 'cluster'; >>  [stat] = freqstatistics(cfg,x,y) >> >> does it calculate it properly? >> >> Thank you, >> Best regards, >> Katya >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/neuroimaging/fieldtrip. >> > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From njkillian at GATECH.EDU Wed Apr 8 22:28:13 2009 From: njkillian at GATECH.EDU (Nathan Killian) Date: Wed, 8 Apr 2009 16:28:13 -0400 Subject: problem with freqdescriptives Message-ID: Hello, I was wondering if anyone knew why a particular configuration is not giving me a jackknife result for the power spectrum, even though I am keeping trials. This problem occurs when I use FT20090404, but I at least get something returned for the standard error with FT20080611 (and it at least looked reasonable). I am using this analysis: cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.foilim = [0,100]; cfg.tapsmofrq = 4; cfg.pad = 'maxperlen'; cfg.keeptrials = 'yes'; cfg.keepfourier = 'no'; cfg.keeptapers = 'no'; cfg.pseudovalue = 'no'; cfg.jackknife = 'yes'; cfg.complex = 'complex'; freq = freqanalysis(cfg, data); freqdes = freqdescriptives(cfg, freq); Additionally, I found if you keeptrials and don't set keepfourier you will get an error only with the new version (could be easily fixed in the freqdescriptives function). Thank you for your help! Nathan -- Graduate Student - Georgia Tech Bioengineering Buffalo Lab at Emory-Yerkes: 404.712.9431 Potter Lab at Georgia Tech: 404.385.4083 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Thu Apr 9 00:14:11 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Wed, 8 Apr 2009 23:14:11 +0100 Subject: problem with freqdescriptives In-Reply-To: Message-ID: Dear Nathan, If you rely on this specific functionality of freqdescriptives I would advice you to copy the old version into your fieldtrip-folder. There are indeed some bugs in the more recent versions of freqdescriptives which have been introduced along the way, but I (and others) did not yet find time to fix it. We anyway hope to soon move to a new implementation of freqdescriptives, which does not seem to make the patching worthwile. Yours, Jan-Mathijs On Apr 8, 2009, at 9:28 PM, Nathan Killian wrote: > Hello, > > I was wondering if anyone knew why a particular configuration is > not giving me a jackknife result for the power spectrum, even > though I am keeping trials. This problem occurs when I use > FT20090404, but I at least get something returned for the standard > error with FT20080611 (and it at least looked reasonable). I am > using this analysis: > cfg.output = 'powandcsd'; > cfg.method = 'mtmfft'; > cfg.foilim = [0,100]; > cfg.tapsmofrq = 4; > cfg.pad = 'maxperlen'; > cfg.keeptrials = 'yes'; > cfg.keepfourier = 'no'; > cfg.keeptapers = 'no'; > cfg.pseudovalue = 'no'; > cfg.jackknife = 'yes'; > cfg.complex = 'complex'; > freq = freqanalysis(cfg, data); > freqdes = freqdescriptives(cfg, freq); > > Additionally, I found if you keeptrials and don't set keepfourier > you will get an error only with the new version (could be easily > fixed in the freqdescriptives function). > > Thank you for your help! > > Nathan > > -- > Graduate Student - Georgia Tech Bioengineering > Buffalo Lab at Emory-Yerkes: 404.712.9431 > Potter Lab at Georgia Tech: 404.385.4083 > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From E.J.M.vanWingerden at UVA.NL Thu Apr 9 09:59:53 2009 From: E.J.M.vanWingerden at UVA.NL (Wingerden, E.J.M. van) Date: Thu, 9 Apr 2009 09:59:53 +0200 Subject: Star-P support In-Reply-To: A<7FFBC71A-F30A-48F5-8295-153E9575B5EC@psy.gla.ac.uk> Message-ID: Dear developers, Buried in the code for freqanalysis_mtmconvol.m I found a comment about a possible implementation of parallel data processing using star-P (line 466). Is this a feature that is under development at the moment? I have some experience with star-P myself and found that using FieldTrip in combination with a star-P computing cluster is quite hampered by the fact that structures cannot be passed as broadcast arguments when the computations are distributed. Have you found ways to circumvent this problem? In my opinion, the FieldTrip code could greatly benefit from parallel computing when splitting across channels, or trials even. However, since usually datasets are split at a high level function while the actual computation takes place within a low level function, the fact that structs containing the parameters that are necessary for the computation need to be passed as arguments between these functions makes it pretty hard to make them star-P compatible. Are you in contact with the star-P developers? I would imagine that they are very interested in the programming needs of a large user community/potential customers as we have here. best regards, marijn van wingerden Mr. Marijn van Wingerden, M.Sc. PhD-candidate Cognitive & Systems Neuroscience (CSN) Centre for NeuroScience (CNS) section of Swammerdam Institute for Life Sciences (SILS) University of Amsterdam, Faculty of Science Kruislaan 320, 1098 SM Amsterdam, The Netherlands Tel: +31 20 525 7713/7547 Fax: +31 20 525 7709 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From michael.wibral at WEB.DE Thu Apr 9 12:05:59 2009 From: michael.wibral at WEB.DE (Michael Wibral) Date: Thu, 9 Apr 2009 12:05:59 +0200 Subject: second level statistics Message-ID: Dear Fieldtrippers, I have computed sourcestatistics (task vs. baseline) at the single subject level for two separate conditions (Cond 1 and Cond2) I then use these t-values source images to comapre the activations between the two conditions at the multi-subject level. Works fine. My question is whether there is any straightforward way in fieldtrip to recycle these results (sourcespace t-value images) for a multisubject analysis for task versus baseline for condition separately. What appeals to me is that these data (t-values) are 'normalized' in a meaningful way across subjects already. Would it be statistically valid to create a virtual "baseline-against-baseline" dataset (with all t-values equal to zero, of course) and test against this? Or would it be better to do sourceanalysis once more to get task and baseline source power for each subject and condition and then do the regular source statistics task-vs-basline for each condition? Any suggestions welcom, Michael Wibral ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: From susannah.murphy at PSYCH.OX.AC.UK Thu Apr 9 12:06:05 2009 From: susannah.murphy at PSYCH.OX.AC.UK (Susannah Murphy) Date: Thu, 9 Apr 2009 11:06:05 +0100 Subject: second level statistics In-Reply-To: <941146944@web.de> Message-ID: Thanks for your message. I am out of the office until Tuesday 14th April. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Thu Apr 9 21:55:48 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Thu, 9 Apr 2009 21:55:48 +0200 Subject: help w/ sourceplot Message-ID: Well, by changing MATLAB to a newer version while using the same Fieldtrip I got the problem solved. Now I can get "sourceplot" to display the MRI images. That's great! Jim On Wed, 8 Apr 2009 08:59:54 +0200, Jim Li wrote: >Dear Jan-Mathijs, > >You're right: The "amp;" shouldn't be there, it's just a random thing popped >up during copying. > >I followed your recommendation to debug and, when crash happened, I got >this: > > >------------------ >K>> param > >param = > > {} {} 'anatomy' 'inside' > >K>> i > >i = > > 1 > >K>> ['avg.' param{i}] >??? Error using ==> horzcat >The following error occurred converting from char to cell: >Error using ==> cell >Conversion to cell from char is not possible. > >------------------ > >Apparently the "{}" is the source of error. > >Tracing further, I think the following two lines of code in "sourceplot.m" seems >to be the source of error since they lead to the two "{}" in the above- >mentioned "param": >if ~isfield(cfg, 'funparameter'), cfg.funparameter = []; end >if ~isfield(cfg, 'maskparameter'), cfg.maskparameter = []; end > > >The "segmentedmriF" I used in "sourceplot(cfg,segmentedmriF)" is like this: >------------ >K>> segmentedmriF > >segmentedmriF = > > dim: [256 256 256] > transform: [4x4 double] > gray: [256x256x256 double] > white: [256x256x256 double] > csf: [256x256x256 double] > cfg: [1x1 struct] > anatomy: [256x256x256 uint16] >------------------- > >So, should the 'funparameter' and 'maskparameter' be specified >in "segmentedmriF" before running the sourceplot? If so, what should they be? > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Fri Apr 10 20:01:58 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Fri, 10 Apr 2009 20:01:58 +0200 Subject: can I combine subplot and multiplotTFR to get multiple epochs displayed on 1 page? Message-ID: Dear Fieldtripper, I tried something like this to do two multiplotTFR plot on one page, but it didn't work: TF = freqanalysis(cfg,data); TF2 = freqanalysis(cfg,data2); subplot(2,1,1); multiplotTFR(cfg,TF); subplot(2,1,2); multiplotTFR(cfg,TF); Any idea how to combine subplot and multiplotTFR to get multiple "multiplotTFR" plots displayed on 1 page? Thanks, Jim ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From todavidkim at GMAIL.COM Fri Apr 10 22:59:08 2009 From: todavidkim at GMAIL.COM (David Kim) Date: Fri, 10 Apr 2009 13:59:08 -0700 Subject: Help with dipole-fitting simultaneous MEG/EEG data Message-ID: Dear Fieldtrip users, I have been working on solving dipole-fitting problem of a simultaneous MEG/EEG data with Fieldtrip. The MEG and EEG sensor definitions (275, 64) is generated to conform to Fieldtrip standard. A 4 shell volume conduction model for EEG and 1 shell model for MEG have been generated to conform to Fieldtrip standard. Given the stimulus, I'm assuming that a single dipole drives the signal in both EEG and MEG. Therefore, I would like to use Fieldtrip to find a dipole that best describes the simultaneously acquired MEG/EEG data in the following sense: A single dipole fit with 9 characteristic values consisting of: dipole position. 3 values, (x,y,z) dipole moment (given the dipole position) that best fits MEG data. 3 dipole moment (given the dipole position) that best fits EEG data. 3 Currently, Fieldtrip has compute_leadfield.m function which can take a cell of multiple volume and sensor definitions as described in line 22 and 23 of the code. % sens = {senseeg, sensmeg} % vol = {voleeg, volmeg} With compute_leadfield.m, I can perform the dipole-fitting, but this requires custom scripts outside of Fieldtrip which can get messy and vary from data to data. I would much rather have the process be done within the Fieldtrip environment where the process is more robust and streamlined. It would be ideal to have the data pass through to dipfit_error() subroutine defined in dipole_fit.m function, where the modifications to dipfit_error() definition would determine the outcome of the fit. It appears to me, however, both dipolefitting.m and dipole_fit.m are not made to process multiple sensor definitions. For example, line 166 of dipole_fit.m reads, "error('simultaneous EEG and MEG not supported');" Is simultaneous EEG/MEG processing of data already implemented in Fieldtrip that I'm not aware of? If not what steps could we take to implement such a feature? Thank you. David Kim ---------------------------------------------------------------------- UCSF/UC Berkeley Bioengineering Graduate Group todavidkim at gmail.com (510) 643-7571 http://cornea.berkeley.edu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From lwn_07 at YAHOO.COM.CN Sun Apr 12 06:03:11 2009 From: lwn_07 at YAHOO.COM.CN (=?utf-8?B?5p2O5Y2r5aic?=) Date: Sun, 12 Apr 2009 12:03:11 +0800 Subject: Ask for help :How can I read the weights file of SAM spatial filter? Message-ID: Dear fieldtripers,       I want to read the SAM spatial filters of my MEG data recorded by CTF151 MEG system in a motor task. It seems the file in a ".svl.max.wts" format describe the "weights" information, but I can't read the out. And I found that there was a "read_ctf_coef.m" file in "eeglab plugins" which is copyrighted to Robert, can returns the spatial filter cofficients for CTF MEG system, and these cofficients were not read from a file but already existed. Is this "cofficients" and my weights the same thing?       The description of function "read_ctf_coef" is as follows:   function [coef] = read_ctf_coef % READ_CTF_COEF returns the spatial filter coefficients for the CTF MEG system % that has been installed at the F.C. Donders Centre (id 1706) % % This function actually does not read the coefficients from a file, but the % coefficients themselves are included in this function. % % The original location of the coefficients included in this file is % odin:/opt/ctf/hardware/M016/M017_1706.coef % Copyright (C) 2003, Robert Oostenveld          Best Wishes!                                                                                            Weina LI                                                                                         2009.04.12 ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Roozbeh.Rezaie at UTH.TMC.EDU Mon Apr 13 16:12:53 2009 From: Roozbeh.Rezaie at UTH.TMC.EDU (Rezaie, Roozbeh) Date: Mon, 13 Apr 2009 09:12:53 -0500 Subject: ISACM 2009- Call For Abstracts Message-ID: ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2009 ISACM Conference Call for Abstracts.pdf Type: application/pdf Size: 127099 bytes Desc: 2009 ISACM Conference Call for Abstracts.pdf URL: From chintan_student at YAHOO.CO.IN Mon Apr 13 20:57:17 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Tue, 14 Apr 2009 00:27:17 +0530 Subject: regarding start Message-ID: Dear sir, i just started learning fieldtrip.  can u tell me how to run the tutorial scripts in matlab.  Check out the all-new Messenger 9.0! Go to http://in.messenger.yahoo.com/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From megjim1 at GMAIL.COM Mon Apr 13 23:35:59 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Mon, 13 Apr 2009 23:35:59 +0200 Subject: Makefile for Linux 64 Message-ID: Dear FTer: We're thinking of buying a 64-bit Quad-core PC w/ big memory(>=16GB), then install a Linux OS (CentOS 4) and run Fieldtrip on it. According to the first question asked by Christine below, there seems to be a problem w/ SPM2. Is that still an issue or is it solved by now? Are there any other issues to pay attention to w/ 64-bit linux? Thanks a lot, Jim On Tue, 18 Sep 2007 17:03:59 +0200, Christine Tillmann wrote: >Hi, > >we are trying to get the fieldtrip beamforming on our linux 64 bit >systems going. As we understand it, there is currently no way around >using spm2. Spm2's mex files however are not compiled for linux 64 bit >and the makefile that's available on the web suffers from the tab/space >delimiter problem. >Does anyone have a makefile for spm2 that works on linux 64 bit? > >Or, else is there a way around spm2? E.g. by using the output of >mriviewer and the localspheres command directly? Or by beamforming in >CTF and feeding its output to sourcestatistics? > >And one last thing: does anyone use the mri files from trhe >CTF-MRIviewer that came with version 5.4.0 yet? > >Thanks, >Christine > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From gflandin at FIL.ION.UCL.AC.UK Wed Apr 15 12:27:10 2009 From: gflandin at FIL.ION.UCL.AC.UK (Guillaume Flandin) Date: Wed, 15 Apr 2009 11:27:10 +0100 Subject: Makefile for Linux 64 In-Reply-To: Message-ID: Dear Jim, some 64bit Linux MEX files for SPM2 are available from here: ftp://ftp.fil.ion.ucl.ac.uk/spm/spm2_updates/ The website mentioned in previous email is the SPM wikibooks: http://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Linux#Compilation_notes_for_SPM2: I also attach a SPM2 Makefile that contains instructions for Linux64 compilation, in case the provided compiled MEX files do not work on your platform. Best regards, Guillaume. Jim Li wrote: > Dear FTer: > > We're thinking of buying a 64-bit Quad-core PC w/ big memory(>=16GB), then > install a Linux OS (CentOS 4) and run Fieldtrip on it. According to the first > question asked by Christine below, there seems to be a problem w/ SPM2. Is > that still an issue or is it solved by now? Are there any other issues to pay > attention to w/ 64-bit linux? > > > Thanks a lot, > > Jim > > On Tue, 18 Sep 2007 17:03:59 +0200, Christine Tillmann FRANKFURT.MPG.DE> wrote: > >> Hi, >> >> we are trying to get the fieldtrip beamforming on our linux 64 bit >> systems going. As we understand it, there is currently no way around >> using spm2. Spm2's mex files however are not compiled for linux 64 bit >> and the makefile that's available on the web suffers from the tab/space >> delimiter problem. >> Does anyone have a makefile for spm2 that works on linux 64 bit? >> >> Or, else is there a way around spm2? E.g. by using the output of >> mriviewer and the localspheres command directly? Or by beamforming in >> CTF and feeding its output to sourcestatistics? >> >> And one last thing: does anyone use the mri files from trhe >> CTF-MRIviewer that came with version 5.4.0 yet? >> >> Thanks, >> Christine -- Guillaume Flandin, PhD Wellcome Trust Centre for Neuroimaging University College London 12 Queen Square London WC1N 3BG ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Makefile URL: From chintan_student at YAHOO.CO.IN Wed Apr 15 16:33:20 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Wed, 15 Apr 2009 20:03:20 +0530 Subject: [FIELD TRIP] regarding define trial Message-ID: folks,   I am going through the tutorials of fieldtrip.  When I try to run the example scripts on matlab, I am getting an error regarding the functions which are undefined such as definetrial or preprocessing.  Please guide me to built the functions on fieldtrip.     Thanking you   Chintan Check out the all-new Messenger 9.0! Go to http://in.messenger.yahoo.com/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Wed Apr 15 16:44:58 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Wed, 15 Apr 2009 15:44:58 +0100 Subject: [FIELD TRIP] regarding define trial In-Reply-To: <692084.73060.qm@web95408.mail.in2.yahoo.com> Message-ID: Dear Chintan, You probably still have to add the fieldtrip folder to you matlab- path, after you downloaded the most recent fieldtrip version. Yours, JM On Apr 15, 2009, at 3:33 PM, shah chintan wrote: > folks, > > I am going through the tutorials of fieldtrip. When I try to run > the example scripts on matlab, I am getting an error regarding the > functions which are undefined such as definetrial or > preprocessing. Please guide me to built the functions on fieldtrip. > > > Thanking you > > Chintan > > Add more friends to your messenger and enjoy! Invite them now. > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lwn_07 at YAHOO.COM.CN Wed Apr 15 16:19:41 2009 From: lwn_07 at YAHOO.COM.CN (=?utf-8?B?5p2O5Y2r5aic?=) Date: Wed, 15 Apr 2009 22:19:41 +0800 Subject: =?utf-8?Q?=E5=9B=9E=E5=A4=8D=EF=BC=9A?= [FIELDTRIP] Ask for help :How can I read the weights file of SAM spatial filter? Message-ID: I found a way to read the weigts in http://kurage.nimh.nih.gov/meglab/Meg/Readwts may help someone else     --- 09年4月12日，周日, 李卫娜 写道： 发件人: 李卫娜 主题: [FIELDTRIP] Ask for help :How can I read the weights file of SAM spatial filter? 收件人: FIELDTRIP at NIC.SURFNET.NL 日期: 2009年4月12日,周日,下午12:03 Dear fieldtripers,       I want to read the SAM spatial filters of my MEG data recorded by CTF151 MEG system in a motor task. It seems the file in a ".svl.max.wts" format describe the "weights" information, but I can't read the out. And I found that there was a "read_ctf_coef.m" file in "eeglab plugins" which is copyrighted to Robert, can returns the spatial filter cofficients for CTF MEG system, and these cofficients were not read from a file but already existed. Is this "cofficients" and my weights the same thing?       The description of function "read_ctf_coef" is as follows:   function [coef] = read_ctf_coef % READ_CTF_COEF returns the spatial filter coefficients for the CTF MEG system % that has been installed at the F.C. Donders Centre (id 1706) % % This function actually does not read the coefficients from a file, but the % coefficients themselves are included in this function. % % The original location of the coefficients included in this file is % odin:/opt/ctf/hardware/M016/M017_1706.coef % Copyright (C) 2003, Robert Oostenveld          Best Wishes!                                                                                            Weina LI                                                                                         2009.04.12 好玩贺卡等你发，邮箱贺卡全新上线！ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at GMAIL.COM Wed Apr 15 17:27:29 2009 From: julian.keil at GMAIL.COM (Julian Keil) Date: Wed, 15 Apr 2009 17:27:29 +0200 Subject: Plot ECoG-Electrodes Message-ID: Hello, we have recently begun to work with ECoG data. Now we would like to plot results from timelock and freqanalysis. Is there any possibility to plot the (known) electrode position onto the brain using sourceplot? Thanks a lot Julian Dipl. Psych. Julian Keil OBOB-Lab University of Konstanz Department of Psychology P.O. Box D23 78457 Konstanz Germany Tel: ++49 - (0)7531 - 88 42 50 Fax: ++49 - (0)7531 - 88 28 91 Email: julian.keil at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Wed Apr 15 17:30:51 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Wed, 15 Apr 2009 21:00:51 +0530 Subject: [FIELD TRIP] regarding define trial Message-ID: Dear schofflen, Do you mean to say that I need to download all the zip files along with the directory and locate them to some folder.  And then locate matlab to that folder.   Best   Chintan --- On Wed, 15/4/09, jan-mathijs schoffelen wrote: From: jan-mathijs schoffelen Subject: Re: [FIELDTRIP] [FIELD TRIP] regarding define trial To: FIELDTRIP at NIC.SURFNET.NL Date: Wednesday, 15 April, 2009, 8:14 PM Dear Chintan, You probably still have to add the fieldtrip folder to you matlab-path, after you downloaded the most recent fieldtrip version. Yours, JM On Apr 15, 2009, at 3:33 PM, shah chintan wrote: folks,   I am going through the tutorials of fieldtrip.  When I try to run the example scripts on matlab, I am getting an error regarding the functions which are undefined such as definetrial or preprocessing.  Please guide me to built the functions on fieldtrip.     Thanking you   Chintan Add more friends to your messenger and enjoy! Invite them now. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Wed Apr 15 19:42:49 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Wed, 15 Apr 2009 23:12:49 +0530 Subject: regarding directory files. Message-ID: Dear folks, Currently I am working on field trip tutorials.  I downloaded all the zip files and directories.  Can anybody tell me where to put directory files and how to locate on matlab.   Best regards,   Chintan Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Wed Apr 15 21:19:20 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Wed, 15 Apr 2009 20:19:20 +0100 Subject: regarding directory files. In-Reply-To: <84601.71472.qm@web95404.mail.in2.yahoo.com> Message-ID: Dear Chintan, I am afraid that the problem you have at the moment is unrelated to FieldTrip, but rather a general matlab issue. It does not matter where you put the files, as long as you tell matlab where to find them. If you put the files in, say, C: \mydirectory\fieldtrip, then you should issue the following command from the matlab command-line: addpath(genpath('C:\mydirectory \fieldtrip')), or you can specify the path using the set path utility (and then you have to add with subdirectories). If this all sounds unfamiliar to you, I strongly advise you to look into the matlab documentation to learn how to work with matlab. Yours, Jan-Mathijs On Apr 15, 2009, at 6:42 PM, shah chintan wrote: > Dear folks, > Currently I am working on field trip tutorials. I downloaded all > the zip files and directories. Can anybody tell me where to put > directory files and how to locate on matlab. > > Best regards, > > Chintan > > Download prohibited? No problem. CHAT from any browser, without > download. > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Wed Apr 15 21:23:44 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Thu, 16 Apr 2009 00:53:44 +0530 Subject: regarding directory files. Message-ID: Dear Sir,   I am very glad with your reply.  Actually I am not finding any .mat files in the installed package of matlab.  And the directories that is available at fieldtrip are all .mat files, So I am not getting where to put those directories.  Can you specify which version of matlab is compatible with fieldtrip. I am usig MATLAB 7.4.0.   Best Regards,   Chintan --- On Thu, 16/4/09, jan-mathijs schoffelen wrote: From: jan-mathijs schoffelen Subject: Re: [FIELDTRIP] regarding directory files. To: FIELDTRIP at NIC.SURFNET.NL Date: Thursday, 16 April, 2009, 12:49 AM Dear Chintan, I am afraid that the problem you have at the moment is unrelated to FieldTrip, but rather a general matlab issue. It does not matter where you put the files, as long as you tell matlab where to find them. If you put the files in, say, C:\mydirectory\fieldtrip, then you should issue the following command from the matlab command-line: addpath(genpath('C:\mydirectory\fieldtrip')), or you can specify the path using the set path utility (and then you have to add with subdirectories). If this all sounds unfamiliar to you, I strongly advise you to look into the matlab documentation to learn how to work with matlab. Yours, Jan-Mathijs   On Apr 15, 2009, at 6:42 PM, shah chintan wrote: Dear folks, Currently I am working on field trip tutorials.  I downloaded all the zip files and directories.  Can anybody tell me where to put directory files and how to locate on matlab.   Best regards,   Chintan Download prohibited? No problem. CHAT from any browser, without download. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Wed Apr 15 21:48:48 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Thu, 16 Apr 2009 01:18:48 +0530 Subject: regarding definetrial and preprocessing Message-ID: Folks,   I am working on fieldtrip tutorials.  I downloaded all the files and directories from tutorials.  Now when I run the scripts, an error occurs that definetrial and preprocessing functions are undefined.  Please help me in  building these functions.   Best Regards,   Chintan Connect with friends all over the world. Get Yahoo! India Messenger at http://in.messenger.yahoo.com/?wm=n/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From megjim1 at GMAIL.COM Fri Apr 17 04:11:06 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Fri, 17 Apr 2009 04:11:06 +0200 Subject: Makefile for Linux 64 Message-ID: Dear Guillaume, That's great! I'm downloading them now. Thanks a lot for your wonderful help, :) Jim On Wed, 15 Apr 2009 11:27:10 +0100, Guillaume Flandin wrote: >Dear Jim, > >some 64bit Linux MEX files for SPM2 are available from here: >ftp://ftp.fil.ion.ucl.ac.uk/spm/spm2_updates/ > >The website mentioned in previous email is the SPM wikibooks: >http://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Linux#Compilation_not es_for_SPM2: > >I also attach a SPM2 Makefile that contains instructions for Linux64 >compilation, in case the provided compiled MEX files do not work on your >platform. > >Best regards, >Guillaume. > > >Jim Li wrote: >> Dear FTer: >> >> We're thinking of buying a 64-bit Quad-core PC w/ big memory(>=16GB), then >> install a Linux OS (CentOS 4) and run Fieldtrip on it. According to the first >> question asked by Christine below, there seems to be a problem w/ SPM2. Is >> that still an issue or is it solved by now? Are there any other issues to pay >> attention to w/ 64-bit linux? >> >> >> Thanks a lot, >> >> Jim >> >> On Tue, 18 Sep 2007 17:03:59 +0200, Christine Tillmann > FRANKFURT.MPG.DE> wrote: >> >>> Hi, >>> >>> we are trying to get the fieldtrip beamforming on our linux 64 bit >>> systems going. As we understand it, there is currently no way around >>> using spm2. Spm2's mex files however are not compiled for linux 64 bit >>> and the makefile that's available on the web suffers from the tab/space >>> delimiter problem. >>> Does anyone have a makefile for spm2 that works on linux 64 bit? >>> >>> Or, else is there a way around spm2? E.g. by using the output of >>> mriviewer and the localspheres command directly? Or by beamforming in >>> CTF and feeding its output to sourcestatistics? >>> >>> And one last thing: does anyone use the mri files from trhe >>> CTF-MRIviewer that came with version 5.4.0 yet? >>> >>> Thanks, >>> Christine > > > >-- >Guillaume Flandin, PhD >Wellcome Trust Centre for Neuroimaging >University College London >12 Queen Square >London WC1N 3BG > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >#!make -f ># ># @(#)Makefile 2.16 John Ashburner 03/05/12 ># Note that changes have been made outside SCCS ># $Id$ ># >#################################################### ########################### ># ># Suggestions for how to make this file a bit more elegant are welcome. So far ># it works under SunOS and Linux (at the FIL) and some Windows systems ># ># $Log$ ># >#################################################### ########################### > >#################################################### ########################### ># Default make >#################################################### ########################### >unknown: > @ make `uname` >tidy: > @ make clean.`uname` > >#################################################### ########################### ># Architecture specific makes >#################################################### ########################### > >MEX = mex -O >CC = cc ># mex output object suffix >MOSUF = o >CHMODIT = chmod 644 >RANLIB = >ADDED_OBS= >ADDED_MEX= > >SunOS: > make all SUF=mexsol CC="cc -xO5" MEX="mex COPTIMFLAGS=-xO5" >Linux: > make all SUF=mexglx CC="gcc -O3 -funroll-loops" MEX="mex COPTIMFLAGS='-O3 -funroll-loops'" >Linux.5: > make all SUF=mexlx CC="gcc -O3 -funroll-loops" MEX="mex COPTIMFLAGS='-O3 -funroll-loops'" >HP-UX: > make all SUF=mexhp7 CC="cc -O +z -Ae +DAportable" MEX="mex COPTIMFLAGS=-O" >IRIX: > make all SUF=mexsg CC="cc -O -mips2" MEX="mex" >IRIX64: > make all SUF=mexsg64 CC="cc -O -mips4 -64" MEX="mex" >AIX: > make all SUF=mexrs6 >OSF1: > make all SUF=mexaxp >MAC: > make all SUF=mexmac RANLIB="ranlib spm_vol_utils.mexmac.a" > >Linux.A64: ># The '-fPIC' option is nexessary to allow the linking proces to complete. ># '-march=x86-64' provides generic optimisations for both Opteron and 64bit Xeon. ># If the code is running on a 64bit Xeon you can change '-march=x86-64' to ># '-march=nocona', when running on an Opteron, change it to '- march=opteron'. ># Also possibly use '-march=k8' for 64 bit Athlon. > make all SUF=mexa64 CC="gcc -O3 -funroll-loops -fPIC -march=x86- 64 -mfpmath=sse"\ > MEX="mex COPTIMFLAGS='-O3 -funroll-loops -fPIC -march=x86- 64 -mfpmath=sse'" > >#windows: ># make all SUF=dll MOSUF=obj CHMODIT="echo > null" ADDED_OBS=win32mmap.dll.o ADDED_MEX=spm_win32utils.dll >windows: ># Consider adding either of the following, depending on your platform: ># -march=pentium3 ># -march=pentium4 > make all SUF=dll CC="gcc -mno-cygwin -O3 -funroll-loops -fomit- frame-pointer -march=pentium4 -mfpmath=sse -DSPM_WIN32" MEX="mex.bat - DSPM_WIN32" MOSUF=obj CHMODIT="echo > NUL" ADDED_OBS=win32mmap.dll.o ADDED_MEX=spm_win32utils.dll > >#################################################### ########################### ># Architecture specific cleaning >#################################################### ########################### >clean.SunOS: > make clean SUF=mexsol >clean.Linux: > make clean SUF=mexglx >clean.Linux.5: > make clean SUF=mexlx >clean.Linux.A64: > make clean SUF=mexa64 >clean.HP-UX: > make clean SUF=mexhp7 >clean.IRIX: > make clean SUF=mexsg >clean.IRIX64: > make clean SUF=mexsg64 >clean.AIX: > make clean SUF=mexrs6 >clean.OSF1: > make clean SUF=mexaxp >clean.MAC: > make clean SUF=mexmac >clean.windows: > make clean SUF=dll > >#################################################### ########################### ># Objects to go in the archive and mexfiles >#################################################### ########################### > >SUF = unknown > >OBS = utils_uchar.$(SUF).o utils_short.$(SUF).o utils_int.$(SUF).o \ > utils_schar.$(SUF).o utils_ushort.$(SUF).o utils_uint.$(SUF).o\ > utils_float.$(SUF).o utils_double.$(SUF).o\ > utils_short_s.$(SUF).o utils_int_s.$(SUF).o\ > utils_ushort_s.$(SUF).o utils_uint_s.$(SUF).o\ > utils_float_s.$(SUF).o utils_double_s.$(SUF).o\ > spm_make_lookup.$(SUF).o spm_getdata.$(SUF).o spm_vol_access.$(SUF).o\ > spm_mapping.$(SUF).o $(ADDED_OBS) > >SPMMEX =\ > spm_sample_vol.$(SUF) spm_slice_vol.$(SUF) spm_brainwarp.$(SUF)\ > spm_add.$(SUF) spm_conv_vol.$(SUF) spm_render_vol.$(SUF)\ > spm_global.$(SUF) spm_resels_vol.$(SUF)\ > spm_atranspa.$(SUF) spm_list_files.$(SUF) spm_unlink.$(SUF)\ > spm_krutil.$(SUF) spm_project.$(SUF) spm_hist2.$(SUF) spm_max.$(SUF)\ > spm_clusters.$(SUF) spm_bsplinc.$(SUF) spm_bsplins.$(SUF)\ > spm_bias_mex.$(SUF) spm_dilate.$(SUF) $(ADDED_MEX) > >#################################################### ########################### ># The main ways to run make >#################################################### ########################### > >all: verb.$(SUF) $(SPMMEX) > @ echo "_____________________________________________________________ " > @ echo "" > @ echo " FINISHED" > @ echo "_____________________________________________________________ " > @ echo "" > >very_clean: clean > @ echo "_____________________________________________________________ " > @ echo "" > @ echo " Deleting mex and archive (.a) files" > @ echo "_____________________________________________________________ " > @ echo "" > rm -f $(SPMMEX) spm_vol_utils.$(SUF).a > >clean: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo " Deleting object (.o) files" > @ echo "_____________________________________________________________ " > @ echo "" > rm -f $(OBS) > >archive: spm_vol_utils.$(SUF).a > >#################################################### ########################### ># Compile spm_vol_utils.c with various flags >#################################################### ########################### > >spm_vol_utils.$(SUF).a: $(OBS) > rm -f $@ > ar rcv $@ $(OBS) > $(RANLIB) > @ $(CHMODIT) $@ > >UTILS=spm_vol_utils.c spm_sys_deps.h spm_make_lookup.h spm_getdata.h > >utils_uchar.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_CHAR > @ $(CHMODIT) $@ > >utils_short.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_SHORT > @ $(CHMODIT) $@ > >utils_int.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_INT > @ $(CHMODIT) $@ > >utils_schar.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_CHAR > @ $(CHMODIT) $@ > >utils_ushort.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_SHORT > @ $(CHMODIT) $@ > >utils_uint.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_INT > @ $(CHMODIT) $@ > >utils_float.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_FLOAT > @ $(CHMODIT) $@ > >utils_double.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_DOUBLE > @ $(CHMODIT) $@ > >utils_short_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_SHORT - DSPM_BYTESWAP > @ $(CHMODIT) $@ > >utils_int_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_INT - DSPM_BYTESWAP > @ $(CHMODIT) $@ > >utils_ushort_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_SHORT - DSPM_BYTESWAP > @ $(CHMODIT) $@ > >utils_uint_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_INT - DSPM_BYTESWAP > @ $(CHMODIT) $@ > >utils_float_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_FLOAT -DSPM_BYTESWAP > @ $(CHMODIT) $@ > >utils_double_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_DOUBLE -DSPM_BYTESWAP > @ $(CHMODIT) $@ > >#################################################### ########################### ># Compile a few additional C routines for linking >#################################################### ########################### > >%.$(SUF).o : %.c spm_sys_deps.h > $(CC) -c -o $@ $< > @ $(CHMODIT) $@ > >spm_getdata.$(SUF).o: spm_getdata.c spm_sys_deps.h > >spm_vol_access.$(SUF).o: spm_vol_access.c spm_vol_access.h spm_datatypes.h > >spm_make_lookup.$(SUF).o: spm_make_lookup.c spm_sys_deps.h > >spm_getdata.$(SUF).o: spm_getdata.c > >spm_mapping.$(SUF).o: spm_mapping.c spm_sys_deps.h spm_mapping.h spm_datatypes.h > $(MEX) -c spm_mapping.c > mv spm_mapping.$(MOSUF) $@ > @ $(CHMODIT) $@ > >win32mmap.$(SUF).o: win32mmap.c win32mmap.h > $(CC) -c -o $@ win32mmap.c > @ $(CHMODIT) $@ > >#################################################### ########################### ># Compile the mex files themselves >#################################################### ########################### > >%.$(SUF) : %.c spm_sys_deps.h > $(MEX) $< > @ $(CHMODIT) $@ > >spm_add.$(SUF): spm_add.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h > $(MEX) spm_add.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_brainwarp.$(SUF): spm_brainwarp.c spm_vol_utils.$(SUF).a spm_matfuns.c\ > spm_sys_deps.h spm_mapping.h > $(MEX) spm_brainwarp.c spm_vol_utils.$(SUF).a spm_matfuns.c > @ $(CHMODIT) $@ > >spm_bsplinc.$(SUF): spm_bsplinc.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h spm_datatypes.h > $(MEX) spm_bsplinc.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_bsplins.$(SUF): spm_bsplins.c spm_sys_deps.h > $(MEX) spm_bsplins.c > @ $(CHMODIT) $@ > >spm_conv_vol.$(SUF): spm_conv_vol.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h spm_datatypes.h > $(MEX) spm_conv_vol.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_global.$(SUF): spm_global.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h > $(MEX) spm_global.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_atranspa.$(SUF): spm_atranspa.c spm_sys_deps.h > >spm_unlink.$(SUF): spm_unlink.c spm_sys_deps.h > >spm_max.$(SUF): spm_max.c spm_sys_deps.h > >spm_clusters.$(SUF): spm_clusters.c spm_sys_deps.h > >spm_hist2.$(SUF): spm_hist2.c spm_sys_deps.h > >spm_krutil.$(SUF): spm_krutil.c spm_sys_deps.h > >spm_dilate.$(SUF): spm_dilate.c > >spm_list_files.$(SUF): spm_list_files.c spm_sys_deps.h > >spm_project.$(SUF): spm_project.c spm_sys_deps.h > >spm_render_vol.$(SUF): spm_render_vol.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h > $(MEX) spm_render_vol.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_resels_vol.$(SUF): spm_resels_vol.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h > $(MEX) spm_resels_vol.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_sample_vol.$(SUF): spm_sample_vol.c spm_vol_utils.$(SUF).a spm_mapping.h > $(MEX) spm_sample_vol.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_slice_vol.$(SUF): spm_slice_vol.c spm_vol_utils.$(SUF).a spm_mapping.h > $(MEX) spm_slice_vol.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_bias_mex.$(SUF): spm_bias_mex.c spm_vol_utils.$(SUF).a spm_mapping.h > $(MEX) spm_bias_mex.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_win32utils.$(SUF): spm_win32utils.c > $(MEX) spm_win32utils.c > @ $(CHMODIT) $@ > >#################################################### ########################### ># Assorted architecture dependent messages >#################################################### ########################### > >verb.unknown: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "PROBLEM: Dont know how to do this." > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexhp7: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "unix compile for hpux cc, and maybe aix cc" > @ echo "" > @ echo "Under HPUX 10.20 with MATLAB 5.2.1 and gcc, you may wish" > @ echo "to modify this Makefile to say something like:" > @ echo ' CC=gcc -O -fpic' > @ echo ' MEX=mex COPTIMFLAGS=-O -f gccopts.sh' > @ echo "where the gccopts.sh file is modified to remove the +z" > @ echo "(which is used with version 9.0 and possibly also 10.0)." > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexsg: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Feedback from users with R10000 O2 and R10000 Indigo2 systems" > @ echo "running IRIX6.5 suggests that the cmex program with Matlab 5.x" > @ echo "compiles with the old 32bit (o32) instruction set (MIPS2) only," > @ echo "while cc by default compiles with the new32 bit (n32 or MIPS4)." > @ echo "Matlab 5.x only likes o32 for O2 R10000 systems." > @ echo "" > @ echo "We also suggest you modify your options file mexopts.sh in" > @ echo 'the sgi section: change LD="ld" to LD="ld -o32"' > @ echo "this tells the linker to use o32 instead of n32." > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexsg64: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "not optimised sgi 64 bit compile for CC" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.dll: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Windows compile with gcc/mingw" > @ echo "see http://www.mrc- cbu.cam.ac.uk/Imaging/gnumex20.html" > @ echo "for instructions about installing gcc/mingw for" > @ echo "compiling Mex files." > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexsol: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Unix compile for Sun cc" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexlx: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Linux compilation (Matlab 5.x) - using gcc" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexglx: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Linux compilation (Matlab 6.x) - using gcc" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexaxp: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "keep your fingers crossed" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexmac: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Unix compile for MacOS X" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexa64: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Unix compile for Linux A64" > @ echo "_____________________________________________________________ " > @ echo "" > > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From cmuehl at GMAIL.COM Fri Apr 17 15:01:26 2009 From: cmuehl at GMAIL.COM (Christian Muehl) Date: Fri, 17 Apr 2009 15:01:26 +0200 Subject: CfP Workshop on Affective Brain-Computer Interfaces (aBCI '09) Message-ID: -------------------------------------------------------------- Call for Papers -------------------------------------------------------------- Workshop on Affective Brain-Computer Interfaces (held in conjunction with ACII’09) Amsterdam, The Netherlands, 09.09.2009 -------------------------------------------------------------- Overview: ------------ This workshop will explore the advantages and limitations of using neurophysiological signals as a modality for the automatic recognition of affective and cognitive states, as well as the possibilities to use this information about the user state in innovative and adaptive applications. Theme of the workshop: ------------------------------ Recent research efforts in brain-computer interfaces (BCI) show that brain activity can be used as an active/voluntary, or passive/involuntary control modality in man-machine interaction. While active BCI paradigms received a lot of attention in recent years, research on passive approaches to BCI is still lacking concerted activity. However, it has been shown more than once that brain activations can carry information about the affective and cognitive state of a subject, and that the interaction between humans and machines can be aided by the recognition of those user states. To achieve robust passive BCIs, efforts from applied and basic sciences have to be combined. On the one hand, applied fields such as affective computing aim at the development of applications that adapt to changes in the user states and thereby enrich the interaction, leading to a more natural and effective usability. On the other hand, basic research in neuroscience advances our understanding of the neural processes associated with emotions. Furthermore, similar advancements are being made for more cognitive mental states, for example attention, fatigue, and work load, which strongly interact with affective states. We encourage submissions exploring one or more of the following topics: * emotion elicitation and data collection for affective BCI * detection of affective and cognitive states with BCI and other modalities * adaptive interfaces and affective BCI Goal of the workshop: --------------------------- The goal of the workshop is to bring researchers from the communities of brain computer interfacing, affective computing, neuroergonomics, affective and cognitive neuroscience together to present state-of-the-art progress and visions on the various intersections between those disciplines. Paper submissions: ----------------------- Papers should be 8 - 15 pages long and in the format of the CTIT Series Proceedings. They should have a clear relationship to brain-computer interfacing and to one or more of the other topics listed above. Technical papers, as well as survey papers and empirical papers are eligible. The accepted papers will be published in the workshop proceedings (CTIT Series, ISSN Number available). Please submit your papers in PDF format to ABCI at ewi.utwente.nl . Important Dates: --------------------- Paper Submission: 15.06.2009 Acceptance Note: 15.07.2009 Camera-ready versions: 15.08.2009 Further information can be found on the workshop website. Workshop Website: http://hmi.ewi.utwente.nl/abci2009 Email: ABCI at ewi.utwente.nl Programme Chairs: ----------------------- * Brendan Allison, Technical University Graz, Austria * Stephen Dunne, StarLabs Barcelona, Spain * Dirk Heylen, University of Twente, The Netherlands * Anton Nijholt, University of Twente, The Netherlands Local Organizer: ------------------- * Christian Muehl, University of Twente, The Netherlands Programme Committee: ----------------------------- * Egon van den Broek, University of Twente, The Netherlands * Anne-Marie Brouwer, TNO Soesterberg, The Netherlands * Peter Desain, Radboud University Nijmegen, The Netherlands * Stephen Fairclough, John Moores University Liverpool, United Kingdom * Didier Grandjean, University of Geneva, Switzerland * Markus Junghöfer, University Münster, Germany * Jonghwa Kim, University Augsburg, Germany * Gary Garcia Molina, Philips Research Eindhoven, The Netherlands * Ioannis Patras, Queen Mary University of London, United Kingdom * Gert Pfurtscheller, Technical University Graz, Austria * Thierry Pun, University of Geneva, Switzerland ------------------------------------------------------------------------ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From djs32 at BUFFALO.EDU Fri Apr 17 15:15:23 2009 From: djs32 at BUFFALO.EDU (Daniel Stolzberg) Date: Fri, 17 Apr 2009 09:15:23 -0400 Subject: regarding definetrial and preprocessing In-Reply-To: <919266.15252.qm@web95407.mail.in2.yahoo.com> Message-ID: Hello Chintan, Have you set the path to the new directories? File -> Set Path -Dan On Wed, Apr 15, 2009 at 3:48 PM, shah chintan wrote: > Folks, > > I am working on fieldtrip tutorials. I downloaded all the files and > directories from tutorials. Now when I run the scripts, an error occurs > that definetrial and preprocessing functions are undefined. Please help me > in building these functions. > > Best Regards, > > Chintan > > ------------------------------ > Add more friends to your messenger and enjoy! Invite them now. > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Fri Apr 17 19:02:19 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Fri, 17 Apr 2009 22:32:19 +0530 Subject: regarding definetrial and preprocessing Message-ID: Hello Dan, Thank you very much for your reply.  New directories does not contain these functions.  every time I locate to the directories that i downloaded.    Chintan --- On Fri, 17/4/09, Daniel Stolzberg wrote: From: Daniel Stolzberg Subject: Re: [FIELDTRIP] regarding definetrial and preprocessing To: FIELDTRIP at NIC.SURFNET.NL Date: Friday, 17 April, 2009, 6:45 PM Hello Chintan, Have you set the path to the new directories?  File -> Set Path -Dan On Wed, Apr 15, 2009 at 3:48 PM, shah chintan wrote: Folks,   I am working on fieldtrip tutorials.  I downloaded all the files and directories from tutorials.  Now when I run the scripts, an error occurs that definetrial and preprocessing functions are undefined.  Please help me in  building these functions.   Best Regards,   Chintan Add more friends to your messenger and enjoy! Invite them now. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at MAC.COM Fri Apr 17 20:06:18 2009 From: nathanweisz at MAC.COM (Nathan Weisz) Date: Fri, 17 Apr 2009 20:06:18 +0200 Subject: regarding definetrial and preprocessing In-Reply-To: <581826.87029.qm@web95411.mail.in2.yahoo.com> Message-ID: dear chintan, you mean the functions define are not in the folders you downloaded? that sounds weird, but perhaps you have downloaded a release where (theoretically) some problems occured and nobody noticed so far, as most people don't update their fieldtrip folders on a daily basis. however unlikely, try downloading an older fieldtrip version and take another look if you can find those functions. are you sure that you click on the "Save" button when setting the path and not just "Ok"? when you type "path" from the command line, can you find the relevant fieldtrip folders? like others have mentioned before your issue could be more Matlab than fieldtrip related. try to consult some colleague familiar with Matlab. good luck! n On 17.04.2009, at 19:02, shah chintan wrote: > Hello Dan, > Thank you very much for your reply. New directories does not > contain these functions. every time I locate to the directories > that i downloaded. > > Chintan > > --- On Fri, 17/4/09, Daniel Stolzberg wrote: > > From: Daniel Stolzberg > Subject: Re: [FIELDTRIP] regarding definetrial and preprocessing > To: FIELDTRIP at NIC.SURFNET.NL > Date: Friday, 17 April, 2009, 6:45 PM > > Hello Chintan, > > Have you set the path to the new directories? File -> Set Path > > -Dan > > On Wed, Apr 15, 2009 at 3:48 PM, shah chintan > wrote: > Folks, > > I am working on fieldtrip tutorials. I downloaded all the files and > directories from tutorials. Now when I run the scripts, an error > occurs that definetrial and preprocessing functions are undefined. > Please help me in building these functions. > > Best Regards, > > Chintan > > Add more friends to your messenger and enjoy! Invite them now. > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > http://listserv.surfnet.nl/archives/fieldtrip.html > http://www.ru.nl/fcdonders/fieldtrip/ > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > http://listserv.surfnet.nl/archives/fieldtrip.html > http://www.ru.nl/fcdonders/fieldtrip/ > > Add more friends to your messenger and enjoy! Invite them now. > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Fri Apr 17 22:55:12 2009 From: chintan_student at YAHOO.CO.IN (Chintan Shah) Date: Sat, 18 Apr 2009 02:25:12 +0530 Subject: Regarding define trial, preprocessing and reject visual Message-ID: Dear sir, I am really glad with your replies.  I thank you from the bottom of my heart.  I downloaded all the files and directories from the tutorial data. Now none of these directories include the functions like definetrial, preprocessing and reject visual. So when everytime I try to run the tutorial scripts locating matlab to the folder containing downloaded files and directories, I get an error that those functions are undefined.  Please help me to build these functions.   Best Regards,   Chintan Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingrid.nieuwenhuis at DONDERS.RU.NL Sat Apr 18 09:21:11 2009 From: ingrid.nieuwenhuis at DONDERS.RU.NL (Ingrid Nieuwenhuis) Date: Sat, 18 Apr 2009 09:21:11 +0200 Subject: Regarding define trial, preprocessing and reject visual Message-ID: Dear Chintan, Did you download the fieldtrip toolbox? If you go to "download" (http://fieldtrip.fcdonders.nl/download) you can se that you can download the "FieldTrip toolbox" and the "tutorial data". I think you only downloaded the tutorial date (also because you somewhere refer to .mat files and not to .m files). .mat files are files containing the data, .m files are files containing scripts (functions) that together make the toolbox. As said before this is all really basic Matlab knowledge. Hope this solves your problem, Best Ingrid _____ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Chintan Shah Sent: Friday, April 17, 2009 10:55 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] Regarding define trial, preprocessing and reject visual Dear sir, I am really glad with your replies. I thank you from the bottom of my heart. I downloaded all the files and directories from the tutorial data. Now none of these directories include the functions like definetrial, preprocessing and reject visual. So when everytime I try to run the tutorial scripts locating matlab to the folder containing downloaded files and directories, I get an error that those functions are undefined. Please help me to build these functions. Best Regards, Chintan _____ Add more friends to your messenger and enjoy! Invite them now. