From g.flandin at ucl.ac.uk Mon Apr 3 18:36:42 2017 From: g.flandin at ucl.ac.uk (Guillaume Flandin) Date: Mon, 3 Apr 2017 17:36:42 +0100 Subject: [FieldTrip] compiling ft_volumenormalise In-Reply-To: References: Message-ID: <58E27A1A.7080307@ucl.ac.uk> Dear Anne, The way we compile SPM is to use the '-a' flag as you did but with a directory instead of individual files (e.g. '-a', '~/Documents/fieldtrip/'); by doing so, all the files from the specified directory as well as all the files from subdirectories will be included so that you don't have to rely on the automatic file dependency analysis mcc performs. Best regards, Guillaume. On 15/03/17 12:29, Anne Urai wrote: > If anyone encounters the same problem, compilation works if I manually > add a bunch of spm functions (which are not recognised by mcc, probably > because they are in a class definition folder). > > Specifically, including > > '-a', '~/Documents/fieldtrip/external/spm8/spm.m', ... > '-a', '~/Documents/fieldtrip/external/spm8/templates/T1.nii', ... > '-a', '~/Documents/fieldtrip/external/freesurfer/MRIread', ... > '-a', '~/code/Tools/spmbug/dim.m', ... > '-a', '~/code/Tools/spmbug/dtype.m', ... > '-a', '~/code/Tools/spmbug/fname.m', ... > '-a', '~/code/Tools/spmbug/offset.m', ... > '-a', '~/code/Tools/spmbug/scl_slope.m', ... > '-a', '~/code/Tools/spmbug/scl_inter.m', ... > '-a', '~/code/Tools/spmbug/permission.m', ... > '-a', '~/code/Tools/spmbug/niftistruc.m', ... > '-a', '~/code/Tools/spmbug/read_hdr.m', ... > '-a', '~/code/Tools/spmbug/getdict.m', ... > '-a', '~/code/Tools/spmbug/read_extras.m', ... > '-a', '~/code/Tools/spmbug/read_hdr_raw.m', ... > > does the trick. > > Happy compiling, > Anne > > On 1 March 2017 at 19:38, Anne Urai > wrote: > > Hi FieldTrippers, > > I compile my code to run on the supercomputer cluster (without many > matlab licenses), which usually works fine when I do something like: > > /addpath('~/Documents/fieldtrip');/ > /ft_defaults; / > /addpath('~/Documents/fieldtrip/external/spm8');/ > /mcc('-mv', '-N', '-p', 'stats', '-p', 'images', '-p', 'signal', .../ > / '-R', '-nodisplay', '-R', '-singleCompThread', fname);/ > > However, compiling the ft_volumenormalise function gives me some > problems. Specifically, if source is the result of my beamformer > analysis, this code > > / cfg = [];/ > / cfg.parameter = 'pow';/ > / cfg.nonlinear = 'no'; % can warp back to individual/ > / cfg.template = > '/home/aeurai/Documents/fieldtrip/external/spm8/templates/T1.nii';/ > / cfg.write = 'no';/ > / cfg.keepinside = 'no'; % otherwise, > ft_sourcegrandaverage will bug/ > / source = ft_volumenormalise(cfg, source);/ > > works fine when running it within Matlab. However, when I run the > executable after compiling (which completes without error), a > low-level spm function throws the following error: > > /the input is source data with 16777216 brainordinates on a [256 256 > 256] grid/ > /Warning: could not reshape "freq" to the expected dimensions/ > /> In ft_datatype_volume (line 136)/ > /In ft_checkdata (line 350)/ > /In ft_volumenormalise (line 98)/ > /In B6b_sourceContrast_volNormalise (line 57)/ > /Converting the coordinate system from ctf to spm/ > /Undefined function 'fname' for input arguments of type 'struct'/ > /Error in file_array (line 32)/ > /Error in spm_create_vol>create_vol (line 77)/ > /Error in spm_create_vol (line 16)/ > /Error in volumewrite_spm (line 71)/ > /Error in ft_write_mri (line 65)/ > /Error in align_ctf2spm (line 168)/ > /Error in ft_convert_coordsys (line 95)/ > /Error in ft_volumenormalise (line 124)/ > /Error in B6b_sourceContrast_volNormalise (line 57)/ > /MATLAB:UndefinedFunction/ > > I'd be very grateful for hints from anyone who's successfully > compiled the ft_normalise function! Adding the template T1.nii file, > spm8 or freesurfer at compilation does not solve the problem. > Thanks, > > — > Anne E. Urai, MSc > PhD student | Institut für Neurophysiologie und Pathophysiologie > Universitätsklinikum Hamburg-Eppendorf | Martinistrasse 52, 20246 | > Hamburg, Germany > www.anneurai.net / @AnneEUrai > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Guillaume Flandin, PhD Wellcome Trust Centre for Neuroimaging University College London 12 Queen Square London WC1N 3BG From d.painter1 at uq.edu.au Tue Apr 4 03:41:09 2017 From: d.painter1 at uq.edu.au (David Painter) Date: Tue, 4 Apr 2017 01:41:09 +0000 Subject: [FieldTrip] Realtime buffer - possible to spawn multiple buffer threads using non-default values for host and port? In-Reply-To: <1491269842991.43690@uq.edu.au> References: <1491269842991.43690@uq.edu.au> Message-ID: <1491270069170.592@uq.edu.au> Dear Fieldtrippers, I've been using Fieldtrip's buffer.exe in conjunction with biosemi2ft.exe to read EEG data in realtime. I'd like to use buffer.exe to communicate EEG analysis results between Matlab sessions. I was wondering whether it's possible to spawn multiple buffer threads on separate ports? Host 'localhost' and port 1972 are already occupied by reading data from the amplifier. I'd like to use a separate port for additional communication during