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lmoranr at GMAIL.COM Sat Apr 18 13:20:15 2009 From: lmoranr at GMAIL.COM (=?ISO-8859-1?Q?Luis_Mor=E1n?=) Date: Sat, 18 Apr 2009 13:20:15 +0200 Subject: Help with dipolesimulation Message-ID: Hi dear Fieldtrippers!! I'm trying to make a dipolesimulation with two dipoles. I need to use different frequencies and phases for each dipole and I don't know very well how to modify the dipolesimulation function. Any advice? Thanks in advance Best regards -- Luis Morán Rodríguez Bioengineering Group Universidad Politecnica Madrid ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Sun Apr 19 15:15:30 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Sun, 19 Apr 2009 14:15:30 +0100 Subject: Help with dipolesimulation In-Reply-To: <52b4c8f20904180420x74d16065l77baa5009993abe9@mail.gmail.com> Message-ID: Dear Luis, I guess that the desired functionality is already there, the only thing which you have to do is specifying your input configuration meaningfully. The most relevant line is line 215, which states (more or less) trial = lf * dipmom * dipsignal; lf contains the leadfield (forward model) for the dipoles at the positions in cfg.dip.pos, and has dimensionality Nchan x (Ndipolex3), so it is a concatenation (in the columns) of the single position's leadfields. dipsignal is an NdipolexNtime matrix containing the dipoles' time series. For the matrix product to work, dipmom should be of dimensionaity (Ndipolex3)xNdipole (right?). This is the key to the solution to your problem: cfg.dip.mom should be something like [orix1 0;oriy1 0; oriz1 0;0 orix2;0 oriy2;0 oriz2], with ori(xyz)(1/2) specifying the moments of your dipoles. I hope this helps, Jan-Mathijs On Apr 18, 2009, at 12:20 PM, Luis Morán wrote: > Hi dear Fieldtrippers!! > > I'm trying to make a dipolesimulation with two dipoles. I need to > use different frequencies and phases for each dipole and I don't > know very well how to modify the dipolesimulation function. > > Any advice? > > Thanks in advance > > Best regards > -- > Luis Morán Rodríguez > > Bioengineering Group > Universidad Politecnica Madrid > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From lmoranr at GMAIL.COM Sun Apr 19 19:22:20 2009 From: lmoranr at GMAIL.COM (=?ISO-8859-1?Q?Luis_Mor=E1n?=) Date: Sun, 19 Apr 2009 19:22:20 +0200 Subject: Help with dipolesimulation In-Reply-To: <4AA43C77-0BA6-40DC-B71C-91BF0AE3BCEE@psy.gla.ac.uk> Message-ID: But that doesn't solve my problem. I've completed the simulation with 2 dipoles but using the same frequencies and phases. What I need is use a different frequency in each dipole As I understand the dipolesimulation function at 'cfg.frequency' we can specify only a value Any other advice? Thanks a lot in advance 2009/4/19 jan-mathijs schoffelen > Dear Luis, > > I guess that the desired functionality is already there, the only thing > which you have to do is specifying your input configuration meaningfully. > The most relevant line is line 215, which states (more or less) trial = lf > * dipmom * dipsignal; > > lf contains the leadfield (forward model) for the dipoles at the positions > in cfg.dip.pos, and has dimensionality Nchan x (Ndipolex3), so it is a > concatenation (in the columns) of the single position's leadfields. > dipsignal is an NdipolexNtime matrix containing the dipoles' time series. > For the matrix product to work, dipmom should be of dimensionaity > (Ndipolex3)xNdipole (right?). This is the key to the solution to your > problem: > > cfg.dip.mom should be something like [orix1 0;oriy1 0; oriz1 0;0 orix2;0 > oriy2;0 oriz2], with ori(xyz)(1/2) specifying the moments of your dipoles. > > I hope this helps, > > Jan-Mathijs > > > > On Apr 18, 2009, at 12:20 PM, Luis Morán wrote: > > Hi dear Fieldtrippers!! >> >> I'm trying to make a dipolesimulation with two dipoles. I need to use >> different frequencies and phases for each dipole and I don't know very well >> how to modify the dipolesimulation function. >> >> Any advice? >> >> Thanks in advance >> >> Best regards >> -- >> Luis Morán Rodríguez >> >> Bioengineering Group >> Universidad Politecnica Madrid >> ---------------------------------- >> >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and >> EEG analysis. >> >> http://listserv.surfnet.nl/archives/fieldtrip.html >> >> http://www.ru.nl/fcdonders/fieldtrip/ >> >> > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > -- Luis Morán Rodríguez Altentic lmoran at altentic.com ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sklein at BERKELEY.EDU Sun Apr 19 19:46:50 2009 From: sklein at BERKELEY.EDU (Stanley Klein) Date: Sun, 19 Apr 2009 10:46:50 -0700 Subject: Help with dipolesimulation In-Reply-To: <9016c9f10904191044n247312c0t7e231c9356d10e36@mail.gmail.com> Message-ID: Luis, Phase doesn't make much sense if frequencies are different. In your simulation are you doing stimulation with two frequencies (SSVEP)? If so then you can do the simulation with two dipoles each with two frequencies. If you aren't doing stimulation then I'd think you'd just want to choose one frequency (say with an octave banwidth) for doing your source localization. Does Fieldtrip have good tools for doing that sort of localization? Stan On Sun, Apr 19, 2009 at 10:22 AM, Luis Morán wrote: > But that doesn't solve my problem. I've completed the simulation with 2 > dipoles but using the same frequencies and phases. What I need is use a > different frequency in each dipole > > As I understand the dipolesimulation function at 'cfg.frequency' we can > specify only a value > > Any other advice? > > Thanks a lot in advance > > > 2009/4/19 jan-mathijs schoffelen > > Dear Luis, >> >> I guess that the desired functionality is already there, the only thing >> which you have to do is specifying your input configuration meaningfully. >> The most relevant line is line 215, which states (more or less) trial = lf >> * dipmom * dipsignal; >> >> lf contains the leadfield (forward model) for the dipoles at the positions >> in cfg.dip.pos, and has dimensionality Nchan x (Ndipolex3), so it is a >> concatenation (in the columns) of the single position's leadfields. >> dipsignal is an NdipolexNtime matrix containing the dipoles' time series. >> For the matrix product to work, dipmom should be of dimensionaity >> (Ndipolex3)xNdipole (right?). This is the key to the solution to your >> problem: >> >> cfg.dip.mom should be something like [orix1 0;oriy1 0; oriz1 0;0 orix2;0 >> oriy2;0 oriz2], with ori(xyz)(1/2) specifying the moments of your dipoles. >> >> I hope this helps, >> >> Jan-Mathijs >> >> >> >> On Apr 18, 2009, at 12:20 PM, Luis Morán wrote: >> >> Hi dear Fieldtrippers!! >>> >>> I'm trying to make a dipolesimulation with two dipoles. I need to use >>> different frequencies and phases for each dipole and I don't know very well >>> how to modify the dipolesimulation function. >>> >>> Any advice? >>> >>> Thanks in advance >>> >>> Best regards >>> -- >>> Luis Morán Rodríguez >>> >>> Bioengineering Group >>> Universidad Politecnica Madrid >>> ---------------------------------- >>> >>> The aim of this list is to facilitate the discussion between users of the >>> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and >>> EEG analysis. >>> >>> http://listserv.surfnet.nl/archives/fieldtrip.html >>> >>> http://www.ru.nl/fcdonders/fieldtrip/ >>> >>> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/neuroimaging/fieldtrip. >> > > > > -- > Luis Morán Rodríguez > > Altentic > > lmoran at altentic.com > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.litvak at ION.UCL.AC.UK Mon Apr 20 01:25:00 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Mon, 20 Apr 2009 00:25:00 +0100 Subject: Help with dipolesimulation In-Reply-To: <9016c9f10904191046i974d987x4fbba9b311ed4525@mail.gmail.com> Message-ID: Dear Luis, What Jan-Mathijs was saying is that you can use the dipolesimulation function to project any arbitrary source waveform to the sensors. There are some limited tools in the function to create such a waveform on the fly (cfg.frequency) but a much more flexible way would be to create the waveforms in your own script using Matlab tools and then just use dipolesimulation to project them (with cfg.dip.mom as JM explained). Also since the summation of sources is linear, you can run dipolesimulation several times with different inputs and then add the resulting data. You can use freqsimulation function for generating your source waveforms or use your own code. Stanley is partially right that phase locking only makes sense for the same frequency (although there might be more complex relations having to do with phase across frequencies), but that's another issue. Large part of Fieldtrip is about localizing oscillatory activity. That's exactly what beamforming is for, particularly DICS. Best, Vladimir On Sun, Apr 19, 2009 at 6:46 PM, Stanley Klein wrote: > Luis, > Phase doesn't make much sense if frequencies are different. > In your simulation are you doing stimulation with two frequencies (SSVEP)? > If so then you can do the simulation with two dipoles each with two > frequencies. If you aren't doing stimulation then I'd think you'd just want > to choose one frequency (say with an octave banwidth) for doing your source > localization. > > Does Fieldtrip have good tools for doing that sort of localization? > Stan > > On Sun, Apr 19, 2009 at 10:22 AM, Luis Morán wrote: >> >> But that doesn't solve my problem.  I've completed the simulation with 2 >> dipoles but using the same frequencies and phases. What I need is use a >> different frequency in each dipole >> >> As I understand the dipolesimulation function at 'cfg.frequency' we can >> specify only a value >> >> Any other advice? >> >> Thanks a lot in advance >> >> >> 2009/4/19 jan-mathijs schoffelen >>> >>> Dear Luis, >>> >>> I guess that the desired functionality is already there, the only thing >>> which you have to do is specifying your input configuration meaningfully. >>> The most relevant line is line 215, which states (more or less) trial = >>> lf * dipmom * dipsignal; >>> >>> lf contains the leadfield (forward model) for the dipoles at the >>> positions in cfg.dip.pos, and has dimensionality Nchan x (Ndipolex3), so it >>> is a concatenation (in the columns) of the single position's leadfields. >>> dipsignal is an NdipolexNtime matrix containing the dipoles' time series. >>> For the matrix product to work, dipmom should be of dimensionaity >>> (Ndipolex3)xNdipole (right?). This is the key to the solution to your >>> problem: >>> >>> cfg.dip.mom should be something like  [orix1 0;oriy1 0; oriz1 0;0 orix2;0 >>> oriy2;0 oriz2], with ori(xyz)(1/2) specifying the moments of your dipoles. >>> >>> I hope this helps, >>> >>> Jan-Mathijs >>> >>> >>> On Apr 18, 2009, at 12:20 PM, Luis Morán wrote: >>> >>>> Hi dear Fieldtrippers!! >>>> >>>> I'm trying to make a dipolesimulation with two dipoles. I need to use >>>> different frequencies and phases for each dipole and I don't know very well >>>> how to modify the dipolesimulation function. >>>> >>>> Any advice? >>>> >>>> Thanks in advance >>>> >>>> Best regards >>>> -- >>>> Luis Morán Rodríguez >>>> >>>> Bioengineering Group >>>> Universidad Politecnica Madrid >>>> ---------------------------------- >>>> >>>> The aim of this list is to facilitate the discussion between users of >>>> the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG >>>> and EEG analysis. >>>> >>>> http://listserv.surfnet.nl/archives/fieldtrip.html >>>> >>>> http://www.ru.nl/fcdonders/fieldtrip/ >>>> >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users of the >>> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG >>> and EEG analysis. See also >>> http://listserv.surfnet.nl/archives/fieldtrip.html and >>> http://www.ru.nl/neuroimaging/fieldtrip. >> >> >> >> -- >> Luis Morán Rodríguez >> >> Altentic >> >> lmoran at altentic.com >> >> ---------------------------------- >> >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and >> EEG analysis. >> >> http://listserv.surfnet.nl/archives/fieldtrip.html >> >> http://www.ru.nl/fcdonders/fieldtrip/ > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bleichner.martin at GMAIL.COM Mon Apr 20 11:24:00 2009 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Mon, 20 Apr 2009 11:24:00 +0200 Subject: Reconstructing signal form powerspctrm Message-ID: Hi there, is there a function in fieldtrip which allows to reconstruct the signal from the powspctrm? Thanks a lot best, Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.maris at DONDERS.RU.NL Mon Apr 20 11:44:01 2009 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Mon, 20 Apr 2009 11:44:01 +0200 Subject: Reconstructing signal form powerspctrm In-Reply-To: Message-ID: Hi Martin, is there a function in fieldtrip which allows to reconstruct the signal from the powspctrm? Let me answer this question, to take away some load from the shoulders of Jan-Mathijs, whos is becoming the prime signal processing/source reconstruction expert on this discussion list. The answer is that such a function does not exist. In fact, what you ask is not possible. It is possible to reconstruct a signal from a Fourier transform (using the inverse Fourier transform), but it is not possible to reconstruct a signal from the squared amplitude of the Fourier transform (which is the power spectrum - or at least the most common estimate of the power spectrum). In the power spectrum the phase information is lost, and therefore you cannot reconstruct the signal. Good luck, Eric Thanks a lot best, Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingrid.nieuwenhuis at DONDERS.RU.NL Mon Apr 20 13:24:43 2009 From: ingrid.nieuwenhuis at DONDERS.RU.NL (Ingrid Nieuwenhuis) Date: Mon, 20 Apr 2009 13:24:43 +0200 Subject: Plot ECoG-Electrodes In-Reply-To: <7A52A42D-A57D-4714-9D19-E35E396C7499@gmail.com> Message-ID: Dear Julian, Do you mean that you would like to plot the outcome from timelock or freqanalysis on the brain, or do you just want to plot the electrodes as dots or something on the brain? And do you want to plot it on an MRI (method slice, or ortho), or on the surface of the brain (method surface). There is not standard something implemented in FieldTrip for plotting ECoG data, but if you describe more in detail what you want, we could think along. There is for instance the possibility to make your own layout, based on the electrode positions, so that there can be interpolated between the electrode positions. And also important to know, do you want to plot it for a single subject, or do you have multiple subjects in MNI normalized coordinates? Best Ingrid _____ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Julian Keil Sent: Wednesday, April 15, 2009 5:27 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] Plot ECoG-Electrodes Hello, we have recently begun to work with ECoG data. Now we would like to plot results from timelock and freqanalysis. Is there any possibility to plot the (known) electrode position onto the brain using sourceplot? Thanks a lot Julian Dipl. Psych. Julian Keil OBOB-Lab University of Konstanz Department of Psychology P.O. Box D23 78457 Konstanz Germany Tel: ++49 - (0)7531 - 88 42 50 Fax: ++49 - (0)7531 - 88 28 91 Email: julian.keil at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From megjim1 at GMAIL.COM Mon Apr 20 20:32:34 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Mon, 20 Apr 2009 20:32:34 +0200 Subject: about ICA w/o EEGLAB Message-ID: Dear all, I'm trying to remove cardiac interferences from my MEG signal (gradiometer) channels before doing wavelet analysis. This seems necessary because, when looking at each epoch, the wavelet power @ 10-40Hz are dominated by cardiac interference, and that's the bandwidth of interest. I see some Fieldtrip example script utilizing ICA of EEGLAB to remove cardiac interference. However, someone told me that it can be done in Fieldtrip w/o using EEGLAB. Is this true? If so, I'd appreciate it very much if anyone can send me the code, :) Thanks a lot, Jim ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Mon Apr 20 22:33:59 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Mon, 20 Apr 2009 21:33:59 +0100 Subject: about ICA w/o EEGLAB In-Reply-To: Message-ID: Dear Jim, I don't know whether I understand your question correctly, but Fieldtrip can do it 'without' a full download of EEGLAB, because the necessary ICA-routines are included in fieldtrip's download (and are located in the subfolder external/eeglab/... This means that your mystery someone was right ;o) Cheers, Jan-Mathijs On Apr 20, 2009, at 7:32 PM, Jim Li wrote: > Dear all, > > I'm trying to remove cardiac interferences from my MEG signal > (gradiometer) > channels before doing wavelet analysis. This seems necessary > because, when > looking at each epoch, the wavelet power @ 10-40Hz are dominated by > cardiac interference, and that's the bandwidth of interest. I see > some Fieldtrip > example script utilizing ICA of EEGLAB to remove cardiac interference. > However, someone told me that it can be done in Fieldtrip w/o using > EEGLAB. > Is this true? If so, I'd appreciate it very much if anyone can send > me the > code, :) > > Thanks a lot, > > Jim > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Mon Apr 20 23:13:13 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Mon, 20 Apr 2009 23:13:13 +0200 Subject: about ICA w/o EEGLAB Message-ID: Dear Jan-Mathijs, Thanks a lot for your answer. I see why my "componentanalysis" didn't work w/o downloading EEGLAB now: As users of a 4D system, I'm avoiding your new updated version of read_4d_hdr by sticking to some old (Dec. 2008) version of Fieldtrip, simply because it's been working fine and I'm lazy. But apparently there's no "external/eeglab" subfolder in those old versions (yes, I have several Dec 08 versions). That's why I had to download EEGLAB to get it to work. I wonder since when did you add the subfolder to Fieldtrip? Anyway, I guess it's time to embrace the new Fieldtrip versions and learn the new way to read 4D data. Thanks a lot for your help, :) Jim On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen wrote: >Dear Jim, > >I don't know whether I understand your question correctly, but >Fieldtrip can do it 'without' a full download of EEGLAB, because the >necessary ICA-routines are included in fieldtrip's download (and are >located in the subfolder external/eeglab/... This means that your >mystery someone was right ;o) > >Cheers, >Jan-Mathijs > >On Apr 20, 2009, at 7:32 PM, Jim Li wrote: > >> Dear all, >> >> I'm trying to remove cardiac interferences from my MEG signal >> (gradiometer) >> channels before doing wavelet analysis. This seems necessary >> because, when >> looking at each epoch, the wavelet power @ 10-40Hz are dominated by >> cardiac interference, and that's the bandwidth of interest. I see >> some Fieldtrip >> example script utilizing ICA of EEGLAB to remove cardiac interference. >> However, someone told me that it can be done in Fieldtrip w/o using >> EEGLAB. >> Is this true? If so, I'd appreciate it very much if anyone can send >> me the >> code, :) >> >> Thanks a lot, >> >> Jim >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Mon Apr 20 23:43:18 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Mon, 20 Apr 2009 22:43:18 +0100 Subject: about ICA w/o EEGLAB In-Reply-To: Message-ID: Dear Jim, I'd be happy to try and sort out problems with respect to my intended improvement of read_4d_hdr, because I assume there were some problems initially? It was kind of a bold commit into fieldtrip, I admit that, because I wasn't sure what this would lead to. My intention was partly to spark the involvement of 4D MEG users at other sites so that we could jointly improve the robustness of the code. So far all seems to work well for the Glaswegian 248-magnetometer site, but I am pretty sure this is not the case for all 4D-systems roaming the face of the earth... I would greatly appreciate if you try the most recent fieldtrip version on your data and provide me with feedback and possibly suggestions for improvement of the code. Cheers, Jan-Mathijs On Apr 20, 2009, at 10:13 PM, Jim Li wrote: > Dear Jan-Mathijs, > > Thanks a lot for your answer. I see why my "componentanalysis" > didn't work > w/o downloading EEGLAB now: > > As users of a 4D system, I'm avoiding your new updated version of > read_4d_hdr by sticking to some old (Dec. 2008) version of > Fieldtrip, simply > because it's been working fine and I'm lazy. But apparently there's > no "external/eeglab" subfolder in those old versions (yes, I have > several Dec > 08 versions). That's why I had to download EEGLAB to get it to work. I > wonder since when did you add the subfolder to Fieldtrip? > > Anyway, I guess it's time to embrace the new Fieldtrip versions and > learn the > new way to read 4D data. > > Thanks a lot for your help, :) > > Jim > > > On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen > wrote: > >> Dear Jim, >> >> I don't know whether I understand your question correctly, but >> Fieldtrip can do it 'without' a full download of EEGLAB, because the >> necessary ICA-routines are included in fieldtrip's download (and are >> located in the subfolder external/eeglab/... This means that your >> mystery someone was right ;o) >> >> Cheers, >> Jan-Mathijs >> >> On Apr 20, 2009, at 7:32 PM, Jim Li wrote: >> >>> Dear all, >>> >>> I'm trying to remove cardiac interferences from my MEG signal >>> (gradiometer) >>> channels before doing wavelet analysis. This seems necessary >>> because, when >>> looking at each epoch, the wavelet power @ 10-40Hz are dominated by >>> cardiac interference, and that's the bandwidth of interest. I see >>> some Fieldtrip >>> example script utilizing ICA of EEGLAB to remove cardiac >>> interference. >>> However, someone told me that it can be done in Fieldtrip w/o using >>> EEGLAB. >>> Is this true? If so, I'd appreciate it very much if anyone can send >>> me the >>> code, :) >>> >>> Thanks a lot, >>> >>> Jim >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users >>> of the FieldTrip toolbox, to share experiences and to discuss new >>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the > FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and > EEG analysis. See also http://listserv.surfnet.nl/archives/ > fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From julian.keil at GMAIL.COM Tue Apr 21 09:07:52 2009 From: julian.keil at GMAIL.COM (Julian Keil) Date: Tue, 21 Apr 2009 09:07:52 +0200 Subject: about ICA w/o EEGLAB In-Reply-To: <87D90E00-9069-4600-BD2D-C609E742A906@psy.gla.ac.uk> Message-ID: Dear Jan, the read_4d_hdr also works quite nicely for the Konstanz 148- magnetometer site as far as I can tell. I currently use the 2009-03-22 version of fieldtrip. Greetings Julian Am 20.04.2009 um 23:43 schrieb jan-mathijs schoffelen: > Dear Jim, > > I'd be happy to try and sort out problems with respect to my > intended improvement of read_4d_hdr, because I assume there were > some problems initially? It was kind of a bold commit into > fieldtrip, I admit that, because I wasn't sure what this would lead > to. My intention was partly to spark the involvement of 4D MEG users > at other sites so that we could jointly improve the robustness of > the code. So far all seems to work well for the Glaswegian 248- > magnetometer site, but I am pretty sure this is not the case for all > 4D-systems roaming the face of the earth... I would greatly > appreciate if you try the most recent fieldtrip version on your data > and provide me with feedback and possibly suggestions for > improvement of the code. > > Cheers, > > Jan-Mathijs > > > On Apr 20, 2009, at 10:13 PM, Jim Li wrote: > >> Dear Jan-Mathijs, >> >> Thanks a lot for your answer. I see why my "componentanalysis" >> didn't work >> w/o downloading EEGLAB now: >> >> As users of a 4D system, I'm avoiding your new updated version of >> read_4d_hdr by sticking to some old (Dec. 2008) version of >> Fieldtrip, simply >> because it's been working fine and I'm lazy. But apparently there's >> no "external/eeglab" subfolder in those old versions (yes, I have >> several Dec >> 08 versions). That's why I had to download EEGLAB to get it to >> work. I >> wonder since when did you add the subfolder to Fieldtrip? >> >> Anyway, I guess it's time to embrace the new Fieldtrip versions and >> learn the >> new way to read 4D data. >> >> Thanks a lot for your help, :) >> >> Jim >> >> >> On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen >> wrote: >> >>> Dear Jim, >>> >>> I don't know whether I understand your question correctly, but >>> Fieldtrip can do it 'without' a full download of EEGLAB, because the >>> necessary ICA-routines are included in fieldtrip's download (and are >>> located in the subfolder external/eeglab/... This means that your >>> mystery someone was right ;o) >>> >>> Cheers, >>> Jan-Mathijs >>> >>> On Apr 20, 2009, at 7:32 PM, Jim Li wrote: >>> >>>> Dear all, >>>> >>>> I'm trying to remove cardiac interferences from my MEG signal >>>> (gradiometer) >>>> channels before doing wavelet analysis. This seems necessary >>>> because, when >>>> looking at each epoch, the wavelet power @ 10-40Hz are dominated by >>>> cardiac interference, and that's the bandwidth of interest. I see >>>> some Fieldtrip >>>> example script utilizing ICA of EEGLAB to remove cardiac >>>> interference. >>>> However, someone told me that it can be done in Fieldtrip w/o using >>>> EEGLAB. >>>> Is this true? If so, I'd appreciate it very much if anyone can send >>>> me the >>>> code, :) >>>> >>>> Thanks a lot, >>>> >>>> Jim >>>> >>>> ---------------------------------- >>>> The aim of this list is to facilitate the discussion between users >>>> of the FieldTrip toolbox, to share experiences and to discuss new >>>> ideas for MEG and EEG analysis. See also http:// >>>> listserv.surfnet.nl/ >>>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/ >>>> fieldtrip. >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users >>> of the >> FieldTrip toolbox, to share experiences and to discuss new ideas >> for MEG and >> EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html >> and >> http://www.ru.nl/neuroimaging/fieldtrip. >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html >> and http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Tue Apr 21 10:22:05 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Tue, 21 Apr 2009 09:22:05 +0100 Subject: about ICA w/o EEGLAB In-Reply-To: <4CBC4EEB-7E3A-41A8-B53B-85DDE9BDEEEE@gmail.com> Message-ID: Dear Julian and other 4D-neuroimagers, Thanks for your feedback. There have been some changes in read_4d_hdr bti2grad which might affect performance though, so I would greatly appreciate if you could upgrade to the latest version and see if you are still happy. In a nutshell it boils down to the fact that read_4d_hdr tries to extract the digital weights from the run config-file which were used during acquisition. So far, these weights have not been included in the forward modelling, which is necessary for dipole fitting / source reconstruction. Although I don't expect that the inclusion of the weights (which are a function of the distant reference sensors, and hardly pick up any brain activity to begin with) is going to affect the leadfields to a big extent, not including them is not completely correct. As far as I know (and thanks to Stephan Moratti for pointing it out and Sarang Dalal for some code) there are two versions of the weight- tables which roughly seem to coincide with the type of system: version 1 (number of observations = 1.5: Madrid 148-magnetometer, and most likely also the Konstanz system), and version 2 (number of observations = 1: Glasgow 248-magnetometer). To make a long story short, the version 1 weight table just seems to contain the weights, and no specific list of channel labels facilitating the interpretation of the weights. This is in contrast to the version 2 table, which contains the lists of labels explicitly. Therefore, we would have to guess about the order of the channels and reference channels occurring in the version 1 weight matrix. I'd rather not guess, and prefer to base some hard-coded assumptions on some (pragmatically 1 or 2 ;o) ) observations... This means I would like to compare the list of weights as obtained with read_4d_hdr to the list of weights which the 4D-software should be able to print (I thought the command was something like print_table, or print_config or so). More specifically, given a particular recording in which for example 'supine' weights had been applied, we should compare the 'supine' weight table, to the weights extracted by fieldtrip. In that way we could gain some confidence about the order of the channels. Please note that at the moment no balancing is applied to data containing a 'version 1' weight table, at least if you use a fieldtrip version older than March 26, or more recent than April 2. Yours, Jan-Mathijs On Apr 21, 2009, at 8:07 AM, Julian Keil wrote: > Dear Jan, > > the read_4d_hdr also works quite nicely for the Konstanz 148- > magnetometer site as far as I can tell. > I currently use the 2009-03-22 version of fieldtrip. > > Greetings > > Julian > > Am 20.04.2009 um 23:43 schrieb jan-mathijs schoffelen: > >> Dear Jim, >> >> I'd be happy to try and sort out problems with respect to my >> intended improvement of read_4d_hdr, because I assume there were >> some problems initially? It was kind of a bold commit into >> fieldtrip, I admit that, because I wasn't sure what this would >> lead to. My intention was partly to spark the involvement of 4D >> MEG users at other sites so that we could jointly improve the >> robustness of the code. So far all seems to work well for the >> Glaswegian 248-magnetometer site, but I am pretty sure this is not >> the case for all 4D-systems roaming the face of the earth... I >> would greatly appreciate if you try the most recent fieldtrip >> version on your data and provide me with feedback and possibly >> suggestions for improvement of the code. >> >> Cheers, >> >> Jan-Mathijs >> >> >> On Apr 20, 2009, at 10:13 PM, Jim Li wrote: >> >>> Dear Jan-Mathijs, >>> >>> Thanks a lot for your answer. I see why my "componentanalysis" >>> didn't work >>> w/o downloading EEGLAB now: >>> >>> As users of a 4D system, I'm avoiding your new updated version of >>> read_4d_hdr by sticking to some old (Dec. 2008) version of >>> Fieldtrip, simply >>> because it's been working fine and I'm lazy. But apparently there's >>> no "external/eeglab" subfolder in those old versions (yes, I have >>> several Dec >>> 08 versions). That's why I had to download EEGLAB to get it to >>> work. I >>> wonder since when did you add the subfolder to Fieldtrip? >>> >>> Anyway, I guess it's time to embrace the new Fieldtrip versions >>> and learn the >>> new way to read 4D data. >>> >>> Thanks a lot for your help, :) >>> >>> Jim >>> >>> >>> On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen >>> wrote: >>> >>>> Dear Jim, >>>> >>>> I don't know whether I understand your question correctly, but >>>> Fieldtrip can do it 'without' a full download of EEGLAB, because >>>> the >>>> necessary ICA-routines are included in fieldtrip's download (and >>>> are >>>> located in the subfolder external/eeglab/... This means that your >>>> mystery someone was right ;o) >>>> >>>> Cheers, >>>> Jan-Mathijs >>>> >>>> On Apr 20, 2009, at 7:32 PM, Jim Li wrote: >>>> >>>>> Dear all, >>>>> >>>>> I'm trying to remove cardiac interferences from my MEG signal >>>>> (gradiometer) >>>>> channels before doing wavelet analysis. This seems necessary >>>>> because, when >>>>> looking at each epoch, the wavelet power @ 10-40Hz are >>>>> dominated by >>>>> cardiac interference, and that's the bandwidth of interest. I see >>>>> some Fieldtrip >>>>> example script utilizing ICA of EEGLAB to remove cardiac >>>>> interference. >>>>> However, someone told me that it can be done in Fieldtrip w/o >>>>> using >>>>> EEGLAB. >>>>> Is this true? If so, I'd appreciate it very much if anyone can >>>>> send >>>>> me the >>>>> code, :) >>>>> >>>>> Thanks a lot, >>>>> >>>>> Jim >>>>> >>>>> ---------------------------------- >>>>> The aim of this list is to facilitate the discussion between users >>>>> of the FieldTrip toolbox, to share experiences and to discuss new >>>>> ideas for MEG and EEG analysis. See also http:// >>>>> listserv.surfnet.nl/ >>>>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/ >>>>> fieldtrip. >>>> >>>> ---------------------------------- >>>> The aim of this list is to facilitate the discussion between >>>> users of the >>> FieldTrip toolbox, to share experiences and to discuss new ideas >>> for MEG and >>> EEG analysis. See also http://listserv.surfnet.nl/archives/ >>> fieldtrip.html and >>> http://www.ru.nl/neuroimaging/fieldtrip. >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between >>> users of the FieldTrip toolbox, to share experiences and to >>> discuss new ideas for MEG and EEG analysis. See also http:// >>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >>> neuroimaging/fieldtrip. >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http:// >> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >> neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From amrgermany at YAHOO.COM Tue Apr 21 12:53:04 2009 From: amrgermany at YAHOO.COM (Amr Ayoub) Date: Tue, 21 Apr 2009 10:53:04 +0000 Subject: Reading raw data Message-ID: Dear All, I have raw data that consits of 151 MEG (CTF machine), EOG and EMG channels. The size of each channel is around 15MB. The ERP are time points detected in EEG channels. What is the best way to import the data in order to be preprocessed in FieldTrip? Thanks a lot, Amr ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From amrgermany at YAHOO.COM Tue Apr 21 12:58:41 2009 From: amrgermany at YAHOO.COM (Amr Ayoub) Date: Tue, 21 Apr 2009 10:58:41 +0000 Subject: Reading raw data Message-ID: Dear All, I have raw data that consits of 151 MEG (CTF machine), EOG and EMG channels. The size of each channel is around 15MB. The ERP are time points detected in EEG channels. What is the best way to import the data in order to be preprocessed in FieldTrip? Thanks a lot, Amr ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Wed Apr 22 17:30:24 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Wed, 22 Apr 2009 21:00:24 +0530 Subject: regarding besa to fieldtrip Message-ID: Dear folks,   I just finished with tutorials.  I got some data in besa format.  I have .CNT, .sfp and .foc file format.  Please tell me how to import these files in matlab using fieldtrip functions.   Best Regads,   Chintan Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at MAC.COM Wed Apr 22 17:42:53 2009 From: nathanweisz at MAC.COM (Nathan Weisz) Date: Wed, 22 Apr 2009 17:42:53 +0200 Subject: regarding besa to fieldtrip In-Reply-To: <558191.69376.qm@web95412.mail.in2.yahoo.com> Message-ID: dear chintan, this page is your friend: http://fieldtrip.fcdonders.nl/integrating_with_besa best, nathan On 22.04.2009, at 17:30, shah chintan wrote: > Dear folks, > > I just finished with tutorials. I got some data in besa format. I > have .CNT, .sfp and .foc file format. Please tell me how to import > these files in matlab using fieldtrip functions. > > Best Regads, > > Chintan > > Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! > Edition * Click here! > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From megjim1 at GMAIL.COM Wed Apr 22 18:12:58 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Wed, 22 Apr 2009 18:12:58 +0200 Subject: about biosig folder Message-ID: Dear Jan-Mathijs, Following your recommendation, I downloaded the 041809 Fieldtrip and it reads our data just fine. I'll keep an eye on the outputs as I advance more into the data processing and report suspicious ones, if any. BTW, w/ this new version I get a bunch of annoying messages each time I open MATLAB. What I did is to add this new version of Fieldtrip in MATLAB by clicking "Set Path" and "Add with subfolders...". And the warning messages look like this (just one warning example out of a zillion): ---- Warning: Function C:\Program Files\MATLAB\R2007b\external\fieldtrip-20090418 \external\biosig\private\transpose.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. > In path at 110 In addpath at 89 In startup at 1 In matlabrc at 251 --- All the warning is related to the "fieldtrip-20090418\external\biosig\private\" directory. So, what's the use of this "biosig" folder? Can I just remove it from my "MATLAB search Path" w/o affecting Fieldtrip operations? Thanks, Jim On Tue, 21 Apr 2009 09:22:05 +0100, jan-mathijs schoffelen wrote: >Dear Julian and other 4D-neuroimagers, > >Thanks for your feedback. There have been some changes in read_4d_hdr >bti2grad which might affect performance though, so I would greatly >appreciate if you could upgrade to the latest version and see if you >are still happy. >In a nutshell it boils down to the fact that read_4d_hdr tries to >extract the digital weights from the run config-file which were used >during acquisition. So far, these weights have not been included in >the forward modelling, which is necessary for dipole fitting / source >reconstruction. Although I don't expect that the inclusion of the >weights (which are a function of the distant reference sensors, and >hardly pick up any brain activity to begin with) is going to affect >the leadfields to a big extent, not including them is not completely >correct. >As far as I know (and thanks to Stephan Moratti for pointing it out >and Sarang Dalal for some code) there are two versions of the weight- >tables which roughly seem to coincide with the type of system: >version 1 (number of observations = 1.5: Madrid 148-magnetometer, and >most likely also the Konstanz system), and version 2 (number of >observations = 1: Glasgow 248-magnetometer). To make a long story >short, the version 1 weight table just seems to contain the weights, >and no specific list of channel labels facilitating the >interpretation of the weights. This is in contrast to the version 2 >table, which contains the lists of labels explicitly. Therefore, we >would have to guess about the order of the channels and reference >channels occurring in the version 1 weight matrix. I'd rather not >guess, and prefer to base some hard-coded assumptions on some >(pragmatically 1 or 2 ;o) ) observations... >This means I would like to compare the list of weights as obtained >with read_4d_hdr to the list of weights which the 4D-software should >be able to print (I thought the command was something like >print_table, or print_config or so). More specifically, given a >particular recording in which for example 'supine' weights had been >applied, we should compare the 'supine' weight table, to the weights >extracted by fieldtrip. In that way we could gain some confidence >about the order of the channels. >Please note that at the moment no balancing is applied to data >containing a 'version 1' weight table, at least if you use a >fieldtrip version older than March 26, or more recent than April 2. > >Yours, > >Jan-Mathijs > >On Apr 21, 2009, at 8:07 AM, Julian Keil wrote: > >> Dear Jan, >> >> the read_4d_hdr also works quite nicely for the Konstanz 148- >> magnetometer site as far as I can tell. >> I currently use the 2009-03-22 version of fieldtrip. >> >> Greetings >> >> Julian >> >> Am 20.04.2009 um 23:43 schrieb jan-mathijs schoffelen: >> >>> Dear Jim, >>> >>> I'd be happy to try and sort out problems with respect to my >>> intended improvement of read_4d_hdr, because I assume there were >>> some problems initially? It was kind of a bold commit into >>> fieldtrip, I admit that, because I wasn't sure what this would >>> lead to. My intention was partly to spark the involvement of 4D >>> MEG users at other sites so that we could jointly improve the >>> robustness of the code. So far all seems to work well for the >>> Glaswegian 248-magnetometer site, but I am pretty sure this is not >>> the case for all 4D-systems roaming the face of the earth... I >>> would greatly appreciate if you try the most recent fieldtrip >>> version on your data and provide me with feedback and possibly >>> suggestions for improvement of the code. >>> >>> Cheers, >>> >>> Jan-Mathijs >>> >>> >>> On Apr 20, 2009, at 10:13 PM, Jim Li wrote: >>> >>>> Dear Jan-Mathijs, >>>> >>>> Thanks a lot for your answer. I see why my "componentanalysis" >>>> didn't work >>>> w/o downloading EEGLAB now: >>>> >>>> As users of a 4D system, I'm avoiding your new updated version of >>>> read_4d_hdr by sticking to some old (Dec. 2008) version of >>>> Fieldtrip, simply >>>> because it's been working fine and I'm lazy. But apparently there's >>>> no "external/eeglab" subfolder in those old versions (yes, I have >>>> several Dec >>>> 08 versions). That's why I had to download EEGLAB to get it to >>>> work. I >>>> wonder since when did you add the subfolder to Fieldtrip? >>>> >>>> Anyway, I guess it's time to embrace the new Fieldtrip versions >>>> and learn the >>>> new way to read 4D data. >>>> >>>> Thanks a lot for your help, :) >>>> >>>> Jim >>>> >>>> >>>> On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen >>>> wrote: >>>> >>>>> Dear Jim, >>>>> >>>>> I don't know whether I understand your question correctly, but >>>>> Fieldtrip can do it 'without' a full download of EEGLAB, because >>>>> the >>>>> necessary ICA-routines are included in fieldtrip's download (and >>>>> are >>>>> located in the subfolder external/eeglab/... This means that your >>>>> mystery someone was right ;o) >>>>> >>>>> Cheers, >>>>> Jan-Mathijs >>>>> >>>>> On Apr 20, 2009, at 7:32 PM, Jim Li wrote: >>>>> >>>>>> Dear all, >>>>>> >>>>>> I'm trying to remove cardiac interferences from my MEG signal >>>>>> (gradiometer) >>>>>> channels before doing wavelet analysis. This seems necessary >>>>>> because, when >>>>>> looking at each epoch, the wavelet power @ 10-40Hz are >>>>>> dominated by >>>>>> cardiac interference, and that's the bandwidth of interest. I see >>>>>> some Fieldtrip >>>>>> example script utilizing ICA of EEGLAB to remove cardiac >>>>>> interference. >>>>>> However, someone told me that it can be done in Fieldtrip w/o >>>>>> using >>>>>> EEGLAB. >>>>>> Is this true? If so, I'd appreciate it very much if anyone can >>>>>> send >>>>>> me the >>>>>> code, :) >>>>>> >>>>>> Thanks a lot, >>>>>> >>>>>> Jim >>>>>> >>>>>> ---------------------------------- >>>>>> The aim of this list is to facilitate the discussion between users >>>>>> of the FieldTrip toolbox, to share experiences and to discuss new >>>>>> ideas for MEG and EEG analysis. See also http:// >>>>>> listserv.surfnet.nl/ >>>>>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/ >>>>>> fieldtrip. >>>>> >>>>> ---------------------------------- >>>>> The aim of this list is to facilitate the discussion between >>>>> users of the >>>> FieldTrip toolbox, to share experiences and to discuss new ideas >>>> for MEG and >>>> EEG analysis. See also http://listserv.surfnet.nl/archives/ >>>> fieldtrip.html and >>>> http://www.ru.nl/neuroimaging/fieldtrip. >>>> >>>> ---------------------------------- >>>> The aim of this list is to facilitate the discussion between >>>> users of the FieldTrip toolbox, to share experiences and to >>>> discuss new ideas for MEG and EEG analysis. See also http:// >>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >>>> neuroimaging/fieldtrip. >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users >>> of the FieldTrip toolbox, to share experiences and to discuss new >>> ideas for MEG and EEG analysis. See also http:// >>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >>> neuroimaging/fieldtrip. >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Wed Apr 22 18:23:19 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Wed, 22 Apr 2009 18:23:19 +0200 Subject: Do I need ECG channel to run "artifact_ecg" Message-ID: Dear all, W/ a 041809 Fieldtrip, I tried to run the following lines but got some error (see below). I don't have ECG channel in my data, that's why I use a left-most MEG channel w/ apparent cardiac interferences instead. Any suggestion how to fix the problem? ------------- cfg = []; cfg.trl = data.cfg.previous.trl; cfg.dataset = data.cfg.previous.dataset; cfg.continuous = 'yes' ; cfg.artfctdef.ecg.channel = 'A229'; cfg.artfctdef.ecg.pretim = 0.25; cfg.artfctdef.ecg.psttim = 0.5; cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method cfg.artfctdef.ecg.cutoff = 3; %peak-threshold [cfg, artifact] = artifact_ecg(cfg); current zvalue threshold = 3.000 keep the current value (y/n) ? y ??? Undefined function or variable "labelmlt". Error in ==> channelselection at 344 if findmlt, channel = [channel; labelmlt]; end Error in ==> artifact_ecg at 238 sgn = channelselection(artfctdef.inspect, hdr.label); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From chintan_student at YAHOO.CO.IN Wed Apr 22 18:31:33 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Wed, 22 Apr 2009 22:01:33 +0530 Subject: regarding besa to fieldtrip Message-ID: Dear folks,   I just finished with tutorials.  I got some data in besa format.  I have .CNT, .sfp and .foc file format.  I can process with .sfp format but no clue about the other two. Please tell me how to import these files in matlab using fieldtrip functions.   Best Regads,   Chintan Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition * Click here! ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Thu Apr 23 09:48:07 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Thu, 23 Apr 2009 08:48:07 +0100 Subject: about biosig folder In-Reply-To: Message-ID: Dear Jim, Yes, I suspect that you just can remove the biosig folder from your path. As long as you don't use fieldtrip functionality which depends on functions within the biosig-folder you are fine. Yours, JM On Apr 22, 2009, at 5:12 PM, Jim Li wrote: > Dear Jan-Mathijs, > > Following your recommendation, I downloaded the 041809 Fieldtrip > and it > reads our data just fine. I'll keep an eye on the outputs as I > advance more > into the data processing and report suspicious ones, if any. > > BTW, w/ this new version I get a bunch of annoying messages each > time I > open MATLAB. What I did is to add this new version of Fieldtrip in > MATLAB by > clicking "Set Path" and "Add with subfolders...". And the warning > messages > look like this (just one warning example out of a zillion): > > ---- > Warning: Function C:\Program > Files\MATLAB\R2007b\external\fieldtrip-20090418 > \external\biosig\private\transpose.m > has the same name as a MATLAB builtin. We suggest you rename the > function > to > avoid a potential name conflict. >> In path at 110 > In addpath at 89 > In startup at 1 > In matlabrc at 251 > --- > > All the warning is related to the "fieldtrip-20090418\external > \biosig\private\" > directory. So, what's the use of this "biosig" folder? Can I just > remove it from > my "MATLAB search Path" w/o affecting Fieldtrip operations? > > Thanks, > > Jim > > On Tue, 21 Apr 2009 09:22:05 +0100, jan-mathijs schoffelen > wrote: > >> Dear Julian and other 4D-neuroimagers, >> >> Thanks for your feedback. There have been some changes in read_4d_hdr >> bti2grad which might affect performance though, so I would greatly >> appreciate if you could upgrade to the latest version and see if you >> are still happy. >> In a nutshell it boils down to the fact that read_4d_hdr tries to >> extract the digital weights from the run config-file which were used >> during acquisition. So far, these weights have not been included in >> the forward modelling, which is necessary for dipole fitting / source >> reconstruction. Although I don't expect that the inclusion of the >> weights (which are a function of the distant reference sensors, and >> hardly pick up any brain activity to begin with) is going to affect >> the leadfields to a big extent, not including them is not completely >> correct. >> As far as I know (and thanks to Stephan Moratti for pointing it out >> and Sarang Dalal for some code) there are two versions of the weight- >> tables which roughly seem to coincide with the type of system: >> version 1 (number of observations = 1.5: Madrid 148-magnetometer, and >> most likely also the Konstanz system), and version 2 (number of >> observations = 1: Glasgow 248-magnetometer). To make a long story >> short, the version 1 weight table just seems to contain the weights, >> and no specific list of channel labels facilitating the >> interpretation of the weights. This is in contrast to the version 2 >> table, which contains the lists of labels explicitly. Therefore, we >> would have to guess about the order of the channels and reference >> channels occurring in the version 1 weight matrix. I'd rather not >> guess, and prefer to base some hard-coded assumptions on some >> (pragmatically 1 or 2 ;o) ) observations... >> This means I would like to compare the list of weights as obtained >> with read_4d_hdr to the list of weights which the 4D-software should >> be able to print (I thought the command was something like >> print_table, or print_config or so). More specifically, given a >> particular recording in which for example 'supine' weights had been >> applied, we should compare the 'supine' weight table, to the weights >> extracted by fieldtrip. In that way we could gain some confidence >> about the order of the channels. >> Please note that at the moment no balancing is applied to data >> containing a 'version 1' weight table, at least if you use a >> fieldtrip version older than March 26, or more recent than April 2. >> >> Yours, >> >> Jan-Mathijs >> >> On Apr 21, 2009, at 8:07 AM, Julian Keil wrote: >> >>> Dear Jan, >>> >>> the read_4d_hdr also works quite nicely for the Konstanz 148- >>> magnetometer site as far as I can tell. >>> I currently use the 2009-03-22 version of fieldtrip. >>> >>> Greetings >>> >>> Julian >>> >>> Am 20.04.2009 um 23:43 schrieb jan-mathijs schoffelen: >>> >>>> Dear Jim, >>>> >>>> I'd be happy to try and sort out problems with respect to my >>>> intended improvement of read_4d_hdr, because I assume there were >>>> some problems initially? It was kind of a bold commit into >>>> fieldtrip, I admit that, because I wasn't sure what this would >>>> lead to. My intention was partly to spark the involvement of 4D >>>> MEG users at other sites so that we could jointly improve the >>>> robustness of the code. So far all seems to work well for the >>>> Glaswegian 248-magnetometer site, but I am pretty sure this is not >>>> the case for all 4D-systems roaming the face of the earth... I >>>> would greatly appreciate if you try the most recent fieldtrip >>>> version on your data and provide me with feedback and possibly >>>> suggestions for improvement of the code. >>>> >>>> Cheers, >>>> >>>> Jan-Mathijs >>>> >>>> >>>> On Apr 20, 2009, at 10:13 PM, Jim Li wrote: >>>> >>>>> Dear Jan-Mathijs, >>>>> >>>>> Thanks a lot for your answer. I see why my "componentanalysis" >>>>> didn't work >>>>> w/o downloading EEGLAB now: >>>>> >>>>> As users of a 4D system, I'm avoiding your new updated version of >>>>> read_4d_hdr by sticking to some old (Dec. 2008) version of >>>>> Fieldtrip, simply >>>>> because it's been working fine and I'm lazy. But apparently >>>>> there's >>>>> no "external/eeglab" subfolder in those old versions (yes, I have >>>>> several Dec >>>>> 08 versions). That's why I had to download EEGLAB to get it to >>>>> work. I >>>>> wonder since when did you add the subfolder to Fieldtrip? >>>>> >>>>> Anyway, I guess it's time to embrace the new Fieldtrip versions >>>>> and learn the >>>>> new way to read 4D data. >>>>> >>>>> Thanks a lot for your help, :) >>>>> >>>>> Jim >>>>> >>>>> >>>>> On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen >>>>> wrote: >>>>> >>>>>> Dear Jim, >>>>>> >>>>>> I don't know whether I understand your question correctly, but >>>>>> Fieldtrip can do it 'without' a full download of EEGLAB, because >>>>>> the >>>>>> necessary ICA-routines are included in fieldtrip's download (and >>>>>> are >>>>>> located in the subfolder external/eeglab/... This means that your >>>>>> mystery someone was right ;o) >>>>>> >>>>>> Cheers, >>>>>> Jan-Mathijs >>>>>> >>>>>> On Apr 20, 2009, at 7:32 PM, Jim Li wrote: >>>>>> >>>>>>> Dear all, >>>>>>> >>>>>>> I'm trying to remove cardiac interferences from my MEG signal >>>>>>> (gradiometer) >>>>>>> channels before doing wavelet analysis. This seems necessary >>>>>>> because, when >>>>>>> looking at each epoch, the wavelet power @ 10-40Hz are >>>>>>> dominated by >>>>>>> cardiac interference, and that's the bandwidth of interest. I >>>>>>> see >>>>>>> some Fieldtrip >>>>>>> example script utilizing ICA of EEGLAB to remove cardiac >>>>>>> interference. >>>>>>> However, someone told me that it can be done in Fieldtrip w/o >>>>>>> using >>>>>>> EEGLAB. >>>>>>> Is this true? If so, I'd appreciate it very much if anyone can >>>>>>> send >>>>>>> me the >>>>>>> code, :) >>>>>>> >>>>>>> Thanks a lot, >>>>>>> >>>>>>> Jim >>>>>>> >>>>>>> ---------------------------------- >>>>>>> The aim of this list is to facilitate the discussion between >>>>>>> users >>>>>>> of the FieldTrip toolbox, to share experiences and to >>>>>>> discuss new >>>>>>> ideas for MEG and EEG analysis. See also http:// >>>>>>> listserv.surfnet.nl/ >>>>>>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/ >>>>>>> fieldtrip. >>>>>> >>>>>> ---------------------------------- >>>>>> The aim of this list is to facilitate the discussion between >>>>>> users of the >>>>> FieldTrip toolbox, to share experiences and to discuss new ideas >>>>> for MEG and >>>>> EEG analysis. See also http://listserv.surfnet.nl/archives/ >>>>> fieldtrip.html and >>>>> http://www.ru.nl/neuroimaging/fieldtrip. >>>>> >>>>> ---------------------------------- >>>>> The aim of this list is to facilitate the discussion between >>>>> users of the FieldTrip toolbox, to share experiences and to >>>>> discuss new ideas for MEG and EEG analysis. See also http:// >>>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >>>>> neuroimaging/fieldtrip. >>>> >>>> ---------------------------------- >>>> The aim of this list is to facilitate the discussion between users >>>> of the FieldTrip toolbox, to share experiences and to discuss new >>>> ideas for MEG and EEG analysis. See also http:// >>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >>>> neuroimaging/fieldtrip. >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users >>> of the FieldTrip toolbox, to share experiences and to discuss new >>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the > FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and > EEG analysis. See also http://listserv.surfnet.nl/archives/ > fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From moratti at MED.UCM.ES Thu Apr 23 09:40:33 2009 From: moratti at MED.UCM.ES (Stephan Moratti) Date: Thu, 23 Apr 2009 09:40:33 +0200 Subject: regarding besa to fieldtrip In-Reply-To: Message-ID: Yo can export your data in BESA to .avr (ASCII) .mul (ASCII multiplexed) and .dat (simple binary, you will also get a header file .generic). With besa2fieldtrip you can read in your data easily, then. best, Stephan -- *Stephan Moratti, PhD/ /**/see also: http://web.me.com/smoratti/ /*Centro de Tecnología Biomédica CBT, Universidad Politécnica de Madrid, en la actualidad (currently at) en el Centro de Magnetoencefalografía Dr. Perez Modrego, Universidad Complutense de Madrid, Faculdad de Medicina, Pabellón 8, Avda. Complutense, s/n, 28040 Madrid, Spain, email: moratti at gbt.tfo.upm.es moratti at med.ucm.es Tel.: +34 91 394 2292 Fax.: +34 91 394 2294 */ /* ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Thu Apr 23 10:00:44 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Thu, 23 Apr 2009 09:00:44 +0100 Subject: Do I need ECG channel to run "artifact_ecg" In-Reply-To: Message-ID: Dear Jim, The reason for your crash is probably related to the fact that the default settings for artifact_ecg have been defined with a ctf-system in mind. Artifact_ecg will provide some feedback as to how the QRS- complex-locked MEG signals look, by picking a subset of channels as defined by cfg.artfctdef.ecg.inspect. By default this is set to all channels named 'MLTxx'. Since in your megsystem the sensors are named 'Axx', fieldtrip cannot make sense out of the default and crashes. Just specify your own (subset of) channel(s) to inspect. Good luck Jan-Mathijs On Apr 22, 2009, at 5:23 PM, Jim Li wrote: > Dear all, > > > W/ a 041809 Fieldtrip, I tried to run the following lines but got > some error (see > below). I don't have ECG channel in my data, that's why I use a > left-most > MEG channel w/ apparent cardiac interferences instead. Any > suggestion how > to fix the problem? > > ------------- > cfg = []; > cfg.trl = data.cfg.previous.trl; > cfg.dataset = data.cfg.previous.dataset; > cfg.continuous = 'yes' ; > cfg.artfctdef.ecg.channel = 'A229'; > cfg.artfctdef.ecg.pretim = 0.25; > cfg.artfctdef.ecg.psttim = 0.5; > cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method > cfg.artfctdef.ecg.cutoff = 3; %peak-threshold > [cfg, artifact] = artifact_ecg(cfg); > > current zvalue threshold = 3.000 > keep the current value (y/n) ? > y > ??? Undefined function or variable "labelmlt". > > Error in ==> channelselection at 344 > if findmlt, channel = [channel; labelmlt]; end > > Error in ==> artifact_ecg at 238 > sgn = channelselection(artfctdef.inspect, hdr.label); > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From A.Stancak at LIVERPOOL.AC.UK Thu Apr 23 10:01:15 2009 From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej) Date: Thu, 23 Apr 2009 09:01:15 +0100 Subject: Do I need ECG channel to run "artifact_ecg" In-Reply-To: Message-ID: Dear Jim-Li, I probably faced the same error message when I was writing my script for ECG artefact removal. I remember to get rid of this error message by putting the ECG channel label into brackets: cfg.artfctdef.ecg.channel = {'A229'}; I hope I have not mislead you as I am a FieldTrip novice, but it is maybe worth trying. Best wishes Andrej Andrej Stancak, PhD. Professor for normal physiology Senior lecturer in psychology School of Psychology Eleanor Rathbone Building Bedford Street South L69 7ZA Liverpool United Kingdom Phone: 0044 0151 7946951 E-mail: a.stancak at liverpool.ac.uk (primary)         stancak at lf3.cuni.cz (secondary) Office hours: Mo 10-12, Wed 10-12 -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jim Li Sent: 22 April 2009 17:23 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] Do I need ECG channel to run "artifact_ecg" Dear all, W/ a 041809 Fieldtrip, I tried to run the following lines but got some error (see below). I don't have ECG channel in my data, that's why I use a left-most MEG channel w/ apparent cardiac interferences instead. Any suggestion how to fix the problem? ------------- cfg = []; cfg.trl = data.cfg.previous.trl; cfg.dataset = data.cfg.previous.dataset; cfg.continuous = 'yes' ; cfg.artfctdef.ecg.channel = 'A229'; cfg.artfctdef.ecg.pretim = 0.25; cfg.artfctdef.ecg.psttim = 0.5; cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method cfg.artfctdef.ecg.cutoff = 3; %peak-threshold [cfg, artifact] = artifact_ecg(cfg); current zvalue threshold = 3.000 keep the current value (y/n) ? y ??? Undefined function or variable "labelmlt". Error in ==> channelselection at 344 if findmlt, channel = [channel; labelmlt]; end Error in ==> artifact_ecg at 238 sgn = channelselection(artfctdef.inspect, hdr.label); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Thu Apr 23 16:25:50 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Thu, 23 Apr 2009 16:25:50 +0200 Subject: Do I need ECG channel to run "artifact_ecg" Message-ID: Dear Andrej, Thanks a lot for your feedback. I tried your recommendation of "cfg.artfctdef.ecg.channel = {'A229'};" but I got the same message. In fact, last night by a little debugging I figured out why the error message occured. And the solution is to simply add this line before doing artifact_ecg: cfg.artfctdef.ecg.inspect = {'A229'}; And that worked beautifully. cheers, Jim On Thu, 23 Apr 2009 09:01:15 +0100, Stancak, Andrej wrote: >Dear Jim-Li, > > I probably faced the same error message when I was writing my script for ECG artefact removal. I remember to get rid of this error message by putting the ECG channel label into brackets: > > cfg.artfctdef.ecg.channel = {'A229'}; > > > I hope I have not mislead you as I am a FieldTrip novice, but it is maybe worth trying. > >Best wishes >Andrej > > > >Andrej Stancak, PhD. >Professor for normal physiology >Senior lecturer in psychology > >School of Psychology >Eleanor Rathbone Building >Bedford Street South >L69 7ZA >Liverpool >United Kingdom > >Phone: 0044 0151 7946951 >E-mail: a.stancak at liverpool.ac.uk (primary) >        stancak at lf3.cuni.cz (secondary) > >Office hours: Mo 10-12, Wed 10-12 > > >-----Original Message----- >From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jim Li >Sent: 22 April 2009 17:23 >To: FIELDTRIP at NIC.SURFNET.NL >Subject: [FIELDTRIP] Do I need ECG channel to run "artifact_ecg" > >Dear all, > > >W/ a 041809 Fieldtrip, I tried to run the following lines but got some error (see >below). I don't have ECG channel in my data, that's why I use a left-most >MEG channel w/ apparent cardiac interferences instead. Any suggestion how >to fix the problem? > >------------- >cfg = []; >cfg.trl = data.cfg.previous.trl; >cfg.dataset = data.cfg.previous.dataset; >cfg.continuous = 'yes' ; >cfg.artfctdef.ecg.channel = 'A229'; >cfg.artfctdef.ecg.pretim = 0.25; >cfg.artfctdef.ecg.psttim = 0.5; >cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method >cfg.artfctdef.ecg.cutoff = 3; %peak-threshold >[cfg, artifact] = artifact_ecg(cfg); > >current zvalue threshold = 3.000 >keep the current value (y/n) ? >y >??? Undefined function or variable "labelmlt". > >Error in ==> channelselection at 344 >if findmlt, channel = [channel; labelmlt]; end > >Error in ==> artifact_ecg at 238 >sgn = channelselection(artfctdef.inspect, hdr.label); > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Thu Apr 23 17:47:53 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Thu, 23 Apr 2009 17:47:53 +0200 Subject: Do I need ECG channel to run "artifact_ecg" Message-ID: Dear Jan-Mathijs, Thanks a lot for your feedback. Last night I did a bit of debugging and found out why the crashed happened. In line 116 of "artifact_ecg" it says: if ~isfield(cfg.artfctdef.ecg,'inspect'),cfg.artfctdef.ecg.inspect = {'MLT' 'MRT'}; end That's the cause of my trouble because 4D's system doesn't have channels names like "MLT", "MRT" . So I fixed te problem by adding this line: cfg.artfctdef.ecg.inspect = {'A229'}; before this line: [cfg, artifact] = artifact_ecg(cfg); And it worked! All these fits into your great suggestion very well. And I'm so happy that I don't need to get an ECG channel before doing cardiac artifact rejection. Jim On Thu, 23 Apr 2009 09:00:44 +0100, jan-mathijs schoffelen wrote: >Dear Jim, > >The reason for your crash is probably related to the fact that the >default settings for artifact_ecg have been defined with a ctf-system >in mind. Artifact_ecg will provide some feedback as to how the QRS- >complex-locked MEG signals look, by picking a subset of channels as >defined by cfg.artfctdef.ecg.inspect. By default this is set to all >channels named 'MLTxx'. Since in your megsystem the sensors are named >'Axx', fieldtrip cannot make sense out of the default and crashes. >Just specify your own (subset of) channel(s) to inspect. > >Good luck > >Jan-Mathijs > > > >On Apr 22, 2009, at 5:23 PM, Jim Li wrote: > >> Dear all, >> >> >> W/ a 041809 Fieldtrip, I tried to run the following lines but got >> some error (see >> below). I don't have ECG channel in my data, that's why I use a >> left-most >> MEG channel w/ apparent cardiac interferences instead. Any >> suggestion how >> to fix the problem? >> >> ------------- >> cfg = []; >> cfg.trl = data.cfg.previous.trl; >> cfg.dataset = data.cfg.previous.dataset; >> cfg.continuous = 'yes' ; >> cfg.artfctdef.ecg.channel = 'A229'; >> cfg.artfctdef.ecg.pretim = 0.25; >> cfg.artfctdef.ecg.psttim = 0.5; >> cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method >> cfg.artfctdef.ecg.cutoff = 3; %peak-threshold >> [cfg, artifact] = artifact_ecg(cfg); >> >> current zvalue threshold = 3.000 >> keep the current value (y/n) ? >> y >> ??? Undefined function or variable "labelmlt". >> >> Error in ==> channelselection at 344 >> if findmlt, channel = [channel; labelmlt]; end >> >> Error in ==> artifact_ecg at 238 >> sgn = channelselection(artfctdef.inspect, hdr.label); >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From cmuehl at GMAIL.COM Thu Apr 23 18:05:27 2009 From: cmuehl at GMAIL.COM (Christian Muehl) Date: Thu, 23 Apr 2009 18:05:27 +0200 Subject: BCI game project in the eNTERFACE 09 workshop Message-ID: Call for participants BCI @ eNTERFACE 09 workshop July 13th - August 7th 2009 Genua, Italy Project on Bain-Computer Interfaces: A multi-player game using neurophysiological sensors For a project on Brain-Computer Interfaces in the context of the eNTERFACE 09 workshop in Genua we are searching for interested people with experience in the areas of signal processing, game design, programming or machine learning. The goal of the project is the development of a multiplayer computer game that uses several innovative input modalities. Neural (EEG) and physiological changes (e.g. ECG, respiration, muscle tension) are used in combination with traditional (mouse, keyboards) input devices to actively and passively control the game dynamics. The game will be a platform for the study of an efficient and natural use of Brain-Computer Interaction and physiological sensors within a gaming environment. More detailed information about that particular project and others can be found here: www.infomus.org/enterface09/projectsTeams.php The eNTERFACE 2009 Workshop is being organized this summer in Genova, Italy, from July 13th to August 7th, 2009. The eNTERFACE Workshops present an opportunity of collaborative research and software development by gathering, in a single place, a team of senior project leaders in multimodal interfaces, PhD students, and (undergraduate) students, to work on a pre-specified list of challenges, for the duration of four weeks. Participants are organized in teams of six to eight, all attached to specific projects. Tutorials and state-of-the art surveys on multimodal interfaces and their design will be given every week by invited experts. Senior researchers, PhD students, or undergraduates interested in participating to the Workshop should send their application by emailing the Organizing Committee at enterface09 at casapaganini.org before April 30, 2009. Please check the workshop website for detailed information on the application proceedure: http://www.infomus.org/enterface09/callForParticipation.php ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Thu Apr 23 18:10:22 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Thu, 23 Apr 2009 18:10:22 +0200 Subject: Do I need ECG channel to run "artifact_ecg" Message-ID: Dear Jan-Mathijs, I continued ICA cardiac-removal processing using the example codes in Fieldtrip website. But I encountered this problem: ---------- cfg = []; cfg.method = 'mtmfft'; cfg.output = 'fourier'; cfg.foilim = [0 100]; cfg.taper = 'hanning'; cfg.pad = 'maxperlen'; freq = freqanalysis(cfg, comp_ecg); the input is component data with 248 components and 248 original channels ??? Error using ==> checkdata at 377 This function requires raw data as input. Error in ==> freqanalysis at 165 data = checkdata(data, 'datatype', 'raw', 'feedback', 'yes', 'hasoffset', 'yes'); ----------------- How to deal w/ it? Thanks, Jim On Thu, 23 Apr 2009 09:00:44 +0100, jan-mathijs schoffelen wrote: >Dear Jim, > >The reason for your crash is probably related to the fact that the >default settings for artifact_ecg have been defined with a ctf-system >in mind. Artifact_ecg will provide some feedback as to how the QRS- >complex-locked MEG signals look, by picking a subset of channels as >defined by cfg.artfctdef.ecg.inspect. By default this is set to all >channels named 'MLTxx'. Since in your megsystem the sensors are named >'Axx', fieldtrip cannot make sense out of the default and crashes. >Just specify your own (subset of) channel(s) to inspect. > >Good luck > >Jan-Mathijs > > > >On Apr 22, 2009, at 5:23 PM, Jim Li wrote: > >> Dear all, >> >> >> W/ a 041809 Fieldtrip, I tried to run the following lines but got >> some error (see >> below). I don't have ECG channel in my data, that's why I use a >> left-most >> MEG channel w/ apparent cardiac interferences instead. Any >> suggestion how >> to fix the problem? >> >> ------------- >> cfg = []; >> cfg.trl = data.cfg.previous.trl; >> cfg.dataset = data.cfg.previous.dataset; >> cfg.continuous = 'yes' ; >> cfg.artfctdef.ecg.channel = 'A229'; >> cfg.artfctdef.ecg.pretim = 0.25; >> cfg.artfctdef.ecg.psttim = 0.5; >> cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method >> cfg.artfctdef.ecg.cutoff = 3; %peak-threshold >> [cfg, artifact] = artifact_ecg(cfg); >> >> current zvalue threshold = 3.000 >> keep the current value (y/n) ? >> y >> ??? Undefined function or variable "labelmlt". >> >> Error in ==> channelselection at 344 >> if findmlt, channel = [channel; labelmlt]; end >> >> Error in ==> artifact_ecg at 238 >> sgn = channelselection(artfctdef.inspect, hdr.label); >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From chintan_student at YAHOO.CO.IN Fri Apr 24 04:07:50 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Fri, 24 Apr 2009 07:37:50 +0530 Subject: regarding besa to fieldtrip Message-ID: Dear Jan-Mathijs,   I   Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Fri Apr 24 04:07:51 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Fri, 24 Apr 2009 07:37:51 +0530 Subject: regarding besa to fieldtrip Message-ID: Dear Jan-Mathijs,   I have   Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition http://downloads.yahoo.com/in/firefox/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Fri Apr 24 04:10:08 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Fri, 24 Apr 2009 07:40:08 +0530 Subject: regarding besa to fieldtrip Message-ID: Dear Jan-Mathijs,   I have besa format file of .cnt and .foc format.  Pleas tell me how to import in matlab using fieldtrip functions.  besa2fieldtrip is not working here.   Best Regards,   Chintan Explore your hobbies and interests. Go to http://in.promos.yahoo.com/groups/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at MAC.COM Fri Apr 24 07:22:51 2009 From: nathanweisz at MAC.COM (Nathan Weisz) Date: Fri, 24 Apr 2009 07:22:51 +0200 Subject: regarding besa to fieldtrip In-Reply-To: <355853.55433.qm@web95401.mail.in2.yahoo.com> Message-ID: Dear Chintan, haven you read Stephans answer to your question. here it is again: > Yo can export your data in BESA to .avr (ASCII) .mul (ASCII > multiplexed) and .dat (simple binary, you will also get a header > file .generic). With besa2fieldtrip you can read in your data > easily, then. btw, the help comments within the besa2fieldtrip function as well as the description in the tutorial should have been detailed enough to get you going (examples in the tutorial). if you nevertheless encounter problems when running the function then saying "besa2fieldtrip is not working here" is simply not enough to know what's exactly your problem. please show us how you called the function and e.g. the error message you got. this helps us helping you. best, nathan On 24.04.2009, at 04:10, shah chintan wrote: > Dear Jan-Mathijs, > > I have besa format file of .cnt and .foc format. Pleas tell me how > to import in matlab using fieldtrip functions. besa2fieldtrip is > not working here. > > Best Regards, > > Chintan > > Own a website.Get an unlimited package.Pay next to nothing.* Click > here!. > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.litvak at ION.UCL.AC.UK Fri Apr 24 19:12:45 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Fri, 24 Apr 2009 18:12:45 +0100 Subject: Important message for Neuromag users Message-ID: Dear Neuromag users, We recently found a critical bug in the new MNE reader. The grad structure for Neuromag read with the new reader was incorrect and this would affect source analysis and (to a minor extent) topoplotting. The users who used the old meg_pd reader are not affected. If you think you might be affected by the bug you should update your FT to the latest version and re-read all the grads read with the MNE reader until now from the original fif files. Sorry for the inconvenience, Vladimir ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From chintan_student at YAHOO.CO.IN Fri Apr 24 21:57:15 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Sat, 25 Apr 2009 01:27:15 +0530 Subject: Fw: Re: [FIELDTRIP] regarding besa to fieldtrip Message-ID: --- On Sat, 25/4/09, shah chintan wrote: From: shah chintan Subject: Re: [FIELDTRIP] regarding besa to fieldtrip To: nathanweisz at me.com Date: Saturday, 25 April, 2009, 1:25 AM Dear Sir,   Actually I have a data file of .cnt format and I have .sfp file containing the positions of electrodes.  The data file consist of different signals depending on time.  I can import both the file into matlab.  I dont know how to analyse or produce the graphical picture of messes at different time frequency.    Best Regards,   Chintan --- On Fri, 24/4/09, Nathan Weisz wrote: From: Nathan Weisz Subject: Re: [FIELDTRIP] regarding besa to fieldtrip To: FIELDTRIP at NIC.SURFNET.NL Date: Friday, 24 April, 2009, 10:52 AM Dear Chintan, haven you read Stephans answer to your question. here it is again: Yo can export your data in BESA to .avr (ASCII) .mul (ASCII multiplexed) and .dat (simple binary, you will also get a header file .generic). With besa2fieldtrip you can read in your data easily, then. btw, the help comments within the besa2fieldtrip function as well as the description in the tutorial should have been detailed enough to get you going (examples in the tutorial). if you nevertheless encounter problems when running the function then saying "besa2fieldtrip is not working here" is simply not enough to know what's exactly your problem. please show us how you called the function and e.g. the error message you got. this helps us helping you. best, nathan On 24.04.2009, at 04:10, shah chintan wrote: Dear Jan-Mathijs,   I have besa format file of .cnt and .foc format.  Pleas tell me how to import in matlab using fieldtrip functions.  besa2fieldtrip is not working here.   Best Regards,   Chintan Own a website.Get an unlimited package.Pay next to nothing.* Click here!. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ Bollywood news, movie reviews, film trailers and more! Click here. Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From johnston at KIN.UCALGARY.CA Thu Apr 30 18:55:32 2009 From: johnston at KIN.UCALGARY.CA (Jamie Johnston) Date: Thu, 30 Apr 2009 10:55:32 -0600 Subject: problems with coherence tutorial Message-ID: I am trying to run the coherence tutorial on the website. I have downloaded the SubjectCMC.zip folder but there is no dataset called "SubjectCMC.ds" and I keep running into an error running the code. Any suggestions. Thanks, Jamie _______________ Jamie Johnston, Ph.D. Assistant Professor Faculty of Kinesiology University of Calgary 2500 University Dr. NW Calgary, AB T2N 1N4 Phone: +1 (403) 220-3649 Fax: +1 (403) 284-3553 email: johnston at kin.ucalgary.ca website: http://www.kin.ucalgary.ca/wcm/knes/johnston.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Thu Apr 30 21:18:55 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Thu, 30 Apr 2009 20:18:55 +0100 Subject: problems with coherence tutorial In-Reply-To: Message-ID: Dear Jamie, I tried to download SubjectCMC.zip and I cannot reproduce your problem. I assume that you properly unzipped the folder? If not, that could explain your problem. The zip file is about 360 megabytes, but once unzipped, SubjectCMC.ds should contain a .meg4-file which should be about 664 Mb. Alternatively, you could skip the preprocessing part and start from "computing the cross-spectral densities". The preprocessed data can be obtained by preprocessing the raw data, or you can directly download the processed data file from the ftp-server. Good luck, Jan-Mathijs On Apr 30, 2009, at 5:55 PM, Jamie Johnston wrote: > I am trying to run the coherence tutorial on the website. I have > downloaded the SubjectCMC.zip folder but there is no dataset called > “SubjectCMC.ds” and I keep running into an error running the code. > Any suggestions. > > Thanks, > > Jamie > > _______________ > Jamie Johnston, Ph.D. > Assistant Professor > Faculty of Kinesiology > University of Calgary > 2500 University Dr. NW > Calgary, AB > T2N 1N4 > Phone: +1 (403) 220-3649 > Fax: +1 (403) 284-3553 > email: johnston at kin.ucalgary.ca > website: http://www.kin.ucalgary.ca/wcm/knes/johnston.html > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From megjim1 at GMAIL.COM Thu Apr 30 21:21:01 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Thu, 30 Apr 2009 21:21:01 +0200 Subject: color bar Message-ID: Dear FTer: I wonder if anybody can tell me how to get the full color bar when plotting w/ "singleplotTFR" or "multiplotTFR". I ran the following commands: -------- figure cfg = []; cfg.layout = '4D248.lay'; cfg.ylim = [5 30] cfg.interactive = 'yes'; cfg.showlabels = 'yes'; cfg.colorbar = 'yes'; cfg.channel='A2' singleplotTFR(cfg,TF) ----------- But what I get on the right side of the figure is a colorbar w/ only half of the color (usually the cold colors like blue or green), and the numbers on the right side of the colorbar seem to be wrongly placed (see attachment). How can I get all the colors (both hot and cold) displayed in the colorbar? FYI, I controled the values of TF.powspctrm so that, for the channel displayed (A2), all values before time 0 is 3e-25, and all values after time 0 is 1e-25. But the color bar is telling me that the blue should be 2e-25, which is totally wrong! It's as if something happened that moved the whole colorbar up by half of the data range, then cut off the top of it (i.e. the hot colors). In fact, I think Fig 3 of the online tutorial (http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis) probably suffered from the same problem. Thanks, Jim ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: half_colorbar.TIF Type: image/tiff Size: 97550 bytes Desc: not available URL: From megjim1 at GMAIL.COM Sun Apr 5 18:15:44 2009 From: megjim1 at GMAIL.COM (=?GB2312?Q?Jim?=) Date: Sun, 5 Apr 2009 18:15:44 +0200 Subject: help w/ sourceplot Message-ID: Dear all, Could anyone give me a hint how to solve this problem? I tried to played with the mri of subject1 in the tutorial page (http://fieldtrip.fcdonders.nl/tutorial/beamformer). I downloaded the segmented mri from ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/beamformer/segmentedmriF.mat, then did the following: --------------- load segmentedmriF mri = read_fcdc_mri('Subject01.mri'); segmentedmriF.transform = mri.transform; segmentedmriF.anatomy = mri.anatomy; figure cfg = []; sourceplot(cfg,segmentedmriF); %only mri ----------------------- The error message is like this: -------------------- the input is volume data with dimensions [256 256 256] ??? Error using ==> horzcat The following error occurred converting from char to cell: Error using ==> cell Conversion to cell from char is not possible. Error in ==> fieldtrip-20090404\private\parameterselection at 94 if ~issubfield(data, param{i}) && issubfield(data, ['avg.' param{i}]) Error in ==> volumedownsample at 171 cfg.parameter = parameterselection(cfg.parameter, source); Error in ==> sourceplot at 305 data = volumedownsample(tmpcfg, data); ---------------------------- Here is some information about my computer/softwares: MATLAB Version 7.0.0.19920 (R14). Operating System: Microsoft Windows XP Version 5.1 (Build 2600: Service Pack 3) Java VM Version: Java 1.4.2 with Sun Microsystems Inc. Java HotSpot(TM) Client VM And I downloaded the latest 040409 Fieldtrip. Any idea how to solve the issue? Thanks a lot, Jim ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Mon Apr 6 10:43:33 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Mon, 6 Apr 2009 09:43:33 +0100 Subject: help w/ sourceplot In-Reply-To: Message-ID: Dear Jim, Is the "amp;" in line 94 parameterselection really there, or did it pop up during the copy and paste process? I tried to reproduce your problem, but I did not manage. If removing the "amp;" does not solve your case, you could try to debug the code by typing on the command-line: "dbstop if error" and calling sourceplot after that. When it crashes, you have access to the local workspace of the functions (you can toggle between the different functions in the calling hierarchy by the commands dbup and dbdown) so that you can have a look what is going wrong. Usually, matlab is pretty explicit about what it tries to do (but fails) in its error messages. Yours, Jan-Mathijs On Apr 5, 2009, at 5:15 PM, Jim wrote: > if ~issubfield(data, param{i}) && issubfield(data, ['avg.' param > {i}] ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From vinnik at SISSA.IT Tue Apr 7 13:56:04 2009 From: vinnik at SISSA.IT (Katya Vinnik) Date: Tue, 7 Apr 2009 13:56:04 +0200 Subject: plots and stats with biosemi128.lay In-Reply-To: <3d0f9a750903231119o3cf85f4as3f5ab40bcd80af20@mail.gmail.com> Message-ID: Dear FT users, has anyone of you encountered this warning? Duplicate x-y data points detected: using average of the z values. I'm simply plotting my data with cfg.layout      = 'biosemi128.lay'; and it gives me strange plots like the one here: picasaweb.google.com/lh/photo/qmd3BgpeEDegPo4kHdRW0w?feat=directlink basically data from channels B19 and 21 and D22 and 24 are overlayed (circled in red on the pictures). This message appears also with topoplot functions. In the layout file, howether ,positions of this electrodes are different (see below). Do you think it can affect cluster-based multiple comparison correction? For example, if I use cfg.layout      = 'biosemi128.lay'; cfg.correctm = 'cluster';  [stat] = freqstatistics(cfg,x,y) does it calculate it properly? Thank you, Best regards, Katya ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Wed Apr 8 08:59:54 2009 From: megjim1 at GMAIL.COM (=?GB2312?Q?Jim_Li?=) Date: Wed, 8 Apr 2009 08:59:54 +0200 Subject: help w/ sourceplot Message-ID: Dear Jan-Mathijs, You're right: The "amp;" shouldn't be there, it's just a random thing popped up during copying. I followed your recommendation to debug and, when crash happened, I got this: ------------------ K>> param param = {} {} 'anatomy' 'inside' K>> i i = 1 K>> ['avg.' param{i}] ??? Error using ==> horzcat The following error occurred converting from char to cell: Error using ==> cell Conversion to cell from char is not possible. ------------------ Apparently the "{}" is the source of error. Tracing further, I think the following two lines of code in "sourceplot.m" seems to be the source of error since they lead to the two "{}" in the above- mentioned "param": if ~isfield(cfg, 'funparameter'), cfg.funparameter = []; end if ~isfield(cfg, 'maskparameter'), cfg.maskparameter = []; end The "segmentedmriF" I used in "sourceplot(cfg,segmentedmriF)" is like this: ------------ K>> segmentedmriF segmentedmriF = dim: [256 256 256] transform: [4x4 double] gray: [256x256x256 double] white: [256x256x256 double] csf: [256x256x256 double] cfg: [1x1 struct] anatomy: [256x256x256 uint16] ------------------- So, should the 'funparameter' and 'maskparameter' be specified in "segmentedmriF" before running the sourceplot? If so, what should they be? ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Wed Apr 8 15:04:29 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Wed, 8 Apr 2009 15:04:29 +0200 Subject: Need help with BVA files In-Reply-To: Message-ID: Hi Martijn It seems that you are using the trialfun_brainvision.m function to define trials. At least, if I try to replicate your problem it seems that definetrial sets cfg.trialfun to trialfun_brainvision (see line 156). The data format specific trialfuns (like trialfun_brainvision) are not maintained any more because they have been replaced wit a more general way of handling the events and the trial definition. Recent versions of fieldtrip also don't include the trialfun_brainvision any more. Please update your fieldtrip to the latest version and try again. You can use trialfun_general or you can write your own function for the trial definition (see for example http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition) best regards, Robert On 31 Mar 2009, at 15:23, Martijn Barendregt wrote: > I'm trying to process some E.E.G. data that I've exported from > BrainVision > Analyzer. But when I run my script (see below) I don't get any > errors but > the 'time' field in the raw_data struct will be all zeros. Because > of this I > can't do anything with the data. > > What can I do to get the time values in correctly? > > Kinds regards, > > Martijn Barendregt > > My code: > cfg = []; > cfg.datafile = 'somefile.dat'; > cfg.headerfile = 'somefile.vhdr'; > cfg.trialdef.trgfile = 'somefile.vmkr'; > cfg.trialdef.eventtype = 'Stimulus'; > cfg.trialdef.eventvalue = 'M22'; > cfg.traildef.prestim = 3; > cfg.traildef.poststim = 3; > cfg.trialdef.segment = 'no'; > cfg.trialdef.timezero = 'no'; > > [cfg] = definetrial(cfg); > > raw_data = preprocessing(cfg); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Wed Apr 8 15:20:25 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Wed, 8 Apr 2009 15:20:25 +0200 Subject: plots and stats with biosemi128.lay In-Reply-To: <3d0f9a750904070456i59c8d768na2f83e98cb3bf0a3@mail.gmail.com> Message-ID: Dear Katya If I do >> cfg.layout = 'biosemi128.lay' >> layoutplot(cfg) then I get attached figure (which you should be able to reproduce). Looking carefully it seems that D39 is lying on top of another channel. If I then do d = dist(lay.pos') imagesc(d==0) then I see that there are multiple off-diagonal elements in the distance matrix (i.e. a 128x128 matrix containing the distance bwteen all pairs) that are zero. So there are multiple channels overlapping. I don't know why that is and at the moment I don't know where the biosemi layouts were coming from. The only information that I have from the log is revision 1.1 date: 2005/06/15 08:21:08; author: roboos; state: Exp; new layout files, based on excel sheet from biosemi I don't know the details of this excel sheet any more, but probably the excel sheet was already wrong. But to come to your prime question: does it affect clustering? Yes it will. You are using the layout to define neighbours. If the layout is flawed, the neighbour definition might also be flawed. Please use the neighbourselection function to make a neighbour definition explicitely and check the neighbours by looking at the output of the neighbourselection function. best regards, Robert PS it would be nice if you could provide a better layout for the biosemi128 cap ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 1.png Type: image/png Size: 37404 bytes Desc: not available URL: -------------- next part -------------- On 7 Apr 2009, at 13:56, Katya Vinnik wrote: > Dear FT users, > > has anyone of you encountered this warning? > Duplicate x-y data points detected: using average of the z values. > > I'm simply plotting my data with cfg.layout = > 'biosemi128.lay'; > > and it gives me strange plots like the one here: > picasaweb.google.com/lh/photo/qmd3BgpeEDegPo4kHdRW0w?feat=directlink > > basically data from channels B19 and 21 and D22 and 24 are overlayed > (circled in red on the pictures). > This message appears also with topoplot functions. In the layout file, > howether ,positions of this electrodes are different (see below). > > Do you think it can affect cluster-based multiple comparison > correction? > > For example, if I use > > cfg.layout = 'biosemi128.lay'; > cfg.correctm = 'cluster'; > [stat] = freqstatistics(cfg,x,y) > > does it calculate it properly? > > Thank you, > Best regards, > Katya > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From lulswinnik at GMAIL.COM Wed Apr 8 17:19:19 2009 From: lulswinnik at GMAIL.COM (Katya Vinnik) Date: Wed, 8 Apr 2009 17:19:19 +0200 Subject: plots and stats with biosemi128.lay In-Reply-To: Message-ID: Thank you, Robert! Regards, Katya 2009/4/8 Robert Oostenveld : > Dear Katya > > If I do >>> cfg.layout = 'biosemi128.lay' >>> layoutplot(cfg) > > then I get attached figure (which you should be able to reproduce). Looking > carefully it seems that D39 is lying on top of another channel. > > If I then do > d = dist(lay.pos') > imagesc(d==0) > > then I see that there are multiple off-diagonal elements in the distance > matrix (i.e. a 128x128 matrix containing the distance bwteen all pairs) that > are zero.  So there are multiple channels overlapping. I don't know why that > is and at the moment I don't know where the biosemi layouts were coming > from. The only information that I have from the log is >  revision 1.1 >  date: 2005/06/15 08:21:08;  author: roboos;  state: Exp; >  new layout files, based on excel sheet from biosemi > > I don't know the details of this excel sheet any more, but probably the > excel sheet was already wrong. > > But to come to your prime question: does it affect clustering? Yes it will. > You are using the layout to define neighbours. If the layout is flawed, the > neighbour definition might also be flawed. Please use the neighbourselection > function to make a neighbour definition explicitely and check the neighbours > by looking at the output of the neighbourselection function. > > > best regards, > Robert > > PS it would be nice if you could provide a better layout for the biosemi128 > cap > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > > > > On 7 Apr 2009, at 13:56, Katya Vinnik wrote: > >> Dear FT users, >> >> has anyone of you encountered this warning? >> Duplicate x-y data points detected: using average of the z values. >> >> I'm simply plotting my data with       cfg.layout      = 'biosemi128.lay'; >> >> and it gives me strange plots  like the one here: >> picasaweb.google.com/lh/photo/qmd3BgpeEDegPo4kHdRW0w?feat=directlink >> >> basically data from channels B19 and 21 and D22 and 24 are overlayed >> (circled in red on the pictures). >> This message appears also with topoplot functions. In the layout file, >> howether ,positions of this electrodes are different (see below). >> >> Do you think it can affect cluster-based multiple comparison correction? >> >> For example, if I use >> >> cfg.layout      = 'biosemi128.lay'; >> cfg.correctm = 'cluster'; >>  [stat] = freqstatistics(cfg,x,y) >> >> does it calculate it properly? >> >> Thank you, >> Best regards, >> Katya >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/neuroimaging/fieldtrip. >> > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From njkillian at GATECH.EDU Wed Apr 8 22:28:13 2009 From: njkillian at GATECH.EDU (Nathan Killian) Date: Wed, 8 Apr 2009 16:28:13 -0400 Subject: problem with freqdescriptives Message-ID: Hello, I was wondering if anyone knew why a particular configuration is not giving me a jackknife result for the power spectrum, even though I am keeping trials. This problem occurs when I use FT20090404, but I at least get something returned for the standard error with FT20080611 (and it at least looked reasonable). I am using this analysis: cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.foilim = [0,100]; cfg.tapsmofrq = 4; cfg.pad = 'maxperlen'; cfg.keeptrials = 'yes'; cfg.keepfourier = 'no'; cfg.keeptapers = 'no'; cfg.pseudovalue = 'no'; cfg.jackknife = 'yes'; cfg.complex = 'complex'; freq = freqanalysis(cfg, data); freqdes = freqdescriptives(cfg, freq); Additionally, I found if you keeptrials and don't set keepfourier you will get an error only with the new version (could be easily fixed in the freqdescriptives function). Thank you for your help! Nathan -- Graduate Student - Georgia Tech Bioengineering Buffalo Lab at Emory-Yerkes: 404.712.9431 Potter Lab at Georgia Tech: 404.385.4083 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Thu Apr 9 00:14:11 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Wed, 8 Apr 2009 23:14:11 +0100 Subject: problem with freqdescriptives In-Reply-To: Message-ID: Dear Nathan, If you rely on this specific functionality of freqdescriptives I would advice you to copy the old version into your fieldtrip-folder. There are indeed some bugs in the more recent versions of freqdescriptives which have been introduced along the way, but I (and others) did not yet find time to fix it. We anyway hope to soon move to a new implementation of freqdescriptives, which does not seem to make the patching worthwile. Yours, Jan-Mathijs On Apr 8, 2009, at 9:28 PM, Nathan Killian wrote: > Hello, > > I was wondering if anyone knew why a particular configuration is > not giving me a jackknife result for the power spectrum, even > though I am keeping trials. This problem occurs when I use > FT20090404, but I at least get something returned for the standard > error with FT20080611 (and it at least looked reasonable). I am > using this analysis: > cfg.output = 'powandcsd'; > cfg.method = 'mtmfft'; > cfg.foilim = [0,100]; > cfg.tapsmofrq = 4; > cfg.pad = 'maxperlen'; > cfg.keeptrials = 'yes'; > cfg.keepfourier = 'no'; > cfg.keeptapers = 'no'; > cfg.pseudovalue = 'no'; > cfg.jackknife = 'yes'; > cfg.complex = 'complex'; > freq = freqanalysis(cfg, data); > freqdes = freqdescriptives(cfg, freq); > > Additionally, I found if you keeptrials and don't set keepfourier > you will get an error only with the new version (could be easily > fixed in the freqdescriptives function). > > Thank you for your help! > > Nathan > > -- > Graduate Student - Georgia Tech Bioengineering > Buffalo Lab at Emory-Yerkes: 404.712.9431 > Potter Lab at Georgia Tech: 404.385.4083 > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From E.J.M.vanWingerden at UVA.NL Thu Apr 9 09:59:53 2009 From: E.J.M.vanWingerden at UVA.NL (Wingerden, E.J.M. van) Date: Thu, 9 Apr 2009 09:59:53 +0200 Subject: Star-P support In-Reply-To: A<7FFBC71A-F30A-48F5-8295-153E9575B5EC@psy.gla.ac.uk> Message-ID: Dear developers, Buried in the code for freqanalysis_mtmconvol.m I found a comment about a possible implementation of parallel data processing using star-P (line 466). Is this a feature that is under development at the moment? I have some experience with star-P myself and found that using FieldTrip in combination with a star-P computing cluster is quite hampered by the fact that structures cannot be passed as broadcast arguments when the computations are distributed. Have you found ways to circumvent this problem? In my opinion, the FieldTrip code could greatly benefit from parallel computing when splitting across channels, or trials even. However, since usually datasets are split at a high level function while the actual computation takes place within a low level function, the fact that structs containing the parameters that are necessary for the computation need to be passed as arguments between these functions makes it pretty hard to make them star-P compatible. Are you in contact with the star-P developers? I would imagine that they are very interested in the programming needs of a large user community/potential customers as we have here. best regards, marijn van wingerden Mr. Marijn van Wingerden, M.Sc. PhD-candidate Cognitive & Systems Neuroscience (CSN) Centre for NeuroScience (CNS) section of Swammerdam Institute for Life Sciences (SILS) University of Amsterdam, Faculty of Science Kruislaan 320, 1098 SM Amsterdam, The Netherlands Tel: +31 20 525 7713/7547 Fax: +31 20 525 7709 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From michael.wibral at WEB.DE Thu Apr 9 12:05:59 2009 From: michael.wibral at WEB.DE (Michael Wibral) Date: Thu, 9 Apr 2009 12:05:59 +0200 Subject: second level statistics Message-ID: Dear Fieldtrippers, I have computed sourcestatistics (task vs. baseline) at the single subject level for two separate conditions (Cond 1 and Cond2) I then use these t-values source images to comapre the activations between the two conditions at the multi-subject level. Works fine. My question is whether there is any straightforward way in fieldtrip to recycle these results (sourcespace t-value images) for a multisubject analysis for task versus baseline for condition separately. What appeals to me is that these data (t-values) are 'normalized' in a meaningful way across subjects already. Would it be statistically valid to create a virtual "baseline-against-baseline" dataset (with all t-values equal to zero, of course) and test against this? Or would it be better to do sourceanalysis once more to get task and baseline source power for each subject and condition and then do the regular source statistics task-vs-basline for each condition? Any suggestions welcom, Michael Wibral ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: From susannah.murphy at PSYCH.OX.AC.UK Thu Apr 9 12:06:05 2009 From: susannah.murphy at PSYCH.OX.AC.UK (Susannah Murphy) Date: Thu, 9 Apr 2009 11:06:05 +0100 Subject: second level statistics In-Reply-To: <941146944@web.de> Message-ID: Thanks for your message. I am out of the office until Tuesday 14th April. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Thu Apr 9 21:55:48 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Thu, 9 Apr 2009 21:55:48 +0200 Subject: help w/ sourceplot Message-ID: Well, by changing MATLAB to a newer version while using the same Fieldtrip I got the problem solved. Now I can get "sourceplot" to display the MRI images. That's great! Jim On Wed, 8 Apr 2009 08:59:54 +0200, Jim Li wrote: >Dear Jan-Mathijs, > >You're right: The "amp;" shouldn't be there, it's just a random thing popped >up during copying. > >I followed your recommendation to debug and, when crash happened, I got >this: > > >------------------ >K>> param > >param = > > {} {} 'anatomy' 'inside' > >K>> i > >i = > > 1 > >K>> ['avg.' param{i}] >??? Error using ==> horzcat >The following error occurred converting from char to cell: >Error using ==> cell >Conversion to cell from char is not possible. > >------------------ > >Apparently the "{}" is the source of error. > >Tracing further, I think the following two lines of code in "sourceplot.m" seems >to be the source of error since they lead to the two "{}" in the above- >mentioned "param": >if ~isfield(cfg, 'funparameter'), cfg.funparameter = []; end >if ~isfield(cfg, 'maskparameter'), cfg.maskparameter = []; end > > >The "segmentedmriF" I used in "sourceplot(cfg,segmentedmriF)" is like this: >------------ >K>> segmentedmriF > >segmentedmriF = > > dim: [256 256 256] > transform: [4x4 double] > gray: [256x256x256 double] > white: [256x256x256 double] > csf: [256x256x256 double] > cfg: [1x1 struct] > anatomy: [256x256x256 uint16] >------------------- > >So, should the 'funparameter' and 'maskparameter' be specified >in "segmentedmriF" before running the sourceplot? If so, what should they be? > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Fri Apr 10 20:01:58 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Fri, 10 Apr 2009 20:01:58 +0200 Subject: can I combine subplot and multiplotTFR to get multiple epochs displayed on 1 page? Message-ID: Dear Fieldtripper, I tried something like this to do two multiplotTFR plot on one page, but it didn't work: TF = freqanalysis(cfg,data); TF2 = freqanalysis(cfg,data2); subplot(2,1,1); multiplotTFR(cfg,TF); subplot(2,1,2); multiplotTFR(cfg,TF); Any idea how to combine subplot and multiplotTFR to get multiple "multiplotTFR" plots displayed on 1 page? Thanks, Jim ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From todavidkim at GMAIL.COM Fri Apr 10 22:59:08 2009 From: todavidkim at GMAIL.COM (David Kim) Date: Fri, 10 Apr 2009 13:59:08 -0700 Subject: Help with dipole-fitting simultaneous MEG/EEG data Message-ID: Dear Fieldtrip users, I have been working on solving dipole-fitting problem of a simultaneous MEG/EEG data with Fieldtrip. The MEG and EEG sensor definitions (275, 64) is generated to conform to Fieldtrip standard. A 4 shell volume conduction model for EEG and 1 shell model for MEG have been generated to conform to Fieldtrip standard. Given the stimulus, I'm assuming that a single dipole drives the signal in both EEG and MEG. Therefore, I would like to use Fieldtrip to find a dipole that best describes the simultaneously acquired MEG/EEG data in the following sense: A single dipole fit with 9 characteristic values consisting of: dipole position. 3 values, (x,y,z) dipole moment (given the dipole position) that best fits MEG data. 3 dipole moment (given the dipole position) that best fits EEG data. 3 Currently, Fieldtrip has compute_leadfield.m function which can take a cell of multiple volume and sensor definitions as described in line 22 and 23 of the code. % sens = {senseeg, sensmeg} % vol = {voleeg, volmeg} With compute_leadfield.m, I can perform the dipole-fitting, but this requires custom scripts outside of Fieldtrip which can get messy and vary from data to data. I would much rather have the process be done within the Fieldtrip environment where the process is more robust and streamlined. It would be ideal to have the data pass through to dipfit_error() subroutine defined in dipole_fit.m function, where the modifications to dipfit_error() definition would determine the outcome of the fit. It appears to me, however, both dipolefitting.m and dipole_fit.m are not made to process multiple sensor definitions. For example, line 166 of dipole_fit.m reads, "error('simultaneous EEG and MEG not supported');" Is simultaneous EEG/MEG processing of data already implemented in Fieldtrip that I'm not aware of? If not what steps could we take to implement such a feature? Thank you. David Kim ---------------------------------------------------------------------- UCSF/UC Berkeley Bioengineering Graduate Group todavidkim at gmail.com (510) 643-7571 http://cornea.berkeley.edu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From lwn_07 at YAHOO.COM.CN Sun Apr 12 06:03:11 2009 From: lwn_07 at YAHOO.COM.CN (=?utf-8?B?5p2O5Y2r5aic?=) Date: Sun, 12 Apr 2009 12:03:11 +0800 Subject: Ask for help :How can I read the weights file of SAM spatial filter? Message-ID: Dear fieldtripers,       I want to read the SAM spatial filters of my MEG data recorded by CTF151 MEG system in a motor task. It seems the file in a ".svl.max.wts" format describe the "weights" information, but I can't read the out. And I found that there was a "read_ctf_coef.m" file in "eeglab plugins" which is copyrighted to Robert, can returns the spatial filter cofficients for CTF MEG system, and these cofficients were not read from a file but already existed. Is this "cofficients" and my weights the same thing?       The description of function "read_ctf_coef" is as follows:   function [coef] = read_ctf_coef % READ_CTF_COEF returns the spatial filter coefficients for the CTF MEG system % that has been installed at the F.C. Donders Centre (id 1706) % % This function actually does not read the coefficients from a file, but the % coefficients themselves are included in this function. % % The original location of the coefficients included in this file is % odin:/opt/ctf/hardware/M016/M017_1706.coef % Copyright (C) 2003, Robert Oostenveld          Best Wishes!                                                                                            Weina LI                                                                                         2009.04.12 ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Roozbeh.Rezaie at UTH.TMC.EDU Mon Apr 13 16:12:53 2009 From: Roozbeh.Rezaie at UTH.TMC.EDU (Rezaie, Roozbeh) Date: Mon, 13 Apr 2009 09:12:53 -0500 Subject: ISACM 2009- Call For Abstracts Message-ID: ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2009 ISACM Conference Call for Abstracts.pdf Type: application/pdf Size: 127099 bytes Desc: 2009 ISACM Conference Call for Abstracts.pdf URL: From chintan_student at YAHOO.CO.IN Mon Apr 13 20:57:17 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Tue, 14 Apr 2009 00:27:17 +0530 Subject: regarding start Message-ID: Dear sir, i just started learning fieldtrip.  can u tell me how to run the tutorial scripts in matlab.  Check out the all-new Messenger 9.0! Go to http://in.messenger.yahoo.com/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From megjim1 at GMAIL.COM Mon Apr 13 23:35:59 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Mon, 13 Apr 2009 23:35:59 +0200 Subject: Makefile for Linux 64 Message-ID: Dear FTer: We're thinking of buying a 64-bit Quad-core PC w/ big memory(>=16GB), then install a Linux OS (CentOS 4) and run Fieldtrip on it. According to the first question asked by Christine below, there seems to be a problem w/ SPM2. Is that still an issue or is it solved by now? Are there any other issues to pay attention to w/ 64-bit linux? Thanks a lot, Jim On Tue, 18 Sep 2007 17:03:59 +0200, Christine Tillmann wrote: >Hi, > >we are trying to get the fieldtrip beamforming on our linux 64 bit >systems going. As we understand it, there is currently no way around >using spm2. Spm2's mex files however are not compiled for linux 64 bit >and the makefile that's available on the web suffers from the tab/space >delimiter problem. >Does anyone have a makefile for spm2 that works on linux 64 bit? > >Or, else is there a way around spm2? E.g. by using the output of >mriviewer and the localspheres command directly? Or by beamforming in >CTF and feeding its output to sourcestatistics? > >And one last thing: does anyone use the mri files from trhe >CTF-MRIviewer that came with version 5.4.0 yet? > >Thanks, >Christine > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From gflandin at FIL.ION.UCL.AC.UK Wed Apr 15 12:27:10 2009 From: gflandin at FIL.ION.UCL.AC.UK (Guillaume Flandin) Date: Wed, 15 Apr 2009 11:27:10 +0100 Subject: Makefile for Linux 64 In-Reply-To: Message-ID: Dear Jim, some 64bit Linux MEX files for SPM2 are available from here: ftp://ftp.fil.ion.ucl.ac.uk/spm/spm2_updates/ The website mentioned in previous email is the SPM wikibooks: http://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Linux#Compilation_notes_for_SPM2: I also attach a SPM2 Makefile that contains instructions for Linux64 compilation, in case the provided compiled MEX files do not work on your platform. Best regards, Guillaume. Jim Li wrote: > Dear FTer: > > We're thinking of buying a 64-bit Quad-core PC w/ big memory(>=16GB), then > install a Linux OS (CentOS 4) and run Fieldtrip on it. According to the first > question asked by Christine below, there seems to be a problem w/ SPM2. Is > that still an issue or is it solved by now? Are there any other issues to pay > attention to w/ 64-bit linux? > > > Thanks a lot, > > Jim > > On Tue, 18 Sep 2007 17:03:59 +0200, Christine Tillmann FRANKFURT.MPG.DE> wrote: > >> Hi, >> >> we are trying to get the fieldtrip beamforming on our linux 64 bit >> systems going. As we understand it, there is currently no way around >> using spm2. Spm2's mex files however are not compiled for linux 64 bit >> and the makefile that's available on the web suffers from the tab/space >> delimiter problem. >> Does anyone have a makefile for spm2 that works on linux 64 bit? >> >> Or, else is there a way around spm2? E.g. by using the output of >> mriviewer and the localspheres command directly? Or by beamforming in >> CTF and feeding its output to sourcestatistics? >> >> And one last thing: does anyone use the mri files from trhe >> CTF-MRIviewer that came with version 5.4.0 yet? >> >> Thanks, >> Christine -- Guillaume Flandin, PhD Wellcome Trust Centre for Neuroimaging University College London 12 Queen Square London WC1N 3BG ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Makefile URL: From chintan_student at YAHOO.CO.IN Wed Apr 15 16:33:20 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Wed, 15 Apr 2009 20:03:20 +0530 Subject: [FIELD TRIP] regarding define trial Message-ID: folks,   I am going through the tutorials of fieldtrip.  When I try to run the example scripts on matlab, I am getting an error regarding the functions which are undefined such as definetrial or preprocessing.  Please guide me to built the functions on fieldtrip.     Thanking you   Chintan Check out the all-new Messenger 9.0! Go to http://in.messenger.yahoo.com/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Wed Apr 15 16:44:58 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Wed, 15 Apr 2009 15:44:58 +0100 Subject: [FIELD TRIP] regarding define trial In-Reply-To: <692084.73060.qm@web95408.mail.in2.yahoo.com> Message-ID: Dear Chintan, You probably still have to add the fieldtrip folder to you matlab- path, after you downloaded the most recent fieldtrip version. Yours, JM On Apr 15, 2009, at 3:33 PM, shah chintan wrote: > folks, > > I am going through the tutorials of fieldtrip. When I try to run > the example scripts on matlab, I am getting an error regarding the > functions which are undefined such as definetrial or > preprocessing. Please guide me to built the functions on fieldtrip. > > > Thanking you > > Chintan > > Add more friends to your messenger and enjoy! Invite them now. > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lwn_07 at YAHOO.COM.CN Wed Apr 15 16:19:41 2009 From: lwn_07 at YAHOO.COM.CN (=?utf-8?B?5p2O5Y2r5aic?=) Date: Wed, 15 Apr 2009 22:19:41 +0800 Subject: =?utf-8?Q?=E5=9B=9E=E5=A4=8D=EF=BC=9A?= [FIELDTRIP] Ask for help :How can I read the weights file of SAM spatial filter? Message-ID: I found a way to read the weigts in http://kurage.nimh.nih.gov/meglab/Meg/Readwts may help someone else     --- 09年4月12日，周日, 李卫娜 写道： 发件人: 李卫娜 主题: [FIELDTRIP] Ask for help :How can I read the weights file of SAM spatial filter? 收件人: FIELDTRIP at NIC.SURFNET.NL 日期: 2009年4月12日,周日,下午12:03 Dear fieldtripers,       I want to read the SAM spatial filters of my MEG data recorded by CTF151 MEG system in a motor task. It seems the file in a ".svl.max.wts" format describe the "weights" information, but I can't read the out. And I found that there was a "read_ctf_coef.m" file in "eeglab plugins" which is copyrighted to Robert, can returns the spatial filter cofficients for CTF MEG system, and these cofficients were not read from a file but already existed. Is this "cofficients" and my weights the same thing?       The description of function "read_ctf_coef" is as follows:   function [coef] = read_ctf_coef % READ_CTF_COEF returns the spatial filter coefficients for the CTF MEG system % that has been installed at the F.C. Donders Centre (id 1706) % % This function actually does not read the coefficients from a file, but the % coefficients themselves are included in this function. % % The original location of the coefficients included in this file is % odin:/opt/ctf/hardware/M016/M017_1706.coef % Copyright (C) 2003, Robert Oostenveld          Best Wishes!                                                                                            Weina LI                                                                                         2009.04.12 好玩贺卡等你发，邮箱贺卡全新上线！ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at GMAIL.COM Wed Apr 15 17:27:29 2009 From: julian.keil at GMAIL.COM (Julian Keil) Date: Wed, 15 Apr 2009 17:27:29 +0200 Subject: Plot ECoG-Electrodes Message-ID: Hello, we have recently begun to work with ECoG data. Now we would like to plot results from timelock and freqanalysis. Is there any possibility to plot the (known) electrode position onto the brain using sourceplot? Thanks a lot Julian Dipl. Psych. Julian Keil OBOB-Lab University of Konstanz Department of Psychology P.O. Box D23 78457 Konstanz Germany Tel: ++49 - (0)7531 - 88 42 50 Fax: ++49 - (0)7531 - 88 28 91 Email: julian.keil at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Wed Apr 15 17:30:51 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Wed, 15 Apr 2009 21:00:51 +0530 Subject: [FIELD TRIP] regarding define trial Message-ID: Dear schofflen, Do you mean to say that I need to download all the zip files along with the directory and locate them to some folder.  And then locate matlab to that folder.   Best   Chintan --- On Wed, 15/4/09, jan-mathijs schoffelen wrote: From: jan-mathijs schoffelen Subject: Re: [FIELDTRIP] [FIELD TRIP] regarding define trial To: FIELDTRIP at NIC.SURFNET.NL Date: Wednesday, 15 April, 2009, 8:14 PM Dear Chintan, You probably still have to add the fieldtrip folder to you matlab-path, after you downloaded the most recent fieldtrip version. Yours, JM On Apr 15, 2009, at 3:33 PM, shah chintan wrote: folks,   I am going through the tutorials of fieldtrip.  When I try to run the example scripts on matlab, I am getting an error regarding the functions which are undefined such as definetrial or preprocessing.  Please guide me to built the functions on fieldtrip.     Thanking you   Chintan Add more friends to your messenger and enjoy! Invite them now. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Wed Apr 15 19:42:49 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Wed, 15 Apr 2009 23:12:49 +0530 Subject: regarding directory files. Message-ID: Dear folks, Currently I am working on field trip tutorials.  I downloaded all the zip files and directories.  Can anybody tell me where to put directory files and how to locate on matlab.   Best regards,   Chintan Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Wed Apr 15 21:19:20 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Wed, 15 Apr 2009 20:19:20 +0100 Subject: regarding directory files. In-Reply-To: <84601.71472.qm@web95404.mail.in2.yahoo.com> Message-ID: Dear Chintan, I am afraid that the problem you have at the moment is unrelated to FieldTrip, but rather a general matlab issue. It does not matter where you put the files, as long as you tell matlab where to find them. If you put the files in, say, C: \mydirectory\fieldtrip, then you should issue the following command from the matlab command-line: addpath(genpath('C:\mydirectory \fieldtrip')), or you can specify the path using the set path utility (and then you have to add with subdirectories). If this all sounds unfamiliar to you, I strongly advise you to look into the matlab documentation to learn how to work with matlab. Yours, Jan-Mathijs On Apr 15, 2009, at 6:42 PM, shah chintan wrote: > Dear folks, > Currently I am working on field trip tutorials. I downloaded all > the zip files and directories. Can anybody tell me where to put > directory files and how to locate on matlab. > > Best regards, > > Chintan > > Download prohibited? No problem. CHAT from any browser, without > download. > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Wed Apr 15 21:23:44 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Thu, 16 Apr 2009 00:53:44 +0530 Subject: regarding directory files. Message-ID: Dear Sir,   I am very glad with your reply.  Actually I am not finding any .mat files in the installed package of matlab.  And the directories that is available at fieldtrip are all .mat files, So I am not getting where to put those directories.  Can you specify which version of matlab is compatible with fieldtrip. I am usig MATLAB 7.4.0.   Best Regards,   Chintan --- On Thu, 16/4/09, jan-mathijs schoffelen wrote: From: jan-mathijs schoffelen Subject: Re: [FIELDTRIP] regarding directory files. To: FIELDTRIP at NIC.SURFNET.NL Date: Thursday, 16 April, 2009, 12:49 AM Dear Chintan, I am afraid that the problem you have at the moment is unrelated to FieldTrip, but rather a general matlab issue. It does not matter where you put the files, as long as you tell matlab where to find them. If you put the files in, say, C:\mydirectory\fieldtrip, then you should issue the following command from the matlab command-line: addpath(genpath('C:\mydirectory\fieldtrip')), or you can specify the path using the set path utility (and then you have to add with subdirectories). If this all sounds unfamiliar to you, I strongly advise you to look into the matlab documentation to learn how to work with matlab. Yours, Jan-Mathijs   On Apr 15, 2009, at 6:42 PM, shah chintan wrote: Dear folks, Currently I am working on field trip tutorials.  I downloaded all the zip files and directories.  Can anybody tell me where to put directory files and how to locate on matlab.   Best regards,   Chintan Download prohibited? No problem. CHAT from any browser, without download. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Wed Apr 15 21:48:48 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Thu, 16 Apr 2009 01:18:48 +0530 Subject: regarding definetrial and preprocessing Message-ID: Folks,   I am working on fieldtrip tutorials.  I downloaded all the files and directories from tutorials.  Now when I run the scripts, an error occurs that definetrial and preprocessing functions are undefined.  Please help me in  building these functions.   Best Regards,   Chintan Connect with friends all over the world. Get Yahoo! India Messenger at http://in.messenger.yahoo.com/?wm=n/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From megjim1 at GMAIL.COM Fri Apr 17 04:11:06 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Fri, 17 Apr 2009 04:11:06 +0200 Subject: Makefile for Linux 64 Message-ID: Dear Guillaume, That's great! I'm downloading them now. Thanks a lot for your wonderful help, :) Jim On Wed, 15 Apr 2009 11:27:10 +0100, Guillaume Flandin wrote: >Dear Jim, > >some 64bit Linux MEX files for SPM2 are available from here: >ftp://ftp.fil.ion.ucl.ac.uk/spm/spm2_updates/ > >The website mentioned in previous email is the SPM wikibooks: >http://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Linux#Compilation_not es_for_SPM2: > >I also attach a SPM2 Makefile that contains instructions for Linux64 >compilation, in case the provided compiled MEX files do not work on your >platform. > >Best regards, >Guillaume. > > >Jim Li wrote: >> Dear FTer: >> >> We're thinking of buying a 64-bit Quad-core PC w/ big memory(>=16GB), then >> install a Linux OS (CentOS 4) and run Fieldtrip on it. According to the first >> question asked by Christine below, there seems to be a problem w/ SPM2. Is >> that still an issue or is it solved by now? Are there any other issues to pay >> attention to w/ 64-bit linux? >> >> >> Thanks a lot, >> >> Jim >> >> On Tue, 18 Sep 2007 17:03:59 +0200, Christine Tillmann > FRANKFURT.MPG.DE> wrote: >> >>> Hi, >>> >>> we are trying to get the fieldtrip beamforming on our linux 64 bit >>> systems going. As we understand it, there is currently no way around >>> using spm2. Spm2's mex files however are not compiled for linux 64 bit >>> and the makefile that's available on the web suffers from the tab/space >>> delimiter problem. >>> Does anyone have a makefile for spm2 that works on linux 64 bit? >>> >>> Or, else is there a way around spm2? E.g. by using the output of >>> mriviewer and the localspheres command directly? Or by beamforming in >>> CTF and feeding its output to sourcestatistics? >>> >>> And one last thing: does anyone use the mri files from trhe >>> CTF-MRIviewer that came with version 5.4.0 yet? >>> >>> Thanks, >>> Christine > > > >-- >Guillaume Flandin, PhD >Wellcome Trust Centre for Neuroimaging >University College London >12 Queen Square >London WC1N 3BG > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >#!make -f ># ># @(#)Makefile 2.16 John Ashburner 03/05/12 ># Note that changes have been made outside SCCS ># $Id$ ># >#################################################### ########################### ># ># Suggestions for how to make this file a bit more elegant are welcome. So far ># it works under SunOS and Linux (at the FIL) and some Windows systems ># ># $Log$ ># >#################################################### ########################### > >#################################################### ########################### ># Default make >#################################################### ########################### >unknown: > @ make `uname` >tidy: > @ make clean.`uname` > >#################################################### ########################### ># Architecture specific makes >#################################################### ########################### > >MEX = mex -O >CC = cc ># mex output object suffix >MOSUF = o >CHMODIT = chmod 644 >RANLIB = >ADDED_OBS= >ADDED_MEX= > >SunOS: > make all SUF=mexsol CC="cc -xO5" MEX="mex COPTIMFLAGS=-xO5" >Linux: > make all SUF=mexglx CC="gcc -O3 -funroll-loops" MEX="mex COPTIMFLAGS='-O3 -funroll-loops'" >Linux.5: > make all SUF=mexlx CC="gcc -O3 -funroll-loops" MEX="mex COPTIMFLAGS='-O3 -funroll-loops'" >HP-UX: > make all SUF=mexhp7 CC="cc -O +z -Ae +DAportable" MEX="mex COPTIMFLAGS=-O" >IRIX: > make all SUF=mexsg CC="cc -O -mips2" MEX="mex" >IRIX64: > make all SUF=mexsg64 CC="cc -O -mips4 -64" MEX="mex" >AIX: > make all SUF=mexrs6 >OSF1: > make all SUF=mexaxp >MAC: > make all SUF=mexmac RANLIB="ranlib spm_vol_utils.mexmac.a" > >Linux.A64: ># The '-fPIC' option is nexessary to allow the linking proces to complete. ># '-march=x86-64' provides generic optimisations for both Opteron and 64bit Xeon. ># If the code is running on a 64bit Xeon you can change '-march=x86-64' to ># '-march=nocona', when running on an Opteron, change it to '- march=opteron'. ># Also possibly use '-march=k8' for 64 bit Athlon. > make all SUF=mexa64 CC="gcc -O3 -funroll-loops -fPIC -march=x86- 64 -mfpmath=sse"\ > MEX="mex COPTIMFLAGS='-O3 -funroll-loops -fPIC -march=x86- 64 -mfpmath=sse'" > >#windows: ># make all SUF=dll MOSUF=obj CHMODIT="echo > null" ADDED_OBS=win32mmap.dll.o ADDED_MEX=spm_win32utils.dll >windows: ># Consider adding either of the following, depending on your platform: ># -march=pentium3 ># -march=pentium4 > make all SUF=dll CC="gcc -mno-cygwin -O3 -funroll-loops -fomit- frame-pointer -march=pentium4 -mfpmath=sse -DSPM_WIN32" MEX="mex.bat - DSPM_WIN32" MOSUF=obj CHMODIT="echo > NUL" ADDED_OBS=win32mmap.dll.o ADDED_MEX=spm_win32utils.dll > >#################################################### ########################### ># Architecture specific cleaning >#################################################### ########################### >clean.SunOS: > make clean SUF=mexsol >clean.Linux: > make clean SUF=mexglx >clean.Linux.5: > make clean SUF=mexlx >clean.Linux.A64: > make clean SUF=mexa64 >clean.HP-UX: > make clean SUF=mexhp7 >clean.IRIX: > make clean SUF=mexsg >clean.IRIX64: > make clean SUF=mexsg64 >clean.AIX: > make clean SUF=mexrs6 >clean.OSF1: > make clean SUF=mexaxp >clean.MAC: > make clean SUF=mexmac >clean.windows: > make clean SUF=dll > >#################################################### ########################### ># Objects to go in the archive and mexfiles >#################################################### ########################### > >SUF = unknown > >OBS = utils_uchar.$(SUF).o utils_short.$(SUF).o utils_int.$(SUF).o \ > utils_schar.$(SUF).o utils_ushort.$(SUF).o utils_uint.$(SUF).o\ > utils_float.$(SUF).o utils_double.$(SUF).o\ > utils_short_s.$(SUF).o utils_int_s.$(SUF).o\ > utils_ushort_s.$(SUF).o utils_uint_s.$(SUF).o\ > utils_float_s.$(SUF).o utils_double_s.$(SUF).o\ > spm_make_lookup.$(SUF).o spm_getdata.$(SUF).o spm_vol_access.$(SUF).o\ > spm_mapping.$(SUF).o $(ADDED_OBS) > >SPMMEX =\ > spm_sample_vol.$(SUF) spm_slice_vol.$(SUF) spm_brainwarp.$(SUF)\ > spm_add.$(SUF) spm_conv_vol.$(SUF) spm_render_vol.$(SUF)\ > spm_global.$(SUF) spm_resels_vol.$(SUF)\ > spm_atranspa.$(SUF) spm_list_files.$(SUF) spm_unlink.$(SUF)\ > spm_krutil.$(SUF) spm_project.$(SUF) spm_hist2.$(SUF) spm_max.$(SUF)\ > spm_clusters.$(SUF) spm_bsplinc.$(SUF) spm_bsplins.$(SUF)\ > spm_bias_mex.$(SUF) spm_dilate.$(SUF) $(ADDED_MEX) > >#################################################### ########################### ># The main ways to run make >#################################################### ########################### > >all: verb.$(SUF) $(SPMMEX) > @ echo "_____________________________________________________________ " > @ echo "" > @ echo " FINISHED" > @ echo "_____________________________________________________________ " > @ echo "" > >very_clean: clean > @ echo "_____________________________________________________________ " > @ echo "" > @ echo " Deleting mex and archive (.a) files" > @ echo "_____________________________________________________________ " > @ echo "" > rm -f $(SPMMEX) spm_vol_utils.$(SUF).a > >clean: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo " Deleting object (.o) files" > @ echo "_____________________________________________________________ " > @ echo "" > rm -f $(OBS) > >archive: spm_vol_utils.$(SUF).a > >#################################################### ########################### ># Compile spm_vol_utils.c with various flags >#################################################### ########################### > >spm_vol_utils.$(SUF).a: $(OBS) > rm -f $@ > ar rcv $@ $(OBS) > $(RANLIB) > @ $(CHMODIT) $@ > >UTILS=spm_vol_utils.c spm_sys_deps.h spm_make_lookup.h spm_getdata.h > >utils_uchar.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_CHAR > @ $(CHMODIT) $@ > >utils_short.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_SHORT > @ $(CHMODIT) $@ > >utils_int.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_INT > @ $(CHMODIT) $@ > >utils_schar.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_CHAR > @ $(CHMODIT) $@ > >utils_ushort.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_SHORT > @ $(CHMODIT) $@ > >utils_uint.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_INT > @ $(CHMODIT) $@ > >utils_float.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_FLOAT > @ $(CHMODIT) $@ > >utils_double.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_DOUBLE > @ $(CHMODIT) $@ > >utils_short_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_SHORT - DSPM_BYTESWAP > @ $(CHMODIT) $@ > >utils_int_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_INT - DSPM_BYTESWAP > @ $(CHMODIT) $@ > >utils_ushort_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_SHORT - DSPM_BYTESWAP > @ $(CHMODIT) $@ > >utils_uint_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_INT - DSPM_BYTESWAP > @ $(CHMODIT) $@ > >utils_float_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_FLOAT -DSPM_BYTESWAP > @ $(CHMODIT) $@ > >utils_double_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_DOUBLE -DSPM_BYTESWAP > @ $(CHMODIT) $@ > >#################################################### ########################### ># Compile a few additional C routines for linking >#################################################### ########################### > >%.$(SUF).o : %.c spm_sys_deps.h > $(CC) -c -o $@ $< > @ $(CHMODIT) $@ > >spm_getdata.$(SUF).o: spm_getdata.c spm_sys_deps.h > >spm_vol_access.$(SUF).o: spm_vol_access.c spm_vol_access.h spm_datatypes.h > >spm_make_lookup.$(SUF).o: spm_make_lookup.c spm_sys_deps.h > >spm_getdata.$(SUF).o: spm_getdata.c > >spm_mapping.$(SUF).o: spm_mapping.c spm_sys_deps.h spm_mapping.h spm_datatypes.h > $(MEX) -c spm_mapping.c > mv spm_mapping.$(MOSUF) $@ > @ $(CHMODIT) $@ > >win32mmap.$(SUF).o: win32mmap.c win32mmap.h > $(CC) -c -o $@ win32mmap.c > @ $(CHMODIT) $@ > >#################################################### ########################### ># Compile the mex files themselves >#################################################### ########################### > >%.$(SUF) : %.c spm_sys_deps.h > $(MEX) $< > @ $(CHMODIT) $@ > >spm_add.$(SUF): spm_add.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h > $(MEX) spm_add.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_brainwarp.$(SUF): spm_brainwarp.c spm_vol_utils.$(SUF).a spm_matfuns.c\ > spm_sys_deps.h spm_mapping.h > $(MEX) spm_brainwarp.c spm_vol_utils.$(SUF).a spm_matfuns.c > @ $(CHMODIT) $@ > >spm_bsplinc.$(SUF): spm_bsplinc.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h spm_datatypes.h > $(MEX) spm_bsplinc.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_bsplins.$(SUF): spm_bsplins.c spm_sys_deps.h > $(MEX) spm_bsplins.c > @ $(CHMODIT) $@ > >spm_conv_vol.$(SUF): spm_conv_vol.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h spm_datatypes.h > $(MEX) spm_conv_vol.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_global.$(SUF): spm_global.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h > $(MEX) spm_global.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_atranspa.$(SUF): spm_atranspa.c spm_sys_deps.h > >spm_unlink.$(SUF): spm_unlink.c spm_sys_deps.h > >spm_max.$(SUF): spm_max.c spm_sys_deps.h > >spm_clusters.$(SUF): spm_clusters.c spm_sys_deps.h > >spm_hist2.$(SUF): spm_hist2.c spm_sys_deps.h > >spm_krutil.$(SUF): spm_krutil.c spm_sys_deps.h > >spm_dilate.$(SUF): spm_dilate.c > >spm_list_files.$(SUF): spm_list_files.c spm_sys_deps.h > >spm_project.$(SUF): spm_project.c spm_sys_deps.h > >spm_render_vol.$(SUF): spm_render_vol.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h > $(MEX) spm_render_vol.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_resels_vol.$(SUF): spm_resels_vol.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h > $(MEX) spm_resels_vol.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_sample_vol.$(SUF): spm_sample_vol.c spm_vol_utils.$(SUF).a spm_mapping.h > $(MEX) spm_sample_vol.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_slice_vol.$(SUF): spm_slice_vol.c spm_vol_utils.$(SUF).a spm_mapping.h > $(MEX) spm_slice_vol.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_bias_mex.$(SUF): spm_bias_mex.c spm_vol_utils.$(SUF).a spm_mapping.h > $(MEX) spm_bias_mex.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_win32utils.$(SUF): spm_win32utils.c > $(MEX) spm_win32utils.c > @ $(CHMODIT) $@ > >#################################################### ########################### ># Assorted architecture dependent messages >#################################################### ########################### > >verb.unknown: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "PROBLEM: Dont know how to do this." > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexhp7: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "unix compile for hpux cc, and maybe aix cc" > @ echo "" > @ echo "Under HPUX 10.20 with MATLAB 5.2.1 and gcc, you may wish" > @ echo "to modify this Makefile to say something like:" > @ echo ' CC=gcc -O -fpic' > @ echo ' MEX=mex COPTIMFLAGS=-O -f gccopts.sh' > @ echo "where the gccopts.sh file is modified to remove the +z" > @ echo "(which is used with version 9.0 and possibly also 10.0)." > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexsg: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Feedback from users with R10000 O2 and R10000 Indigo2 systems" > @ echo "running IRIX6.5 suggests that the cmex program with Matlab 5.x" > @ echo "compiles with the old 32bit (o32) instruction set (MIPS2) only," > @ echo "while cc by default compiles with the new32 bit (n32 or MIPS4)." > @ echo "Matlab 5.x only likes o32 for O2 R10000 systems." > @ echo "" > @ echo "We also suggest you modify your options file mexopts.sh in" > @ echo 'the sgi section: change LD="ld" to LD="ld -o32"' > @ echo "this tells the linker to use o32 instead of n32." > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexsg64: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "not optimised sgi 64 bit compile for CC" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.dll: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Windows compile with gcc/mingw" > @ echo "see http://www.mrc- cbu.cam.ac.uk/Imaging/gnumex20.html" > @ echo "for instructions about installing gcc/mingw for" > @ echo "compiling Mex files." > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexsol: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Unix compile for Sun cc" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexlx: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Linux compilation (Matlab 5.x) - using gcc" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexglx: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Linux compilation (Matlab 6.x) - using gcc" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexaxp: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "keep your fingers crossed" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexmac: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Unix compile for MacOS X" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexa64: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Unix compile for Linux A64" > @ echo "_____________________________________________________________ " > @ echo "" > > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From cmuehl at GMAIL.COM Fri Apr 17 15:01:26 2009 From: cmuehl at GMAIL.COM (Christian Muehl) Date: Fri, 17 Apr 2009 15:01:26 +0200 Subject: CfP Workshop on Affective Brain-Computer Interfaces (aBCI '09) Message-ID: -------------------------------------------------------------- Call for Papers -------------------------------------------------------------- Workshop on Affective Brain-Computer Interfaces (held in conjunction with ACII’09) Amsterdam, The Netherlands, 09.09.2009 -------------------------------------------------------------- Overview: ------------ This workshop will explore the advantages and limitations of using neurophysiological signals as a modality for the automatic recognition of affective and cognitive states, as well as the possibilities to use this information about the user state in innovative and adaptive applications. Theme of the workshop: ------------------------------ Recent research efforts in brain-computer interfaces (BCI) show that brain activity can be used as an active/voluntary, or passive/involuntary control modality in man-machine interaction. While active BCI paradigms received a lot of attention in recent years, research on passive approaches to BCI is still lacking concerted activity. However, it has been shown more than once that brain activations can carry information about the affective and cognitive state of a subject, and that the interaction between humans and machines can be aided by the recognition of those user states. To achieve robust passive BCIs, efforts from applied and basic sciences have to be combined. On the one hand, applied fields such as affective computing aim at the development of applications that adapt to changes in the user states and thereby enrich the interaction, leading to a more natural and effective usability. On the other hand, basic research in neuroscience advances our understanding of the neural processes associated with emotions. Furthermore, similar advancements are being made for more cognitive mental states, for example attention, fatigue, and work load, which strongly interact with affective states. We encourage submissions exploring one or more of the following topics: * emotion elicitation and data collection for affective BCI * detection of affective and cognitive states with BCI and other modalities * adaptive interfaces and affective BCI Goal of the workshop: --------------------------- The goal of the workshop is to bring researchers from the communities of brain computer interfacing, affective computing, neuroergonomics, affective and cognitive neuroscience together to present state-of-the-art progress and visions on the various intersections between those disciplines. Paper submissions: ----------------------- Papers should be 8 - 15 pages long and in the format of the CTIT Series Proceedings. They should have a clear relationship to brain-computer interfacing and to one or more of the other topics listed above. Technical papers, as well as survey papers and empirical papers are eligible. The accepted papers will be published in the workshop proceedings (CTIT Series, ISSN Number available). Please submit your papers in PDF format to ABCI at ewi.utwente.nl . Important Dates: --------------------- Paper Submission: 15.06.2009 Acceptance Note: 15.07.2009 Camera-ready versions: 15.08.2009 Further information can be found on the workshop website. Workshop Website: http://hmi.ewi.utwente.nl/abci2009 Email: ABCI at ewi.utwente.nl Programme Chairs: ----------------------- * Brendan Allison, Technical University Graz, Austria * Stephen Dunne, StarLabs Barcelona, Spain * Dirk Heylen, University of Twente, The Netherlands * Anton Nijholt, University of Twente, The Netherlands Local Organizer: ------------------- * Christian Muehl, University of Twente, The Netherlands Programme Committee: ----------------------------- * Egon van den Broek, University of Twente, The Netherlands * Anne-Marie Brouwer, TNO Soesterberg, The Netherlands * Peter Desain, Radboud University Nijmegen, The Netherlands * Stephen Fairclough, John Moores University Liverpool, United Kingdom * Didier Grandjean, University of Geneva, Switzerland * Markus Junghöfer, University Münster, Germany * Jonghwa Kim, University Augsburg, Germany * Gary Garcia Molina, Philips Research Eindhoven, The Netherlands * Ioannis Patras, Queen Mary University of London, United Kingdom * Gert Pfurtscheller, Technical University Graz, Austria * Thierry Pun, University of Geneva, Switzerland ------------------------------------------------------------------------ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From djs32 at BUFFALO.EDU Fri Apr 17 15:15:23 2009 From: djs32 at BUFFALO.EDU (Daniel Stolzberg) Date: Fri, 17 Apr 2009 09:15:23 -0400 Subject: regarding definetrial and preprocessing In-Reply-To: <919266.15252.qm@web95407.mail.in2.yahoo.com> Message-ID: Hello Chintan, Have you set the path to the new directories? File -> Set Path -Dan On Wed, Apr 15, 2009 at 3:48 PM, shah chintan wrote: > Folks, > > I am working on fieldtrip tutorials. I downloaded all the files and > directories from tutorials. Now when I run the scripts, an error occurs > that definetrial and preprocessing functions are undefined. Please help me > in building these functions. > > Best Regards, > > Chintan > > ------------------------------ > Add more friends to your messenger and enjoy! Invite them now. > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Fri Apr 17 19:02:19 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Fri, 17 Apr 2009 22:32:19 +0530 Subject: regarding definetrial and preprocessing Message-ID: Hello Dan, Thank you very much for your reply.  New directories does not contain these functions.  every time I locate to the directories that i downloaded.    Chintan --- On Fri, 17/4/09, Daniel Stolzberg wrote: From: Daniel Stolzberg Subject: Re: [FIELDTRIP] regarding definetrial and preprocessing To: FIELDTRIP at NIC.SURFNET.NL Date: Friday, 17 April, 2009, 6:45 PM Hello Chintan, Have you set the path to the new directories?  File -> Set Path -Dan On Wed, Apr 15, 2009 at 3:48 PM, shah chintan wrote: Folks,   I am working on fieldtrip tutorials.  I downloaded all the files and directories from tutorials.  Now when I run the scripts, an error occurs that definetrial and preprocessing functions are undefined.  Please help me in  building these functions.   Best Regards,   Chintan Add more friends to your messenger and enjoy! Invite them now. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at MAC.COM Fri Apr 17 20:06:18 2009 From: nathanweisz at MAC.COM (Nathan Weisz) Date: Fri, 17 Apr 2009 20:06:18 +0200 Subject: regarding definetrial and preprocessing In-Reply-To: <581826.87029.qm@web95411.mail.in2.yahoo.com> Message-ID: dear chintan, you mean the functions define are not in the folders you downloaded? that sounds weird, but perhaps you have downloaded a release where (theoretically) some problems occured and nobody noticed so far, as most people don't update their fieldtrip folders on a daily basis. however unlikely, try downloading an older fieldtrip version and take another look if you can find those functions. are you sure that you click on the "Save" button when setting the path and not just "Ok"? when you type "path" from the command line, can you find the relevant fieldtrip folders? like others have mentioned before your issue could be more Matlab than fieldtrip related. try to consult some colleague familiar with Matlab. good luck! n On 17.04.2009, at 19:02, shah chintan wrote: > Hello Dan, > Thank you very much for your reply. New directories does not > contain these functions. every time I locate to the directories > that i downloaded. > > Chintan > > --- On Fri, 17/4/09, Daniel Stolzberg wrote: > > From: Daniel Stolzberg > Subject: Re: [FIELDTRIP] regarding definetrial and preprocessing > To: FIELDTRIP at NIC.SURFNET.NL > Date: Friday, 17 April, 2009, 6:45 PM > > Hello Chintan, > > Have you set the path to the new directories? File -> Set Path > > -Dan > > On Wed, Apr 15, 2009 at 3:48 PM, shah chintan > wrote: > Folks, > > I am working on fieldtrip tutorials. I downloaded all the files and > directories from tutorials. Now when I run the scripts, an error > occurs that definetrial and preprocessing functions are undefined. > Please help me in building these functions. > > Best Regards, > > Chintan > > Add more friends to your messenger and enjoy! Invite them now. > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > http://listserv.surfnet.nl/archives/fieldtrip.html > http://www.ru.nl/fcdonders/fieldtrip/ > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > http://listserv.surfnet.nl/archives/fieldtrip.html > http://www.ru.nl/fcdonders/fieldtrip/ > > Add more friends to your messenger and enjoy! Invite them now. > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Fri Apr 17 22:55:12 2009 From: chintan_student at YAHOO.CO.IN (Chintan Shah) Date: Sat, 18 Apr 2009 02:25:12 +0530 Subject: Regarding define trial, preprocessing and reject visual Message-ID: Dear sir, I am really glad with your replies.  I thank you from the bottom of my heart.  I downloaded all the files and directories from the tutorial data. Now none of these directories include the functions like definetrial, preprocessing and reject visual. So when everytime I try to run the tutorial scripts locating matlab to the folder containing downloaded files and directories, I get an error that those functions are undefined.  Please help me to build these functions.   Best Regards,   Chintan Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingrid.nieuwenhuis at DONDERS.RU.NL Sat Apr 18 09:21:11 2009 From: ingrid.nieuwenhuis at DONDERS.RU.NL (Ingrid Nieuwenhuis) Date: Sat, 18 Apr 2009 09:21:11 +0200 Subject: Regarding define trial, preprocessing and reject visual Message-ID: Dear Chintan, Did you download the fieldtrip toolbox? If you go to "download" (http://fieldtrip.fcdonders.nl/download) you can se that you can download the "FieldTrip toolbox" and the "tutorial data". I think you only downloaded the tutorial date (also because you somewhere refer to .mat files and not to .m files). .mat files are files containing the data, .m files are files containing scripts (functions) that together make the toolbox. As said before this is all really basic Matlab knowledge. Hope this solves your problem, Best Ingrid _____ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Chintan Shah Sent: Friday, April 17, 2009 10:55 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] Regarding define trial, preprocessing and reject visual Dear sir, I am really glad with your replies. I thank you from the bottom of my heart. I downloaded all the files and directories from the tutorial data. Now none of these directories include the functions like definetrial, preprocessing and reject visual. So when everytime I try to run the tutorial scripts locating matlab to the folder containing downloaded files and directories, I get an error that those functions are undefined. Please help me to build these functions. Best Regards, Chintan _____ Add more friends to your messenger and enjoy! Invite them now. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lmoranr at GMAIL.COM Sat Apr 18 13:20:15 2009 From: lmoranr at GMAIL.COM (=?ISO-8859-1?Q?Luis_Mor=E1n?=) Date: Sat, 18 Apr 2009 13:20:15 +0200 Subject: Help with dipolesimulation Message-ID: Hi dear Fieldtrippers!! I'm trying to make a dipolesimulation with two dipoles. I need to use different frequencies and phases for each dipole and I don't know very well how to modify the dipolesimulation function. Any advice? Thanks in advance Best regards -- Luis Morán Rodríguez Bioengineering Group Universidad Politecnica Madrid ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Sun Apr 19 15:15:30 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Sun, 19 Apr 2009 14:15:30 +0100 Subject: Help with dipolesimulation In-Reply-To: <52b4c8f20904180420x74d16065l77baa5009993abe9@mail.gmail.com> Message-ID: Dear Luis, I guess that the desired functionality is already there, the only thing which you have to do is specifying your input configuration meaningfully. The most relevant line is line 215, which states (more or less) trial = lf * dipmom * dipsignal; lf contains the leadfield (forward model) for the dipoles at the positions in cfg.dip.pos, and has dimensionality Nchan x (Ndipolex3), so it is a concatenation (in the columns) of the single position's leadfields. dipsignal is an NdipolexNtime matrix containing the dipoles' time series. For the matrix product to work, dipmom should be of dimensionaity (Ndipolex3)xNdipole (right?). This is the key to the solution to your problem: cfg.dip.mom should be something like [orix1 0;oriy1 0; oriz1 0;0 orix2;0 oriy2;0 oriz2], with ori(xyz)(1/2) specifying the moments of your dipoles. I hope this helps, Jan-Mathijs On Apr 18, 2009, at 12:20 PM, Luis Morán wrote: > Hi dear Fieldtrippers!! > > I'm trying to make a dipolesimulation with two dipoles. I need to > use different frequencies and phases for each dipole and I don't > know very well how to modify the dipolesimulation function. > > Any advice? > > Thanks in advance > > Best regards > -- > Luis Morán Rodríguez > > Bioengineering Group > Universidad Politecnica Madrid > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From lmoranr at GMAIL.COM Sun Apr 19 19:22:20 2009 From: lmoranr at GMAIL.COM (=?ISO-8859-1?Q?Luis_Mor=E1n?=) Date: Sun, 19 Apr 2009 19:22:20 +0200 Subject: Help with dipolesimulation In-Reply-To: <4AA43C77-0BA6-40DC-B71C-91BF0AE3BCEE@psy.gla.ac.uk> Message-ID: But that doesn't solve my problem. I've completed the simulation with 2 dipoles but using the same frequencies and phases. What I need is use a different frequency in each dipole As I understand the dipolesimulation function at 'cfg.frequency' we can specify only a value Any other advice? Thanks a lot in advance 2009/4/19 jan-mathijs schoffelen > Dear Luis, > > I guess that the desired functionality is already there, the only thing > which you have to do is specifying your input configuration meaningfully. > The most relevant line is line 215, which states (more or less) trial = lf > * dipmom * dipsignal; > > lf contains the leadfield (forward model) for the dipoles at the positions > in cfg.dip.pos, and has dimensionality Nchan x (Ndipolex3), so it is a > concatenation (in the columns) of the single position's leadfields. > dipsignal is an NdipolexNtime matrix containing the dipoles' time series. > For the matrix product to work, dipmom should be of dimensionaity > (Ndipolex3)xNdipole (right?). This is the key to the solution to your > problem: > > cfg.dip.mom should be something like [orix1 0;oriy1 0; oriz1 0;0 orix2;0 > oriy2;0 oriz2], with ori(xyz)(1/2) specifying the moments of your dipoles. > > I hope this helps, > > Jan-Mathijs > > > > On Apr 18, 2009, at 12:20 PM, Luis Morán wrote: > > Hi dear Fieldtrippers!! >> >> I'm trying to make a dipolesimulation with two dipoles. I need to use >> different frequencies and phases for each dipole and I don't know very well >> how to modify the dipolesimulation function. >> >> Any advice? >> >> Thanks in advance >> >> Best regards >> -- >> Luis Morán Rodríguez >> >> Bioengineering Group >> Universidad Politecnica Madrid >> ---------------------------------- >> >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and >> EEG analysis. >> >> http://listserv.surfnet.nl/archives/fieldtrip.html >> >> http://www.ru.nl/fcdonders/fieldtrip/ >> >> > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > -- Luis Morán Rodríguez Altentic lmoran at altentic.com ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sklein at BERKELEY.EDU Sun Apr 19 19:46:50 2009 From: sklein at BERKELEY.EDU (Stanley Klein) Date: Sun, 19 Apr 2009 10:46:50 -0700 Subject: Help with dipolesimulation In-Reply-To: <9016c9f10904191044n247312c0t7e231c9356d10e36@mail.gmail.com> Message-ID: Luis, Phase doesn't make much sense if frequencies are different. In your simulation are you doing stimulation with two frequencies (SSVEP)? If so then you can do the simulation with two dipoles each with two frequencies. If you aren't doing stimulation then I'd think you'd just want to choose one frequency (say with an octave banwidth) for doing your source localization. Does Fieldtrip have good tools for doing that sort of localization? Stan On Sun, Apr 19, 2009 at 10:22 AM, Luis Morán wrote: > But that doesn't solve my problem. I've completed the simulation with 2 > dipoles but using the same frequencies and phases. What I need is use a > different frequency in each dipole > > As I understand the dipolesimulation function at 'cfg.frequency' we can > specify only a value > > Any other advice? > > Thanks a lot in advance > > > 2009/4/19 jan-mathijs schoffelen > > Dear Luis, >> >> I guess that the desired functionality is already there, the only thing >> which you have to do is specifying your input configuration meaningfully. >> The most relevant line is line 215, which states (more or less) trial = lf >> * dipmom * dipsignal; >> >> lf contains the leadfield (forward model) for the dipoles at the positions >> in cfg.dip.pos, and has dimensionality Nchan x (Ndipolex3), so it is a >> concatenation (in the columns) of the single position's leadfields. >> dipsignal is an NdipolexNtime matrix containing the dipoles' time series. >> For the matrix product to work, dipmom should be of dimensionaity >> (Ndipolex3)xNdipole (right?). This is the key to the solution to your >> problem: >> >> cfg.dip.mom should be something like [orix1 0;oriy1 0; oriz1 0;0 orix2;0 >> oriy2;0 oriz2], with ori(xyz)(1/2) specifying the moments of your dipoles. >> >> I hope this helps, >> >> Jan-Mathijs >> >> >> >> On Apr 18, 2009, at 12:20 PM, Luis Morán wrote: >> >> Hi dear Fieldtrippers!! >>> >>> I'm trying to make a dipolesimulation with two dipoles. I need to use >>> different frequencies and phases for each dipole and I don't know very well >>> how to modify the dipolesimulation function. >>> >>> Any advice? >>> >>> Thanks in advance >>> >>> Best regards >>> -- >>> Luis Morán Rodríguez >>> >>> Bioengineering Group >>> Universidad Politecnica Madrid >>> ---------------------------------- >>> >>> The aim of this list is to facilitate the discussion between users of the >>> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and >>> EEG analysis. >>> >>> http://listserv.surfnet.nl/archives/fieldtrip.html >>> >>> http://www.ru.nl/fcdonders/fieldtrip/ >>> >>> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/neuroimaging/fieldtrip. >> > > > > -- > Luis Morán Rodríguez > > Altentic > > lmoran at altentic.com > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.litvak at ION.UCL.AC.UK Mon Apr 20 01:25:00 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Mon, 20 Apr 2009 00:25:00 +0100 Subject: Help with dipolesimulation In-Reply-To: <9016c9f10904191046i974d987x4fbba9b311ed4525@mail.gmail.com> Message-ID: Dear Luis, What Jan-Mathijs was saying is that you can use the dipolesimulation function to project any arbitrary source waveform to the sensors. There are some limited tools in the function to create such a waveform on the fly (cfg.frequency) but a much more flexible way would be to create the waveforms in your own script using Matlab tools and then just use dipolesimulation to project them (with cfg.dip.mom as JM explained). Also since the summation of sources is linear, you can run dipolesimulation several times with different inputs and then add the resulting data. You can use freqsimulation function for generating your source waveforms or use your own code. Stanley is partially right that phase locking only makes sense for the same frequency (although there might be more complex relations having to do with phase across frequencies), but that's another issue. Large part of Fieldtrip is about localizing oscillatory activity. That's exactly what beamforming is for, particularly DICS. Best, Vladimir On Sun, Apr 19, 2009 at 6:46 PM, Stanley Klein wrote: > Luis, > Phase doesn't make much sense if frequencies are different. > In your simulation are you doing stimulation with two frequencies (SSVEP)? > If so then you can do the simulation with two dipoles each with two > frequencies. If you aren't doing stimulation then I'd think you'd just want > to choose one frequency (say with an octave banwidth) for doing your source > localization. > > Does Fieldtrip have good tools for doing that sort of localization? > Stan > > On Sun, Apr 19, 2009 at 10:22 AM, Luis Morán wrote: >> >> But that doesn't solve my problem.  