neurofeedback, but the only value for "port" that seems to work is 1972. "Host" accepts the values of 'localhost' and the current ip4 config address of the computer but can't seem to allow remote connections. Does anyone know if host and port can accept values other than "localhost" and "1972"? I couldn't many explicit examples on this procedure online, so I've posted my code for future reference. David University of Queensland Windows 7 & 10, 64-bit - Matlab R2016b 64-bit % matlab code % direct.realtime ---> where buffer.exe and related files are located: % buffer.exe % pthreadGC2-w64.dll % buffer.mexw32 % pthreadGC2.dll % Labview_DLL.dll % buffer.mexw64 % biosemi2ft.exe % libgcc_s_dw2-1.dll % biosemi_config.txt % libstdc++-6.dll !taskkill /F /IM cmd.exe /T !taskkill /F /IM buffer.exe /T system( ['e: -& cd "' direct.realtime '" & buffer.exe -&'] ); % start buffer.exe cfg.host = 'localhost'; % <---- CAN THESE VALUES CHANGE? cfg.port = uint32( 1972 ); % <----- CAN THESE VALUES CHANGE? cfg.nchans = uint32( 1 ); dat.nchans = uint32( 32 ); dat.nsamples = uint32( 200 ); dat.nevents = uint32( 0 ); dat.fsample = uint32( 200 ); dat.data_type = uint32( 9 ); % single precision data dat.bufsize = uint32( dat.nsamples * dat.nchans * 4 ); dat.buf = single( rand(dat.nsamples,dat.nchans ) ); buffer('put_hdr', dat, cfg.host, cfg.port); % hdr = buffer('get_hdr', [], cfg.host, cfg.port); % ----- read header buffer('put_dat', dat, cfg.host, cfg.port); % hdr = buffer('get_hdr', [], cfg.host, cfg.port); % ----- read header begsample = 1; endsample = 200; dat = buffer('get_dat', [begsample-1 endsample-1], cfg.host, cfg.port); -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarang at cfin.au.dk Tue Apr 4 14:21:00 2017 From: sarang at cfin.au.dk (Sarang S. Dalal) Date: Tue, 4 Apr 2017 12:21:00 +0000 Subject: [FieldTrip] April 10 deadline for MEG Nord conference (Aarhus, May 9-10 2017) Message-ID: <51C59DAA-ECA6-45B1-8EEF-501485EF59BE@cfin.au.dk> Dear all, The abstract submission and registration deadline is coming up on April 10 for the MEG Nord conference at Aarhus University, Denmark, to be held on May 9-10 (+ satellite on May 8). The preliminary program and a link to the registration/submission page can be found at: http://cfin.au.dk/meg-nord-2017/ Please feel free to advertise and forward this information to your colleagues and mailing lists. Note that you can choose between three submission types: poster (default), blitz talk (3 min – to be evaluated) and site symposium (restricted to participating Nordic MEG sites). The latter is to be agreed within each site prior to submission, and the designated individuals should submit their details individually; other submission types are open to all. Note that we do not have the capacity to book accommodation, so please use your favorite booking system. While there are no hotels on-site, any centrally located accommodation in Aarhus would be within easy reach from the AU Lakeside auditorium. For flights, in addition to Aarhus airport (connected mainly to Nordic capitals and London), please consider Billund and Aalborg as well (many direct connections throughout Europe). There are also train connections from Copenhagen and Hamburg. We look forward to welcoming you at MEG Nord 2017! On behalf of the organising committee: Yury Shtyrov, Sarang Dalal, Christopher Bailey From sarang at cfin.au.dk Thu Apr 6 16:13:18 2017 From: sarang at cfin.au.dk (Sarang S. Dalal) Date: Thu, 6 Apr 2017 14:13:18 +0000 Subject: [FieldTrip] OpenMEEG binaries are not correctly installed In-Reply-To: References: Message-ID: Hi Rachel, Contrary to what the message says, you might actually have the OpenMEEG binaries properly installed. :-) You do get the expected output when you ran system('om_assemble’)… The problem is that the program that checks for it (om_checkombin.m) simply doesn’t know how to check for it on Windows. Have a look in om_checkombin.m … maybe you can figure out how to properly check on Windows, or otherwise simply force status = 0 as a temporary hack. Cheers, Sarang On 31 Mar 2017, at 17:40, Rachel S > wrote: Hello fieldtrip community, My name is Rachel and I am a Master student working on a project on Ecog. I am trying to use ft_prepare_headmodel with cfg = 'openmeeg' and I get the error "OpenMEEG binaries are not correctly installed". I use a Windows machine and I already add the openmeeg install folder to 'PATH'. When I ran system('om_assemble'), the output is: om_assemble version 2.1.0 (799) compiled at Aug 17 2011 19:50:41 Not enough arguments Please try "om_assemble -h" or "om_assemble --help " ans = 0 Any suggestions? Thanks in advance. Best wishes, Rachel _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Apr 7 09:10:29 2017 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 7 Apr 2017 09:10:29 +0200 Subject: [FieldTrip] Realtime buffer - possible to spawn multiple buffer threads using non-default values for host and port? In-Reply-To: <1491270069170.592@uq.edu.au> References: <1491269842991.43690@uq.edu.au> <1491270069170.592@uq.edu.au> Message-ID: <6759BA3E-A2E1-456E-8847-73190BE4FF63@donders.ru.nl> Hi David, The buffer mex allows you to start a buffer server within MATLAB. However, the low-level C code does not allow multiple (posix) threads to be started to support multiple buffers in a single executable (i.e. in MATLAB), since the threads would all be reading/writing at the same piece of memory. So the only way to go is to start multiple executables. The way that I usually do this is by starting multiple instances of buffer.exe, specifying for each which port it should listen to. If you start a command line prompt, you can cd to the fieldtrip/realtime/bin/win32 directory and start buffer.exe where you specify the port number. Repeat that (in multiple command windows) for each of the buffers, each with a separate port. The buffer always runs on the computer where you start it. So the answer to the question “can the buffer run on another computer than localhost?” is no. But the code that reads and/or writes to the buffer can connect to another computer. Please note that the firewall settings have to allow for this. On http://www.fieldtriptoolbox.org/development/realtime/fmri you can find an example for a pipeline that involves two buffers. Furthermore I recommend that you do not use the buffer.mex file (it is in private for a good reason!), but rather that you use ft_read_data and ft_write_data. At that level you can also find plenty of examples, e.g. starting at http://www.fieldtriptoolbox.org/getting_started/realtime and looking at the code in fieldtrip/realtime/example. best Robert > On 04 Apr 2017, at 03:41, David Painter wrote: > > Dear Fieldtrippers, > > I've been using Fieldtrip's buffer.exe in conjunction with biosemi2ft.exe to read EEG data in realtime. > > I'd like to use buffer.exe to communicate EEG analysis results between Matlab sessions. I was wondering whether it's possible to spawn multiple buffer threads on separate ports? Host 'localhost' and port 1972 are already occupied by reading data from the amplifier. I'd like to use a separate port for additional communication during neurofeedback, but the only value for "port" that seems to work is 1972. "Host" accepts the values of 'localhost' and the current ip4 config address of the computer but can't seem to allow remote connections. > > Does anyone know if host and port can accept values other than "localhost" and "1972"? > > I couldn't many explicit examples on this procedure online, so I've posted my code for future reference. > > David > University of Queensland > Windows 7 & 10, 64-bit - Matlab R2016b 64-bit > > % matlab code > > % direct.realtime ---> where buffer.exe and related files are located: > % buffer.exe > % pthreadGC2-w64.dll > % buffer.mexw32 > % pthreadGC2.dll > % Labview_DLL.dll > % buffer.mexw64 > % biosemi2ft.exe > % libgcc_s_dw2-1.dll > % biosemi_config.txt > % libstdc++-6.dll > > !taskkill /F /IM cmd.exe /T > !taskkill /F /IM buffer.exe /T > system( ['e: -& cd "' direct.realtime '" & buffer.exe -&'] ); % start buffer.exe > > cfg.host = 'localhost'; % <---- CAN THESE VALUES CHANGE? > cfg.port = uint32( 1972 ); % <----- CAN THESE VALUES CHANGE? > > cfg.nchans = uint32( 1 ); > dat.nchans = uint32( 32 ); > dat.nsamples = uint32( 200 ); > dat.nevents = uint32( 0 ); > dat.fsample = uint32( 200 ); > dat.data_type = uint32( 9 ); % single precision data > dat.bufsize = uint32( dat.nsamples * dat.nchans * 4 ); > dat.buf = single( rand(dat.nsamples,dat.nchans ) ); > > buffer('put_hdr', dat, cfg.host, cfg.port); > % hdr = buffer('get_hdr', [], cfg.host, cfg.port); % ----- read header > buffer('put_dat', dat, cfg.host, cfg.port); > % hdr = buffer('get_hdr', [], cfg.host, cfg.port); % ----- read header > > begsample = 1; > endsample = 200; > > dat = buffer('get_dat', [begsample-1 endsample-1], cfg.host, cfg.port); > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Apr 7 09:21:07 2017 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 7 Apr 2017 09:21:07 +0200 Subject: [FieldTrip] compiling ft_volumenormalise In-Reply-To: References: Message-ID: <0F4760EF-55E7-4C00-8106-6A16CD4F70CD@donders.ru.nl> Hi Anne I opened this feature request http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2787 some time back. I made an initial implementation in a separate branch at https://github.com/robertoostenveld/fieldtrip/tree/bug2787-standalone If you look at https://github.com/fieldtrip/fieldtrip/compare/master...robertoostenveld:bug2787-standalone you can see the changes. It follows the strategy that we used for the compiled megconnectome application for the human connectome project (see https://www.humanconnectome.org/documentation/HCP-pipelines/meg-pipeline.html ), i.e. it compiles into an application which can take a script as argument and which “evals” that script. This allows for the flexibility of making changes to the pipeline and cfg settings without having to recompile. best Robert PS If you can use a single interactive MATLAB session on a head node or compute node from the cluster, you can also look into using the ‘compile’ option in qsubcellfun. See http://www.fieldtriptoolbox.org/faq#distributed_computing > On 15 Mar 2017, at 