I've completed the simulation with 2 >> dipoles but using the same frequencies and phases. What I need is use a >> different frequency in each dipole >> >> As I understand the dipolesimulation function at 'cfg.frequency' we can >> specify only a value >> >> Any other advice? >> >> Thanks a lot in advance >> >> >> 2009/4/19 jan-mathijs schoffelen >>> >>> Dear Luis, >>> >>> I guess that the desired functionality is already there, the only thing >>> which you have to do is specifying your input configuration meaningfully. >>> The most relevant line is line 215, which states (more or less) trial = >>> lf * dipmom * dipsignal; >>> >>> lf contains the leadfield (forward model) for the dipoles at the >>> positions in cfg.dip.pos, and has dimensionality Nchan x (Ndipolex3), so it >>> is a concatenation (in the columns) of the single position's leadfields. >>> dipsignal is an NdipolexNtime matrix containing the dipoles' time series. >>> For the matrix product to work, dipmom should be of dimensionaity >>> (Ndipolex3)xNdipole (right?). This is the key to the solution to your >>> problem: >>> >>> cfg.dip.mom should be something like  [orix1 0;oriy1 0; oriz1 0;0 orix2;0 >>> oriy2;0 oriz2], with ori(xyz)(1/2) specifying the moments of your dipoles. >>> >>> I hope this helps, >>> >>> Jan-Mathijs >>> >>> >>> On Apr 18, 2009, at 12:20 PM, Luis Morán wrote: >>> >>>> Hi dear Fieldtrippers!! >>>> >>>> I'm trying to make a dipolesimulation with two dipoles. I need to use >>>> different frequencies and phases for each dipole and I don't know very well >>>> how to modify the dipolesimulation function. >>>> >>>> Any advice? >>>> >>>> Thanks in advance >>>> >>>> Best regards >>>> -- >>>> Luis Morán Rodríguez >>>> >>>> Bioengineering Group >>>> Universidad Politecnica Madrid >>>> ---------------------------------- >>>> >>>> The aim of this list is to facilitate the discussion between users of >>>> the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG >>>> and EEG analysis. >>>> >>>> http://listserv.surfnet.nl/archives/fieldtrip.html >>>> >>>> http://www.ru.nl/fcdonders/fieldtrip/ >>>> >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users of the >>> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG >>> and EEG analysis. See also >>> http://listserv.surfnet.nl/archives/fieldtrip.html and >>> http://www.ru.nl/neuroimaging/fieldtrip. >> >> >> >> -- >> Luis Morán Rodríguez >> >> Altentic >> >> lmoran at altentic.com >> >> ---------------------------------- >> >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and >> EEG analysis. >> >> http://listserv.surfnet.nl/archives/fieldtrip.html >> >> http://www.ru.nl/fcdonders/fieldtrip/ > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bleichner.martin at GMAIL.COM Mon Apr 20 11:24:00 2009 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Mon, 20 Apr 2009 11:24:00 +0200 Subject: Reconstructing signal form powerspctrm Message-ID: Hi there, is there a function in fieldtrip which allows to reconstruct the signal from the powspctrm? Thanks a lot best, Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.maris at DONDERS.RU.NL Mon Apr 20 11:44:01 2009 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Mon, 20 Apr 2009 11:44:01 +0200 Subject: Reconstructing signal form powerspctrm In-Reply-To: Message-ID: Hi Martin, is there a function in fieldtrip which allows to reconstruct the signal from the powspctrm? Let me answer this question, to take away some load from the shoulders of Jan-Mathijs, whos is becoming the prime signal processing/source reconstruction expert on this discussion list. The answer is that such a function does not exist. In fact, what you ask is not possible. It is possible to reconstruct a signal from a Fourier transform (using the inverse Fourier transform), but it is not possible to reconstruct a signal from the squared amplitude of the Fourier transform (which is the power spectrum - or at least the most common estimate of the power spectrum). In the power spectrum the phase information is lost, and therefore you cannot reconstruct the signal. Good luck, Eric Thanks a lot best, Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingrid.nieuwenhuis at DONDERS.RU.NL Mon Apr 20 13:24:43 2009 From: ingrid.nieuwenhuis at DONDERS.RU.NL (Ingrid Nieuwenhuis) Date: Mon, 20 Apr 2009 13:24:43 +0200 Subject: Plot ECoG-Electrodes In-Reply-To: <7A52A42D-A57D-4714-9D19-E35E396C7499@gmail.com> Message-ID: Dear Julian, Do you mean that you would like to plot the outcome from timelock or freqanalysis on the brain, or do you just want to plot the electrodes as dots or something on the brain? And do you want to plot it on an MRI (method slice, or ortho), or on the surface of the brain (method surface). There is not standard something implemented in FieldTrip for plotting ECoG data, but if you describe more in detail what you want, we could think along. There is for instance the possibility to make your own layout, based on the electrode positions, so that there can be interpolated between the electrode positions. And also important to know, do you want to plot it for a single subject, or do you have multiple subjects in MNI normalized coordinates? Best Ingrid _____ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Julian Keil Sent: Wednesday, April 15, 2009 5:27 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] Plot ECoG-Electrodes Hello, we have recently begun to work with ECoG data. Now we would like to plot results from timelock and freqanalysis. Is there any possibility to plot the (known) electrode position onto the brain using sourceplot? Thanks a lot Julian Dipl. Psych. Julian Keil OBOB-Lab University of Konstanz Department of Psychology P.O. Box D23 78457 Konstanz Germany Tel: ++49 - (0)7531 - 88 42 50 Fax: ++49 - (0)7531 - 88 28 91 Email: julian.keil at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From megjim1 at GMAIL.COM Mon Apr 20 20:32:34 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Mon, 20 Apr 2009 20:32:34 +0200 Subject: about ICA w/o EEGLAB Message-ID: Dear all, I'm trying to remove cardiac interferences from my MEG signal (gradiometer) channels before doing wavelet analysis. This seems necessary because, when looking at each epoch, the wavelet power @ 10-40Hz are dominated by cardiac interference, and that's the bandwidth of interest. I see some Fieldtrip example script utilizing ICA of EEGLAB to remove cardiac interference. However, someone told me that it can be done in Fieldtrip w/o using EEGLAB. Is this true? If so, I'd appreciate it very much if anyone can send me the code, :) Thanks a lot, Jim ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Mon Apr 20 22:33:59 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Mon, 20 Apr 2009 21:33:59 +0100 Subject: about ICA w/o EEGLAB In-Reply-To: Message-ID: Dear Jim, I don't know whether I understand your question correctly, but Fieldtrip can do it 'without' a full download of EEGLAB, because the necessary ICA-routines are included in fieldtrip's download (and are located in the subfolder external/eeglab/... This means that your mystery someone was right ;o) Cheers, Jan-Mathijs On Apr 20, 2009, at 7:32 PM, Jim Li wrote: > Dear all, > > I'm trying to remove cardiac interferences from my MEG signal > (gradiometer) > channels before doing wavelet analysis. This seems necessary > because, when > looking at each epoch, the wavelet power @ 10-40Hz are dominated by > cardiac interference, and that's the bandwidth of interest. I see > some Fieldtrip > example script utilizing ICA of EEGLAB to remove cardiac interference. > However, someone told me that it can be done in Fieldtrip w/o using > EEGLAB. > Is this true? If so, I'd appreciate it very much if anyone can send > me the > code, :) > > Thanks a lot, > > Jim > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Mon Apr 20 23:13:13 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Mon, 20 Apr 2009 23:13:13 +0200 Subject: about ICA w/o EEGLAB Message-ID: Dear Jan-Mathijs, Thanks a lot for your answer. I see why my "componentanalysis" didn't work w/o downloading EEGLAB now: As users of a 4D system, I'm avoiding your new updated version of read_4d_hdr by sticking to some old (Dec. 2008) version of Fieldtrip, simply because it's been working fine and I'm lazy. But apparently there's no "external/eeglab" subfolder in those old versions (yes, I have several Dec 08 versions). That's why I had to download EEGLAB to get it to work. I wonder since when did you add the subfolder to Fieldtrip? Anyway, I guess it's time to embrace the new Fieldtrip versions and learn the new way to read 4D data. Thanks a lot for your help, :) Jim On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen wrote: >Dear Jim, > >I don't know whether I understand your question correctly, but >Fieldtrip can do it 'without' a full download of EEGLAB, because the >necessary ICA-routines are included in fieldtrip's download (and are >located in the subfolder external/eeglab/... This means that your >mystery someone was right ;o) > >Cheers, >Jan-Mathijs > >On Apr 20, 2009, at 7:32 PM, Jim Li wrote: > >> Dear all, >> >> I'm trying to remove cardiac interferences from my MEG signal >> (gradiometer) >> channels before doing wavelet analysis. This seems necessary >> because, when >> looking at each epoch, the wavelet power @ 10-40Hz are dominated by >> cardiac interference, and that's the bandwidth of interest. I see >> some Fieldtrip >> example script utilizing ICA of EEGLAB to remove cardiac interference. >> However, someone told me that it can be done in Fieldtrip w/o using >> EEGLAB. >> Is this true? If so, I'd appreciate it very much if anyone can send >> me the >> code, :) >> >> Thanks a lot, >> >> Jim >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Mon Apr 20 23:43:18 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Mon, 20 Apr 2009 22:43:18 +0100 Subject: about ICA w/o EEGLAB In-Reply-To: Message-ID: Dear Jim, I'd be happy to try and sort out problems with respect to my intended improvement of read_4d_hdr, because I assume there were some problems initially? It was kind of a bold commit into fieldtrip, I admit that, because I wasn't sure what this would lead to. My intention was partly to spark the involvement of 4D MEG users at other sites so that we could jointly improve the robustness of the code. So far all seems to work well for the Glaswegian 248-magnetometer site, but I am pretty sure this is not the case for all 4D-systems roaming the face of the earth... I would greatly appreciate if you try the most recent fieldtrip version on your data and provide me with feedback and possibly suggestions for improvement of the code. Cheers, Jan-Mathijs On Apr 20, 2009, at 10:13 PM, Jim Li wrote: > Dear Jan-Mathijs, > > Thanks a lot for your answer. I see why my "componentanalysis" > didn't work > w/o downloading EEGLAB now: > > As users of a 4D system, I'm avoiding your new updated version of > read_4d_hdr by sticking to some old (Dec. 2008) version of > Fieldtrip, simply > because it's been working fine and I'm lazy. But apparently there's > no "external/eeglab" subfolder in those old versions (yes, I have > several Dec > 08 versions). That's why I had to download EEGLAB to get it to work. I > wonder since when did you add the subfolder to Fieldtrip? > > Anyway, I guess it's time to embrace the new Fieldtrip versions and > learn the > new way to read 4D data. > > Thanks a lot for your help, :) > > Jim > > > On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen > wrote: > >> Dear Jim, >> >> I don't know whether I understand your question correctly, but >> Fieldtrip can do it 'without' a full download of EEGLAB, because the >> necessary ICA-routines are included in fieldtrip's download (and are >> located in the subfolder external/eeglab/... This means that your >> mystery someone was right ;o) >> >> Cheers, >> Jan-Mathijs >> >> On Apr 20, 2009, at 7:32 PM, Jim Li wrote: >> >>> Dear all, >>> >>> I'm trying to remove cardiac interferences from my MEG signal >>> (gradiometer) >>> channels before doing wavelet analysis. This seems necessary >>> because, when >>> looking at each epoch, the wavelet power @ 10-40Hz are dominated by >>> cardiac interference, and that's the bandwidth of interest. I see >>> some Fieldtrip >>> example script utilizing ICA of EEGLAB to remove cardiac >>> interference. >>> However, someone told me that it can be done in Fieldtrip w/o using >>> EEGLAB. >>> Is this true? If so, I'd appreciate it very much if anyone can send >>> me the >>> code, :) >>> >>> Thanks a lot, >>> >>> Jim >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users >>> of the FieldTrip toolbox, to share experiences and to discuss new >>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the > FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and > EEG analysis. See also http://listserv.surfnet.nl/archives/ > fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From julian.keil at GMAIL.COM Tue Apr 21 09:07:52 2009 From: julian.keil at GMAIL.COM (Julian Keil) Date: Tue, 21 Apr 2009 09:07:52 +0200 Subject: about ICA w/o EEGLAB In-Reply-To: <87D90E00-9069-4600-BD2D-C609E742A906@psy.gla.ac.uk> Message-ID: Dear Jan, the read_4d_hdr also works quite nicely for the Konstanz 148- magnetometer site as far as I can tell. I currently use the 2009-03-22 version of fieldtrip. Greetings Julian Am 20.04.2009 um 23:43 schrieb jan-mathijs schoffelen: > Dear Jim, > > I'd be happy to try and sort out problems with respect to my > intended improvement of read_4d_hdr, because I assume there were > some problems initially? It was kind of a bold commit into > fieldtrip, I admit that, because I wasn't sure what this would lead > to. My intention was partly to spark the involvement of 4D MEG users > at other sites so that we could jointly improve the robustness of > the code. So far all seems to work well for the Glaswegian 248- > magnetometer site, but I am pretty sure this is not the case for all > 4D-systems roaming the face of the earth... I would greatly > appreciate if you try the most recent fieldtrip version on your data > and provide me with feedback and possibly suggestions for > improvement of the code. > > Cheers, > > Jan-Mathijs > > > On Apr 20, 2009, at 10:13 PM, Jim Li wrote: > >> Dear Jan-Mathijs, >> >> Thanks a lot for your answer. I see why my "componentanalysis" >> didn't work >> w/o downloading EEGLAB now: >> >> As users of a 4D system, I'm avoiding your new updated version of >> read_4d_hdr by sticking to some old (Dec. 2008) version of >> Fieldtrip, simply >> because it's been working fine and I'm lazy. But apparently there's >> no "external/eeglab" subfolder in those old versions (yes, I have >> several Dec >> 08 versions). That's why I had to download EEGLAB to get it to >> work. I >> wonder since when did you add the subfolder to Fieldtrip? >> >> Anyway, I guess it's time to embrace the new Fieldtrip versions and >> learn the >> new way to read 4D data. >> >> Thanks a lot for your help, :) >> >> Jim >> >> >> On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen >> wrote: >> >>> Dear Jim, >>> >>> I don't know whether I understand your question correctly, but >>> Fieldtrip can do it 'without' a full download of EEGLAB, because the >>> necessary ICA-routines are included in fieldtrip's download (and are >>> located in the subfolder external/eeglab/... This means that your >>> mystery someone was right ;o) >>> >>> Cheers, >>> Jan-Mathijs >>> >>> On Apr 20, 2009, at 7:32 PM, Jim Li wrote: >>> >>>> Dear all, >>>> >>>> I'm trying to remove cardiac interferences from my MEG signal >>>> (gradiometer) >>>> channels before doing wavelet analysis. This seems necessary >>>> because, when >>>> looking at each epoch, the wavelet power @ 10-40Hz are dominated by >>>> cardiac interference, and that's the bandwidth of interest. I see >>>> some Fieldtrip >>>> example script utilizing ICA of EEGLAB to remove cardiac >>>> interference. >>>> However, someone told me that it can be done in Fieldtrip w/o using >>>> EEGLAB. >>>> Is this true? If so, I'd appreciate it very much if anyone can send >>>> me the >>>> code, :) >>>> >>>> Thanks a lot, >>>> >>>> Jim >>>> >>>> ---------------------------------- >>>> The aim of this list is to facilitate the discussion between users >>>> of the FieldTrip toolbox, to share experiences and to discuss new >>>> ideas for MEG and EEG analysis. See also http:// >>>> listserv.surfnet.nl/ >>>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/ >>>> fieldtrip. >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users >>> of the >> FieldTrip toolbox, to share experiences and to discuss new ideas >> for MEG and >> EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html >> and >> http://www.ru.nl/neuroimaging/fieldtrip. >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html >> and http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Tue Apr 21 10:22:05 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Tue, 21 Apr 2009 09:22:05 +0100 Subject: about ICA w/o EEGLAB In-Reply-To: <4CBC4EEB-7E3A-41A8-B53B-85DDE9BDEEEE@gmail.com> Message-ID: Dear Julian and other 4D-neuroimagers, Thanks for your feedback. There have been some changes in read_4d_hdr bti2grad which might affect performance though, so I would greatly appreciate if you could upgrade to the latest version and see if you are still happy. In a nutshell it boils down to the fact that read_4d_hdr tries to extract the digital weights from the run config-file which were used during acquisition. So far, these weights have not been included in the forward modelling, which is necessary for dipole fitting / source reconstruction. Although I don't expect that the inclusion of the weights (which are a function of the distant reference sensors, and hardly pick up any brain activity to begin with) is going to affect the leadfields to a big extent, not including them is not completely correct. As far as I know (and thanks to Stephan Moratti for pointing it out and Sarang Dalal for some code) there are two versions of the weight- tables which roughly seem to coincide with the type of system: version 1 (number of observations = 1.5: Madrid 148-magnetometer, and most likely also the Konstanz system), and version 2 (number of observations = 1: Glasgow 248-magnetometer). To make a long story short, the version 1 weight table just seems to contain the weights, and no specific list of channel labels facilitating the interpretation of the weights. This is in contrast to the version 2 table, which contains the lists of labels explicitly. Therefore, we would have to guess about the order of the channels and reference channels occurring in the version 1 weight matrix. I'd rather not guess, and prefer to base some hard-coded assumptions on some (pragmatically 1 or 2 ;o) ) observations... This means I would like to compare the list of weights as obtained with read_4d_hdr to the list of weights which the 4D-software should be able to print (I thought the command was something like print_table, or print_config or so). More specifically, given a particular recording in which for example 'supine' weights had been applied, we should compare the 'supine' weight table, to the weights extracted by fieldtrip. In that way we could gain some confidence about the order of the channels. Please note that at the moment no balancing is applied to data containing a 'version 1' weight table, at least if you use a fieldtrip version older than March 26, or more recent than April 2. Yours, Jan-Mathijs On Apr 21, 2009, at 8:07 AM, Julian Keil wrote: > Dear Jan, > > the read_4d_hdr also works quite nicely for the Konstanz 148- > magnetometer site as far as I can tell. > I currently use the 2009-03-22 version of fieldtrip. > > Greetings > > Julian > > Am 20.04.2009 um 23:43 schrieb jan-mathijs schoffelen: > >> Dear Jim, >> >> I'd be happy to try and sort out problems with respect to my >> intended improvement of read_4d_hdr, because I assume there were >> some problems initially? It was kind of a bold commit into >> fieldtrip, I admit that, because I wasn't sure what this would >> lead to. My intention was partly to spark the involvement of 4D >> MEG users at other sites so that we could jointly improve the >> robustness of the code. So far all seems to work well for the >> Glaswegian 248-magnetometer site, but I am pretty sure this is not >> the case for all 4D-systems roaming the face of the earth... I >> would greatly appreciate if you try the most recent fieldtrip >> version on your data and provide me with feedback and possibly >> suggestions for improvement of the code. >> >> Cheers, >> >> Jan-Mathijs >> >> >> On Apr 20, 2009, at 10:13 PM, Jim Li wrote: >> >>> Dear Jan-Mathijs, >>> >>> Thanks a lot for your answer. I see why my "componentanalysis" >>> didn't work >>> w/o downloading EEGLAB now: >>> >>> As users of a 4D system, I'm avoiding your new updated version of >>> read_4d_hdr by sticking to some old (Dec. 2008) version of >>> Fieldtrip, simply >>> because it's been working fine and I'm lazy. But apparently there's >>> no "external/eeglab" subfolder in those old versions (yes, I have >>> several Dec >>> 08 versions). That's why I had to download EEGLAB to get it to >>> work. I >>> wonder since when did you add the subfolder to Fieldtrip? >>> >>> Anyway, I guess it's time to embrace the new Fieldtrip versions >>> and learn the >>> new way to read 4D data. >>> >>> Thanks a lot for your help, :) >>> >>> Jim >>> >>> >>> On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen >>> wrote: >>> >>>> Dear Jim, >>>> >>>> I don't know whether I understand your question correctly, but >>>> Fieldtrip can do it 'without' a full download of EEGLAB, because >>>> the >>>> necessary ICA-routines are included in fieldtrip's download (and >>>> are >>>> located in the subfolder external/eeglab/... This means that your >>>> mystery someone was right ;o) >>>> >>>> Cheers, >>>> Jan-Mathijs >>>> >>>> On Apr 20, 2009, at 7:32 PM, Jim Li wrote: >>>> >>>>> Dear all, >>>>> >>>>> I'm trying to remove cardiac interferences from my MEG signal >>>>> (gradiometer) >>>>> channels before doing wavelet analysis. This seems necessary >>>>> because, when >>>>> looking at each epoch, the wavelet power @ 10-40Hz are >>>>> dominated by >>>>> cardiac interference, and that's the bandwidth of interest. I see >>>>> some Fieldtrip >>>>> example script utilizing ICA of EEGLAB to remove cardiac >>>>> interference. >>>>> However, someone told me that it can be done in Fieldtrip w/o >>>>> using >>>>> EEGLAB. >>>>> Is this true? If so, I'd appreciate it very much if anyone can >>>>> send >>>>> me the >>>>> code, :) >>>>> >>>>> Thanks a lot, >>>>> >>>>> Jim >>>>> >>>>> ---------------------------------- >>>>> The aim of this list is to facilitate the discussion between users >>>>> of the FieldTrip toolbox, to share experiences and to discuss new >>>>> ideas for MEG and EEG analysis. See also http:// >>>>> listserv.surfnet.nl/ >>>>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/ >>>>> fieldtrip. >>>> >>>> ---------------------------------- >>>> The aim of this list is to facilitate the discussion between >>>> users of the >>> FieldTrip toolbox, to share experiences and to discuss new ideas >>> for MEG and >>> EEG analysis. See also http://listserv.surfnet.nl/archives/ >>> fieldtrip.html and >>> http://www.ru.nl/neuroimaging/fieldtrip. >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between >>> users of the FieldTrip toolbox, to share experiences and to >>> discuss new ideas for MEG and EEG analysis. See also http:// >>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >>> neuroimaging/fieldtrip. >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http:// >> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >> neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From amrgermany at YAHOO.COM Tue Apr 21 12:53:04 2009 From: amrgermany at YAHOO.COM (Amr Ayoub) Date: Tue, 21 Apr 2009 10:53:04 +0000 Subject: Reading raw data Message-ID: Dear All, I have raw data that consits of 151 MEG (CTF machine), EOG and EMG channels. The size of each channel is around 15MB. The ERP are time points detected in EEG channels. What is the best way to import the data in order to be preprocessed in FieldTrip? Thanks a lot, Amr ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From amrgermany at YAHOO.COM Tue Apr 21 12:58:41 2009 From: amrgermany at YAHOO.COM (Amr Ayoub) Date: Tue, 21 Apr 2009 10:58:41 +0000 Subject: Reading raw data Message-ID: Dear All, I have raw data that consits of 151 MEG (CTF machine), EOG and EMG channels. The size of each channel is around 15MB. The ERP are time points detected in EEG channels. What is the best way to import the data in order to be preprocessed in FieldTrip? Thanks a lot, Amr ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Wed Apr 22 17:30:24 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Wed, 22 Apr 2009 21:00:24 +0530 Subject: regarding besa to fieldtrip Message-ID: Dear folks,   I just finished with tutorials.  I got some data in besa format.  I have .CNT, .sfp and .foc file format.  Please tell me how to import these files in matlab using fieldtrip functions.   Best Regads,   Chintan Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at MAC.COM Wed Apr 22 17:42:53 2009 From: nathanweisz at MAC.COM (Nathan Weisz) Date: Wed, 22 Apr 2009 17:42:53 +0200 Subject: regarding besa to fieldtrip In-Reply-To: <558191.69376.qm@web95412.mail.in2.yahoo.com> Message-ID: dear chintan, this page is your friend: http://fieldtrip.fcdonders.nl/integrating_with_besa best, nathan On 22.04.2009, at 17:30, shah chintan wrote: > Dear folks, > > I just finished with tutorials. I got some data in besa format. I > have .CNT, .sfp and .foc file format. Please tell me how to import > these files in matlab using fieldtrip functions. > > Best Regads, > > Chintan > > Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! > Edition * Click here! > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From megjim1 at GMAIL.COM Wed Apr 22 18:12:58 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Wed, 22 Apr 2009 18:12:58 +0200 Subject: about biosig folder Message-ID: Dear Jan-Mathijs, Following your recommendation, I downloaded the 041809 Fieldtrip and it reads our data just fine. I'll keep an eye on the outputs as I advance more into the data processing and report suspicious ones, if any. BTW, w/ this new version I get a bunch of annoying messages each time I open MATLAB. What I did is to add this new version of Fieldtrip in MATLAB by clicking "Set Path" and "Add with subfolders...". And the warning messages look like this (just one warning example out of a zillion): ---- Warning: Function C:\Program Files\MATLAB\R2007b\external\fieldtrip-20090418 \external\biosig\private\transpose.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. > In path at 110 In addpath at 89 In startup at 1 In matlabrc at 251 --- All the warning is related to the "fieldtrip-20090418\external\biosig\private\" directory. So, what's the use of this "biosig" folder? Can I just remove it from my "MATLAB search Path" w/o affecting Fieldtrip operations? Thanks, Jim On Tue, 21 Apr 2009 09:22:05 +0100, jan-mathijs schoffelen wrote: >Dear Julian and other 4D-neuroimagers, > >Thanks for your feedback. There have been some changes in read_4d_hdr >bti2grad which might affect performance though, so I would greatly >appreciate if you could upgrade to the latest version and see if you >are still happy. >In a nutshell it boils down to the fact that read_4d_hdr tries to >extract the digital weights from the run config-file which were used >during acquisition. So far, these weights have not been included in >the forward modelling, which is necessary for dipole fitting / source >reconstruction. Although I don't expect that the inclusion of the >weights (which are a function of the distant reference sensors, and >hardly pick up any brain activity to begin with) is going to affect >the leadfields to a big extent, not including them is not completely >correct. >As far as I know (and thanks to Stephan Moratti for pointing it out >and Sarang Dalal for some code) there are two versions of the weight- >tables which roughly seem to coincide with the type of system: >version 1 (number of observations = 1.5: Madrid 148-magnetometer, and >most likely also the Konstanz system), and version 2 (number of >observations = 1: Glasgow 248-magnetometer). To make a long story >short, the version 1 weight table just seems to contain the weights, >and no specific list of channel labels facilitating the >interpretation of the weights. This is in contrast to the version 2 >table, which contains the lists of labels explicitly. Therefore, we >would have to guess about the order of the channels and reference >channels occurring in the version 1 weight matrix. I'd rather not >guess, and prefer to base some hard-coded assumptions on some >(pragmatically 1 or 2 ;o) ) observations... >This means I would like to compare the list of weights as obtained >with read_4d_hdr to the list of weights which the 4D-software should >be able to print (I thought the command was something like >print_table, or print_config or so). More specifically, given a >particular recording in which for example 'supine' weights had been >applied, we should compare the 'supine' weight table, to the weights >extracted by fieldtrip. In that way we could gain some confidence >about the order of the channels. >Please note that at the moment no balancing is applied to data >containing a 'version 1' weight table, at least if you use a >fieldtrip version older than March 26, or more recent than April 2. > >Yours, > >Jan-Mathijs > >On Apr 21, 2009, at 8:07 AM, Julian Keil wrote: > >> Dear Jan, >> >> the read_4d_hdr also works quite nicely for the Konstanz 148- >> magnetometer site as far as I can tell. >> I currently use the 2009-03-22 version of fieldtrip. >> >> Greetings >> >> Julian >> >> Am 20.04.2009 um 23:43 schrieb jan-mathijs schoffelen: >> >>> Dear Jim, >>> >>> I'd be happy to try and sort out problems with respect to my >>> intended improvement of read_4d_hdr, because I assume there were >>> some problems initially? It was kind of a bold commit into >>> fieldtrip, I admit that, because I wasn't sure what this would >>> lead to. My intention was partly to spark the involvement of 4D >>> MEG users at other sites so that we could jointly improve the >>> robustness of the code. So far all seems to work well for the >>> Glaswegian 248-magnetometer site, but I am pretty sure this is not >>> the case for all 4D-systems roaming the face of the earth... I >>> would greatly appreciate if you try the most recent fieldtrip >>> version on your data and provide me with feedback and possibly >>> suggestions for improvement of the code. >>> >>> Cheers, >>> >>> Jan-Mathijs >>> >>> >>> On Apr 20, 2009, at 10:13 PM, Jim Li wrote: >>> >>>> Dear Jan-Mathijs, >>>> >>>> Thanks a lot for your answer. I see why my "componentanalysis" >>>> didn't work >>>> w/o downloading EEGLAB now: >>>> >>>> As users of a 4D system, I'm avoiding your new updated version of >>>> read_4d_hdr by sticking to some old (Dec. 2008) version of >>>> Fieldtrip, simply >>>> because it's been working fine and I'm lazy. But apparently there's >>>> no "external/eeglab" subfolder in those old versions (yes, I have >>>> several Dec >>>> 08 versions). That's why I had to download EEGLAB to get it to >>>> work. I >>>> wonder since when did you add the subfolder to Fieldtrip? >>>> >>>> Anyway, I guess it's time to embrace the new Fieldtrip versions >>>> and learn the >>>> new way to read 4D data. >>>> >>>> Thanks a lot for your help, :) >>>> >>>> Jim >>>> >>>> >>>> On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen >>>> wrote: >>>> >>>>> Dear Jim, >>>>> >>>>> I don't know whether I understand your question correctly, but >>>>> Fieldtrip can do it 'without' a full download of EEGLAB, because >>>>> the >>>>> necessary ICA-routines are included in fieldtrip's download (and >>>>> are >>>>> located in the subfolder external/eeglab/... This means that your >>>>> mystery someone was right ;o) >>>>> >>>>> Cheers, >>>>> Jan-Mathijs >>>>> >>>>> On Apr 20, 2009, at 7:32 PM, Jim Li wrote: >>>>> >>>>>> Dear all, >>>>>> >>>>>> I'm trying to remove cardiac interferences from my MEG signal >>>>>> (gradiometer) >>>>>> channels before doing wavelet analysis. This seems necessary >>>>>> because, when >>>>>> looking at each epoch, the wavelet power @ 10-40Hz are >>>>>> dominated by >>>>>> cardiac interference, and that's the bandwidth of interest. I see >>>>>> some Fieldtrip >>>>>> example script utilizing ICA of EEGLAB to remove cardiac >>>>>> interference. >>>>>> However, someone told me that it can be done in Fieldtrip w/o >>>>>> using >>>>>> EEGLAB. >>>>>> Is this true? If so, I'd appreciate it very much if anyone can >>>>>> send >>>>>> me the >>>>>> code, :) >>>>>> >>>>>> Thanks a lot, >>>>>> >>>>>> Jim >>>>>> >>>>>> ---------------------------------- >>>>>> The aim of this list is to facilitate the discussion between users >>>>>> of the FieldTrip toolbox, to share experiences and to discuss new >>>>>> ideas for MEG and EEG analysis. See also http:// >>>>>> listserv.surfnet.nl/ >>>>>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/ >>>>>> fieldtrip. >>>>> >>>>> ---------------------------------- >>>>> The aim of this list is to facilitate the discussion between >>>>> users of the >>>> FieldTrip toolbox, to share experiences and to discuss new ideas >>>> for MEG and >>>> EEG analysis. See also http://listserv.surfnet.nl/archives/ >>>> fieldtrip.html and >>>> http://www.ru.nl/neuroimaging/fieldtrip. >>>> >>>> ---------------------------------- >>>> The aim of this list is to facilitate the discussion between >>>> users of the FieldTrip toolbox, to share experiences and to >>>> discuss new ideas for MEG and EEG analysis. See also http:// >>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >>>> neuroimaging/fieldtrip. >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users >>> of the FieldTrip toolbox, to share experiences and to discuss new >>> ideas for MEG and EEG analysis. See also http:// >>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >>> neuroimaging/fieldtrip. >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Wed Apr 22 18:23:19 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Wed, 22 Apr 2009 18:23:19 +0200 Subject: Do I need ECG channel to run "artifact_ecg" Message-ID: Dear all, W/ a 041809 Fieldtrip, I tried to run the following lines but got some error (see below). I don't have ECG channel in my data, that's why I use a left-most MEG channel w/ apparent cardiac interferences instead. Any suggestion how to fix the problem? ------------- cfg = []; cfg.trl = data.cfg.previous.trl; cfg.dataset = data.cfg.previous.dataset; cfg.continuous = 'yes' ; cfg.artfctdef.ecg.channel = 'A229'; cfg.artfctdef.ecg.pretim = 0.25; cfg.artfctdef.ecg.psttim = 0.5; cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method cfg.artfctdef.ecg.cutoff = 3; %peak-threshold [cfg, artifact] = artifact_ecg(cfg); current zvalue threshold = 3.000 keep the current value (y/n) ? y ??? Undefined function or variable "labelmlt". Error in ==> channelselection at 344 if findmlt, channel = [channel; labelmlt]; end Error in ==> artifact_ecg at 238 sgn = channelselection(artfctdef.inspect, hdr.label); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From chintan_student at YAHOO.CO.IN Wed Apr 22 18:31:33 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Wed, 22 Apr 2009 22:01:33 +0530 Subject: regarding besa to fieldtrip Message-ID: Dear folks,   I just finished with tutorials.  I got some data in besa format.  I have .CNT, .sfp and .foc file format.  I can process with .sfp format but no clue about the other two. Please tell me how to import these files in matlab using fieldtrip functions.   Best Regads,   Chintan Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition * Click here! ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Thu Apr 23 09:48:07 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Thu, 23 Apr 2009 08:48:07 +0100 Subject: about biosig folder In-Reply-To: Message-ID: Dear Jim, Yes, I suspect that you just can remove the biosig folder from your path. As long as you don't use fieldtrip functionality which depends on functions within the biosig-folder you are fine. Yours, JM On Apr 22, 2009, at 5:12 PM, Jim Li wrote: > Dear Jan-Mathijs, > > Following your recommendation, I downloaded the 041809 Fieldtrip > and it > reads our data just fine. I'll keep an eye on the outputs as I > advance more > into the data processing and report suspicious ones, if any. > > BTW, w/ this new version I get a bunch of annoying messages each > time I > open MATLAB. What I did is to add this new version of Fieldtrip in > MATLAB by > clicking "Set Path" and "Add with subfolders...". And the warning > messages > look like this (just one warning example out of a zillion): > > ---- > Warning: Function C:\Program > Files\MATLAB\R2007b\external\fieldtrip-20090418 > \external\biosig\private\transpose.m > has the same name as a MATLAB builtin. We suggest you rename the > function > to > avoid a potential name conflict. >> In path at 110 > In addpath at 89 > In startup at 1 > In matlabrc at 251 > --- > > All the warning is related to the "fieldtrip-20090418\external > \biosig\private\" > directory. So, what's the use of this "biosig" folder? Can I just > remove it from > my "MATLAB search Path" w/o affecting Fieldtrip operations? > > Thanks, > > Jim > > On Tue, 21 Apr 2009 09:22:05 +0100, jan-mathijs schoffelen > wrote: > >> Dear Julian and other 4D-neuroimagers, >> >> Thanks for your feedback. There have been some changes in read_4d_hdr >> bti2grad which might affect performance though, so I would greatly >> appreciate if you could upgrade to the latest version and see if you >> are still happy. >> In a nutshell it boils down to the fact that read_4d_hdr tries to >> extract the digital weights from the run config-file which were used >> during acquisition. So far, these weights have not been included in >> the forward modelling, which is necessary for dipole fitting / source >> reconstruction. Although I don't expect that the inclusion of the >> weights (which are a function of the distant reference sensors, and >> hardly pick up any brain activity to begin with) is going to affect >> the leadfields to a big extent, not including them is not completely >> correct. >> As far as I know (and thanks to Stephan Moratti for pointing it out >> and Sarang Dalal for some code) there are two versions of the weight- >> tables which roughly seem to coincide with the type of system: >> version 1 (number of observations = 1.5: Madrid 148-magnetometer, and >> most likely also the Konstanz system), and version 2 (number of >> observations = 1: Glasgow 248-magnetometer). To make a long story >> short, the version 1 weight table just seems to contain the weights, >> and no specific list of channel labels facilitating the >> interpretation of the weights. This is in contrast to the version 2 >> table, which contains the lists of labels explicitly. Therefore, we >> would have to guess about the order of the channels and reference >> channels occurring in the version 1 weight matrix. I'd rather not >> guess, and prefer to base some hard-coded assumptions on some >> (pragmatically 1 or 2 ;o) ) observations... >> This means I would like to compare the list of weights as obtained >> with read_4d_hdr to the list of weights which the 4D-software should >> be able to print (I thought the command was something like >> print_table, or print_config or so). More specifically, given a >> particular recording in which for example 'supine' weights had been >> applied, we should compare the 'supine' weight table, to the weights >> extracted by fieldtrip. In that way we could gain some confidence >> about the order of the channels. >> Please note that at the moment no balancing is applied to data >> containing a 'version 1' weight table, at least if you use a >> fieldtrip version older than March 26, or more recent than April 2. >> >> Yours, >> >> Jan-Mathijs >> >> On Apr 21, 2009, at 8:07 AM, Julian Keil wrote: >> >>> Dear Jan, >>> >>> the read_4d_hdr also works quite nicely for the Konstanz 148- >>> magnetometer site as far as I can tell. >>> I currently use the 2009-03-22 version of fieldtrip. >>> >>> Greetings >>> >>> Julian >>> >>> Am 20.04.2009 um 23:43 schrieb jan-mathijs schoffelen: >>> >>>> Dear Jim, >>>> >>>> I'd be happy to try and sort out problems with respect to my >>>> intended improvement of read_4d_hdr, because I assume there were >>>> some problems initially? It was kind of a bold commit into >>>> fieldtrip, I admit that, because I wasn't sure what this would >>>> lead to. My intention was partly to spark the involvement of 4D >>>> MEG users at other sites so that we could jointly improve the >>>> robustness of the code. So far all seems to work well for the >>>> Glaswegian 248-magnetometer site, but I am pretty sure this is not >>>> the case for all 4D-systems roaming the face of the earth... I >>>> would greatly appreciate if you try the most recent fieldtrip >>>> version on your data and provide me with feedback and possibly >>>> suggestions for improvement of the code. >>>> >>>> Cheers, >>>> >>>> Jan-Mathijs >>>> >>>> >>>> On Apr 20, 2009, at 10:13 PM, Jim Li wrote: >>>> >>>>> Dear Jan-Mathijs, >>>>> >>>>> Thanks a lot for your answer. I see why my "componentanalysis" >>>>> didn't work >>>>> w/o downloading EEGLAB now: >>>>> >>>>> As users of a 4D system, I'm avoiding your new updated version of >>>>> read_4d_hdr by sticking to some old (Dec. 2008) version of >>>>> Fieldtrip, simply >>>>> because it's been working fine and I'm lazy. But apparently >>>>> there's >>>>> no "external/eeglab" subfolder in those old versions (yes, I have >>>>> several Dec >>>>> 08 versions). That's why I had to download EEGLAB to get it to >>>>> work. I >>>>> wonder since when did you add the subfolder to Fieldtrip? >>>>> >>>>> Anyway, I guess it's time to embrace the new Fieldtrip versions >>>>> and learn the >>>>> new way to read 4D data. >>>>> >>>>> Thanks a lot for your help, :) >>>>> >>>>> Jim >>>>> >>>>> >>>>> On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen >>>>> wrote: >>>>> >>>>>> Dear Jim, >>>>>> >>>>>> I don't know whether I understand your question correctly, but >>>>>> Fieldtrip can do it 'without' a full download of EEGLAB, because >>>>>> the >>>>>> necessary ICA-routines are included in fieldtrip's download (and >>>>>> are >>>>>> located in the subfolder external/eeglab/... This means that your >>>>>> mystery someone was right ;o) >>>>>> >>>>>> Cheers, >>>>>> Jan-Mathijs >>>>>> >>>>>> On Apr 20, 2009, at 7:32 PM, Jim Li wrote: >>>>>> >>>>>>> Dear all, >>>>>>> >>>>>>> I'm trying to remove cardiac interferences from my MEG signal >>>>>>> (gradiometer) >>>>>>> channels before doing wavelet analysis. This seems necessary >>>>>>> because, when >>>>>>> looking at each epoch, the wavelet power @ 10-40Hz are >>>>>>> dominated by >>>>>>> cardiac interference, and that's the bandwidth of interest. I >>>>>>> see >>>>>>> some Fieldtrip >>>>>>> example script utilizing ICA of EEGLAB to remove cardiac >>>>>>> interference. >>>>>>> However, someone told me that it can be done in Fieldtrip w/o >>>>>>> using >>>>>>> EEGLAB. >>>>>>> Is this true? If so, I'd appreciate it very much if anyone can >>>>>>> send >>>>>>> me the >>>>>>> code, :) >>>>>>> >>>>>>> Thanks a lot, >>>>>>> >>>>>>> Jim >>>>>>> >>>>>>> ---------------------------------- >>>>>>> The aim of this list is to facilitate the discussion between >>>>>>> users >>>>>>> of the FieldTrip toolbox, to share experiences and to >>>>>>> discuss new >>>>>>> ideas for MEG and EEG analysis. See also http:// >>>>>>> listserv.surfnet.nl/ >>>>>>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/ >>>>>>> fieldtrip. >>>>>> >>>>>> ---------------------------------- >>>>>> The aim of this list is to facilitate the discussion between >>>>>> users of the >>>>> FieldTrip toolbox, to share experiences and to discuss new ideas >>>>> for MEG and >>>>> EEG analysis. See also http://listserv.surfnet.nl/archives/ >>>>> fieldtrip.html and >>>>> http://www.ru.nl/neuroimaging/fieldtrip. >>>>> >>>>> ---------------------------------- >>>>> The aim of this list is to facilitate the discussion between >>>>> users of the FieldTrip toolbox, to share experiences and to >>>>> discuss new ideas for MEG and EEG analysis. See also http:// >>>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >>>>> neuroimaging/fieldtrip. >>>> >>>> ---------------------------------- >>>> The aim of this list is to facilitate the discussion between users >>>> of the FieldTrip toolbox, to share experiences and to discuss new >>>> ideas for MEG and EEG analysis. See also http:// >>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >>>> neuroimaging/fieldtrip. >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users >>> of the FieldTrip toolbox, to share experiences and to discuss new >>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the > FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and > EEG analysis. See also http://listserv.surfnet.nl/archives/ > fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From moratti at MED.UCM.ES Thu Apr 23 09:40:33 2009 From: moratti at MED.UCM.ES (Stephan Moratti) Date: Thu, 23 Apr 2009 09:40:33 +0200 Subject: regarding besa to fieldtrip In-Reply-To: Message-ID: Yo can export your data in BESA to .avr (ASCII) .mul (ASCII multiplexed) and .dat (simple binary, you will also get a header file .generic). With besa2fieldtrip you can read in your data easily, then. best, Stephan -- *Stephan Moratti, PhD/ /**/see also: http://web.me.com/smoratti/ /*Centro de Tecnología Biomédica CBT, Universidad Politécnica de Madrid, en la actualidad (currently at) en el Centro de Magnetoencefalografía Dr. Perez Modrego, Universidad Complutense de Madrid, Faculdad de Medicina, Pabellón 8, Avda. Complutense, s/n, 28040 Madrid, Spain, email: moratti at gbt.tfo.upm.es moratti at med.ucm.es Tel.: +34 91 394 2292 Fax.: +34 91 394 2294 */ /* ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Thu Apr 23 10:00:44 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Thu, 23 Apr 2009 09:00:44 +0100 Subject: Do I need ECG channel to run "artifact_ecg" In-Reply-To: Message-ID: Dear Jim, The reason for your crash is probably related to the fact that the default settings for artifact_ecg have been defined with a ctf-system in mind. Artifact_ecg will provide some feedback as to how the QRS- complex-locked MEG signals look, by picking a subset of channels as defined by cfg.artfctdef.ecg.inspect. By default this is set to all channels named 'MLTxx'. Since in your megsystem the sensors are named 'Axx', fieldtrip cannot make sense out of the default and crashes. Just specify your own (subset of) channel(s) to inspect. Good luck Jan-Mathijs On Apr 22, 2009, at 5:23 PM, Jim Li wrote: > Dear all, > > > W/ a 041809 Fieldtrip, I tried to run the following lines but got > some error (see > below). I don't have ECG channel in my data, that's why I use a > left-most > MEG channel w/ apparent cardiac interferences instead. Any > suggestion how > to fix the problem? > > ------------- > cfg = []; > cfg.trl = data.cfg.previous.trl; > cfg.dataset = data.cfg.previous.dataset; > cfg.continuous = 'yes' ; > cfg.artfctdef.ecg.channel = 'A229'; > cfg.artfctdef.ecg.pretim = 0.25; > cfg.artfctdef.ecg.psttim = 0.5; > cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method > cfg.artfctdef.ecg.cutoff = 3; %peak-threshold > [cfg, artifact] = artifact_ecg(cfg); > > current zvalue threshold = 3.000 > keep the current value (y/n) ? > y > ??? Undefined function or variable "labelmlt". > > Error in ==> channelselection at 344 > if findmlt, channel = [channel; labelmlt]; end > > Error in ==> artifact_ecg at 238 > sgn = channelselection(artfctdef.inspect, hdr.label); > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From A.Stancak at LIVERPOOL.AC.UK Thu Apr 23 10:01:15 2009 From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej) Date: Thu, 23 Apr 2009 09:01:15 +0100 Subject: Do I need ECG channel to run "artifact_ecg" In-Reply-To: Message-ID: Dear Jim-Li, I probably faced the same error message when I was writing my script for ECG artefact removal. I remember to get rid of this error message by putting the ECG channel label into brackets: cfg.artfctdef.ecg.channel = {'A229'}; I hope I have not mislead you as I am a FieldTrip novice, but it is maybe worth trying. Best wishes Andrej Andrej Stancak, PhD. Professor for normal physiology Senior lecturer in psychology School of Psychology Eleanor Rathbone Building Bedford Street South L69 7ZA Liverpool United Kingdom Phone: 0044 0151 7946951 E-mail: a.stancak at liverpool.ac.uk (primary)         stancak at lf3.cuni.cz (secondary) Office hours: Mo 10-12, Wed 10-12 -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jim Li Sent: 22 April 2009 17:23 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] Do I need ECG channel to run "artifact_ecg" Dear all, W/ a 041809 Fieldtrip, I tried to run the following lines but got some error (see below). I don't have ECG channel in my data, that's why I use a left-most MEG channel w/ apparent cardiac interferences instead. Any suggestion how to fix the problem? ------------- cfg = []; cfg.trl = data.cfg.previous.trl; cfg.dataset = data.cfg.previous.dataset; cfg.continuous = 'yes' ; cfg.artfctdef.ecg.channel = 'A229'; cfg.artfctdef.ecg.pretim = 0.25; cfg.artfctdef.ecg.psttim = 0.5; cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method cfg.artfctdef.ecg.cutoff = 3; %peak-threshold [cfg, artifact] = artifact_ecg(cfg); current zvalue threshold = 3.000 keep the current value (y/n) ? y ??? Undefined function or variable "labelmlt". Error in ==> channelselection at 344 if findmlt, channel = [channel; labelmlt]; end Error in ==> artifact_ecg at 238 sgn = channelselection(artfctdef.inspect, hdr.label); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Thu Apr 23 16:25:50 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Thu, 23 Apr 2009 16:25:50 +0200 Subject: Do I need ECG channel to run "artifact_ecg" Message-ID: Dear Andrej, Thanks a lot for your feedback. I tried your recommendation of "cfg.artfctdef.ecg.channel = {'A229'};" but I got the same message. In fact, last night by a little debugging I figured out why the error message occured. And the solution is to simply add this line before doing artifact_ecg: cfg.artfctdef.ecg.inspect = {'A229'}; And that worked beautifully. cheers, Jim On Thu, 23 Apr 2009 09:01:15 +0100, Stancak, Andrej wrote: >Dear Jim-Li, > > I probably faced the same error message when I was writing my script for ECG artefact removal. I remember to get rid of this error message by putting the ECG channel label into brackets: > > cfg.artfctdef.ecg.channel = {'A229'}; > > > I hope I have not mislead you as I am a FieldTrip novice, but it is maybe worth trying. > >Best wishes >Andrej > > > >Andrej Stancak, PhD. >Professor for normal physiology >Senior lecturer in psychology > >School of Psychology >Eleanor Rathbone Building >Bedford Street South >L69 7ZA >Liverpool >United Kingdom > >Phone: 0044 0151 7946951 >E-mail: a.stancak at liverpool.ac.uk (primary) >        stancak at lf3.cuni.cz (secondary) > >Office hours: Mo 10-12, Wed 10-12 > > >-----Original Message----- >From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jim Li >Sent: 22 April 2009 17:23 >To: FIELDTRIP at NIC.SURFNET.NL >Subject: [FIELDTRIP] Do I need ECG channel to run "artifact_ecg" > >Dear all, > > >W/ a 041809 Fieldtrip, I tried to run the following lines but got some error (see >below). I don't have ECG channel in my data, that's why I use a left-most >MEG channel w/ apparent cardiac interferences instead. Any suggestion how >to fix the problem? > >------------- >cfg = []; >cfg.trl = data.cfg.previous.trl; >cfg.dataset = data.cfg.previous.dataset; >cfg.continuous = 'yes' ; >cfg.artfctdef.ecg.channel = 'A229'; >cfg.artfctdef.ecg.pretim = 0.25; >cfg.artfctdef.ecg.psttim = 0.5; >cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method >cfg.artfctdef.ecg.cutoff = 3; %peak-threshold >[cfg, artifact] = artifact_ecg(cfg); > >current zvalue threshold = 3.000 >keep the current value (y/n) ? >y >??? Undefined function or variable "labelmlt". > >Error in ==> channelselection at 344 >if findmlt, channel = [channel; labelmlt]; end > >Error in ==> artifact_ecg at 238 >sgn = channelselection(artfctdef.inspect, hdr.label); > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Thu Apr 23 17:47:53 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Thu, 23 Apr 2009 17:47:53 +0200 Subject: Do I need ECG channel to run "artifact_ecg" Message-ID: Dear Jan-Mathijs, Thanks a lot for your feedback. Last night I did a bit of debugging and found out why the crashed happened. In line 116 of "artifact_ecg" it says: if ~isfield(cfg.artfctdef.ecg,'inspect'),cfg.artfctdef.ecg.inspect = {'MLT' 'MRT'}; end That's the cause of my trouble because 4D's system doesn't have channels names like "MLT", "MRT" . So I fixed te problem by adding this line: cfg.artfctdef.ecg.inspect = {'A229'}; before this line: [cfg, artifact] = artifact_ecg(cfg); And it worked! All these fits into your great suggestion very well. And I'm so happy that I don't need to get an ECG channel before doing cardiac artifact rejection. Jim On Thu, 23 Apr 2009 09:00:44 +0100, jan-mathijs schoffelen wrote: >Dear Jim, > >The reason for your crash is probably related to the fact that the >default settings for artifact_ecg have been defined with a ctf-system >in mind. Artifact_ecg will provide some feedback as to how the QRS- >complex-locked MEG signals look, by picking a subset of channels as >defined by cfg.artfctdef.ecg.inspect. By default this is set to all >channels named 'MLTxx'. Since in your megsystem the sensors are named >'Axx', fieldtrip cannot make sense out of the default and crashes. >Just specify your own (subset of) channel(s) to inspect. > >Good luck > >Jan-Mathijs > > > >On Apr 22, 2009, at 5:23 PM, Jim Li wrote: > >> Dear all, >> >> >> W/ a 041809 Fieldtrip, I tried to run the following lines but got >> some error (see >> below). I don't have ECG channel in my data, that's why I use a >> left-most >> MEG channel w/ apparent cardiac interferences instead. Any >> suggestion how >> to fix the problem? >> >> ------------- >> cfg = []; >> cfg.trl = data.cfg.previous.trl; >> cfg.dataset = data.cfg.previous.dataset; >> cfg.continuous = 'yes' ; >> cfg.artfctdef.ecg.channel = 'A229'; >> cfg.artfctdef.ecg.pretim = 0.25; >> cfg.artfctdef.ecg.psttim = 0.5; >> cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method >> cfg.artfctdef.ecg.cutoff = 3; %peak-threshold >> [cfg, artifact] = artifact_ecg(cfg); >> >> current zvalue threshold = 3.000 >> keep the current value (y/n) ? >> y >> ??? Undefined function or variable "labelmlt". >> >> Error in ==> channelselection at 344 >> if findmlt, channel = [channel; labelmlt]; end >> >> Error in ==> artifact_ecg at 238 >> sgn = channelselection(artfctdef.inspect, hdr.label); >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From cmuehl at GMAIL.COM Thu Apr 23 18:05:27 2009 From: cmuehl at GMAIL.COM (Christian Muehl) Date: Thu, 23 Apr 2009 18:05:27 +0200 Subject: BCI game project in the eNTERFACE 09 workshop Message-ID: Call for participants BCI @ eNTERFACE 09 workshop July 13th - August 7th 2009 Genua, Italy Project on Bain-Computer Interfaces: A multi-player game using neurophysiological sensors For a project on Brain-Computer Interfaces in the context of the eNTERFACE 09 workshop in Genua we are searching for interested people with experience in the areas of signal processing, game design, programming or machine learning. The goal of the project is the development of a multiplayer computer game that uses several innovative input modalities. Neural (EEG) and physiological changes (e.g. ECG, respiration, muscle tension) are used in combination with traditional (mouse, keyboards) input devices to actively and passively control the game dynamics. The game will be a platform for the study of an efficient and natural use of Brain-Computer Interaction and physiological sensors within a gaming environment. More detailed information about that particular project and others can be found here: www.infomus.org/enterface09/projectsTeams.php The eNTERFACE 2009 Workshop is being organized this summer in Genova, Italy, from July 13th to August 7th, 2009. The eNTERFACE Workshops present an opportunity of collaborative research and software development by gathering, in a single place, a team of senior project leaders in multimodal interfaces, PhD students, and (undergraduate) students, to work on a pre-specified list of challenges, for the duration of four weeks. Participants are organized in teams of six to eight, all attached to specific projects. Tutorials and state-of-the art surveys on multimodal interfaces and their design will be given every week by invited experts. Senior researchers, PhD students, or undergraduates interested in participating to the Workshop should send their application by emailing the Organizing Committee at enterface09 at casapaganini.org before April 30, 2009. Please check the workshop website for detailed information on the application proceedure: http://www.infomus.org/enterface09/callForParticipation.php ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Thu Apr 23 18:10:22 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Thu, 23 Apr 2009 18:10:22 +0200 Subject: Do I need ECG channel to run "artifact_ecg" Message-ID: Dear Jan-Mathijs, I continued ICA cardiac-removal processing using the example codes in Fieldtrip website. But I encountered this problem: ---------- cfg = []; cfg.method = 'mtmfft'; cfg.output = 'fourier'; cfg.foilim = [0 100]; cfg.taper = 'hanning'; cfg.pad = 'maxperlen'; freq = freqanalysis(cfg, comp_ecg); the input is component data with 248 components and 248 original channels ??? Error using ==> checkdata at 377 This function requires raw data as input. Error in ==> freqanalysis at 165 data = checkdata(data, 'datatype', 'raw', 'feedback', 'yes', 'hasoffset', 'yes'); ----------------- How to deal w/ it? Thanks, Jim On Thu, 23 Apr 2009 09:00:44 +0100, jan-mathijs schoffelen wrote: >Dear Jim, > >The reason for your crash is probably related to the fact that the >default settings for artifact_ecg have been defined with a ctf-system >in mind. Artifact_ecg will provide some feedback as to how the QRS- >complex-locked MEG signals look, by picking a subset of channels as >defined by cfg.artfctdef.ecg.inspect. By default this is set to all >channels named 'MLTxx'. Since in your megsystem the sensors are named >'Axx', fieldtrip cannot make sense out of the default and crashes. >Just specify your own (subset of) channel(s) to inspect. > >Good luck > >Jan-Mathijs > > > >On Apr 22, 2009, at 5:23 PM, Jim Li wrote: > >> Dear all, >> >> >> W/ a 041809 Fieldtrip, I tried to run the following lines but got >> some error (see >> below). I don't have ECG channel in my data, that's why I use a >> left-most >> MEG channel w/ apparent cardiac interferences instead. Any >> suggestion how >> to fix the problem? >> >> ------------- >> cfg = []; >> cfg.trl = data.cfg.previous.trl; >> cfg.dataset = data.cfg.previous.dataset; >> cfg.continuous = 'yes' ; >> cfg.artfctdef.ecg.channel = 'A229'; >> cfg.artfctdef.ecg.pretim = 0.25; >> cfg.artfctdef.ecg.psttim = 0.5; >> cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method >> cfg.artfctdef.ecg.cutoff = 3; %peak-threshold >> [cfg, artifact] = artifact_ecg(cfg); >> >> current zvalue threshold = 3.000 >> keep the current value (y/n) ? >> y >> ??? Undefined function or variable "labelmlt". >> >> Error in ==> channelselection at 344 >> if findmlt, channel = [channel; labelmlt]; end >> >> Error in ==> artifact_ecg at 238 >> sgn = channelselection(artfctdef.inspect, hdr.label); >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From chintan_student at YAHOO.CO.IN Fri Apr 24 04:07:50 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Fri, 24 Apr 2009 07:37:50 +0530 Subject: regarding besa to fieldtrip Message-ID: Dear Jan-Mathijs,   I   Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Fri Apr 24 04:07:51 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Fri, 24 Apr 2009 07:37:51 +0530 Subject: regarding besa to fieldtrip Message-ID: Dear Jan-Mathijs,   I have   Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition http://downloads.yahoo.com/in/firefox/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Fri Apr 24 04:10:08 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Fri, 24 Apr 2009 07:40:08 +0530 Subject: regarding besa to fieldtrip Message-ID: Dear Jan-Mathijs,   I have besa format file of .cnt and .foc format.  