13:29, Anne Urai wrote: > > If anyone encounters the same problem, compilation works if I manually add a bunch of spm functions (which are not recognised by mcc, probably because they are in a class definition folder). > > Specifically, including > > '-a', '~/Documents/fieldtrip/external/spm8/spm.m', ... > '-a', '~/Documents/fieldtrip/external/spm8/templates/T1.nii', ... > '-a', '~/Documents/fieldtrip/external/freesurfer/MRIread', ... > '-a', '~/code/Tools/spmbug/dim.m', ... > '-a', '~/code/Tools/spmbug/dtype.m', ... > '-a', '~/code/Tools/spmbug/fname.m', ... > '-a', '~/code/Tools/spmbug/offset.m', ... > '-a', '~/code/Tools/spmbug/scl_slope.m', ... > '-a', '~/code/Tools/spmbug/scl_inter.m', ... > '-a', '~/code/Tools/spmbug/permission.m', ... > '-a', '~/code/Tools/spmbug/niftistruc.m', ... > '-a', '~/code/Tools/spmbug/read_hdr.m', ... > '-a', '~/code/Tools/spmbug/getdict.m', ... > '-a', '~/code/Tools/spmbug/read_extras.m', ... > '-a', '~/code/Tools/spmbug/read_hdr_raw.m', ... > > does the trick. > > Happy compiling, > Anne > > On 1 March 2017 at 19:38, Anne Urai > wrote: > Hi FieldTrippers, > > I compile my code to run on the supercomputer cluster (without many matlab licenses), which usually works fine when I do something like: > > addpath('~/Documents/fieldtrip'); > ft_defaults; > addpath('~/Documents/fieldtrip/external/spm8'); > mcc('-mv', '-N', '-p', 'stats', '-p', 'images', '-p', 'signal', ... > '-R', '-nodisplay', '-R', '-singleCompThread', fname); > > However, compiling the ft_volumenormalise function gives me some problems. Specifically, if source is the result of my beamformer analysis, this code > > cfg = []; > cfg.parameter = 'pow'; > cfg.nonlinear = 'no'; % can warp back to individual > cfg.template = '/home/aeurai/Documents/fieldtrip/external/spm8/templates/T1.nii'; > cfg.write = 'no'; > cfg.keepinside = 'no'; % otherwise, ft_sourcegrandaverage will bug > source = ft_volumenormalise(cfg, source); > > works fine when running it within Matlab. However, when I run the executable after compiling (which completes without error), a low-level spm function throws the following error: > > the input is source data with 16777216 brainordinates on a [256 256 256] grid > Warning: could not reshape "freq" to the expected dimensions > > In ft_datatype_volume (line 136) > In ft_checkdata (line 350) > In ft_volumenormalise (line 98) > In B6b_sourceContrast_volNormalise (line 57) > Converting the coordinate system from ctf to spm > Undefined function 'fname' for input arguments of type 'struct' > Error in file_array (line 32) > Error in spm_create_vol>create_vol (line 77) > Error in spm_create_vol (line 16) > Error in volumewrite_spm (line 71) > Error in ft_write_mri (line 65) > Error in align_ctf2spm (line 168) > Error in ft_convert_coordsys (line 95) > Error in ft_volumenormalise (line 124) > Error in B6b_sourceContrast_volNormalise (line 57) > MATLAB:UndefinedFunction > > I'd be very grateful for hints from anyone who's successfully compiled the ft_normalise function! Adding the template T1.nii file, spm8 or freesurfer at compilation does not solve the problem. > Thanks, > > — > Anne E. Urai, MSc > PhD student | Institut für Neurophysiologie und Pathophysiologie > Universitätsklinikum Hamburg-Eppendorf | Martinistrasse 52, 20246 | Hamburg, Germany > www.anneurai.net / @AnneEUrai > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From bart at vision.rutgers.edu Fri Apr 7 09:40:52 2017 From: bart at vision.rutgers.edu (Bart Krekelberg) Date: Fri, 07 Apr 2017 07:40:52 +0000 Subject: [FieldTrip] Postdoctoral Position at Rutgers University Message-ID: Postdoctoral Position at Rutgers University: Neural mechanisms of perception in schizophrenia and bipolar disorder using EEG and transcranial current stimulation. The Division of Schizophrenia Research and Center for Molecular and Behavioral Neuroscience at Rutgers University in New Jersey are seeking to hire a full-time postdoctoral fellow. The overall goal of the project is to use EEG and transcranial current stimulation (tDCS ,tACS) to investigate the neurobiological basis of perceptual differences in schizophrenia and bipolar disorder. The ideal candidate will have a doctoral degree in psychology, neuroscience, cognitive science, or a related field, will be proficient in designing and performing EEG experiments with human participants, and will have a strong affinity with sophisticated data analysis (for instance, using Matlab). The successful candidate will play a pivotal role in the design and further development of experimental protocols, organizing study data, analyzing data, writing up, and presenting scientific results. There will also be significant opportunity for designing and conducting original research of the candidate’s choosing. The Rutgers Newark Campus and the Center for Molecular and Behavioral Neuroscience provide a diverse and stimulating scientific environment. Collaborations are possible with investigators at other affiliated departments and institutions including Rutgers University Brain Imaging Center (http://rubic.rutgers.edu/), Rutgers Center for Cognitive Science ( http://ruccs.rutgers.edu), and Rutgers-Princeton Center for Computational Cognitive Neuropsychiatry (https://ccnp.princeton.edu/about-ccnp/). An infinite amount of cultural stimulation is only a 15 minute train ride away, in New York City. An appointment at NIH postdoctoral salary scales will be made for one year, with the possibility to renew for one or more additional years. Rutgers University is an equal opportunity, affirmative action institution; underrepresented minorities are encouraged to apply. The start date is flexible. Interested applicants should send a CV, cover letter, representative publications, and the names of three references to Caren Alexander ( alexanch at ubhc.rutgers.edu), using the subject heading “Postdoc Search 2017”. Informal inquiries regarding the position are welcome and may be directed to Brian Keane, (brian.keane at rutgers.edu; www.briankeane.org) or Bart Krekelberg (bart at vision.rutgers.edu; www.vision.rutgers.edu) -------------- next part -------------- An HTML attachment was scrubbed... URL: From M.Wimber at bham.ac.uk Fri Apr 7 12:04:43 2017 From: M.Wimber at bham.ac.uk (Maria Wimber) Date: Fri, 7 Apr 2017 10:04:43 +0000 Subject: [FieldTrip] Postdoc for human single neuron project in Birmingham Message-ID: The Memory Group in Birmingham (www.memorybham.com) currently has an open position for a postdoctoral research fellow, funded by a 5-year European Research Council (ERC) grant awarded to Dr Maria Wimber (www.memorybham.com/maria-wimber). The project aims to map the time course of remembering in the human brain, using memory-related patterns of neural activity. It uses a multimodal brain imaging approach, including intracranial EEG, EEG-fMRI, MEG, and high-field fMRI. The postdoc will mainly be involved in the iEEG aspects of the project, including LFP and single-unit recordings from the human medial temporal lobes. These are conducted in close collaboration with the Queen Elisabeth Hospital Birmingham (UK), and other members of the Birmingham Memory Group. We encourage applications from researchers with a strong background in electrophysiology - human or animal - and a general interest in memory. The post is open for applications until April 19th 2017. More details about the position and an application link can be found at www.jobs.ac.uk/job/AYA233/research-fellow For more information, please feel free to contact the PI directly by email at m.wimber at bham.ac.uk. ---------------------- Dr Maria Wimber Senior Lecturer School of Psychology University of Birmingham tel +44 121 4144659 www.memorybham.com/maria-wimber -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Apr 7 14:27:59 2017 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 7 Apr 2017 14:27:59 +0200 Subject: [FieldTrip] new look and feel for the Fieldtrip website Message-ID: Dear FieldTrip users Now that the FieldTrip toolkit course that we hosted here in Nijmegen is over, I have moved the website over to a new version of the dokuwiki content management system (i.e. the PHP code that runs underneath the website). Read on below for the motivation... The old version of the dokuwiki software was flagged by some online scanners as being sensitive to malware, and I received reports that at some universities it was blocked. Although there is no reason to asume that the FT wiki was malicious in any way (the whole site is carefully monitored and locked down), it is of course annoying if it gets flagged as such. The drawback of the new version of the website is that the old template is not compatible, so right now the wiki has a different look and feel. All content is exactly the same, and we will try to get the original appearance back. For those of you for whom the website was blocked: it will take some time before it gets scanned once more (which I suppose happens automatically, as I never requested for it). That means that www.fieldtriptoolbox.org might remain in some blacklist database for some time. You can use new.fieldtriptoolbox.org as a temporary alternative. It points to exactly the same site, but operates over a different web address and proxy server. best regards, Robert PS we could use some help with the website. If you know a bit of PHP/HTML/CSS - or possibly even have dokuwiki experience - and want to help us out, please send me a personal message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tfkustermann at gmail.com Fri Apr 7 17:45:09 2017 From: tfkustermann at gmail.com (Thomas Kustermann) Date: Fri, 7 Apr 2017 17:45:09 +0200 Subject: [FieldTrip] how to make the cfg.selectfeature work in ft_databrowser? In-Reply-To: References: Message-ID: Hello Diego, taking a look at the underlying code it seems that while multiple input arguments to cfg.selectfeature are accepted and passed on to artfctdef.xxx.artifact (line 403), the function then attempts to select the current artifact from cfg.selectfeature even when multiple arguments are entered. opt.ftsel = find(strcmp(artlabel,cfg.selectfeature)); % current artifact/feature being selected (line 629) You could either change this line to: opt.ftsel = find(strcmp(artlabel,cfg.selectfeature{1})); % current artifact/feature being selected automatically selecting the first input argument to cfg.selectfeature as default selection in ft_databrowser or you could write them to the cfg.artfctdef.xxx.artifact manually: cfg.selectfeature = 'a'; cfg.artfctdef.a.artifact = zeros(0,2); cfg.artfctdef.b.artifact = zeros(0,2); ... Best, Thomas On Fri, Mar 31, 2017 at 4:40 PM, Diego Lozano-Soldevilla < dlozanosoldevilla at gmail.com> wrote: > Hi all, > > I'm using ft_databrowser to inspect sleep data and I want to visually mark > different events (spindles, k-complexes, artifacts, so forth) and asign > them to different cfg.artfctdef.xxx.artifact substructures. Could somebody > help me to mark different artifact trial types using the cfg.selectfeature > option? Please find below the code and data to reproduce the error I got. > I'm using the very last fieldtrip version on windows with matlab 7.9b. > > Thanks beforehand, > > Diego > > > > data = []; > data.label = {'Fpz';'F7';'F3';'Fz';'F4';'F8';'C3';'Cz';'C4';'P3';'Pz';' > P4';'O1';'Oz';'O2'}; > data.fsample = 250; > data.trial{1} = rand(size(data.label,1),data.fsample*30); > data.time{1} = (1:data.fsample*30)./data.fsample; > > cfg = []; > cfg.length = 2; > cfg.overlap = 0; > trl = ft_redefinetrial(cfg,data); > > > cfg = []; > cfg.channel = 'all'; > cfg.blocksize = 2; > cfg.selectfeature = {'a';'b'}; > cfg.viewmode = 'vertical'; > events = ft_databrowser(cfg,trl); > > > the input is raw data with 15 channels and 15 trials > detected 0 a artifacts > detected 0 b artifacts > ??? Error using ==> plus > Matrix dimensions must agree. > > Error in ==> ft_databrowser at 745 > hsel = [1 2 3] + (opt.ftsel-1) .*3; > > ??? Reference to non-existent field 'trlvis'. > > Error in ==> ft_databrowser>redraw_cb at 1639 > begsample = opt.trlvis(opt.trlop, 1); > > Error in ==> ft_databrowser>winresize_cb at 2250 > redraw_cb(h,eventdata); > > ??? Error while evaluating figure ResizeFcn > > > > Virus-free. > www.avast.com > > <#m_-281810346689554922_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joeboe at umich.edu Fri Apr 7 20:23:32 2017 From: joeboe at umich.edu (Joseph Lee) Date: Fri, 7 Apr 2017 14:23:32 -0400 Subject: [FieldTrip] Inquiry about Field-Trip usage for multi-channel sources Message-ID: Dear Field Trip Community I am Joe from the Computational Unit of the Center for Consciousness Science, University of Michigan. We are somewhat new to forward modelling and are currently undertaking a project to generate 128 scalp-level channel signals from the 78 source-level signals. We are using the "ft_compute_leadfield" function of FieldTrip in order to accomplish that goal. Is this a valid approach for our goal or were those functions designed for a different purpose? Any comments on this will be helpful for us. Thank you very much. Best, Joe Research Assistant Center for Consciousness Science, University of Michigan Medical School, Ann Arbor, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: From timeehan at gmail.com Fri Apr 7 20:32:49 2017 From: timeehan at gmail.com (Tim Meehan) Date: Fri, 7 Apr 2017 14:32:49 -0400 Subject: [FieldTrip] iEEG square wave 'notch' artifact Message-ID: Dear FieldTrippers, I have a recurring artifact in my iEEG data, a very brief (10-15 ms) square-wave-like 'notch' that occurs intermittently and across many channels. It also varies in polarity and amplitude, seemingly randomly. Here's a link showing an example trial containing many of these artifacts: https://drive.google.com/open?id=0B4m5PGO25j3mYkVPUEI5aDZERDA As of now I've been advised to throw out trials in which these occur, but they are very frequent during some sessions. I wonder if alternatively there is some way to selectively remove these? My guess is one could do some sort of template matching to identify when they occur and interpolate across, but I have no idea how to do that or if it's feasible. Does anyone have any insight? Thank you, Tim -------------- next part -------------- An HTML attachment was scrubbed... URL: From dlozanosoldevilla at gmail.com Fri Apr 7 20:34:52 2017 From: dlozanosoldevilla at gmail.com (Diego Lozano-Soldevilla) Date: Fri, 7 Apr 2017 20:34:52 +0200 Subject: [FieldTrip] how to make the cfg.selectfeature work in ft_databrowser? In-Reply-To: References: Message-ID: Hi Thomas, Thank you for your response. It seems is not working well so I'll file a bug and figure out how to fix it. best, Diego On 7 April 2017 at 17:45, Thomas Kustermann wrote: > Hello Diego, > > taking a look at the underlying code it seems that while multiple input > arguments to cfg.selectfeature are accepted and passed on to > artfctdef.xxx.artifact (line 403), the function then attempts to select the > current artifact from cfg.selectfeature even when multiple arguments are > entered. > opt.ftsel = find(strcmp(artlabel,cfg.selectfeature)); % current > artifact/feature being selected (line 629) > > You could either change this line to: > opt.ftsel = find(strcmp(artlabel,cfg.selectfeature{1})); % current > artifact/feature being selected > > automatically