Pleas tell me how to import in matlab using fieldtrip functions.  besa2fieldtrip is not working here.   Best Regards,   Chintan Explore your hobbies and interests. Go to http://in.promos.yahoo.com/groups/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at MAC.COM Fri Apr 24 07:22:51 2009 From: nathanweisz at MAC.COM (Nathan Weisz) Date: Fri, 24 Apr 2009 07:22:51 +0200 Subject: regarding besa to fieldtrip In-Reply-To: <355853.55433.qm@web95401.mail.in2.yahoo.com> Message-ID: Dear Chintan, haven you read Stephans answer to your question. here it is again: > Yo can export your data in BESA to .avr (ASCII) .mul (ASCII > multiplexed) and .dat (simple binary, you will also get a header > file .generic). With besa2fieldtrip you can read in your data > easily, then. btw, the help comments within the besa2fieldtrip function as well as the description in the tutorial should have been detailed enough to get you going (examples in the tutorial). if you nevertheless encounter problems when running the function then saying "besa2fieldtrip is not working here" is simply not enough to know what's exactly your problem. please show us how you called the function and e.g. the error message you got. this helps us helping you. best, nathan On 24.04.2009, at 04:10, shah chintan wrote: > Dear Jan-Mathijs, > > I have besa format file of .cnt and .foc format. Pleas tell me how > to import in matlab using fieldtrip functions. besa2fieldtrip is > not working here. > > Best Regards, > > Chintan > > Own a website.Get an unlimited package.Pay next to nothing.* Click > here!. > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.litvak at ION.UCL.AC.UK Fri Apr 24 19:12:45 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Fri, 24 Apr 2009 18:12:45 +0100 Subject: Important message for Neuromag users Message-ID: Dear Neuromag users, We recently found a critical bug in the new MNE reader. The grad structure for Neuromag read with the new reader was incorrect and this would affect source analysis and (to a minor extent) topoplotting. The users who used the old meg_pd reader are not affected. If you think you might be affected by the bug you should update your FT to the latest version and re-read all the grads read with the MNE reader until now from the original fif files. Sorry for the inconvenience, Vladimir ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From chintan_student at YAHOO.CO.IN Fri Apr 24 21:57:15 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Sat, 25 Apr 2009 01:27:15 +0530 Subject: Fw: Re: [FIELDTRIP] regarding besa to fieldtrip Message-ID: --- On Sat, 25/4/09, shah chintan wrote: From: shah chintan Subject: Re: [FIELDTRIP] regarding besa to fieldtrip To: nathanweisz at me.com Date: Saturday, 25 April, 2009, 1:25 AM Dear Sir,   Actually I have a data file of .cnt format and I have .sfp file containing the positions of electrodes.  The data file consist of different signals depending on time.  I can import both the file into matlab.  I dont know how to analyse or produce the graphical picture of messes at different time frequency.    Best Regards,   Chintan --- On Fri, 24/4/09, Nathan Weisz wrote: From: Nathan Weisz Subject: Re: [FIELDTRIP] regarding besa to fieldtrip To: FIELDTRIP at NIC.SURFNET.NL Date: Friday, 24 April, 2009, 10:52 AM Dear Chintan, haven you read Stephans answer to your question. here it is again: Yo can export your data in BESA to .avr (ASCII) .mul (ASCII multiplexed) and .dat (simple binary, you will also get a header file .generic). With besa2fieldtrip you can read in your data easily, then. btw, the help comments within the besa2fieldtrip function as well as the description in the tutorial should have been detailed enough to get you going (examples in the tutorial). if you nevertheless encounter problems when running the function then saying "besa2fieldtrip is not working here" is simply not enough to know what's exactly your problem. please show us how you called the function and e.g. the error message you got. this helps us helping you. best, nathan On 24.04.2009, at 04:10, shah chintan wrote: Dear Jan-Mathijs,   I have besa format file of .cnt and .foc format.  Pleas tell me how to import in matlab using fieldtrip functions.  besa2fieldtrip is not working here.   Best Regards,   Chintan Own a website.Get an unlimited package.Pay next to nothing.* Click here!. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ Bollywood news, movie reviews, film trailers and more! Click here. Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From johnston at KIN.UCALGARY.CA Thu Apr 30 18:55:32 2009 From: johnston at KIN.UCALGARY.CA (Jamie Johnston) Date: Thu, 30 Apr 2009 10:55:32 -0600 Subject: problems with coherence tutorial Message-ID: I am trying to run the coherence tutorial on the website. I have downloaded the SubjectCMC.zip folder but there is no dataset called "SubjectCMC.ds" and I keep running into an error running the code. Any suggestions. Thanks, Jamie _______________ Jamie Johnston, Ph.D. Assistant Professor Faculty of Kinesiology University of Calgary 2500 University Dr. NW Calgary, AB T2N 1N4 Phone: +1 (403) 220-3649 Fax: +1 (403) 284-3553 email: johnston at kin.ucalgary.ca website: http://www.kin.ucalgary.ca/wcm/knes/johnston.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Thu Apr 30 21:18:55 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Thu, 30 Apr 2009 20:18:55 +0100 Subject: problems with coherence tutorial In-Reply-To: Message-ID: Dear Jamie, I tried to download SubjectCMC.zip and I cannot reproduce your problem. I assume that you properly unzipped the folder? If not, that could explain your problem. The zip file is about 360 megabytes, but once unzipped, SubjectCMC.ds should contain a .meg4-file which should be about 664 Mb. Alternatively, you could skip the preprocessing part and start from "computing the cross-spectral densities". The preprocessed data can be obtained by preprocessing the raw data, or you can directly download the processed data file from the ftp-server. Good luck, Jan-Mathijs On Apr 30, 2009, at 5:55 PM, Jamie Johnston wrote: > I am trying to run the coherence tutorial on the website. I have > downloaded the SubjectCMC.zip folder but there is no dataset called > “SubjectCMC.ds” and I keep running into an error running the code. > Any suggestions. > > Thanks, > > Jamie > > _______________ > Jamie Johnston, Ph.D. > Assistant Professor > Faculty of Kinesiology > University of Calgary > 2500 University Dr. NW > Calgary, AB > T2N 1N4 > Phone: +1 (403) 220-3649 > Fax: +1 (403) 284-3553 > email: johnston at kin.ucalgary.ca > website: http://www.kin.ucalgary.ca/wcm/knes/johnston.html > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From megjim1 at GMAIL.COM Thu Apr 30 21:21:01 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Thu, 30 Apr 2009 21:21:01 +0200 Subject: color bar Message-ID: Dear FTer: I wonder if anybody can tell me how to get the full color bar when plotting w/ "singleplotTFR" or "multiplotTFR". I ran the following commands: -------- figure cfg = []; cfg.layout = '4D248.lay'; cfg.ylim = [5 30] cfg.interactive = 'yes'; cfg.showlabels = 'yes'; cfg.colorbar = 'yes'; cfg.channel='A2' singleplotTFR(cfg,TF) ----------- But what I get on the right side of the figure is a colorbar w/ only half of the color (usually the cold colors like blue or green), and the numbers on the right side of the colorbar seem to be wrongly placed (see attachment). How can I get all the colors (both hot and cold) displayed in the colorbar? FYI, I controled the values of TF.powspctrm so that, for the channel displayed (A2), all values before time 0 is 3e-25, and all values after time 0 is 1e-25. But the color bar is telling me that the blue should be 2e-25, which is totally wrong! It's as if something happened that moved the whole colorbar up by half of the data range, then cut off the top of it (i.e. the hot colors). In fact, I think Fig 3 of the online tutorial (http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis) probably suffered from the same problem. Thanks, Jim ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: half_colorbar.TIF Type: image/tiff Size: 97550 bytes Desc: not available URL: From megjim1 at GMAIL.COM Sun Apr 5 18:15:44 2009 From: megjim1 at GMAIL.COM (=?GB2312?Q?Jim?=) Date: Sun, 5 Apr 2009 18:15:44 +0200 Subject: help w/ sourceplot Message-ID: Dear all, Could anyone give me a hint how to solve this problem? I tried to played with the mri of subject1 in the tutorial page (http://fieldtrip.fcdonders.nl/tutorial/beamformer). I downloaded the segmented mri from ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/beamformer/segmentedmriF.mat, then did the following: --------------- load segmentedmriF mri = read_fcdc_mri('Subject01.mri'); segmentedmriF.transform = mri.transform; segmentedmriF.anatomy = mri.anatomy; figure cfg = []; sourceplot(cfg,segmentedmriF); %only mri ----------------------- The error message is like this: -------------------- the input is volume data with dimensions [256 256 256] ??? Error using ==> horzcat The following error occurred converting from char to cell: Error using ==> cell Conversion to cell from char is not possible. Error in ==> fieldtrip-20090404\private\parameterselection at 94 if ~issubfield(data, param{i}) && issubfield(data, ['avg.' param{i}]) Error in ==> volumedownsample at 171 cfg.parameter = parameterselection(cfg.parameter, source); Error in ==> sourceplot at 305 data = volumedownsample(tmpcfg, data); ---------------------------- Here is some information about my computer/softwares: MATLAB Version 7.0.0.19920 (R14). Operating System: Microsoft Windows XP Version 5.1 (Build 2600: Service Pack 3) Java VM Version: Java 1.4.2 with Sun Microsystems Inc. Java HotSpot(TM) Client VM And I downloaded the latest 040409 Fieldtrip. Any idea how to solve the issue? Thanks a lot, Jim ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Mon Apr 6 10:43:33 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Mon, 6 Apr 2009 09:43:33 +0100 Subject: help w/ sourceplot In-Reply-To: Message-ID: Dear Jim, Is the "amp;" in line 94 parameterselection really there, or did it pop up during the copy and paste process? I tried to reproduce your problem, but I did not manage. If removing the "amp;" does not solve your case, you could try to debug the code by typing on the command-line: "dbstop if error" and calling sourceplot after that. When it crashes, you have access to the local workspace of the functions (you can toggle between the different functions in the calling hierarchy by the commands dbup and dbdown) so that you can have a look what is going wrong. Usually, matlab is pretty explicit about what it tries to do (but fails) in its error messages. Yours, Jan-Mathijs On Apr 5, 2009, at 5:15 PM, Jim wrote: > if ~issubfield(data, param{i}) && issubfield(data, ['avg.' param > {i}] ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From vinnik at SISSA.IT Tue Apr 7 13:56:04 2009 From: vinnik at SISSA.IT (Katya Vinnik) Date: Tue, 7 Apr 2009 13:56:04 +0200 Subject: plots and stats with biosemi128.lay In-Reply-To: <3d0f9a750903231119o3cf85f4as3f5ab40bcd80af20@mail.gmail.com> Message-ID: Dear FT users, has anyone of you encountered this warning? Duplicate x-y data points detected: using average of the z values. I'm simply plotting my data with cfg.layout      = 'biosemi128.lay'; and it gives me strange plots like the one here: picasaweb.google.com/lh/photo/qmd3BgpeEDegPo4kHdRW0w?feat=directlink basically data from channels B19 and 21 and D22 and 24 are overlayed (circled in red on the pictures). This message appears also with topoplot functions. In the layout file, howether ,positions of this electrodes are different (see below). Do you think it can affect cluster-based multiple comparison correction? For example, if I use cfg.layout      = 'biosemi128.lay'; cfg.correctm = 'cluster';  [stat] = freqstatistics(cfg,x,y) does it calculate it properly? Thank you, Best regards, Katya ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Wed Apr 8 08:59:54 2009 From: megjim1 at GMAIL.COM (=?GB2312?Q?Jim_Li?=) Date: Wed, 8 Apr 2009 08:59:54 +0200 Subject: help w/ sourceplot Message-ID: Dear Jan-Mathijs, You're right: The "amp;" shouldn't be there, it's just a random thing popped up during copying. I followed your recommendation to debug and, when crash happened, I got this: ------------------ K>> param param = {} {} 'anatomy' 'inside' K>> i i = 1 K>> ['avg.' param{i}] ??? Error using ==> horzcat The following error occurred converting from char to cell: Error using ==> cell Conversion to cell from char is not possible. ------------------ Apparently the "{}" is the source of error. Tracing further, I think the following two lines of code in "sourceplot.m" seems to be the source of error since they lead to the two "{}" in the above- mentioned "param": if ~isfield(cfg, 'funparameter'), cfg.funparameter = []; end if ~isfield(cfg, 'maskparameter'), cfg.maskparameter = []; end The "segmentedmriF" I used in "sourceplot(cfg,segmentedmriF)" is like this: ------------ K>> segmentedmriF segmentedmriF = dim: [256 256 256] transform: [4x4 double] gray: [256x256x256 double] white: [256x256x256 double] csf: [256x256x256 double] cfg: [1x1 struct] anatomy: [256x256x256 uint16] ------------------- So, should the 'funparameter' and 'maskparameter' be specified in "segmentedmriF" before running the sourceplot? If so, what should they be? ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Wed Apr 8 15:04:29 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Wed, 8 Apr 2009 15:04:29 +0200 Subject: Need help with BVA files In-Reply-To: Message-ID: Hi Martijn It seems that you are using the trialfun_brainvision.m function to define trials. At least, if I try to replicate your problem it seems that definetrial sets cfg.trialfun to trialfun_brainvision (see line 156). The data format specific trialfuns (like trialfun_brainvision) are not maintained any more because they have been replaced wit a more general way of handling the events and the trial definition. Recent versions of fieldtrip also don't include the trialfun_brainvision any more. Please update your fieldtrip to the latest version and try again. You can use trialfun_general or you can write your own function for the trial definition (see for example http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition) best regards, Robert On 31 Mar 2009, at 15:23, Martijn Barendregt wrote: > I'm trying to process some E.E.G. data that I've exported from > BrainVision > Analyzer. But when I run my script (see below) I don't get any > errors but > the 'time' field in the raw_data struct will be all zeros. Because > of this I > can't do anything with the data. > > What can I do to get the time values in correctly? > > Kinds regards, > > Martijn Barendregt > > My code: > cfg = []; > cfg.datafile = 'somefile.dat'; > cfg.headerfile = 'somefile.vhdr'; > cfg.trialdef.trgfile = 'somefile.vmkr'; > cfg.trialdef.eventtype = 'Stimulus'; > cfg.trialdef.eventvalue = 'M22'; > cfg.traildef.prestim = 3; > cfg.traildef.poststim = 3; > cfg.trialdef.segment = 'no'; > cfg.trialdef.timezero = 'no'; > > [cfg] = definetrial(cfg); > > raw_data = preprocessing(cfg); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Wed Apr 8 15:20:25 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Wed, 8 Apr 2009 15:20:25 +0200 Subject: plots and stats with biosemi128.lay In-Reply-To: <3d0f9a750904070456i59c8d768na2f83e98cb3bf0a3@mail.gmail.com> Message-ID: Dear Katya If I do >> cfg.layout = 'biosemi128.lay' >> layoutplot(cfg) then I get attached figure (which you should be able to reproduce). Looking carefully it seems that D39 is lying on top of another channel. If I then do d = dist(lay.pos') imagesc(d==0) then I see that there are multiple off-diagonal elements in the distance matrix (i.e. a 128x128 matrix containing the distance bwteen all pairs) that are zero. So there are multiple channels overlapping. I don't know why that is and at the moment I don't know where the biosemi layouts were coming from. The only information that I have from the log is revision 1.1 date: 2005/06/15 08:21:08; author: roboos; state: Exp; new layout files, based on excel sheet from biosemi I don't know the details of this excel sheet any more, but probably the excel sheet was already wrong. But to come to your prime question: does it affect clustering? Yes it will. You are using the layout to define neighbours. If the layout is flawed, the neighbour definition might also be flawed. Please use the neighbourselection function to make a neighbour definition explicitely and check the neighbours by looking at the output of the neighbourselection function. best regards, Robert PS it would be nice if you could provide a better layout for the biosemi128 cap ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 1.png Type: image/png Size: 37404 bytes Desc: not available URL: -------------- next part -------------- On 7 Apr 2009, at 13:56, Katya Vinnik wrote: > Dear FT users, > > has anyone of you encountered this warning? > Duplicate x-y data points detected: using average of the z values. > > I'm simply plotting my data with cfg.layout = > 'biosemi128.lay'; > > and it gives me strange plots like the one here: > picasaweb.google.com/lh/photo/qmd3BgpeEDegPo4kHdRW0w?feat=directlink > > basically data from channels B19 and 21 and D22 and 24 are overlayed > (circled in red on the pictures). > This message appears also with topoplot functions. In the layout file, > howether ,positions of this electrodes are different (see below). > > Do you think it can affect cluster-based multiple comparison > correction? > > For example, if I use > > cfg.layout = 'biosemi128.lay'; > cfg.correctm = 'cluster'; > [stat] = freqstatistics(cfg,x,y) > > does it calculate it properly? > > Thank you, > Best regards, > Katya > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From lulswinnik at GMAIL.COM Wed Apr 8 17:19:19 2009 From: lulswinnik at GMAIL.COM (Katya Vinnik) Date: Wed, 8 Apr 2009 17:19:19 +0200 Subject: plots and stats with biosemi128.lay In-Reply-To: Message-ID: Thank you, Robert! Regards, Katya 2009/4/8 Robert Oostenveld : > Dear Katya > > If I do >>> cfg.layout = 'biosemi128.lay' >>> layoutplot(cfg) > > then I get attached figure (which you should be able to reproduce). Looking > carefully it seems that D39 is lying on top of another channel. > > If I then do > d = dist(lay.pos') > imagesc(d==0) > > then I see that there are multiple off-diagonal elements in the distance > matrix (i.e. a 128x128 matrix containing the distance bwteen all pairs) that > are zero.  So there are multiple channels overlapping. I don't know why that > is and at the moment I don't know where the biosemi layouts were coming > from. The only information that I have from the log is >  revision 1.1 >  date: 2005/06/15 08:21:08;  author: roboos;  state: Exp; >  new layout files, based on excel sheet from biosemi > > I don't know the details of this excel sheet any more, but probably the > excel sheet was already wrong. > > But to come to your prime question: does it affect clustering? Yes it will. > You are using the layout to define neighbours. If the layout is flawed, the > neighbour definition might also be flawed. Please use the neighbourselection > function to make a neighbour definition explicitely and check the neighbours > by looking at the output of the neighbourselection function. > > > best regards, > Robert > > PS it would be nice if you could provide a better layout for the biosemi128 > cap > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > > > > On 7 Apr 2009, at 13:56, Katya Vinnik wrote: > >> Dear FT users, >> >> has anyone of you encountered this warning? >> Duplicate x-y data points detected: using average of the z values. >> >> I'm simply plotting my data with       cfg.layout      = 'biosemi128.lay'; >> >> and it gives me strange plots  like the one here: >> picasaweb.google.com/lh/photo/qmd3BgpeEDegPo4kHdRW0w?feat=directlink >> >> basically data from channels B19 and 21 and D22 and 24 are overlayed >> (circled in red on the pictures). >> This message appears also with topoplot functions. In the layout file, >> howether ,positions of this electrodes are different (see below). >> >> Do you think it can affect cluster-based multiple comparison correction? >> >> For example, if I use >> >> cfg.layout      = 'biosemi128.lay'; >> cfg.correctm = 'cluster'; >>  [stat] = freqstatistics(cfg,x,y) >> >> does it calculate it properly? >> >> Thank you, >> Best regards, >> Katya >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/neuroimaging/fieldtrip. >> > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From njkillian at GATECH.EDU Wed Apr 8 22:28:13 2009 From: njkillian at GATECH.EDU (Nathan Killian) Date: Wed, 8 Apr 2009 16:28:13 -0400 Subject: problem with freqdescriptives Message-ID: Hello, I was wondering if anyone knew why a particular configuration is not giving me a jackknife result for the power spectrum, even though I am keeping trials. This problem occurs when I use FT20090404, but I at least get something returned for the standard error with FT20080611 (and it at least looked reasonable). I am using this analysis: cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.foilim = [0,100]; cfg.tapsmofrq = 4; cfg.pad = 'maxperlen'; cfg.keeptrials = 'yes'; cfg.keepfourier = 'no'; cfg.keeptapers = 'no'; cfg.pseudovalue = 'no'; cfg.jackknife = 'yes'; cfg.complex = 'complex'; freq = freqanalysis(cfg, data); freqdes = freqdescriptives(cfg, freq); Additionally, I found if you keeptrials and don't set keepfourier you will get an error only with the new version (could be easily fixed in the freqdescriptives function). Thank you for your help! Nathan -- Graduate Student - Georgia Tech Bioengineering Buffalo Lab at Emory-Yerkes: 404.712.9431 Potter Lab at Georgia Tech: 404.385.4083 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Thu Apr 9 00:14:11 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Wed, 8 Apr 2009 23:14:11 +0100 Subject: problem with freqdescriptives In-Reply-To: Message-ID: Dear Nathan, If you rely on this specific functionality of freqdescriptives I would advice you to copy the old version into your fieldtrip-folder. There are indeed some bugs in the more recent versions of freqdescriptives which have been introduced along the way, but I (and others) did not yet find time to fix it. We anyway hope to soon move to a new implementation of freqdescriptives, which does not seem to make the patching worthwile. Yours, Jan-Mathijs On Apr 8, 2009, at 9:28 PM, Nathan Killian wrote: > Hello, > > I was wondering if anyone knew why a particular configuration is > not giving me a jackknife result for the power spectrum, even > though I am keeping trials. This problem occurs when I use > FT20090404, but I at least get something returned for the standard > error with FT20080611 (and it at least looked reasonable). I am > using this analysis: > cfg.output = 'powandcsd'; > cfg.method = 'mtmfft'; > cfg.foilim = [0,100]; > cfg.tapsmofrq = 4; > cfg.pad = 'maxperlen'; > cfg.keeptrials = 'yes'; > cfg.keepfourier = 'no'; > cfg.keeptapers = 'no'; > cfg.pseudovalue = 'no'; > cfg.jackknife = 'yes'; > cfg.complex = 'complex'; > freq = freqanalysis(cfg, data); > freqdes = freqdescriptives(cfg, freq); > > Additionally, I found if you keeptrials and don't set keepfourier > you will get an error only with the new version (could be easily > fixed in the freqdescriptives function). > > Thank you for your help! > > Nathan > > -- > Graduate Student - Georgia Tech Bioengineering > Buffalo Lab at Emory-Yerkes: 404.712.9431 > Potter Lab at Georgia Tech: 404.385.4083 > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From E.J.M.vanWingerden at UVA.NL Thu Apr 9 09:59:53 2009 From: E.J.M.vanWingerden at UVA.NL (Wingerden, E.J.M. van) Date: Thu, 9 Apr 2009 09:59:53 +0200 Subject: Star-P support In-Reply-To: A<7FFBC71A-F30A-48F5-8295-153E9575B5EC@psy.gla.ac.uk> Message-ID: Dear developers, Buried in the code for freqanalysis_mtmconvol.m I found a comment about a possible implementation of parallel data processing using star-P (line 466). Is this a feature that is under development at the moment? I have some experience with star-P myself and found that using FieldTrip in combination with a star-P computing cluster is quite hampered by the fact that structures cannot be passed as broadcast arguments when the computations are distributed. Have you found ways to circumvent this problem? In my opinion, the FieldTrip code could greatly benefit from parallel computing when splitting across channels, or trials even. However, since usually datasets are split at a high level function while the actual computation takes place within a low level function, the fact that structs containing the parameters that are necessary for the computation need to be passed as arguments between these functions makes it pretty hard to make them star-P compatible. Are you in contact with the star-P developers? I would imagine that they are very interested in the programming needs of a large user community/potential customers as we have here. best regards, marijn van wingerden Mr. Marijn van Wingerden, M.Sc. PhD-candidate Cognitive & Systems Neuroscience (CSN) Centre for NeuroScience (CNS) section of Swammerdam Institute for Life Sciences (SILS) University of Amsterdam, Faculty of Science Kruislaan 320, 1098 SM Amsterdam, The Netherlands Tel: +31 20 525 7713/7547 Fax: +31 20 525 7709 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From michael.wibral at WEB.DE Thu Apr 9 12:05:59 2009 From: michael.wibral at WEB.DE (Michael Wibral) Date: Thu, 9 Apr 2009 12:05:59 +0200 Subject: second level statistics Message-ID: Dear Fieldtrippers, I have computed sourcestatistics (task vs. baseline) at the single subject level for two separate conditions (Cond 1 and Cond2) I then use these t-values source images to comapre the activations between the two conditions at the multi-subject level. Works fine. My question is whether there is any straightforward way in fieldtrip to recycle these results (sourcespace t-value images) for a multisubject analysis for task versus baseline for condition separately. What appeals to me is that these data (t-values) are 'normalized' in a meaningful way across subjects already. Would it be statistically valid to create a virtual "baseline-against-baseline" dataset (with all t-values equal to zero, of course) and test against this? Or would it be better to do sourceanalysis once more to get task and baseline source power for each subject and condition and then do the regular source statistics task-vs-basline for each condition? Any suggestions welcom, Michael Wibral ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: From susannah.murphy at PSYCH.OX.AC.UK Thu Apr 9 12:06:05 2009 From: susannah.murphy at PSYCH.OX.AC.UK (Susannah Murphy) Date: Thu, 9 Apr 2009 11:06:05 +0100 Subject: second level statistics In-Reply-To: <941146944@web.de> Message-ID: Thanks for your message. I am out of the office until Tuesday 14th April. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Thu Apr 9 21:55:48 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Thu, 9 Apr 2009 21:55:48 +0200 Subject: help w/ sourceplot Message-ID: Well, by changing MATLAB to a newer version while using the same Fieldtrip I got the problem solved. Now I can get "sourceplot" to display the MRI images. That's great! Jim On Wed, 8 Apr 2009 08:59:54 +0200, Jim Li wrote: >Dear Jan-Mathijs, > >You're right: The "amp;" shouldn't be there, it's just a random thing popped >up during copying. > >I followed your recommendation to debug and, when crash happened, I got >this: > > >------------------ >K>> param > >param = > > {} {} 'anatomy' 'inside' > >K>> i > >i = > > 1 > >K>> ['avg.' param{i}] >??? Error using ==> horzcat >The following error occurred converting from char to cell: >Error using ==> cell >Conversion to cell from char is not possible. > >------------------ > >Apparently the "{}" is the source of error. > >Tracing further, I think the following two lines of code in "sourceplot.m" seems >to be the source of error since they lead to the two "{}" in the above- >mentioned "param": >if ~isfield(cfg, 'funparameter'), cfg.funparameter = []; end >if ~isfield(cfg, 'maskparameter'), cfg.maskparameter = []; end > > >The "segmentedmriF" I used in "sourceplot(cfg,segmentedmriF)" is like this: >------------ >K>> segmentedmriF > >segmentedmriF = > > dim: [256 256 256] > transform: [4x4 double] > gray: [256x256x256 double] > white: [256x256x256 double] > csf: [256x256x256 double] > cfg: [1x1 struct] > anatomy: [256x256x256 uint16] >------------------- > >So, should the 'funparameter' and 'maskparameter' be specified >in "segmentedmriF" before running the sourceplot? If so, what should they be? > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Fri Apr 10 20:01:58 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Fri, 10 Apr 2009 20:01:58 +0200 Subject: can I combine subplot and multiplotTFR to get multiple epochs displayed on 1 page? Message-ID: Dear Fieldtripper, I tried something like this to do two multiplotTFR plot on one page, but it didn't work: TF = freqanalysis(cfg,data); TF2 = freqanalysis(cfg,data2); subplot(2,1,1); multiplotTFR(cfg,TF); subplot(2,1,2); multiplotTFR(cfg,TF); Any idea how to combine subplot and multiplotTFR to get multiple "multiplotTFR" plots displayed on 1 page? Thanks, Jim ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From todavidkim at GMAIL.COM Fri Apr 10 22:59:08 2009 From: todavidkim at GMAIL.COM (David Kim) Date: Fri, 10 Apr 2009 13:59:08 -0700 Subject: Help with dipole-fitting simultaneous MEG/EEG data Message-ID: Dear Fieldtrip users, I have been working on solving dipole-fitting problem of a simultaneous MEG/EEG data with Fieldtrip. The MEG and EEG sensor definitions (275, 64) is generated to conform to Fieldtrip standard. A 4 shell volume conduction model for EEG and 1 shell model for MEG have been generated to conform to Fieldtrip standard. Given the stimulus, I'm assuming that a single dipole drives the signal in both EEG and MEG. Therefore, I would like to use Fieldtrip to find a dipole that best describes the simultaneously acquired MEG/EEG data in the following sense: A single dipole fit with 9 characteristic values consisting of: dipole position. 3 values, (x,y,z) dipole moment (given the dipole position) that best fits MEG data. 3 dipole moment (given the dipole position) that best fits EEG data. 3 Currently, Fieldtrip has compute_leadfield.m function which can take a cell of multiple volume and sensor definitions as described in line 22 and 23 of the code. % sens = {senseeg, sensmeg} % vol = {voleeg, volmeg} With compute_leadfield.m, I can perform the dipole-fitting, but this requires custom scripts outside of Fieldtrip which can get messy and vary from data to data. I would much rather have the process be done within the Fieldtrip environment where the process is more robust and streamlined. It would be ideal to have the data pass through to dipfit_error() subroutine defined in dipole_fit.m function, where the modifications to dipfit_error() definition would determine the outcome of the fit. It appears to me, however, both dipolefitting.m and dipole_fit.m are not made to process multiple sensor definitions. For example, line 166 of dipole_fit.m reads, "error('simultaneous EEG and MEG not supported');" Is simultaneous EEG/MEG processing of data already implemented in Fieldtrip that I'm not aware of? If not what steps could we take to implement such a feature? Thank you. David Kim ---------------------------------------------------------------------- UCSF/UC Berkeley Bioengineering Graduate Group todavidkim at gmail.com (510) 643-7571 http://cornea.berkeley.edu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From lwn_07 at YAHOO.COM.CN Sun Apr 12 06:03:11 2009 From: lwn_07 at YAHOO.COM.CN (=?utf-8?B?5p2O5Y2r5aic?=) Date: Sun, 12 Apr 2009 12:03:11 +0800 Subject: Ask for help :How can I read the weights file of SAM spatial filter? Message-ID: Dear fieldtripers,       I want to read the SAM spatial filters of my MEG data recorded by CTF151 MEG system in a motor task. It seems the file in a ".svl.max.wts" format describe the "weights" information, but I can't read the out. And I found that there was a "read_ctf_coef.m" file in "eeglab plugins" which is copyrighted to Robert, can returns the spatial filter cofficients for CTF MEG system, and these cofficients were not read from a file but already existed. Is this "cofficients" and my weights the same thing?       The description of function "read_ctf_coef" is as follows:   function [coef] = read_ctf_coef % READ_CTF_COEF returns the spatial filter coefficients for the CTF MEG system % that has been installed at the F.C. Donders Centre (id 1706) % % This function actually does not read the coefficients from a file, but the % coefficients themselves are included in this function. % % The original location of the coefficients included in this file is % odin:/opt/ctf/hardware/M016/M017_1706.coef % Copyright (C) 2003, Robert Oostenveld          Best Wishes!                                                                                            Weina LI                                                                                         2009.04.12 ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Roozbeh.Rezaie at UTH.TMC.EDU Mon Apr 13 16:12:53 2009 From: Roozbeh.Rezaie at UTH.TMC.EDU (Rezaie, Roozbeh) Date: Mon, 13 Apr 2009 09:12:53 -0500 Subject: ISACM 2009- Call For Abstracts Message-ID: ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2009 ISACM Conference Call for Abstracts.pdf Type: application/pdf Size: 127099 bytes Desc: 2009 ISACM Conference Call for Abstracts.pdf URL: From chintan_student at YAHOO.CO.IN Mon Apr 13 20:57:17 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Tue, 14 Apr 2009 00:27:17 +0530 Subject: regarding start Message-ID: Dear sir, i just started learning fieldtrip.  can u tell me how to run the tutorial scripts in matlab.  Check out the all-new Messenger 9.0! Go to http://in.messenger.yahoo.com/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From megjim1 at GMAIL.COM Mon Apr 13 23:35:59 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Mon, 13 Apr 2009 23:35:59 +0200 Subject: Makefile for Linux 64 Message-ID: Dear FTer: We're thinking of buying a 64-bit Quad-core PC w/ big memory(>=16GB), then install a Linux OS (CentOS 4) and run Fieldtrip on it. According to the first question asked by Christine below, there seems to be a problem w/ SPM2. Is that still an issue or is it solved by now? Are there any other issues to pay attention to w/ 64-bit linux? Thanks a lot, Jim On Tue, 18 Sep 2007 17:03:59 +0200, Christine Tillmann wrote: >Hi, > >we are trying to get the fieldtrip beamforming on our linux 64 bit >systems going. As we understand it, there is currently no way around >using spm2. Spm2's mex files however are not compiled for linux 64 bit >and the makefile that's available on the web suffers from the tab/space >delimiter problem. >Does anyone have a makefile for spm2 that works on linux 64 bit? > >Or, else is there a way around spm2? E.g. by using the output of >mriviewer and the localspheres command directly? Or by beamforming in >CTF and feeding its output to sourcestatistics? > >And one last thing: does anyone use the mri files from trhe >CTF-MRIviewer that came with version 5.4.0 yet? > >Thanks, >Christine > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From gflandin at FIL.ION.UCL.AC.UK Wed Apr 15 12:27:10 2009 From: gflandin at FIL.ION.UCL.AC.UK (Guillaume Flandin) Date: Wed, 15 Apr 2009 11:27:10 +0100 Subject: Makefile for Linux 64 In-Reply-To: Message-ID: Dear Jim, some 64bit Linux MEX files for SPM2 are available from here: ftp://ftp.fil.ion.ucl.ac.uk/spm/spm2_updates/ The website mentioned in previous email is the SPM wikibooks: http://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Linux#Compilation_notes_for_SPM2: I also attach a SPM2 Makefile that contains instructions for Linux64 compilation, in case the provided compiled MEX files do not work on your platform. Best regards, Guillaume. Jim Li wrote: > Dear FTer: > > We're thinking of buying a 64-bit Quad-core PC w/ big memory(>=16GB), then > install a Linux OS (CentOS 4) and run Fieldtrip on it. According to the first > question asked by Christine below, there seems to be a problem w/ SPM2. Is > that still an issue or is it solved by now? Are there any other issues to pay > attention to w/ 64-bit linux? > > > Thanks a lot, > > Jim > > On Tue, 18 Sep 2007 17:03:59 +0200, Christine Tillmann FRANKFURT.MPG.DE> wrote: > >> Hi, >> >> we are trying to get the fieldtrip beamforming on our linux 64 bit >> systems going. As we understand it, there is currently no way around >> using spm2. Spm2's mex files however are not compiled for linux 64 bit >> and the makefile that's available on the web suffers from the tab/space >> delimiter problem. >> Does anyone have a makefile for spm2 that works on linux 64 bit? >> >> Or, else is there a way around spm2? E.g. by using the output of >> mriviewer and the localspheres command directly? Or by beamforming in >> CTF and feeding its output to sourcestatistics? >> >> And one last thing: does anyone use the mri files from trhe >> CTF-MRIviewer that came with version 5.4.0 yet? >> >> Thanks, >> Christine -- Guillaume Flandin, PhD Wellcome Trust Centre for Neuroimaging University College London 12 Queen Square London WC1N 3BG ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Makefile URL: From chintan_student at YAHOO.CO.IN Wed Apr 15 16:33:20 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Wed, 15 Apr 2009 20:03:20 +0530 Subject: [FIELD TRIP] regarding define trial Message-ID: folks,   I am going through the tutorials of fieldtrip.  When I try to run the example scripts on matlab, I am getting an error regarding the functions which are undefined such as definetrial or preprocessing.  Please guide me to built the functions on fieldtrip.     Thanking you   Chintan Check out the all-new Messenger 9.0! Go to http://in.messenger.yahoo.com/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Wed Apr 15 16:44:58 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Wed, 15 Apr 2009 15:44:58 +0100 Subject: [FIELD TRIP] regarding define trial In-Reply-To: <692084.73060.qm@web95408.mail.in2.yahoo.com> Message-ID: Dear Chintan, You probably still have to add the fieldtrip folder to you matlab- path, after you downloaded the most recent fieldtrip version. Yours, JM On Apr 15, 2009, at 3:33 PM, shah chintan wrote: > folks, > > I am going through the tutorials of fieldtrip. When I try to run > the example scripts on matlab, I am getting an error regarding the > functions which are undefined such as definetrial or > preprocessing. Please guide me to built the functions on fieldtrip. > > > Thanking you > > Chintan > > Add more friends to your messenger and enjoy! Invite them now. > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lwn_07 at YAHOO.COM.CN Wed Apr 15 16:19:41 2009 From: lwn_07 at YAHOO.COM.CN (=?utf-8?B?5p2O5Y2r5aic?=) Date: Wed, 15 Apr 2009 22:19:41 +0800 Subject: =?utf-8?Q?=E5=9B=9E=E5=A4=8D=EF=BC=9A?= [FIELDTRIP] Ask for help :How can I read the weights file of SAM spatial filter? Message-ID: I found a way to read the weigts in http://kurage.nimh.nih.gov/meglab/Meg/Readwts may help someone else     --- 09年4月12日，周日, 李卫娜 写道： 发件人: 李卫娜 主题: [FIELDTRIP] Ask for help :How can I read the weights file of SAM spatial filter? 收件人: FIELDTRIP at NIC.SURFNET.NL 日期: 2009年4月12日,周日,下午12:03 Dear fieldtripers,       I want to read the SAM spatial filters of my MEG data recorded by CTF151 MEG system in a motor task. It seems the file in a ".svl.max.wts" format describe the "weights" information, but I can't read the out. And I found that there was a "read_ctf_coef.m" file in "eeglab plugins" which is copyrighted to Robert, can returns the spatial filter cofficients for CTF MEG system, and these cofficients were not read from a file but already existed. Is this "cofficients" and my weights the same thing?       The description of function "read_ctf_coef" is as follows:   function [coef] = read_ctf_coef % READ_CTF_COEF returns the spatial filter coefficients for the CTF MEG system % that has been installed at the F.C. Donders Centre (id 1706) % % This function actually does not read the coefficients from a file, but the % coefficients themselves are included in this function. % % The original location of the coefficients included in this file is % odin:/opt/ctf/hardware/M016/M017_1706.coef % Copyright (C) 2003, Robert Oostenveld          Best Wishes!                                                                                            Weina LI                                                                                         2009.04.12 好玩贺卡等你发，邮箱贺卡全新上线！ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at GMAIL.COM Wed Apr 15 17:27:29 2009 From: julian.keil at GMAIL.COM (Julian Keil) Date: Wed, 15 Apr 2009 17:27:29 +0200 Subject: Plot ECoG-Electrodes Message-ID: Hello, we have recently begun to work with ECoG data. Now we would like to plot results from timelock and freqanalysis. Is there any possibility to plot the (known) electrode position onto the brain using sourceplot? Thanks a lot Julian Dipl. Psych. Julian Keil OBOB-Lab University of Konstanz Department of Psychology P.O. Box D23 78457 Konstanz Germany Tel: ++49 - (0)7531 - 88 42 50 Fax: ++49 - (0)7531 - 88 28 91 Email: julian.keil at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Wed Apr 15 17:30:51 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Wed, 15 Apr 2009 21:00:51 +0530 Subject: [FIELD TRIP] regarding define trial Message-ID: Dear schofflen, Do you mean to say that I need to download all the zip files along with the directory and locate them to some folder.  And then locate matlab to that folder.   Best   Chintan --- On Wed, 15/4/09, jan-mathijs schoffelen wrote: From: jan-mathijs schoffelen Subject: Re: [FIELDTRIP] [FIELD TRIP] regarding define trial To: FIELDTRIP at NIC.SURFNET.NL Date: Wednesday, 15 April, 2009, 8:14 PM Dear Chintan, You probably still have to add the fieldtrip folder to you matlab-path, after you downloaded the most recent fieldtrip version. Yours, JM On Apr 15, 2009, at 3:33 PM, shah chintan wrote: folks,   I am going through the tutorials of fieldtrip.  When I try to run the example scripts on matlab, I am getting an error regarding the functions which are undefined such as definetrial or preprocessing.  Please guide me to built the functions on fieldtrip.     Thanking you   Chintan Add more friends to your messenger and enjoy! Invite them now. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Wed Apr 15 19:42:49 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Wed, 15 Apr 2009 23:12:49 +0530 Subject: regarding directory files. Message-ID: Dear folks, Currently I am working on field trip tutorials.  I downloaded all the zip files and directories.  Can anybody tell me where to put directory files and how to locate on matlab.   Best regards,   Chintan Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Wed Apr 15 21:19:20 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Wed, 15 Apr 2009 20:19:20 +0100 Subject: regarding directory files. In-Reply-To: <84601.71472.qm@web95404.mail.in2.yahoo.com> Message-ID: Dear Chintan, I am afraid that the problem you have at the moment is unrelated to FieldTrip, but rather a general matlab issue. It does not matter where you put the files, as long as you tell matlab where to find them. If you put the files in, say, C: \mydirectory\fieldtrip, then you should issue the following command from the matlab command-line: addpath(genpath('C:\mydirectory \fieldtrip')), or you can specify the path using the set path utility (and then you have to add with subdirectories). If this all sounds unfamiliar to you, I strongly advise you to look into the matlab documentation to learn how to work with matlab. Yours, Jan-Mathijs On Apr 15, 2009, at 6:42 PM, shah chintan wrote: > Dear folks, > Currently I am working on field trip tutorials. I downloaded all > the zip files and directories. Can anybody tell me where to put > directory files and how to locate on matlab. > > Best regards, > > Chintan > > Download prohibited? No problem. CHAT from any browser, without > download. > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Wed Apr 15 21:23:44 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Thu, 16 Apr 2009 00:53:44 +0530 Subject: regarding directory files. Message-ID: Dear Sir,   I am very glad with your reply.  Actually I am not finding any .mat files in the installed package of matlab.  And the directories that is available at fieldtrip are all .mat files, So I am not getting where to put those directories.  Can you specify which version of matlab is compatible with fieldtrip. I am usig MATLAB 7.4.0.   Best Regards,   Chintan --- On Thu, 16/4/09, jan-mathijs schoffelen wrote: From: jan-mathijs schoffelen Subject: Re: [FIELDTRIP] regarding directory files. To: FIELDTRIP at NIC.SURFNET.NL Date: Thursday, 16 April, 2009, 12:49 AM Dear Chintan, I am afraid that the problem you have at the moment is unrelated to FieldTrip, but rather a general matlab issue. It does not matter where you put the files, as long as you tell matlab where to find them. If you put the files in, say, C:\mydirectory\fieldtrip, then you should issue the following command from the matlab command-line: addpath(genpath('C:\mydirectory\fieldtrip')), or you can specify the path using the set path utility (and then you have to add with subdirectories). If this all sounds unfamiliar to you, I strongly advise you to look into the matlab documentation to learn how to work with matlab. Yours, Jan-Mathijs   On Apr 15, 2009, at 6:42 PM, shah chintan wrote: Dear folks, Currently I am working on field trip tutorials.  I downloaded all the zip files and directories.  Can anybody tell me where to put directory files and how to locate on matlab.   Best regards,   Chintan Download prohibited? No problem. CHAT from any browser, without download. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Wed Apr 15 21:48:48 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Thu, 16 Apr 2009 01:18:48 +0530 Subject: regarding definetrial and preprocessing Message-ID: Folks,   I am working on fieldtrip tutorials.  I downloaded all the files and directories from tutorials.  Now when I run the scripts, an error occurs that definetrial and preprocessing functions are undefined.  Please help me in  building these functions.   