selecting the first input argument to cfg.selectfeature as > default selection in ft_databrowser or you could write them to the cfg.artfctdef.xxx.artifact > manually: > > cfg.selectfeature = 'a'; > cfg.artfctdef.a.artifact = zeros(0,2); > cfg.artfctdef.b.artifact = zeros(0,2); > ... > > Best, > Thomas > > > > On Fri, Mar 31, 2017 at 4:40 PM, Diego Lozano-Soldevilla < > dlozanosoldevilla at gmail.com> wrote: > >> Hi all, >> >> I'm using ft_databrowser to inspect sleep data and I want to visually >> mark different events (spindles, k-complexes, artifacts, so forth) and >> asign them to different cfg.artfctdef.xxx.artifact substructures. Could >> somebody help me to mark different artifact trial types using the >> cfg.selectfeature option? Please find below the code and data to reproduce >> the error I got. I'm using the very last fieldtrip version on windows with >> matlab 7.9b. >> >> Thanks beforehand, >> >> Diego >> >> >> >> data = []; >> data.label = {'Fpz';'F7';'F3';'Fz';'F4';'F8';'C3';'Cz';'C4';'P3';'Pz';'P4 >> ';'O1';'Oz';'O2'}; >> data.fsample = 250; >> data.trial{1} = rand(size(data.label,1),data.fsample*30); >> data.time{1} = (1:data.fsample*30)./data.fsample; >> >> cfg = []; >> cfg.length = 2; >> cfg.overlap = 0; >> trl = ft_redefinetrial(cfg,data); >> >> >> cfg = []; >> cfg.channel = 'all'; >> cfg.blocksize = 2; >> cfg.selectfeature = {'a';'b'}; >> cfg.viewmode = 'vertical'; >> events = ft_databrowser(cfg,trl); >> >> >> the input is raw data with 15 channels and 15 trials >> detected 0 a artifacts >> detected 0 b artifacts >> ??? Error using ==> plus >> Matrix dimensions must agree. >> >> Error in ==> ft_databrowser at 745 >> hsel = [1 2 3] + (opt.ftsel-1) .*3; >> >> ??? Reference to non-existent field 'trlvis'. >> >> Error in ==> ft_databrowser>redraw_cb at 1639 >> begsample = opt.trlvis(opt.trlop, 1); >> >> Error in ==> ft_databrowser>winresize_cb at 2250 >> redraw_cb(h,eventdata); >> >> ??? Error while evaluating figure ResizeFcn >> >> >> >> Virus-free. >> www.avast.com >> >> <#m_3369054593448223812_m_-281810346689554922_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Fri Apr 7 20:56:37 2017 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Fri, 7 Apr 2017 11:56:37 -0700 Subject: [FieldTrip] iEEG square wave 'notch' artifact In-Reply-To: References: Message-ID: Hi Tim, Those may be due to wire tugs, possibly as a result of the subject making (abrupt) movements (of the head). Logically, they are artifacts and need to be dealt with. Hopefully, someone here has found a way to do so effectively. Best, Arjen 2017-04-07 11:32 GMT-07:00 Tim Meehan : > Dear FieldTrippers, > > I have a recurring artifact in my iEEG data, a very brief (10-15 ms) > square-wave-like 'notch' that occurs intermittently and across many > channels. It also varies in polarity and amplitude, seemingly randomly. > Here's a link showing an example trial containing many of these artifacts: > > https://drive.google.com/open?id=0B4m5PGO25j3mYkVPUEI5aDZERDA > > As of now I've been advised to throw out trials in which these occur, but > they are very frequent during some sessions. I wonder if alternatively > there is some way to selectively remove these? My guess is one could do > some sort of template matching to identify when they occur and interpolate > across, but I have no idea how to do that or if it's feasible. Does anyone > have any insight? > > Thank you, > Tim > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From A_Lofts at hotmail.ca Fri Apr 7 23:01:27 2017 From: A_Lofts at hotmail.ca (Andrew Lofts) Date: Fri, 7 Apr 2017 21:01:27 +0000 Subject: [FieldTrip] Fieldtrip Octave MEX files - help Message-ID: Hello Readers, I am attempting to preform dipole fitting using fieldtrip in Octave. I am having trouble whenever the code uses one of the functions that require MEX to work. I have installed liboctave-dev in order for mkoctave to work. Whenever a function such as solid_angle is called it needs to be compiled to a .mex, as preformed in the solid_angle.m file. The call can not find the .c files that are needed. "error: no such file, '/home/jad/EAndrew_Lofts/EyesTest/eeg_pipe_asr_amica/analysis/support/dependencies/eeglab_asr_amica/plugins/Fieldtrip-lite141209/forward/private/solid_angle.m' error: called from bounding_mesh at line 74 column 12 find_outermost_boundary at line 45 column 17 ft_prepare_vol_sens at line 85 column 24 prepare_headmodel at line 94 column 11 ft_dipolefitting at line 233 column 15 dipfit_gridsearch at line 106 column 8 pop_dipfit_gridsearch at line 135 column 10 pop_multifit at line 133 column 13" It appears as if these .c file do no exist. There are plenty of .mex* files in the folder but none of them are recognised by "which solid_angle" except for the one .m file. Can someone help me find the .c files to compile, or help with getting Octave to recognise and run one of the other .mex* variants. Thanks, Andrew Lofts -------------- next part -------------- An HTML attachment was scrubbed... URL: From velmurugan.nimhans at gmail.com Sun Apr 9 02:54:43 2017 From: velmurugan.nimhans at gmail.com (velmurugan jayabal) Date: Sat, 8 Apr 2017 17:54:43 -0700 Subject: [FieldTrip] error in source parcellation and source connectivity analysis Message-ID: Dear Field-trip community, I am having the following errors when computing connectivity analysis. Please any help in this regard would be highly appreciated. Thanks in advance. 1. How to compute atlas based source model grid, from MMP atlas?. Since MMP atlas doesn't contain the *dim *field, the ft_volumelookup function doesn't work prompting me the same error. 2. Alternatively, I had created AAL atlas based source model grid and used to compute source connectivity (img.coh) from PCC beamformer source output. But, I am unable to compute the connectivity value for each parcel using ft_sourceparcellate. I am writing the codes used to derive the same. 3. Is there any acronym or a clear explanation for the parcellation label?. I had read Glasser et al 2016 paper and their resource site. But, I couldn't get complete names or explanation for all the ROIs. CODE: %source is the output of pcc beamformer results. cfg = []; cfg.method ='coh'; cfg.complex = 'absimag'; source_conn_imcoh = ft_connectivityanalysis(cfg, source); atlas =ft_read_atlas ('ROI_MNI_V5.nii'); atlas.pos =source_conn_imcoh.pos; cfg =[]; cfg.method ='mean' cfg.parameter ='cohspctrm'; cfg.parcellation = 'tissue'; parc_conn= ft_sourceparcellate(cfg,source_conn, atlas); I had even tried computing source connectivity interpolation on the atlas before parcellation. But, I am getting a huge array > 50 GB, which exceeds my MATLAB and system limit. -- - sincerely, *Velmurugan Jayabal,* *Magnetoencephalography (MEG) research centre,* *Department of Clinical Neurosciences,* *National Institute of Mental Health and Neurosciences (NIMHANS),* *Bangalore - 560029, Karnataka, India* -------------- next part -------------- An HTML attachment was scrubbed... URL: From Markus.Gschwind at unige.ch Sun Apr 9 11:18:21 2017 From: Markus.Gschwind at unige.ch (Markus Gschwind) Date: Sun, 9 Apr 2017 11:18:21 +0200 Subject: [FieldTrip] Problem with Matlab system commands in OS X (XTerm, Logout, crash, sleep mode) Message-ID: Dear all, I hope to find here an expert who knows an answer to the following problem: I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not able to run big and lengthy matlab jobs because at each logout (which occurs after 2h), Matlab crashes, all results are gone (if they are not save to the HD and XTerm closes. I start Matlab form the XTerm (and not by clicking the App Icon) in order to be able to run system (unix) commands within Matlab. I guess, this behaviour is proper to XTerm, and in case I could find an other way to run system commands from Matlab, probably this could be resolved. Could it be that the running matlab job is not visible to the system which goes to sleep?? For info here the power management info: $ pmset -g custom Battery Power: lidwake 1 autopoweroff 1 autopoweroffdelay 14400 standbydelay 18000 standby 1 ttyskeepawake 0 hibernatemode 3 gpuswitch 2 hibernatefile /var/vm/sleepimage displaysleep 2 sleep 0 acwake 1 halfdim 1 sms 1 lessbright 1 disksleep 10 AC Power: lidwake 1 autopoweroff 1 autopoweroffdelay 14400 standbydelay 18000 standby 0 ttyskeepawake 1 hibernatemode 3 gpuswitch 2 hibernatefile /var/vm/sleepimage womp 1 displaysleep 3 networkoversleep 0 sleep 0 acwake 0 halfdim 1 sms 1 disksleep 60 Many thanks for help! Markus -------------- next part -------------- An HTML attachment was scrubbed... URL: From shoeffner at uos.de Sun Apr 9 12:05:12 2017 From: shoeffner at uos.de (=?UTF-8?Q?Sebastian_H=C3=B6ffner?=) Date: Sun, 09 Apr 2017 10:05:12 +0000 Subject: [FieldTrip] Problem with Matlab system commands in OS X (XTerm, Logout, crash, sleep mode) In-Reply-To: References: Message-ID: Dear Markus, while I don't have a proper solution for your problem with matlab, I can recommend you the little app Caffeine which you should find on the app store. It keeps your Mac awake and should stop your matlab process from terminating. http://lightheadsw.com/caffeine/ Best Sebastian On Sun, Apr 9, 2017, 11:31 Markus Gschwind wrote: > Dear all, > > I hope to find here an expert who knows an answer to the following problem: > > I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not > able to run big and lengthy matlab jobs because at each logout (which > occurs after 2h), Matlab crashes, all results are gone (if they are not > save to the HD and XTerm closes. > > I start Matlab form the XTerm (and not by clicking the App Icon) in order > to be able to run system (unix) commands within Matlab. > > I guess, this behaviour is proper to XTerm, and in case I could find an > other way to run system commands from Matlab, probably this could be > resolved. > > Could it be that the running matlab job is not visible to the system which > goes to sleep?? > > For info here the power management info: > > $ pmset -g custom > Battery Power: > lidwake 1 > autopoweroff 1 > autopoweroffdelay 14400 > standbydelay 18000 > standby 1 > ttyskeepawake 0 > hibernatemode 3 > gpuswitch 2 > hibernatefile /var/vm/sleepimage > displaysleep 2 