Best Regards,   Chintan Connect with friends all over the world. Get Yahoo! India Messenger at http://in.messenger.yahoo.com/?wm=n/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From megjim1 at GMAIL.COM Fri Apr 17 04:11:06 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Fri, 17 Apr 2009 04:11:06 +0200 Subject: Makefile for Linux 64 Message-ID: Dear Guillaume, That's great! I'm downloading them now. Thanks a lot for your wonderful help, :) Jim On Wed, 15 Apr 2009 11:27:10 +0100, Guillaume Flandin wrote: >Dear Jim, > >some 64bit Linux MEX files for SPM2 are available from here: >ftp://ftp.fil.ion.ucl.ac.uk/spm/spm2_updates/ > >The website mentioned in previous email is the SPM wikibooks: >http://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Linux#Compilation_not es_for_SPM2: > >I also attach a SPM2 Makefile that contains instructions for Linux64 >compilation, in case the provided compiled MEX files do not work on your >platform. > >Best regards, >Guillaume. > > >Jim Li wrote: >> Dear FTer: >> >> We're thinking of buying a 64-bit Quad-core PC w/ big memory(>=16GB), then >> install a Linux OS (CentOS 4) and run Fieldtrip on it. According to the first >> question asked by Christine below, there seems to be a problem w/ SPM2. Is >> that still an issue or is it solved by now? Are there any other issues to pay >> attention to w/ 64-bit linux? >> >> >> Thanks a lot, >> >> Jim >> >> On Tue, 18 Sep 2007 17:03:59 +0200, Christine Tillmann > FRANKFURT.MPG.DE> wrote: >> >>> Hi, >>> >>> we are trying to get the fieldtrip beamforming on our linux 64 bit >>> systems going. As we understand it, there is currently no way around >>> using spm2. Spm2's mex files however are not compiled for linux 64 bit >>> and the makefile that's available on the web suffers from the tab/space >>> delimiter problem. >>> Does anyone have a makefile for spm2 that works on linux 64 bit? >>> >>> Or, else is there a way around spm2? E.g. by using the output of >>> mriviewer and the localspheres command directly? Or by beamforming in >>> CTF and feeding its output to sourcestatistics? >>> >>> And one last thing: does anyone use the mri files from trhe >>> CTF-MRIviewer that came with version 5.4.0 yet? >>> >>> Thanks, >>> Christine > > > >-- >Guillaume Flandin, PhD >Wellcome Trust Centre for Neuroimaging >University College London >12 Queen Square >London WC1N 3BG > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >#!make -f ># ># @(#)Makefile 2.16 John Ashburner 03/05/12 ># Note that changes have been made outside SCCS ># $Id$ ># >#################################################### ########################### ># ># Suggestions for how to make this file a bit more elegant are welcome. So far ># it works under SunOS and Linux (at the FIL) and some Windows systems ># ># $Log$ ># >#################################################### ########################### > >#################################################### ########################### ># Default make >#################################################### ########################### >unknown: > @ make `uname` >tidy: > @ make clean.`uname` > >#################################################### ########################### ># Architecture specific makes >#################################################### ########################### > >MEX = mex -O >CC = cc ># mex output object suffix >MOSUF = o >CHMODIT = chmod 644 >RANLIB = >ADDED_OBS= >ADDED_MEX= > >SunOS: > make all SUF=mexsol CC="cc -xO5" MEX="mex COPTIMFLAGS=-xO5" >Linux: > make all SUF=mexglx CC="gcc -O3 -funroll-loops" MEX="mex COPTIMFLAGS='-O3 -funroll-loops'" >Linux.5: > make all SUF=mexlx CC="gcc -O3 -funroll-loops" MEX="mex COPTIMFLAGS='-O3 -funroll-loops'" >HP-UX: > make all SUF=mexhp7 CC="cc -O +z -Ae +DAportable" MEX="mex COPTIMFLAGS=-O" >IRIX: > make all SUF=mexsg CC="cc -O -mips2" MEX="mex" >IRIX64: > make all SUF=mexsg64 CC="cc -O -mips4 -64" MEX="mex" >AIX: > make all SUF=mexrs6 >OSF1: > make all SUF=mexaxp >MAC: > make all SUF=mexmac RANLIB="ranlib spm_vol_utils.mexmac.a" > >Linux.A64: ># The '-fPIC' option is nexessary to allow the linking proces to complete. ># '-march=x86-64' provides generic optimisations for both Opteron and 64bit Xeon. ># If the code is running on a 64bit Xeon you can change '-march=x86-64' to ># '-march=nocona', when running on an Opteron, change it to '- march=opteron'. ># Also possibly use '-march=k8' for 64 bit Athlon. > make all SUF=mexa64 CC="gcc -O3 -funroll-loops -fPIC -march=x86- 64 -mfpmath=sse"\ > MEX="mex COPTIMFLAGS='-O3 -funroll-loops -fPIC -march=x86- 64 -mfpmath=sse'" > >#windows: ># make all SUF=dll MOSUF=obj CHMODIT="echo > null" ADDED_OBS=win32mmap.dll.o ADDED_MEX=spm_win32utils.dll >windows: ># Consider adding either of the following, depending on your platform: ># -march=pentium3 ># -march=pentium4 > make all SUF=dll CC="gcc -mno-cygwin -O3 -funroll-loops -fomit- frame-pointer -march=pentium4 -mfpmath=sse -DSPM_WIN32" MEX="mex.bat - DSPM_WIN32" MOSUF=obj CHMODIT="echo > NUL" ADDED_OBS=win32mmap.dll.o ADDED_MEX=spm_win32utils.dll > >#################################################### ########################### ># Architecture specific cleaning >#################################################### ########################### >clean.SunOS: > make clean SUF=mexsol >clean.Linux: > make clean SUF=mexglx >clean.Linux.5: > make clean SUF=mexlx >clean.Linux.A64: > make clean SUF=mexa64 >clean.HP-UX: > make clean SUF=mexhp7 >clean.IRIX: > make clean SUF=mexsg >clean.IRIX64: > make clean SUF=mexsg64 >clean.AIX: > make clean SUF=mexrs6 >clean.OSF1: > make clean SUF=mexaxp >clean.MAC: > make clean SUF=mexmac >clean.windows: > make clean SUF=dll > >#################################################### ########################### ># Objects to go in the archive and mexfiles >#################################################### ########################### > >SUF = unknown > >OBS = utils_uchar.$(SUF).o utils_short.$(SUF).o utils_int.$(SUF).o \ > utils_schar.$(SUF).o utils_ushort.$(SUF).o utils_uint.$(SUF).o\ > utils_float.$(SUF).o utils_double.$(SUF).o\ > utils_short_s.$(SUF).o utils_int_s.$(SUF).o\ > utils_ushort_s.$(SUF).o utils_uint_s.$(SUF).o\ > utils_float_s.$(SUF).o utils_double_s.$(SUF).o\ > spm_make_lookup.$(SUF).o spm_getdata.$(SUF).o spm_vol_access.$(SUF).o\ > spm_mapping.$(SUF).o $(ADDED_OBS) > >SPMMEX =\ > spm_sample_vol.$(SUF) spm_slice_vol.$(SUF) spm_brainwarp.$(SUF)\ > spm_add.$(SUF) spm_conv_vol.$(SUF) spm_render_vol.$(SUF)\ > spm_global.$(SUF) spm_resels_vol.$(SUF)\ > spm_atranspa.$(SUF) spm_list_files.$(SUF) spm_unlink.$(SUF)\ > spm_krutil.$(SUF) spm_project.$(SUF) spm_hist2.$(SUF) spm_max.$(SUF)\ > spm_clusters.$(SUF) spm_bsplinc.$(SUF) spm_bsplins.$(SUF)\ > spm_bias_mex.$(SUF) spm_dilate.$(SUF) $(ADDED_MEX) > >#################################################### ########################### ># The main ways to run make >#################################################### ########################### > >all: verb.$(SUF) $(SPMMEX) > @ echo "_____________________________________________________________ " > @ echo "" > @ echo " FINISHED" > @ echo "_____________________________________________________________ " > @ echo "" > >very_clean: clean > @ echo "_____________________________________________________________ " > @ echo "" > @ echo " Deleting mex and archive (.a) files" > @ echo "_____________________________________________________________ " > @ echo "" > rm -f $(SPMMEX) spm_vol_utils.$(SUF).a > >clean: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo " Deleting object (.o) files" > @ echo "_____________________________________________________________ " > @ echo "" > rm -f $(OBS) > >archive: spm_vol_utils.$(SUF).a > >#################################################### ########################### ># Compile spm_vol_utils.c with various flags >#################################################### ########################### > >spm_vol_utils.$(SUF).a: $(OBS) > rm -f $@ > ar rcv $@ $(OBS) > $(RANLIB) > @ $(CHMODIT) $@ > >UTILS=spm_vol_utils.c spm_sys_deps.h spm_make_lookup.h spm_getdata.h > >utils_uchar.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_CHAR > @ $(CHMODIT) $@ > >utils_short.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_SHORT > @ $(CHMODIT) $@ > >utils_int.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_INT > @ $(CHMODIT) $@ > >utils_schar.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_CHAR > @ $(CHMODIT) $@ > >utils_ushort.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_SHORT > @ $(CHMODIT) $@ > >utils_uint.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_INT > @ $(CHMODIT) $@ > >utils_float.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_FLOAT > @ $(CHMODIT) $@ > >utils_double.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_DOUBLE > @ $(CHMODIT) $@ > >utils_short_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_SHORT - DSPM_BYTESWAP > @ $(CHMODIT) $@ > >utils_int_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_INT - DSPM_BYTESWAP > @ $(CHMODIT) $@ > >utils_ushort_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_SHORT - DSPM_BYTESWAP > @ $(CHMODIT) $@ > >utils_uint_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_INT - DSPM_BYTESWAP > @ $(CHMODIT) $@ > >utils_float_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_FLOAT -DSPM_BYTESWAP > @ $(CHMODIT) $@ > >utils_double_s.$(SUF).o: $(UTILS) > $(CC) -c -o $@ spm_vol_utils.c -DSPM_DOUBLE -DSPM_BYTESWAP > @ $(CHMODIT) $@ > >#################################################### ########################### ># Compile a few additional C routines for linking >#################################################### ########################### > >%.$(SUF).o : %.c spm_sys_deps.h > $(CC) -c -o $@ $< > @ $(CHMODIT) $@ > >spm_getdata.$(SUF).o: spm_getdata.c spm_sys_deps.h > >spm_vol_access.$(SUF).o: spm_vol_access.c spm_vol_access.h spm_datatypes.h > >spm_make_lookup.$(SUF).o: spm_make_lookup.c spm_sys_deps.h > >spm_getdata.$(SUF).o: spm_getdata.c > >spm_mapping.$(SUF).o: spm_mapping.c spm_sys_deps.h spm_mapping.h spm_datatypes.h > $(MEX) -c spm_mapping.c > mv spm_mapping.$(MOSUF) $@ > @ $(CHMODIT) $@ > >win32mmap.$(SUF).o: win32mmap.c win32mmap.h > $(CC) -c -o $@ win32mmap.c > @ $(CHMODIT) $@ > >#################################################### ########################### ># Compile the mex files themselves >#################################################### ########################### > >%.$(SUF) : %.c spm_sys_deps.h > $(MEX) $< > @ $(CHMODIT) $@ > >spm_add.$(SUF): spm_add.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h > $(MEX) spm_add.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_brainwarp.$(SUF): spm_brainwarp.c spm_vol_utils.$(SUF).a spm_matfuns.c\ > spm_sys_deps.h spm_mapping.h > $(MEX) spm_brainwarp.c spm_vol_utils.$(SUF).a spm_matfuns.c > @ $(CHMODIT) $@ > >spm_bsplinc.$(SUF): spm_bsplinc.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h spm_datatypes.h > $(MEX) spm_bsplinc.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_bsplins.$(SUF): spm_bsplins.c spm_sys_deps.h > $(MEX) spm_bsplins.c > @ $(CHMODIT) $@ > >spm_conv_vol.$(SUF): spm_conv_vol.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h spm_datatypes.h > $(MEX) spm_conv_vol.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_global.$(SUF): spm_global.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h > $(MEX) spm_global.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_atranspa.$(SUF): spm_atranspa.c spm_sys_deps.h > >spm_unlink.$(SUF): spm_unlink.c spm_sys_deps.h > >spm_max.$(SUF): spm_max.c spm_sys_deps.h > >spm_clusters.$(SUF): spm_clusters.c spm_sys_deps.h > >spm_hist2.$(SUF): spm_hist2.c spm_sys_deps.h > >spm_krutil.$(SUF): spm_krutil.c spm_sys_deps.h > >spm_dilate.$(SUF): spm_dilate.c > >spm_list_files.$(SUF): spm_list_files.c spm_sys_deps.h > >spm_project.$(SUF): spm_project.c spm_sys_deps.h > >spm_render_vol.$(SUF): spm_render_vol.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h > $(MEX) spm_render_vol.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_resels_vol.$(SUF): spm_resels_vol.c spm_vol_utils.$(SUF).a\ > spm_sys_deps.h spm_mapping.h > $(MEX) spm_resels_vol.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_sample_vol.$(SUF): spm_sample_vol.c spm_vol_utils.$(SUF).a spm_mapping.h > $(MEX) spm_sample_vol.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_slice_vol.$(SUF): spm_slice_vol.c spm_vol_utils.$(SUF).a spm_mapping.h > $(MEX) spm_slice_vol.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_bias_mex.$(SUF): spm_bias_mex.c spm_vol_utils.$(SUF).a spm_mapping.h > $(MEX) spm_bias_mex.c spm_vol_utils.$(SUF).a > @ $(CHMODIT) $@ > >spm_win32utils.$(SUF): spm_win32utils.c > $(MEX) spm_win32utils.c > @ $(CHMODIT) $@ > >#################################################### ########################### ># Assorted architecture dependent messages >#################################################### ########################### > >verb.unknown: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "PROBLEM: Dont know how to do this." > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexhp7: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "unix compile for hpux cc, and maybe aix cc" > @ echo "" > @ echo "Under HPUX 10.20 with MATLAB 5.2.1 and gcc, you may wish" > @ echo "to modify this Makefile to say something like:" > @ echo ' CC=gcc -O -fpic' > @ echo ' MEX=mex COPTIMFLAGS=-O -f gccopts.sh' > @ echo "where the gccopts.sh file is modified to remove the +z" > @ echo "(which is used with version 9.0 and possibly also 10.0)." > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexsg: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Feedback from users with R10000 O2 and R10000 Indigo2 systems" > @ echo "running IRIX6.5 suggests that the cmex program with Matlab 5.x" > @ echo "compiles with the old 32bit (o32) instruction set (MIPS2) only," > @ echo "while cc by default compiles with the new32 bit (n32 or MIPS4)." > @ echo "Matlab 5.x only likes o32 for O2 R10000 systems." > @ echo "" > @ echo "We also suggest you modify your options file mexopts.sh in" > @ echo 'the sgi section: change LD="ld" to LD="ld -o32"' > @ echo "this tells the linker to use o32 instead of n32." > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexsg64: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "not optimised sgi 64 bit compile for CC" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.dll: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Windows compile with gcc/mingw" > @ echo "see http://www.mrc- cbu.cam.ac.uk/Imaging/gnumex20.html" > @ echo "for instructions about installing gcc/mingw for" > @ echo "compiling Mex files." > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexsol: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Unix compile for Sun cc" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexlx: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Linux compilation (Matlab 5.x) - using gcc" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexglx: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Linux compilation (Matlab 6.x) - using gcc" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexaxp: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "keep your fingers crossed" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexmac: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Unix compile for MacOS X" > @ echo "_____________________________________________________________ " > @ echo "" > >verb.mexa64: > @ echo "_____________________________________________________________ " > @ echo "" > @ echo "Unix compile for Linux A64" > @ echo "_____________________________________________________________ " > @ echo "" > > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From cmuehl at GMAIL.COM Fri Apr 17 15:01:26 2009 From: cmuehl at GMAIL.COM (Christian Muehl) Date: Fri, 17 Apr 2009 15:01:26 +0200 Subject: CfP Workshop on Affective Brain-Computer Interfaces (aBCI '09) Message-ID: -------------------------------------------------------------- Call for Papers -------------------------------------------------------------- Workshop on Affective Brain-Computer Interfaces (held in conjunction with ACII’09) Amsterdam, The Netherlands, 09.09.2009 -------------------------------------------------------------- Overview: ------------ This workshop will explore the advantages and limitations of using neurophysiological signals as a modality for the automatic recognition of affective and cognitive states, as well as the possibilities to use this information about the user state in innovative and adaptive applications. Theme of the workshop: ------------------------------ Recent research efforts in brain-computer interfaces (BCI) show that brain activity can be used as an active/voluntary, or passive/involuntary control modality in man-machine interaction. While active BCI paradigms received a lot of attention in recent years, research on passive approaches to BCI is still lacking concerted activity. However, it has been shown more than once that brain activations can carry information about the affective and cognitive state of a subject, and that the interaction between humans and machines can be aided by the recognition of those user states. To achieve robust passive BCIs, efforts from applied and basic sciences have to be combined. On the one hand, applied fields such as affective computing aim at the development of applications that adapt to changes in the user states and thereby enrich the interaction, leading to a more natural and effective usability. On the other hand, basic research in neuroscience advances our understanding of the neural processes associated with emotions. Furthermore, similar advancements are being made for more cognitive mental states, for example attention, fatigue, and work load, which strongly interact with affective states. We encourage submissions exploring one or more of the following topics: * emotion elicitation and data collection for affective BCI * detection of affective and cognitive states with BCI and other modalities * adaptive interfaces and affective BCI Goal of the workshop: --------------------------- The goal of the workshop is to bring researchers from the communities of brain computer interfacing, affective computing, neuroergonomics, affective and cognitive neuroscience together to present state-of-the-art progress and visions on the various intersections between those disciplines. Paper submissions: ----------------------- Papers should be 8 - 15 pages long and in the format of the CTIT Series Proceedings. They should have a clear relationship to brain-computer interfacing and to one or more of the other topics listed above. Technical papers, as well as survey papers and empirical papers are eligible. The accepted papers will be published in the workshop proceedings (CTIT Series, ISSN Number available). Please submit your papers in PDF format to ABCI at ewi.utwente.nl . Important Dates: --------------------- Paper Submission: 15.06.2009 Acceptance Note: 15.07.2009 Camera-ready versions: 15.08.2009 Further information can be found on the workshop website. Workshop Website: http://hmi.ewi.utwente.nl/abci2009 Email: ABCI at ewi.utwente.nl Programme Chairs: ----------------------- * Brendan Allison, Technical University Graz, Austria * Stephen Dunne, StarLabs Barcelona, Spain * Dirk Heylen, University of Twente, The Netherlands * Anton Nijholt, University of Twente, The Netherlands Local Organizer: ------------------- * Christian Muehl, University of Twente, The Netherlands Programme Committee: ----------------------------- * Egon van den Broek, University of Twente, The Netherlands * Anne-Marie Brouwer, TNO Soesterberg, The Netherlands * Peter Desain, Radboud University Nijmegen, The Netherlands * Stephen Fairclough, John Moores University Liverpool, United Kingdom * Didier Grandjean, University of Geneva, Switzerland * Markus Junghöfer, University Münster, Germany * Jonghwa Kim, University Augsburg, Germany * Gary Garcia Molina, Philips Research Eindhoven, The Netherlands * Ioannis Patras, Queen Mary University of London, United Kingdom * Gert Pfurtscheller, Technical University Graz, Austria * Thierry Pun, University of Geneva, Switzerland ------------------------------------------------------------------------ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From djs32 at BUFFALO.EDU Fri Apr 17 15:15:23 2009 From: djs32 at BUFFALO.EDU (Daniel Stolzberg) Date: Fri, 17 Apr 2009 09:15:23 -0400 Subject: regarding definetrial and preprocessing In-Reply-To: <919266.15252.qm@web95407.mail.in2.yahoo.com> Message-ID: Hello Chintan, Have you set the path to the new directories? File -> Set Path -Dan On Wed, Apr 15, 2009 at 3:48 PM, shah chintan wrote: > Folks, > > I am working on fieldtrip tutorials. I downloaded all the files and > directories from tutorials. Now when I run the scripts, an error occurs > that definetrial and preprocessing functions are undefined. Please help me > in building these functions. > > Best Regards, > > Chintan > > ------------------------------ > Add more friends to your messenger and enjoy! Invite them now. > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Fri Apr 17 19:02:19 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Fri, 17 Apr 2009 22:32:19 +0530 Subject: regarding definetrial and preprocessing Message-ID: Hello Dan, Thank you very much for your reply.  New directories does not contain these functions.  every time I locate to the directories that i downloaded.    Chintan --- On Fri, 17/4/09, Daniel Stolzberg wrote: From: Daniel Stolzberg Subject: Re: [FIELDTRIP] regarding definetrial and preprocessing To: FIELDTRIP at NIC.SURFNET.NL Date: Friday, 17 April, 2009, 6:45 PM Hello Chintan, Have you set the path to the new directories?  File -> Set Path -Dan On Wed, Apr 15, 2009 at 3:48 PM, shah chintan wrote: Folks,   I am working on fieldtrip tutorials.  I downloaded all the files and directories from tutorials.  Now when I run the scripts, an error occurs that definetrial and preprocessing functions are undefined.  Please help me in  building these functions.   Best Regards,   Chintan Add more friends to your messenger and enjoy! Invite them now. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at MAC.COM Fri Apr 17 20:06:18 2009 From: nathanweisz at MAC.COM (Nathan Weisz) Date: Fri, 17 Apr 2009 20:06:18 +0200 Subject: regarding definetrial and preprocessing In-Reply-To: <581826.87029.qm@web95411.mail.in2.yahoo.com> Message-ID: dear chintan, you mean the functions define are not in the folders you downloaded? that sounds weird, but perhaps you have downloaded a release where (theoretically) some problems occured and nobody noticed so far, as most people don't update their fieldtrip folders on a daily basis. however unlikely, try downloading an older fieldtrip version and take another look if you can find those functions. are you sure that you click on the "Save" button when setting the path and not just "Ok"? when you type "path" from the command line, can you find the relevant fieldtrip folders? like others have mentioned before your issue could be more Matlab than fieldtrip related. try to consult some colleague familiar with Matlab. good luck! n On 17.04.2009, at 19:02, shah chintan wrote: > Hello Dan, > Thank you very much for your reply. New directories does not > contain these functions. every time I locate to the directories > that i downloaded. > > Chintan > > --- On Fri, 17/4/09, Daniel Stolzberg wrote: > > From: Daniel Stolzberg > Subject: Re: [FIELDTRIP] regarding definetrial and preprocessing > To: FIELDTRIP at NIC.SURFNET.NL > Date: Friday, 17 April, 2009, 6:45 PM > > Hello Chintan, > > Have you set the path to the new directories? File -> Set Path > > -Dan > > On Wed, Apr 15, 2009 at 3:48 PM, shah chintan > wrote: > Folks, > > I am working on fieldtrip tutorials. I downloaded all the files and > directories from tutorials. Now when I run the scripts, an error > occurs that definetrial and preprocessing functions are undefined. > Please help me in building these functions. > > Best Regards, > > Chintan > > Add more friends to your messenger and enjoy! Invite them now. > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > http://listserv.surfnet.nl/archives/fieldtrip.html > http://www.ru.nl/fcdonders/fieldtrip/ > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > http://listserv.surfnet.nl/archives/fieldtrip.html > http://www.ru.nl/fcdonders/fieldtrip/ > > Add more friends to your messenger and enjoy! Invite them now. > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Fri Apr 17 22:55:12 2009 From: chintan_student at YAHOO.CO.IN (Chintan Shah) Date: Sat, 18 Apr 2009 02:25:12 +0530 Subject: Regarding define trial, preprocessing and reject visual Message-ID: Dear sir, I am really glad with your replies.  I thank you from the bottom of my heart.  I downloaded all the files and directories from the tutorial data. Now none of these directories include the functions like definetrial, preprocessing and reject visual. So when everytime I try to run the tutorial scripts locating matlab to the folder containing downloaded files and directories, I get an error that those functions are undefined.  Please help me to build these functions.   Best Regards,   Chintan Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingrid.nieuwenhuis at DONDERS.RU.NL Sat Apr 18 09:21:11 2009 From: ingrid.nieuwenhuis at DONDERS.RU.NL (Ingrid Nieuwenhuis) Date: Sat, 18 Apr 2009 09:21:11 +0200 Subject: Regarding define trial, preprocessing and reject visual Message-ID: Dear Chintan, Did you download the fieldtrip toolbox? If you go to "download" (http://fieldtrip.fcdonders.nl/download) you can se that you can download the "FieldTrip toolbox" and the "tutorial data". I think you only downloaded the tutorial date (also because you somewhere refer to .mat files and not to .m files). .mat files are files containing the data, .m files are files containing scripts (functions) that together make the toolbox. As said before this is all really basic Matlab knowledge. Hope this solves your problem, Best Ingrid _____ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Chintan Shah Sent: Friday, April 17, 2009 10:55 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] Regarding define trial, preprocessing and reject visual Dear sir, I am really glad with your replies. I thank you from the bottom of my heart. I downloaded all the files and directories from the tutorial data. Now none of these directories include the functions like definetrial, preprocessing and reject visual. So when everytime I try to run the tutorial scripts locating matlab to the folder containing downloaded files and directories, I get an error that those functions are undefined. Please help me to build these functions. Best Regards, Chintan _____ Add more friends to your messenger and enjoy! Invite them now. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lmoranr at GMAIL.COM Sat Apr 18 13:20:15 2009 From: lmoranr at GMAIL.COM (=?ISO-8859-1?Q?Luis_Mor=E1n?=) Date: Sat, 18 Apr 2009 13:20:15 +0200 Subject: Help with dipolesimulation Message-ID: Hi dear Fieldtrippers!! I'm trying to make a dipolesimulation with two dipoles. I need to use different frequencies and phases for each dipole and I don't know very well how to modify the dipolesimulation function. Any advice? Thanks in advance Best regards -- Luis Morán Rodríguez Bioengineering Group Universidad Politecnica Madrid ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Sun Apr 19 15:15:30 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Sun, 19 Apr 2009 14:15:30 +0100 Subject: Help with dipolesimulation In-Reply-To: <52b4c8f20904180420x74d16065l77baa5009993abe9@mail.gmail.com> Message-ID: Dear Luis, I guess that the desired functionality is already there, the only thing which you have to do is specifying your input configuration meaningfully. The most relevant line is line 215, which states (more or less) trial = lf * dipmom * dipsignal; lf contains the leadfield (forward model) for the dipoles at the positions in cfg.dip.pos, and has dimensionality Nchan x (Ndipolex3), so it is a concatenation (in the columns) of the single position's leadfields. dipsignal is an NdipolexNtime matrix containing the dipoles' time series. For the matrix product to work, dipmom should be of dimensionaity (Ndipolex3)xNdipole (right?). This is the key to the solution to your problem: cfg.dip.mom should be something like [orix1 0;oriy1 0; oriz1 0;0 orix2;0 oriy2;0 oriz2], with ori(xyz)(1/2) specifying the moments of your dipoles. I hope this helps, Jan-Mathijs On Apr 18, 2009, at 12:20 PM, Luis Morán wrote: > Hi dear Fieldtrippers!! > > I'm trying to make a dipolesimulation with two dipoles. I need to > use different frequencies and phases for each dipole and I don't > know very well how to modify the dipolesimulation function. > > Any advice? > > Thanks in advance > > Best regards > -- > Luis Morán Rodríguez > > Bioengineering Group > Universidad Politecnica Madrid > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From lmoranr at GMAIL.COM Sun Apr 19 19:22:20 2009 From: lmoranr at GMAIL.COM (=?ISO-8859-1?Q?Luis_Mor=E1n?=) Date: Sun, 19 Apr 2009 19:22:20 +0200 Subject: Help with dipolesimulation In-Reply-To: <4AA43C77-0BA6-40DC-B71C-91BF0AE3BCEE@psy.gla.ac.uk> Message-ID: But that doesn't solve my problem. I've completed the simulation with 2 dipoles but using the same frequencies and phases. What I need is use a different frequency in each dipole As I understand the dipolesimulation function at 'cfg.frequency' we can specify only a value Any other advice? Thanks a lot in advance 2009/4/19 jan-mathijs schoffelen > Dear Luis, > > I guess that the desired functionality is already there, the only thing > which you have to do is specifying your input configuration meaningfully. > The most relevant line is line 215, which states (more or less) trial = lf > * dipmom * dipsignal; > > lf contains the leadfield (forward model) for the dipoles at the positions > in cfg.dip.pos, and has dimensionality Nchan x (Ndipolex3), so it is a > concatenation (in the columns) of the single position's leadfields. > dipsignal is an NdipolexNtime matrix containing the dipoles' time series. > For the matrix product to work, dipmom should be of dimensionaity > (Ndipolex3)xNdipole (right?). This is the key to the solution to your > problem: > > cfg.dip.mom should be something like [orix1 0;oriy1 0; oriz1 0;0 orix2;0 > oriy2;0 oriz2], with ori(xyz)(1/2) specifying the moments of your dipoles. > > I hope this helps, > > Jan-Mathijs > > > > On Apr 18, 2009, at 12:20 PM, Luis Morán wrote: > > Hi dear Fieldtrippers!! >> >> I'm trying to make a dipolesimulation with two dipoles. I need to use >> different frequencies and phases for each dipole and I don't know very well >> how to modify the dipolesimulation function. >> >> Any advice? >> >> Thanks in advance >> >> Best regards >> -- >> Luis Morán Rodríguez >> >> Bioengineering Group >> Universidad Politecnica Madrid >> ---------------------------------- >> >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and >> EEG analysis. >> >> http://listserv.surfnet.nl/archives/fieldtrip.html >> >> http://www.ru.nl/fcdonders/fieldtrip/ >> >> > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > -- Luis Morán Rodríguez Altentic lmoran at altentic.com ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sklein at BERKELEY.EDU Sun Apr 19 19:46:50 2009 From: sklein at BERKELEY.EDU (Stanley Klein) Date: Sun, 19 Apr 2009 10:46:50 -0700 Subject: Help with dipolesimulation In-Reply-To: <9016c9f10904191044n247312c0t7e231c9356d10e36@mail.gmail.com> Message-ID: Luis, Phase doesn't make much sense if frequencies are different. In your simulation are you doing stimulation with two frequencies (SSVEP)? If so then you can do the simulation with two dipoles each with two frequencies. If you aren't doing stimulation then I'd think you'd just want to choose one frequency (say with an octave banwidth) for doing your source localization. Does Fieldtrip have good tools for doing that sort of localization? Stan On Sun, Apr 19, 2009 at 10:22 AM, Luis Morán wrote: > But that doesn't solve my problem. I've completed the simulation with 2 > dipoles but using the same frequencies and phases. What I need is use a > different frequency in each dipole > > As I understand the dipolesimulation function at 'cfg.frequency' we can > specify only a value > > Any other advice? > > Thanks a lot in advance > > > 2009/4/19 jan-mathijs schoffelen > > Dear Luis, >> >> I guess that the desired functionality is already there, the only thing >> which you have to do is specifying your input configuration meaningfully. >> The most relevant line is line 215, which states (more or less) trial = lf >> * dipmom * dipsignal; >> >> lf contains the leadfield (forward model) for the dipoles at the positions >> in cfg.dip.pos, and has dimensionality Nchan x (Ndipolex3), so it is a >> concatenation (in the columns) of the single position's leadfields. >> dipsignal is an NdipolexNtime matrix containing the dipoles' time series. >> For the matrix product to work, dipmom should be of dimensionaity >> (Ndipolex3)xNdipole (right?). This is the key to the solution to your >> problem: >> >> cfg.dip.mom should be something like [orix1 0;oriy1 0; oriz1 0;0 orix2;0 >> oriy2;0 oriz2], with ori(xyz)(1/2) specifying the moments of your dipoles. >> >> I hope this helps, >> >> Jan-Mathijs >> >> >> >> On Apr 18, 2009, at 12:20 PM, Luis Morán wrote: >> >> Hi dear Fieldtrippers!! >>> >>> I'm trying to make a dipolesimulation with two dipoles. I need to use >>> different frequencies and phases for each dipole and I don't know very well >>> how to modify the dipolesimulation function. >>> >>> Any advice? >>> >>> Thanks in advance >>> >>> Best regards >>> -- >>> Luis Morán Rodríguez >>> >>> Bioengineering Group >>> Universidad Politecnica Madrid >>> ---------------------------------- >>> >>> The aim of this list is to facilitate the discussion between users of the >>> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and >>> EEG analysis. >>> >>> http://listserv.surfnet.nl/archives/fieldtrip.html >>> >>> http://www.ru.nl/fcdonders/fieldtrip/ >>> >>> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/neuroimaging/fieldtrip. >> > > > > -- > Luis Morán Rodríguez > > Altentic > > lmoran at altentic.com > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.litvak at ION.UCL.AC.UK Mon Apr 20 01:25:00 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Mon, 20 Apr 2009 00:25:00 +0100 Subject: Help with dipolesimulation In-Reply-To: <9016c9f10904191046i974d987x4fbba9b311ed4525@mail.gmail.com> Message-ID: Dear Luis, What Jan-Mathijs was saying is that you can use the dipolesimulation function to project any arbitrary source waveform to the sensors. There are some limited tools in the function to create such a waveform on the fly (cfg.frequency) but a much more flexible way would be to create the waveforms in your own script using Matlab tools and then just use dipolesimulation to project them (with cfg.dip.mom as JM explained). Also since the summation of sources is linear, you can run dipolesimulation several times with different inputs and then add the resulting data. You can use freqsimulation function for generating your source waveforms or use your own code. Stanley is partially right that phase locking only makes sense for the same frequency (although there might be more complex relations having to do with phase across frequencies), but that's another issue. Large part of Fieldtrip is about localizing oscillatory activity. That's exactly what beamforming is for, particularly DICS. Best, Vladimir On Sun, Apr 19, 2009 at 6:46 PM, Stanley Klein wrote: > Luis, > Phase doesn't make much sense if frequencies are different. > In your simulation are you doing stimulation with two frequencies (SSVEP)? > If so then you can do the simulation with two dipoles each with two > frequencies. If you aren't doing stimulation then I'd think you'd just want > to choose one frequency (say with an octave banwidth) for doing your source > localization. > > Does Fieldtrip have good tools for doing that sort of localization? > Stan > > On Sun, Apr 19, 2009 at 10:22 AM, Luis Morán wrote: >> >> But that doesn't solve my problem.  I've completed the simulation with 2 >> dipoles but using the same frequencies and phases. What I need is use a >> different frequency in each dipole >> >> As I understand the dipolesimulation function at 'cfg.frequency' we can >> specify only a value >> >> Any other advice? >> >> Thanks a lot in advance >> >> >> 2009/4/19 jan-mathijs schoffelen >>> >>> Dear Luis, >>> >>> I guess that the desired functionality is already there, the only thing >>> which you have to do is specifying your input configuration meaningfully. >>> The most relevant line is line 215, which states (more or less) trial = >>> lf * dipmom * dipsignal; >>> >>> lf contains the leadfield (forward model) for the dipoles at the >>> positions in cfg.dip.pos, and has dimensionality Nchan x (Ndipolex3), so it >>> is a concatenation (in the columns) of the single position's leadfields. >>> dipsignal is an NdipolexNtime matrix containing the dipoles' time series. >>> For the matrix product to work, dipmom should be of dimensionaity >>> (Ndipolex3)xNdipole (right?). This is the key to the solution to your >>> problem: >>> >>> cfg.dip.mom should be something like  [orix1 0;oriy1 0; oriz1 0;0 orix2;0 >>> oriy2;0 oriz2], with ori(xyz)(1/2) specifying the moments of your dipoles. >>> >>> I hope this helps, >>> >>> Jan-Mathijs >>> >>> >>> On Apr 18, 2009, at 12:20 PM, Luis Morán wrote: >>> >>>> Hi dear Fieldtrippers!! >>>> >>>> I'm trying to make a dipolesimulation with two dipoles. I need to use >>>> different frequencies and phases for each dipole and I don't know very well >>>> how to modify the dipolesimulation function. >>>> >>>> Any advice? >>>> >>>> Thanks in advance >>>> >>>> Best regards >>>> -- >>>> Luis Morán Rodríguez >>>> >>>> Bioengineering Group >>>> Universidad Politecnica Madrid >>>> ---------------------------------- >>>> >>>> The aim of this list is to facilitate the discussion between users of >>>> the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG >>>> and EEG analysis. >>>> >>>> http://listserv.surfnet.nl/archives/fieldtrip.html >>>> >>>> http://www.ru.nl/fcdonders/fieldtrip/ >>>> >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users of the >>> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG >>> and EEG analysis. See also >>> http://listserv.surfnet.nl/archives/fieldtrip.html and >>> http://www.ru.nl/neuroimaging/fieldtrip. >> >> >> >> -- >> Luis Morán Rodríguez >> >> Altentic >> >> lmoran at altentic.com >> >> ---------------------------------- >> >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and >> EEG analysis. >> >> http://listserv.surfnet.nl/archives/fieldtrip.html >> >> http://www.ru.nl/fcdonders/fieldtrip/ > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bleichner.martin at GMAIL.COM Mon Apr 20 11:24:00 2009 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Mon, 20 Apr 2009 11:24:00 +0200 Subject: Reconstructing signal form powerspctrm Message-ID: Hi there, is there a function in fieldtrip which allows to reconstruct the signal from the powspctrm? Thanks a lot best, Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.maris at DONDERS.RU.NL Mon Apr 20 11:44:01 2009 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Mon, 20 Apr 2009 11:44:01 +0200 Subject: Reconstructing signal form powerspctrm In-Reply-To: Message-ID: Hi Martin, is there a function in fieldtrip which allows to reconstruct the signal from the powspctrm? Let me answer this question, to take away some load from the shoulders of Jan-Mathijs, whos is becoming the prime signal processing/source reconstruction expert on this discussion list. The answer is that such a function does not exist. In fact, what you ask is not possible. It is possible to reconstruct a signal from a Fourier transform (using the inverse Fourier transform), but it is not possible to reconstruct a signal from the squared amplitude of the Fourier transform (which is the power spectrum - or at least the most common estimate of the power spectrum). In the power spectrum the phase information is lost, and therefore you cannot reconstruct the signal. Good luck, Eric Thanks a lot best, Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingrid.nieuwenhuis at DONDERS.RU.NL Mon Apr 20 13:24:43 2009 From: ingrid.nieuwenhuis at DONDERS.RU.NL (Ingrid Nieuwenhuis) Date: Mon, 20 Apr 2009 13:24:43 +0200 Subject: Plot ECoG-Electrodes In-Reply-To: <7A52A42D-A57D-4714-9D19-E35E396C7499@gmail.com> Message-ID: Dear Julian, Do you mean that you would like to plot the outcome from timelock or freqanalysis on the brain, or do you just want to plot the electrodes as dots or something on the brain? And do you want to plot it on an MRI (method slice, or ortho), or on the surface of the brain (method surface). There is not standard something implemented in FieldTrip for plotting ECoG data, but if you describe more in detail what you want, we could think along. There is for instance the possibility to make your own layout, based on the electrode positions, so that there can be interpolated between the electrode positions. And also important to know, do you want to plot it for a single subject, or do you have multiple subjects in MNI normalized coordinates? Best Ingrid _____ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Julian Keil Sent: Wednesday, April 15, 2009 5:27 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] Plot ECoG-Electrodes Hello, we have recently begun to work with ECoG data. Now we would like to plot results from timelock and freqanalysis. Is there any possibility to plot the (known) electrode position onto the brain using sourceplot? Thanks a lot Julian Dipl. Psych. Julian Keil OBOB-Lab University of Konstanz Department of Psychology P.O. Box D23 78457 Konstanz Germany Tel: ++49 - (0)7531 - 88 42 50 Fax: ++49 - (0)7531 - 88 28 91 Email: julian.keil at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From megjim1 at GMAIL.COM Mon Apr 20 20:32:34 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Mon, 20 Apr 2009 20:32:34 +0200 Subject: about ICA w/o EEGLAB Message-ID: Dear all, I'm trying to remove cardiac interferences from my MEG signal (gradiometer) channels before doing wavelet analysis. This seems necessary because, when looking at each epoch, the wavelet power @ 10-40Hz are dominated by cardiac interference, and that's the bandwidth of interest. I see some Fieldtrip example script utilizing ICA of EEGLAB to remove cardiac interference. However, someone told me that it can be done in Fieldtrip w/o using EEGLAB. Is this true? If so, I'd appreciate it very much if anyone can send me the code, :) Thanks a lot, Jim ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Mon Apr 20 22:33:59 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Mon, 20 Apr 2009 21:33:59 +0100 Subject: about ICA w/o EEGLAB In-Reply-To: Message-ID: Dear Jim, I don't know whether I understand your question correctly, but Fieldtrip can do it 'without' a full download of EEGLAB, because the necessary ICA-routines are included in fieldtrip's download (and are located in the subfolder external/eeglab/... This means that your mystery someone was right ;o) Cheers, Jan-Mathijs On Apr 20, 2009, at 7:32 PM, Jim Li wrote: > Dear all, > > I'm trying to remove cardiac interferences from my MEG signal > (gradiometer) > channels before doing wavelet analysis. This seems necessary > because, when > looking at each epoch, the wavelet power @ 10-40Hz are dominated by > cardiac interference, and that's the bandwidth of interest. I see > some Fieldtrip > example script utilizing ICA of EEGLAB to remove cardiac interference. > However, someone told me that it can be done in Fieldtrip w/o using > EEGLAB. > Is this true? If so, I'd appreciate it very much if anyone can send > me the > code, :) > > Thanks a lot, > > Jim > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Mon Apr 20 23:13:13 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Mon, 20 Apr 2009 23:13:13 +0200 Subject: about ICA w/o EEGLAB Message-ID: Dear Jan-Mathijs, Thanks a lot for your answer. I see why my "componentanalysis" didn't work w/o downloading EEGLAB now: As users of a 4D system, I'm avoiding your new updated version of read_4d_hdr by sticking to some old (Dec. 2008) version of Fieldtrip, simply because it's been working fine and I'm lazy. But apparently there's no "external/eeglab" subfolder in those old versions (yes, I have several Dec 08 versions). That's why I had to download EEGLAB to get it to work. I wonder since when did you add the subfolder to Fieldtrip? Anyway, I guess it's time to embrace the new Fieldtrip versions and learn the new way to read 4D data. Thanks a lot for your help, :) Jim On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen wrote: >Dear Jim, > >I don't know whether I understand your question correctly, but >Fieldtrip can do it 'without' a full download of EEGLAB, because the >necessary ICA-routines are included in fieldtrip's download (and are >located in the subfolder external/eeglab/... This means that your >mystery someone was right ;o) > >Cheers, >Jan-Mathijs > >On Apr 20, 2009, at 7:32 PM, Jim Li wrote: > >> Dear all, >> >> I'm trying to remove cardiac interferences from my MEG signal >> (gradiometer) >> channels before doing wavelet analysis. This seems necessary >> because, when >> looking at each epoch, the wavelet power @ 10-40Hz are dominated by >> cardiac interference, and that's the bandwidth of interest. I see >> some Fieldtrip >> example script utilizing ICA of EEGLAB to remove cardiac interference. >> However, someone told me that it can be done in Fieldtrip w/o using >> EEGLAB. >> Is this true? If so, I'd appreciate it very much if anyone can send >> me the >> code, :) >> >> Thanks a lot, >> >> Jim >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Mon Apr 20 23:43:18 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Mon, 20 Apr 2009 22:43:18 +0100 Subject: about ICA w/o EEGLAB In-Reply-To: Message-ID: Dear Jim, I'd be happy to try and sort out problems with respect to my intended improvement of read_4d_hdr, because I assume there were some problems initially? It was kind of a bold commit into fieldtrip, I admit that, because I wasn't sure what this would lead to. My intention was partly to spark the involvement of 4D MEG users at other sites so that we could jointly improve the robustness of the code. So far all seems to work well for the Glaswegian 248-magnetometer site, but I am pretty sure this is not the case for all 4D-systems roaming the face of the earth... I would greatly appreciate if you try the most recent fieldtrip version on your data and provide me with feedback and possibly suggestions for improvement of the code. Cheers, Jan-Mathijs On Apr 20, 2009, at 10:13 PM, Jim Li wrote: > Dear Jan-Mathijs, > > Thanks a lot for your answer. I see why my "componentanalysis" > didn't work > w/o downloading EEGLAB now: > > As users of a 4D system, I'm avoiding your new updated version of > read_4d_hdr by sticking to some old (Dec. 2008) version of > Fieldtrip, simply > because it's been working fine and I'm lazy. But apparently there's > no "external/eeglab" subfolder in those old versions (yes, I have > several Dec > 08 versions). That's why I had to download EEGLAB to get it to work. I > wonder since when did you add the subfolder to Fieldtrip? > > Anyway, I guess it's time to embrace the new Fieldtrip versions and > learn the > new way to read 4D data. > > Thanks a lot for your help, :) > > Jim > > > On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen > wrote: > >> Dear Jim, >> >> I don't know whether I understand your question correctly, but >> Fieldtrip can do it 'without' a full download of EEGLAB, because the >> necessary ICA-routines are included in fieldtrip's download (and are >> located in the subfolder external/eeglab/... This means that your >> mystery someone was right ;o) >> >> Cheers, >> Jan-Mathijs >> >> On Apr 20, 2009, at 7:32 PM, Jim Li wrote: >> >>> Dear all, >>> >>> I'm trying to remove cardiac interferences from my MEG signal >>> (gradiometer) >>> channels before doing wavelet analysis. This seems necessary >>> because, when >>> looking at each epoch, the wavelet power @ 10-40Hz are dominated by >>> cardiac interference, and that's the bandwidth of interest. I see >>> some Fieldtrip >>> example script utilizing ICA of EEGLAB to remove cardiac >>> interference. >>> However, someone told me that it can be done in Fieldtrip w/o using >>> EEGLAB. >>> Is this true? If so, I'd appreciate it very much if anyone can send >>> me the >>> code, :) >>> >>> Thanks a lot, >>> >>> Jim >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users >>> of the FieldTrip toolbox, to share experiences and to discuss new >>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the > FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and > EEG analysis. See also http://listserv.surfnet.nl/archives/ > fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From julian.keil at GMAIL.COM Tue Apr 21 09:07:52 2009 From: julian.keil at GMAIL.COM (Julian Keil) Date: Tue, 21 Apr 2009 09:07:52 +0200 Subject: about ICA w/o EEGLAB In-Reply-To: <87D90E00-9069-4600-BD2D-C609E742A906@psy.gla.ac.uk> Message-ID: Dear Jan, the read_4d_hdr also works quite nicely for the Konstanz 148- magnetometer site as far as I can tell. I currently use the 2009-03-22 version of fieldtrip. Greetings Julian Am 20.04.2009 um 23:43 schrieb jan-mathijs schoffelen: > Dear Jim, > > I'd be happy to try and sort out problems with respect to my > intended improvement of read_4d_hdr, because I assume there were > some problems initially? It was kind of a bold commit into > fieldtrip, I admit that, because I wasn't sure what this would lead > to. My intention was partly to spark the involvement of 4D MEG users > at other sites so that we could jointly improve the robustness of > the code. So far all seems to work well for the Glaswegian 248- > magnetometer site, but I am pretty sure this is not the case for all > 4D-systems roaming the face of the earth... I would greatly > appreciate if you try the most recent fieldtrip version on your data > and provide me with feedback and possibly suggestions for > improvement of the code. > > Cheers, > > Jan-Mathijs > > > On Apr 20, 2009, at 10:13 PM, Jim Li wrote: > >> Dear Jan-Mathijs, >> >> Thanks a lot for your answer. I see why my "componentanalysis" >> didn't work >> w/o downloading EEGLAB now: >> >> As users of a 4D system, I'm avoiding your new updated version of >> read_4d_hdr by sticking to some old (Dec. 2008) version of >> Fieldtrip, simply >> because it's been working fine and I'm lazy. But apparently there's >> no "external/eeglab" subfolder in those old versions (yes, I have >> several Dec >> 08 versions). That's why I had to download EEGLAB to get it to >> work. I >> wonder since when did you add the subfolder to Fieldtrip? >> >> Anyway, I guess it's time to embrace the new Fieldtrip versions and >> learn the >> new way to read 4D data. >> >> Thanks a lot for your help, :) >> >> Jim >> >> >> On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen >> wrote: >> >>> Dear Jim, >>> >>> I don't know whether I understand your question correctly, but >>> Fieldtrip can do it 'without' a full download of EEGLAB, because the >>> necessary ICA-routines are included in fieldtrip's download (and are >>> located in the subfolder external/eeglab/... This means that your >>> mystery someone was right ;o) >>> >>> Cheers, >>> Jan-Mathijs >>> >>> On Apr 20, 2009, at 7:32 PM, Jim Li wrote: >>> >>>> Dear all, >>>> >>>> I'm trying to remove cardiac interferences from my MEG signal >>>> (gradiometer) >>>> channels before doing wavelet analysis. This seems necessary >>>> because, when >>>> looking at each epoch, the wavelet power @ 10-40Hz are dominated by >>>> cardiac interference, and that's the bandwidth of interest. I see >>>> some Fieldtrip >>>> example script utilizing ICA of EEGLAB to remove cardiac >>>> interference. >>>> However, someone told me that it can be done in Fieldtrip w/o using >>>> EEGLAB. >>>> Is this true? If so, I'd appreciate it very much if anyone can send >>>> me the >>>> code, :) >>>> >>>> Thanks a lot, >>>> >>>> Jim >>>> >>>> ---------------------------------- >>>> The aim of this list is to facilitate the discussion between users >>>> of the FieldTrip toolbox, to share experiences and to discuss new >>>> ideas for MEG and EEG analysis. See also http:// >>>> listserv.surfnet.nl/ >>>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/ >>>> fieldtrip. >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users >>> of the >> FieldTrip toolbox, to share experiences and to discuss new ideas >> for MEG and >> EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html >> and >> http://www.ru.nl/neuroimaging/fieldtrip. >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html >> and http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Tue Apr 21 10:22:05 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Tue, 21 Apr 2009 09:22:05 +0100 Subject: about ICA w/o EEGLAB In-Reply-To: <4CBC4EEB-7E3A-41A8-B53B-85DDE9BDEEEE@gmail.com> Message-ID: Dear Julian and other 4D-neuroimagers, Thanks for your feedback. There have been some changes in read_4d_hdr bti2grad which might affect performance though, so I would greatly appreciate if you could upgrade to the latest version and see if you are still happy. In a nutshell it boils down to the fact that read_4d_hdr tries to extract the digital weights from the run config-file which were used during acquisition. So far, these weights have not been included in the forward modelling, which is necessary for dipole fitting / source reconstruction. Although I don't expect that the inclusion of the weights (which are a function of the distant reference sensors, and hardly pick up any brain activity to begin with) is going to affect the leadfields to a big extent, not including them is not completely correct. As far as I know (and thanks to Stephan Moratti for pointing it out and Sarang Dalal for some code) there are two versions of the weight- tables which roughly seem to coincide with the type of system: version 1 (number of observations = 1.5: Madrid 148-magnetometer, and most likely also the Konstanz system), and version 2 (number of observations = 1: Glasgow 248-magnetometer). To make a long story short, the version 1 weight table just seems to contain the weights, and no specific list of channel labels facilitating the interpretation of the weights. This is in contrast to the version 2 table, which contains the lists of labels explicitly. Therefore, we would have to guess about the order of the channels and reference channels occurring in the version 1 weight matrix. I'd rather not guess, and prefer to base some hard-coded assumptions on some (pragmatically 1 or 2 ;o) ) observations... This means I would like to compare the list of weights as obtained with read_4d_hdr to the list of weights which the 4D-software should be able to print (I thought the command was something like print_table, or print_config or so). More specifically, given a particular recording in which for example 'supine' weights had been applied, we should compare the 'supine' weight table, to the weights extracted by fieldtrip. In that way we could gain some confidence about the order of the channels. Please note that at the moment no balancing is applied to data containing a 'version 1' weight table, at least if you use a fieldtrip version older than March 26, or more recent than April 2. Yours, Jan-Mathijs On Apr 21, 2009, at 8:07 AM, Julian Keil wrote: > Dear Jan, > > the read_4d_hdr also works quite nicely for the Konstanz 148- > magnetometer site as far as I can tell. > I currently use the 2009-03-22 version of fieldtrip. > > Greetings > > Julian > > Am 20.04.2009 um 23:43 schrieb jan-mathijs schoffelen: > >> Dear Jim, >> >> I'd be happy to try and sort out problems with respect to my >> intended improvement of read_4d_hdr, because I assume there were >> some problems initially? It was kind of a bold commit into >> fieldtrip, I admit that, because I wasn't sure what this would >> lead to. My intention was partly to spark the involvement of 4D >> MEG users at other sites so that we could jointly improve the >> robustness of the code. So far all seems to work well for the >> Glaswegian 248-magnetometer site, but I am pretty sure this is not >> the case for all 4D-systems roaming the face of the earth... I >> would greatly appreciate if you try the most recent fieldtrip >> version on your data and provide me with feedback and possibly >> suggestions for improvement of the code. >> >> Cheers, >> >> Jan-Mathijs >> >> >> On Apr 20, 2009, at 10:13 PM, Jim Li wrote: >> >>> Dear Jan-Mathijs, >>> >>> Thanks a lot for your answer. I see why my "componentanalysis" >>> didn't work >>> w/o downloading EEGLAB now: >>> >>> As users of a 4D system, I'm avoiding your new updated version of >>> read_4d_hdr by sticking to some old (Dec. 2008) version of >>> Fieldtrip, simply >>> because it's been working fine and I'm lazy. But apparently there's >>> no "external/eeglab" subfolder in those old versions (yes, I have >>> several Dec >>> 08 versions). That's why I had to download EEGLAB to get it to >>> work. I >>> wonder since when did you add the subfolder to Fieldtrip? >>> >>> Anyway, I guess it's time to embrace the new Fieldtrip versions >>> and learn the >>> new way to read 4D data. >>> >>> Thanks a lot for your help, :) >>> >>> Jim >>> >>> >>> On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen >>> wrote: >>> >>>> Dear Jim, >>>> >>>> I don't know whether I understand your question correctly, but >>>> Fieldtrip can do it 'without' a full download of EEGLAB, because >>>> the >>>> necessary ICA-routines are included in fieldtrip's download (and >>>> are >>>> located in the subfolder external/eeglab/... This means that your >>>> mystery someone was right ;o) >>>> >>>> Cheers, >>>> Jan-Mathijs >>>> >>>> On Apr 20, 2009, at 7:32 PM, Jim Li wrote: >>>> >>>>> Dear all, >>>>> >>>>> I'm trying to remove cardiac interferences from my MEG signal >>>>> (gradiometer) >>>>> channels before doing wavelet analysis. This seems necessary >>>>> because, when >>>>> looking at each epoch, the wavelet power @ 10-40Hz are >>>>> dominated by >>>>> cardiac interference, and that's the bandwidth of interest. I see >>>>> some Fieldtrip >>>>> example script utilizing ICA of EEGLAB to remove cardiac >>>>> interference. >>>>> However, someone told me that it can be done in Fieldtrip w/o >>>>> using >>>>> EEGLAB. >>>>> Is this true? If so, I'd appreciate it very much if anyone can >>>>> send >>>>> me the >>>>> code, :) >>>>> >>>>> Thanks a lot, >>>>> >>>>> Jim >>>>> >>>>> ---------------------------------- >>>>> The aim of this list is to facilitate the discussion between users >>>>> of the FieldTrip toolbox, to share experiences and to discuss new >>>>> ideas for MEG and EEG analysis. See also http:// >>>>> listserv.surfnet.nl/ >>>>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/ >>>>> fieldtrip. >>>> >>>> ---------------------------------- >>>> The aim of this list is to facilitate the discussion between >>>> users of the >>> FieldTrip toolbox, to share experiences and to discuss new ideas >>> for MEG and >>> EEG analysis. See also http://listserv.surfnet.nl/archives/ >>> fieldtrip.html and >>> http://www.ru.nl/neuroimaging/fieldtrip. >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between >>> users of the FieldTrip toolbox, to share experiences and to >>> discuss new ideas for MEG and EEG analysis. See also http:// >>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >>> neuroimaging/fieldtrip. >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http:// >> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >> neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From amrgermany at YAHOO.COM Tue Apr 21 12:53:04 2009 From: amrgermany at YAHOO.COM (Amr Ayoub) Date: Tue, 21 Apr 2009 10:53:04 +0000 Subject: Reading raw data Message-ID: Dear All, I have raw data that consits of 151 MEG (CTF machine), EOG and EMG channels. The size of each channel is around 15MB. The ERP are time points detected in EEG channels. What is the best way to import the data in order to be preprocessed in FieldTrip? Thanks a lot, Amr ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From amrgermany at YAHOO.COM Tue Apr 21 12:58:41 2009 From: amrgermany at YAHOO.COM (Amr Ayoub) Date: Tue, 21 Apr 2009 10:58:41 +0000 Subject: Reading raw data Message-ID: Dear All, I have raw data that consits of 151 MEG (CTF machine), EOG and EMG channels. The size of each channel is around 15MB. The ERP are time points detected in EEG channels. What is the best way to import the data in order to be preprocessed in FieldTrip? Thanks a lot, Amr ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Wed Apr 22 17:30:24 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Wed, 22 Apr 2009 21:00:24 +0530 Subject: regarding besa to fieldtrip Message-ID: Dear folks,   I just finished with tutorials.  I got some data in besa format.  I have .CNT, .sfp and .foc file format.  Please tell me how to import these files in matlab using fieldtrip functions.   Best Regads,   Chintan Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at MAC.COM Wed Apr 22 17:42:53 2009 From: nathanweisz at MAC.COM (Nathan Weisz) Date: Wed, 22 Apr 2009 17:42:53 +0200 Subject: regarding besa to fieldtrip In-Reply-To: <558191.69376.qm@web95412.mail.in2.yahoo.com> Message-ID: dear chintan, this page is your friend: http://fieldtrip.fcdonders.nl/integrating_with_besa best, nathan On 22.04.2009, at 17:30, shah chintan wrote: > Dear folks, > > I just finished with tutorials. I got some data in besa format. I > have .CNT, .sfp and .foc file format. Please tell me how to import > these files in matlab using fieldtrip functions. > > Best Regads, > > Chintan > > Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! > Edition * Click here! > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From megjim1 at GMAIL.COM Wed Apr 22 18:12:58 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Wed, 22 Apr 2009 18:12:58 +0200 Subject: about biosig folder Message-ID: Dear Jan-Mathijs, Following your recommendation, I downloaded the 041809 Fieldtrip and it reads our data just fine. I'll keep an eye on the outputs as I advance more into the data processing and report suspicious ones, if any. BTW, w/ this new version I get a bunch of annoying messages each time I open MATLAB. What I did is to add this new version of Fieldtrip in MATLAB by clicking "Set Path" and "Add with subfolders...". And the warning messages look like this (just one warning example out of a zillion): ---- Warning: Function C:\Program Files\MATLAB\R2007b\external\fieldtrip-20090418 \external\biosig\private\transpose.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. > In path at 110 In addpath at 89 In startup at 1 In matlabrc at 251 --- All the warning is related to the "fieldtrip-20090418\external\biosig\private\" directory. So, what's the use of this "biosig" folder? Can I just remove it from my "MATLAB search Path" w/o affecting Fieldtrip operations? Thanks, Jim On Tue, 21 Apr 2009 09:22:05 +0100, jan-mathijs schoffelen wrote: >Dear Julian and other 4D-neuroimagers, > >Thanks for your feedback. There have been some changes in read_4d_hdr >bti2grad which might affect performance though, so I would greatly >appreciate if you could upgrade to the latest version and see if you >are still happy. >In a nutshell it boils down to the fact that read_4d_hdr tries to >extract the digital weights from the run config-file which were used >during acquisition. So far, these weights have not been included in >the forward modelling, which is necessary for dipole fitting / source >reconstruction. Although I don't expect that the inclusion of the >weights (which are a function of the distant reference sensors, and >hardly pick up any brain activity to begin with) is going to affect >the leadfields to a big extent, not including them is not completely >correct. >As far as I know (and thanks to Stephan Moratti for pointing it out >and Sarang Dalal for some code) there are two versions of the weight- >tables which roughly seem to coincide with the type of system: >version 1 (number of observations = 1.5: Madrid 148-magnetometer, and >most likely also the Konstanz system), and version 2 (number of >observations = 1: Glasgow 248-magnetometer). To make a long story >short, the version 1 weight table just seems to contain the weights, >and no specific list of channel labels facilitating the >interpretation of the weights. This is in contrast to the version 2 >table, which contains the lists of labels explicitly. Therefore, we >would have to guess about the order of the channels and reference >channels occurring in the version 1 weight matrix. I'd rather not >guess, and prefer to base some hard-coded assumptions on some >(pragmatically 1 or 2 ;o) ) observations... >This means I would like to compare the list of weights as obtained >with read_4d_hdr to the list of weights which the 4D-software should >be able to print (I thought the command was something like >print_table, or print_config or so). More specifically, given a >particular recording in which for example 'supine' weights had been >applied, we should compare the 'supine' weight table, to the weights >extracted by fieldtrip. In that way we could gain some confidence >about the order of the channels. >Please note that at the moment no balancing is applied to data >containing a 'version 1' weight table, at least if you use a >fieldtrip version older than March 26, or more recent than April 2. > >Yours, > >Jan-Mathijs > >On Apr 21, 2009, at 8:07 AM, Julian Keil wrote: > >> Dear Jan, >> >> the read_4d_hdr also works quite nicely for the Konstanz 148- >> magnetometer site as far as I can tell. >> I currently use the 2009-03-22 version of fieldtrip. >> >> Greetings >> >> Julian >> >> Am 20.04.2009 um 23:43 schrieb jan-mathijs schoffelen: >> >>> Dear Jim, >>> >>> I'd be happy to try and sort out problems with respect to my >>> intended improvement of read_4d_hdr, because I assume there were >>> some problems initially? It was kind of a bold commit into >>> fieldtrip, I admit that, because I wasn't sure what this would >>> lead to. My intention was partly to spark the involvement of 4D >>> MEG users at other sites so that we could jointly improve the >>> robustness of the code. So far all seems to work well for the >>> Glaswegian 248-magnetometer site, but I am pretty sure this is not >>> the case for all 4D-systems roaming the face of the earth... I >>> would greatly appreciate if you try the most recent fieldtrip >>> version on your data and provide me with feedback and possibly >>> suggestions for improvement of the code. >>> >>> Cheers, >>> >>> Jan-Mathijs >>> >>> >>> On Apr 20, 2009, at 10:13 PM, Jim Li wrote: >>> >>>> Dear Jan-Mathijs, >>>> >>>> Thanks a lot for your answer. I see why my "componentanalysis" >>>> didn't work >>>> w/o downloading EEGLAB now: >>>> >>>> As users of a 4D system, I'm avoiding your new updated version of >>>> read_4d_hdr by sticking to some old (Dec. 2008) version of >>>> Fieldtrip, simply >>>> because it's been working fine and I'm lazy. But apparently there's >>>> no "external/eeglab" subfolder in those old versions (yes, I have >>>> several Dec >>>> 08 versions). That's why I had to download EEGLAB to get it to >>>> work. I >>>> wonder since when did you add the subfolder to Fieldtrip? >>>> >>>> Anyway, I guess it's time to embrace the new Fieldtrip versions >>>> and learn the >>>> new way to read 4D data. >>>> >>>> Thanks a lot for your help, :) >>>> >>>> Jim >>>> >>>> >>>> On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen >>>> wrote: >>>> >>>>> Dear Jim, >>>>> >>>>> I don't know whether I understand your question correctly, but >>>>> Fieldtrip can do it 'without' a full download of EEGLAB, because >>>>> the >>>>> necessary ICA-routines are included in fieldtrip's download (and >>>>> are >>>>> located in the subfolder external/eeglab/... This means that your >>>>> mystery someone was right ;o) >>>>> >>>>> Cheers, >>>>> Jan-Mathijs >>>>> >>>>> On Apr 20, 2009, at 7:32 PM, Jim Li wrote: >>>>> >>>>>> Dear all, >>>>>> >>>>>> I'm trying to remove cardiac interferences from my MEG signal >>>>>> (gradiometer) >>>>>> channels before doing wavelet analysis. This seems necessary >>>>>> because, when >>>>>> looking at each epoch, the wavelet power @ 10-40Hz are >>>>>> dominated by >>>>>> cardiac interference, and that's the bandwidth of interest. I see >>>>>> some Fieldtrip >>>>>> example script utilizing ICA of EEGLAB to remove cardiac >>>>>> interference. >>>>>> However, someone told me that it can be done in Fieldtrip w/o >>>>>> using >>>>>> EEGLAB. >>>>>> Is this true? If so, I'd appreciate it very much if anyone can >>>>>> send >>>>>> me the >>>>>> code, :) >>>>>> >>>>>> Thanks a lot, >>>>>> >>>>>> Jim >>>>>> >>>>>> ---------------------------------- >>>>>> The aim of this list is to facilitate the discussion between users >>>>>> of the FieldTrip toolbox, to share experiences and to discuss new >>>>>> ideas for MEG and EEG analysis. See also http:// >>>>>> listserv.surfnet.nl/ >>>>>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/ >>>>>> fieldtrip. >>>>> >>>>> ---------------------------------- >>>>> The aim of this list is to facilitate the discussion between >>>>> users of the >>>> FieldTrip toolbox, to share experiences and to discuss new ideas >>>> for MEG and >>>> EEG analysis. See also http://listserv.surfnet.nl/archives/ >>>> fieldtrip.html and >>>> http://www.ru.nl/neuroimaging/fieldtrip. >>>> >>>> ---------------------------------- >>>> The aim of this list is to facilitate the discussion between >>>> users of the FieldTrip toolbox, to share experiences and to >>>> discuss new ideas for MEG and EEG analysis. See also http:// >>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >>>> neuroimaging/fieldtrip. >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users >>> of the FieldTrip toolbox, to share experiences and to discuss new >>> ideas for MEG and EEG analysis. See also http:// >>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >>> neuroimaging/fieldtrip. >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Wed Apr 22 18:23:19 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Wed, 22 Apr 2009 18:23:19 +0200 Subject: Do I need ECG channel to run "artifact_ecg" Message-ID: Dear all, W/ a 041809 Fieldtrip, I tried to run the following lines but got some error (see below). I don't have ECG channel in my data, that's why I use a left-most MEG channel w/ apparent cardiac interferences instead. Any suggestion how to fix the problem? ------------- cfg = []; cfg.trl = data.cfg.previous.trl; cfg.dataset = data.cfg.previous.dataset; cfg.continuous = 'yes' ; cfg.artfctdef.ecg.channel = 'A229'; cfg.artfctdef.ecg.pretim = 0.25; cfg.artfctdef.ecg.psttim = 0.5; cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method cfg.artfctdef.ecg.cutoff = 3; %peak-threshold [cfg, artifact] = artifact_ecg(cfg); current zvalue threshold = 3.000 keep the current value (y/n) ? y ??? Undefined function or variable "labelmlt". Error in ==> channelselection at 344 if findmlt, channel = [channel; labelmlt]; end Error in ==> artifact_ecg at 238 sgn = channelselection(artfctdef.inspect, hdr.label); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From chintan_student at YAHOO.CO.IN Wed Apr 22 18:31:33 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Wed, 22 Apr 2009 22:01:33 +0530 Subject: regarding besa to fieldtrip Message-ID: Dear folks,   I just finished with tutorials.  I got some data in besa format.  I have .CNT, .sfp and .foc file format.  I can process with .sfp format but no clue about the other two. Please tell me how to import these files in matlab using fieldtrip functions.   Best Regads,   Chintan Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition * Click here! ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Thu Apr 23 09:48:07 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Thu, 23 Apr 2009 08:48:07 +0100 Subject: about biosig folder In-Reply-To: Message-ID: Dear Jim, Yes, I suspect that you just can remove the biosig folder from your path. As long as you don't use fieldtrip functionality which depends on functions within the biosig-folder you are fine. Yours, JM On Apr 22, 2009, at 5:12 PM, Jim Li wrote: > Dear Jan-Mathijs, > > Following your recommendation, I downloaded the 041809 Fieldtrip > and it > reads our data just fine. I'll keep an eye on the outputs as I > advance more > into the data processing and report suspicious ones, if any. > > BTW, w/ this new version I get a bunch of annoying messages each > time I > open MATLAB. What I did is to add this new version of Fieldtrip in > MATLAB by > clicking "Set Path" and "Add with subfolders...". And the warning > messages > look like this (just one warning example out of a zillion): > > ---- > Warning: Function C:\Program > Files\MATLAB\R2007b\external\fieldtrip-20090418 > \external\biosig\private\transpose.m > has the same name as a MATLAB builtin. We suggest you rename the > function > to > avoid a potential name conflict. >> In path at 110 > In addpath at 89 > In startup at 1 > In matlabrc at 251 > --- > > All the warning is related to the "fieldtrip-20090418\external > \biosig\private\" > directory. So, what's the use of this "biosig" folder? Can I just > remove it from > my "MATLAB search Path" w/o affecting Fieldtrip operations? > > Thanks, > > Jim > > On Tue, 21 Apr 2009 09:22:05 +0100, jan-mathijs schoffelen > wrote: > >> Dear Julian and other 4D-neuroimagers, >> >> Thanks for your feedback. There have been some changes in read_4d_hdr >> bti2grad which might affect performance though, so I would greatly >> appreciate if you could upgrade to the latest version and see if you >> are still happy. >> In a nutshell it boils down to the fact that read_4d_hdr tries to >> extract the digital weights from the run config-file which were used >> during acquisition. So far, these weights have not been included in >> the forward modelling, which is necessary for dipole fitting / source >> reconstruction. Although I don't expect that the inclusion of the >> weights (which are a function of the distant reference sensors, and >> hardly pick up any brain activity to begin with) is going to affect >> the leadfields to a big extent, not including them is not completely >> correct. >> As far as I know (and thanks to Stephan Moratti for pointing it out >> and Sarang Dalal for some code) there are two versions of the weight- >> tables which roughly seem to coincide with the type of system: >> version 1 (number of observations = 1.5: Madrid 148-magnetometer, and >> most likely also the Konstanz system), and version 2 (number of >> observations = 1: Glasgow 248-magnetometer). To make a long story >> short, the version 1 weight table just seems to contain the weights, >> and no specific list of channel labels facilitating the >> interpretation of the weights. This is in contrast to the version 2 >> table, which contains the lists of labels explicitly. Therefore, we >> would have to guess about the order of the channels and reference >> channels occurring in the version 1 weight matrix. I'd rather not >> guess, and prefer to base some hard-coded assumptions on some >> (pragmatically 1 or 2 ;o) ) observations... >> This means I would like to compare the list of weights as obtained >> with read_4d_hdr to the list of weights which the 4D-software should >> be able to print (I thought the command was something like >> print_table, or print_config or so). More specifically, given a >> particular recording in which for example 'supine' weights had been >> applied, we should compare the 'supine' weight table, to the weights >> extracted by fieldtrip. In that way we could gain some confidence >> about the order of the channels. >> Please note that at the moment no balancing is applied to data >> containing a 'version 1' weight table, at least if you use a >> fieldtrip version older than March 26, or more recent than April 2. >> >> Yours, >> >> Jan-Mathijs >> >> On Apr 21, 2009, at 8:07 AM, Julian Keil wrote: >> >>> Dear Jan, >>> >>> the read_4d_hdr also works quite nicely for the Konstanz 148- >>> magnetometer site as far as I can tell. >>> I currently use the 2009-03-22 version of fieldtrip. >>> >>> Greetings >>> >>> Julian >>> >>> Am 20.04.2009 um 23:43 schrieb jan-mathijs schoffelen: >>> >>>> Dear Jim, >>>> >>>> I'd be happy to try and sort out problems with respect to my >>>> intended improvement of read_4d_hdr, because I assume there were >>>> some problems initially? It was kind of a bold commit into >>>> fieldtrip, I admit that, because I wasn't sure what this would >>>> lead to. My intention was partly to spark the involvement of 4D >>>> MEG users at other sites so that we could jointly improve the >>>> robustness of the code. So far all seems to work well for the >>>> Glaswegian 248-magnetometer site, but I am pretty sure this is not >>>> the case for all 4D-systems roaming the face of the earth... I >>>> would greatly appreciate if you try the most recent fieldtrip >>>> version on your data and provide me with feedback and possibly >>>> suggestions for improvement of the code. >>>> >>>> Cheers, >>>> >>>> Jan-Mathijs >>>> >>>> >>>> On Apr 20, 2009, at 10:13 PM, Jim Li wrote: >>>> >>>>> Dear Jan-Mathijs, >>>>> >>>>> Thanks a lot for your answer. I see why my "componentanalysis" >>>>> didn't work >>>>> w/o downloading EEGLAB now: >>>>> >>>>> As users of a 4D system, I'm avoiding your new updated version of >>>>> read_4d_hdr by sticking to some old (Dec. 2008) version of >>>>> Fieldtrip, simply >>>>> because it's been working fine and I'm lazy. But apparently >>>>> there's >>>>> no "external/eeglab" subfolder in those old versions (yes, I have >>>>> several Dec >>>>> 08 versions). That's why I had to download EEGLAB to get it to >>>>> work. I >>>>> wonder since when did you add the subfolder to Fieldtrip? >>>>> >>>>> Anyway, I guess it's time to embrace the new Fieldtrip versions >>>>> and learn the >>>>> new way to read 4D data. >>>>> >>>>> Thanks a lot for your help, :) >>>>> >>>>> Jim >>>>> >>>>> >>>>> On Mon, 20 Apr 2009 21:33:59 +0100, jan-mathijs schoffelen >>>>> wrote: >>>>> >>>>>> Dear Jim, >>>>>> >>>>>> I don't know whether I understand your question correctly, but >>>>>> Fieldtrip can do it 'without' a full download of EEGLAB, because >>>>>> the >>>>>> necessary ICA-routines are included in fieldtrip's download (and >>>>>> are >>>>>> located in the subfolder external/eeglab/... This means that your >>>>>> mystery someone was right ;o) >>>>>> >>>>>> Cheers, >>>>>> Jan-Mathijs >>>>>> >>>>>> On Apr 20, 2009, at 7:32 PM, Jim Li wrote: >>>>>> >>>>>>> Dear all, >>>>>>> >>>>>>> I'm trying to remove cardiac interferences from my MEG signal >>>>>>> (gradiometer) >>>>>>> channels before doing wavelet analysis. This seems necessary >>>>>>> because, when >>>>>>> looking at each epoch, the wavelet power @ 10-40Hz are >>>>>>> dominated by >>>>>>> cardiac interference, and that's the bandwidth of interest. I >>>>>>> see >>>>>>> some Fieldtrip >>>>>>> example script utilizing ICA of EEGLAB to remove cardiac >>>>>>> interference. >>>>>>> However, someone told me that it can be done in Fieldtrip w/o >>>>>>> using >>>>>>> EEGLAB. >>>>>>> Is this true? If so, I'd appreciate it very much if anyone can >>>>>>> send >>>>>>> me the >>>>>>> code, :) >>>>>>> >>>>>>> Thanks a lot, >>>>>>> >>>>>>> Jim >>>>>>> >>>>>>> ---------------------------------- >>>>>>> The aim of this list is to facilitate the discussion between >>>>>>> users >>>>>>> of the FieldTrip toolbox, to share experiences and to >>>>>>> discuss new >>>>>>> ideas for MEG and EEG analysis. See also http:// >>>>>>> listserv.surfnet.nl/ >>>>>>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/ >>>>>>> fieldtrip. >>>>>> >>>>>> ---------------------------------- >>>>>> The aim of this list is to facilitate the discussion between >>>>>> users of the >>>>> FieldTrip toolbox, to share experiences and to discuss new ideas >>>>> for MEG and >>>>> EEG analysis. See also http://listserv.surfnet.nl/archives/ >>>>> fieldtrip.html and >>>>> http://www.ru.nl/neuroimaging/fieldtrip. >>>>> >>>>> ---------------------------------- >>>>> The aim of this list is to facilitate the discussion between >>>>> users of the FieldTrip toolbox, to share experiences and to >>>>> discuss new ideas for MEG and EEG analysis. See also http:// >>>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >>>>> neuroimaging/fieldtrip. >>>> >>>> ---------------------------------- >>>> The aim of this list is to facilitate the discussion between users >>>> of the FieldTrip toolbox, to share experiences and to discuss new >>>> ideas for MEG and EEG analysis. See also http:// >>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/ >>>> neuroimaging/fieldtrip. >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users >>> of the FieldTrip toolbox, to share experiences and to discuss new >>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >>> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the > FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and > EEG analysis. See also http://listserv.surfnet.nl/archives/ > fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From moratti at MED.UCM.ES Thu Apr 23 09:40:33 2009 From: moratti at MED.UCM.ES (Stephan Moratti) Date: Thu, 23 Apr 2009 09:40:33 +0200 Subject: regarding besa to fieldtrip In-Reply-To: Message-ID: Yo can export your data in BESA to .avr (ASCII) .mul (ASCII multiplexed) and .dat (simple binary, you will also get a header file .generic). With besa2fieldtrip you can read in your data easily, then. best, Stephan -- *Stephan Moratti, PhD/ /**/see also: http://web.me.com/smoratti/ /*Centro de Tecnología Biomédica CBT, Universidad Politécnica de Madrid, en la actualidad (currently at) en el Centro de Magnetoencefalografía Dr. Perez Modrego, Universidad Complutense de Madrid, Faculdad de Medicina, Pabellón 8, Avda. Complutense, s/n, 28040 Madrid, Spain, email: moratti at gbt.tfo.upm.es moratti at med.ucm.es Tel.: +34 91 394 2292 Fax.: +34 91 394 2294 */ /* ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Thu Apr 23 10:00:44 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Thu, 23 Apr 2009 09:00:44 +0100 Subject: Do I need ECG channel to run "artifact_ecg" In-Reply-To: Message-ID: Dear Jim, The reason for your crash is probably related to the fact that the default settings for artifact_ecg have been defined with a ctf-system in mind. Artifact_ecg will provide some feedback as to how the QRS- complex-locked MEG signals look, by picking a subset of channels as defined by cfg.artfctdef.ecg.inspect. By default this is set to all channels named 'MLTxx'. Since in your megsystem the sensors are named 'Axx', fieldtrip cannot make sense out of the default and crashes. Just specify your own (subset of) channel(s) to inspect. Good luck Jan-Mathijs On Apr 22, 2009, at 5:23 PM, Jim Li wrote: > Dear all, > > > W/ a 041809 Fieldtrip, I tried to run the following lines but got > some error (see > below). I don't have ECG channel in my data, that's why I use a > left-most > MEG channel w/ apparent cardiac interferences instead. Any > suggestion how > to fix the problem? > > ------------- > cfg = []; > cfg.trl = data.cfg.previous.trl; > cfg.dataset = data.cfg.previous.dataset; > cfg.continuous = 'yes' ; > cfg.artfctdef.ecg.channel = 'A229'; > cfg.artfctdef.ecg.pretim = 0.25; > cfg.artfctdef.ecg.psttim = 0.5; > cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method > cfg.artfctdef.ecg.cutoff = 3; %peak-threshold > [cfg, artifact] = artifact_ecg(cfg); > > current zvalue threshold = 3.000 > keep the current value (y/n) ? > y > ??? Undefined function or variable "labelmlt". > > Error in ==> channelselection at 344 > if findmlt, channel = [channel; labelmlt]; end > > Error in ==> artifact_ecg at 238 > sgn = channelselection(artfctdef.inspect, hdr.label); > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From A.Stancak at LIVERPOOL.AC.UK Thu Apr 23 10:01:15 2009 From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej) Date: Thu, 23 Apr 2009 09:01:15 +0100 Subject: Do I need ECG channel to run "artifact_ecg" In-Reply-To: Message-ID: Dear Jim-Li, I probably faced the same error message when I was writing my script for ECG artefact removal. I remember to get rid of this error message by putting the ECG channel label into brackets: cfg.artfctdef.ecg.channel = {'A229'}; I hope I have not mislead you as I am a FieldTrip novice, but it is maybe worth trying. Best wishes Andrej Andrej Stancak, PhD. Professor for normal physiology Senior lecturer in psychology School of Psychology Eleanor Rathbone Building Bedford Street South L69 7ZA Liverpool United Kingdom Phone: 0044 0151 7946951 E-mail: a.stancak at liverpool.ac.uk (primary)         stancak at lf3.cuni.cz (secondary) Office hours: Mo 10-12, Wed 10-12 -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jim Li Sent: 22 April 2009 17:23 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] Do I need ECG channel to run "artifact_ecg" Dear all, W/ a 041809 Fieldtrip, I tried to run the following lines but got some error (see below). I don't have ECG channel in my data, that's why I use a left-most MEG channel w/ apparent cardiac interferences instead. Any suggestion how to fix the problem? ------------- cfg = []; cfg.trl = data.cfg.previous.trl; cfg.dataset = data.cfg.previous.dataset; cfg.continuous = 'yes' ; cfg.artfctdef.ecg.channel = 'A229'; cfg.artfctdef.ecg.pretim = 0.25; cfg.artfctdef.ecg.psttim = 0.5; cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method cfg.artfctdef.ecg.cutoff = 3; %peak-threshold [cfg, artifact] = artifact_ecg(cfg); current zvalue threshold = 3.000 keep the current value (y/n) ? y ??? Undefined function or variable "labelmlt". Error in ==> channelselection at 344 if findmlt, channel = [channel; labelmlt]; end Error in ==> artifact_ecg at 238 sgn = channelselection(artfctdef.inspect, hdr.label); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Thu Apr 23 16:25:50 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Thu, 23 Apr 2009 16:25:50 +0200 Subject: Do I need ECG channel to run "artifact_ecg" Message-ID: Dear Andrej, Thanks a lot for your feedback. I tried your recommendation of "cfg.artfctdef.ecg.channel = {'A229'};" but I got the same message. In fact, last night by a little debugging I figured out why the error message occured. And the solution is to simply add this line before doing artifact_ecg: cfg.artfctdef.ecg.inspect = {'A229'}; And that worked beautifully. cheers, Jim On Thu, 23 Apr 2009 09:01:15 +0100, Stancak, Andrej wrote: >Dear Jim-Li, > > I probably faced the same error message when I was writing my script for ECG artefact removal. I remember to get rid of this error message by putting the ECG channel label into brackets: > > cfg.artfctdef.ecg.channel = {'A229'}; > > > I hope I have not mislead you as I am a FieldTrip novice, but it is maybe worth trying. > >Best wishes >Andrej > > > >Andrej Stancak, PhD. >Professor for normal physiology >Senior lecturer in psychology > >School of Psychology >Eleanor Rathbone Building >Bedford Street South >L69 7ZA >Liverpool >United Kingdom > >Phone: 0044 0151 7946951 >E-mail: a.stancak at liverpool.ac.uk (primary) >        stancak at lf3.cuni.cz (secondary) > >Office hours: Mo 10-12, Wed 10-12 > > >-----Original Message----- >From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jim Li >Sent: 22 April 2009 17:23 >To: FIELDTRIP at NIC.SURFNET.NL >Subject: [FIELDTRIP] Do I need ECG channel to run "artifact_ecg" > >Dear all, > > >W/ a 041809 Fieldtrip, I tried to run the following lines but got some error (see >below). I don't have ECG channel in my data, that's why I use a left-most >MEG channel w/ apparent cardiac interferences instead. Any suggestion how >to fix the problem? > >------------- >cfg = []; >cfg.trl = data.cfg.previous.trl; >cfg.dataset = data.cfg.previous.dataset; >cfg.continuous = 'yes' ; >cfg.artfctdef.ecg.channel = 'A229'; >cfg.artfctdef.ecg.pretim = 0.25; >cfg.artfctdef.ecg.psttim = 0.5; >cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method >cfg.artfctdef.ecg.cutoff = 3; %peak-threshold >[cfg, artifact] = artifact_ecg(cfg); > >current zvalue threshold = 3.000 >keep the current value (y/n) ? >y >??? Undefined function or variable "labelmlt". > >Error in ==> channelselection at 344 >if findmlt, channel = [channel; labelmlt]; end > >Error in ==> artifact_ecg at 238 >sgn = channelselection(artfctdef.inspect, hdr.label); > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Thu Apr 23 17:47:53 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Thu, 23 Apr 2009 17:47:53 +0200 Subject: Do I need ECG channel to run "artifact_ecg" Message-ID: Dear Jan-Mathijs, Thanks a lot for your feedback. Last night I did a bit of debugging and found out why the crashed happened. In line 116 of "artifact_ecg" it says: if ~isfield(cfg.artfctdef.ecg,'inspect'),cfg.artfctdef.ecg.inspect = {'MLT' 'MRT'}; end That's the cause of my trouble because 4D's system doesn't have channels names like "MLT", "MRT" . So I fixed te problem by adding this line: cfg.artfctdef.ecg.inspect = {'A229'}; before this line: [cfg, artifact] = artifact_ecg(cfg); And it worked! All these fits into your great suggestion very well. And I'm so happy that I don't need to get an ECG channel before doing cardiac artifact rejection. Jim On Thu, 23 Apr 2009 09:00:44 +0100, jan-mathijs schoffelen wrote: >Dear Jim, > >The reason for your crash is probably related to the fact that the >default settings for artifact_ecg have been defined with a ctf-system >in mind. Artifact_ecg will provide some feedback as to how the QRS- >complex-locked MEG signals look, by picking a subset of channels as >defined by cfg.artfctdef.ecg.inspect. By default this is set to all >channels named 'MLTxx'. Since in your megsystem the sensors are named >'Axx', fieldtrip cannot make sense out of the default and crashes. >Just specify your own (subset of) channel(s) to inspect. > >Good luck > >Jan-Mathijs > > > >On Apr 22, 2009, at 5:23 PM, Jim Li wrote: > >> Dear all, >> >> >> W/ a 041809 Fieldtrip, I tried to run the following lines but got >> some error (see >> below). I don't have ECG channel in my data, that's why I use a >> left-most >> MEG channel w/ apparent cardiac interferences instead. Any >> suggestion how >> to fix the problem? >> >> ------------- >> cfg = []; >> cfg.trl = data.cfg.previous.trl; >> cfg.dataset = data.cfg.previous.dataset; >> cfg.continuous = 'yes' ; >> cfg.artfctdef.ecg.channel = 'A229'; >> cfg.artfctdef.ecg.pretim = 0.25; >> cfg.artfctdef.ecg.psttim = 0.5; >> cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method >> cfg.artfctdef.ecg.cutoff = 3; %peak-threshold >> [cfg, artifact] = artifact_ecg(cfg); >> >> current zvalue threshold = 3.000 >> keep the current value (y/n) ? >> y >> ??? Undefined function or variable "labelmlt". >> >> Error in ==> channelselection at 344 >> if findmlt, channel = [channel; labelmlt]; end >> >> Error in ==> artifact_ecg at 238 >> sgn = channelselection(artfctdef.inspect, hdr.label); >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From cmuehl at GMAIL.COM Thu Apr 23 18:05:27 2009 From: cmuehl at GMAIL.COM (Christian Muehl) Date: Thu, 23 Apr 2009 18:05:27 +0200 Subject: BCI game project in the eNTERFACE 09 workshop Message-ID: Call for participants BCI @ eNTERFACE 09 workshop July 13th - August 7th 2009 Genua, Italy Project on Bain-Computer Interfaces: A multi-player game using neurophysiological sensors For a project on Brain-Computer Interfaces in the context of the eNTERFACE 09 workshop in Genua we are searching for interested people with experience in the areas of signal processing, game design, programming or machine learning. The goal of the project is the development of a multiplayer computer game that uses several innovative input modalities. Neural (EEG) and physiological changes (e.g. ECG, respiration, muscle tension) are used in combination with traditional (mouse, keyboards) input devices to actively and passively control the game dynamics. The game will be a platform for the study of an efficient and natural use of Brain-Computer Interaction and physiological sensors within a gaming environment. More detailed information about that particular project and others can be found here: www.infomus.org/enterface09/projectsTeams.php The eNTERFACE 2009 Workshop is being organized this summer in Genova, Italy, from July 13th to August 7th, 2009. The eNTERFACE Workshops present an opportunity of collaborative research and software development by gathering, in a single place, a team of senior project leaders in multimodal interfaces, PhD students, and (undergraduate) students, to work on a pre-specified list of challenges, for the duration of four weeks. Participants are organized in teams of six to eight, all attached to specific projects. Tutorials and state-of-the art surveys on multimodal interfaces and their design will be given every week by invited experts. Senior researchers, PhD students, or undergraduates interested in participating to the Workshop should send their application by emailing the Organizing Committee at enterface09 at casapaganini.org before April 30, 2009. Please check the workshop website for detailed information on the application proceedure: http://www.infomus.org/enterface09/callForParticipation.php ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From megjim1 at GMAIL.COM Thu Apr 23 18:10:22 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Thu, 23 Apr 2009 18:10:22 +0200 Subject: Do I need ECG channel to run "artifact_ecg" Message-ID: Dear Jan-Mathijs, I continued ICA cardiac-removal processing using the example codes in Fieldtrip website. But I encountered this problem: ---------- cfg = []; cfg.method = 'mtmfft'; cfg.output = 'fourier'; cfg.foilim = [0 100]; cfg.taper = 'hanning'; cfg.pad = 'maxperlen'; freq = freqanalysis(cfg, comp_ecg); the input is component data with 248 components and 248 original channels ??? Error using ==> checkdata at 377 This function requires raw data as input. Error in ==> freqanalysis at 165 data = checkdata(data, 'datatype', 'raw', 'feedback', 'yes', 'hasoffset', 'yes'); ----------------- How to deal w/ it? Thanks, Jim On Thu, 23 Apr 2009 09:00:44 +0100, jan-mathijs schoffelen wrote: >Dear Jim, > >The reason for your crash is probably related to the fact that the >default settings for artifact_ecg have been defined with a ctf-system >in mind. Artifact_ecg will provide some feedback as to how the QRS- >complex-locked MEG signals look, by picking a subset of channels as >defined by cfg.artfctdef.ecg.inspect. By default this is set to all >channels named 'MLTxx'. Since in your megsystem the sensors are named >'Axx', fieldtrip cannot make sense out of the default and crashes. >Just specify your own (subset of) channel(s) to inspect. > >Good luck > >Jan-Mathijs > > > >On Apr 22, 2009, at 5:23 PM, Jim Li wrote: > >> Dear all, >> >> >> W/ a 041809 Fieldtrip, I tried to run the following lines but got >> some error (see >> below). I don't have ECG channel in my data, that's why I use a >> left-most >> MEG channel w/ apparent cardiac interferences instead. Any >> suggestion how >> to fix the problem? >> >> ------------- >> cfg = []; >> cfg.trl = data.cfg.previous.trl; >> cfg.dataset = data.cfg.previous.dataset; >> cfg.continuous = 'yes' ; >> cfg.artfctdef.ecg.channel = 'A229'; >> cfg.artfctdef.ecg.pretim = 0.25; >> cfg.artfctdef.ecg.psttim = 0.5; >> cfg.artfctdef.ecg.method = 'zvalue'; %peak-detection method >> cfg.artfctdef.ecg.cutoff = 3; %peak-threshold >> [cfg, artifact] = artifact_ecg(cfg); >> >> current zvalue threshold = 3.000 >> keep the current value (y/n) ? >> y >> ??? Undefined function or variable "labelmlt". >> >> Error in ==> channelselection at 344 >> if findmlt, channel = [channel; labelmlt]; end >> >> Error in ==> artifact_ecg at 238 >> sgn = channelselection(artfctdef.inspect, hdr.label); >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the FieldTrip toolbox, to share experiences and to discuss new >> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ >> archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > >---------------------------------- >The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From chintan_student at YAHOO.CO.IN Fri Apr 24 04:07:50 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Fri, 24 Apr 2009 07:37:50 +0530 Subject: regarding besa to fieldtrip Message-ID: Dear Jan-Mathijs,   I   Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Fri Apr 24 04:07:51 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Fri, 24 Apr 2009 07:37:51 +0530 Subject: regarding besa to fieldtrip Message-ID: Dear Jan-Mathijs,   I have   Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition http://downloads.yahoo.com/in/firefox/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chintan_student at YAHOO.CO.IN Fri Apr 24 04:10:08 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Fri, 24 Apr 2009 07:40:08 +0530 Subject: regarding besa to fieldtrip Message-ID: Dear Jan-Mathijs,   I have besa format file of .cnt and .foc format.  Pleas tell me how to import in matlab using fieldtrip functions.  besa2fieldtrip is not working here.   Best Regards,   Chintan Explore your hobbies and interests. Go to http://in.promos.yahoo.com/groups/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at MAC.COM Fri Apr 24 07:22:51 2009 From: nathanweisz at MAC.COM (Nathan Weisz) Date: Fri, 24 Apr 2009 07:22:51 +0200 Subject: regarding besa to fieldtrip In-Reply-To: <355853.55433.qm@web95401.mail.in2.yahoo.com> Message-ID: Dear Chintan, haven you read Stephans answer to your question. here it is again: > Yo can export your data in BESA to .avr (ASCII) .mul (ASCII > multiplexed) and .dat (simple binary, you will also get a header > file .generic). With besa2fieldtrip you can read in your data > easily, then. btw, the help comments within the besa2fieldtrip function as well as the description in the tutorial should have been detailed enough to get you going (examples in the tutorial). if you nevertheless encounter problems when running the function then saying "besa2fieldtrip is not working here" is simply not enough to know what's exactly your problem. please show us how you called the function and e.g. the error message you got. this helps us helping you. best, nathan On 24.04.2009, at 04:10, shah chintan wrote: > Dear Jan-Mathijs, > > I have besa format file of .cnt and .foc format. Pleas tell me how > to import in matlab using fieldtrip functions. besa2fieldtrip is > not working here. > > Best Regards, > > Chintan > > Own a website.Get an unlimited package.Pay next to nothing.* Click > here!. > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.litvak at ION.UCL.AC.UK Fri Apr 24 19:12:45 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Fri, 24 Apr 2009 18:12:45 +0100 Subject: Important message for Neuromag users Message-ID: Dear Neuromag users, We recently found a critical bug in the new MNE reader. The grad structure for Neuromag read with the new reader was incorrect and this would affect source analysis and (to a minor extent) topoplotting. The users who used the old meg_pd reader are not affected. If you think you might be affected by the bug you should update your FT to the latest version and re-read all the grads read with the MNE reader until now from the original fif files. Sorry for the inconvenience, Vladimir ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From chintan_student at YAHOO.CO.IN Fri Apr 24 21:57:15 2009 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Sat, 25 Apr 2009 01:27:15 +0530 Subject: Fw: Re: [FIELDTRIP] regarding besa to fieldtrip Message-ID: --- On Sat, 25/4/09, shah chintan wrote: From: shah chintan Subject: Re: [FIELDTRIP] regarding besa to fieldtrip To: nathanweisz at me.com Date: Saturday, 25 April, 2009, 1:25 AM Dear Sir,   Actually I have a data file of .cnt format and I have .sfp file containing the positions of electrodes.  The data file consist of different signals depending on time.  I can import both the file into matlab.  I dont know how to analyse or produce the graphical picture of messes at different time frequency.    Best Regards,   Chintan --- On Fri, 24/4/09, Nathan Weisz wrote: From: Nathan Weisz Subject: Re: [FIELDTRIP] regarding besa to fieldtrip To: FIELDTRIP at NIC.SURFNET.NL Date: Friday, 24 April, 2009, 10:52 AM Dear Chintan, haven you read Stephans answer to your question. here it is again: Yo can export your data in BESA to .avr (ASCII) .mul (ASCII multiplexed) and .dat (simple binary, you will also get a header file .generic). With besa2fieldtrip you can read in your data easily, then. btw, the help comments within the besa2fieldtrip function as well as the description in the tutorial should have been detailed enough to get you going (examples in the tutorial). if you nevertheless encounter problems when running the function then saying "besa2fieldtrip is not working here" is simply not enough to know what's exactly your problem. please show us how you called the function and e.g. the error message you got. this helps us helping you. best, nathan On 24.04.2009, at 04:10, shah chintan wrote: Dear Jan-Mathijs,   I have besa format file of .cnt and .foc format.  Pleas tell me how to import in matlab using fieldtrip functions.  besa2fieldtrip is not working here.   Best Regards,   Chintan Own a website.Get an unlimited package.Pay next to nothing.* Click here!. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ Bollywood news, movie reviews, film trailers and more! Click here. Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From johnston at KIN.UCALGARY.CA Thu Apr 30 18:55:32 2009 From: johnston at KIN.UCALGARY.CA (Jamie Johnston) Date: Thu, 30 Apr 2009 10:55:32 -0600 Subject: problems with coherence tutorial Message-ID: I am trying to run the coherence tutorial on the website. I have downloaded the SubjectCMC.zip folder but there is no dataset called "SubjectCMC.ds" and I keep running into an error running the code. Any suggestions. Thanks, Jamie _______________ Jamie Johnston, Ph.D. Assistant Professor Faculty of Kinesiology University of Calgary 2500 University Dr. NW Calgary, AB T2N 1N4 Phone: +1 (403) 220-3649 Fax: +1 (403) 284-3553 email: johnston at kin.ucalgary.ca website: http://www.kin.ucalgary.ca/wcm/knes/johnston.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.schoffelen at PSY.GLA.AC.UK Thu Apr 30 21:18:55 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Thu, 30 Apr 2009 20:18:55 +0100 Subject: problems with coherence tutorial In-Reply-To: Message-ID: Dear Jamie, I tried to download SubjectCMC.zip and I cannot reproduce your problem. I assume that you properly unzipped the folder? If not, that could explain your problem. The zip file is about 360 megabytes, but once unzipped, SubjectCMC.ds should contain a .meg4-file which should be about 664 Mb. Alternatively, you could skip the preprocessing part and start from "computing the cross-spectral densities". The preprocessed data can be obtained by preprocessing the raw data, or you can directly download the processed data file from the ftp-server. Good luck, Jan-Mathijs On Apr 30, 2009, at 5:55 PM, Jamie Johnston wrote: > I am trying to run the coherence tutorial on the website. I have > downloaded the SubjectCMC.zip folder but there is no dataset called > “SubjectCMC.ds” and I keep running into an error running the code. > Any suggestions. > > Thanks, > > Jamie > > _______________ > Jamie Johnston, Ph.D. > Assistant Professor > Faculty of Kinesiology > University of Calgary > 2500 University Dr. NW > Calgary, AB > T2N 1N4 > Phone: +1 (403) 220-3649 > Fax: +1 (403) 284-3553 > email: johnston at kin.ucalgary.ca > website: http://www.kin.ucalgary.ca/wcm/knes/johnston.html > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From megjim1 at GMAIL.COM Thu Apr 30 21:21:01 2009 From: megjim1 at GMAIL.COM (Jim Li) Date: Thu, 30 Apr 2009 21:21:01 +0200 Subject: color bar Message-ID: Dear FTer: I wonder if anybody can tell me how to get the full color bar when plotting w/ "singleplotTFR" or "multiplotTFR". I ran the following commands: -------- figure cfg = []; cfg.layout = '4D248.lay'; cfg.ylim = [5 30] cfg.interactive = 'yes'; cfg.showlabels = 'yes'; cfg.colorbar = 'yes'; cfg.channel='A2' singleplotTFR(cfg,TF) ----------- But what I get on the right side of the figure is a colorbar w/ only half of the color (usually the cold colors like blue or green), and the numbers on the right side of the colorbar seem to be wrongly placed (see attachment). How can I get all the colors (both hot and cold) displayed in the colorbar? FYI, I controled the values of TF.powspctrm so that, for the channel displayed (A2), all values before time 0 is 3e-25, and all values after time 0 is 1e-25. But the color bar is telling me that the blue should be 2e-25, which is totally wrong! It's as if something happened that moved the whole colorbar up by half of the data range, then cut off the top of it (i.e. the hot colors). In fact, I think Fig 3 of the online tutorial (http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis) probably suffered from the same problem. Thanks, Jim ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: half_colorbar.TIF Type: image/tiff Size: 97550 bytes Desc: not available URL: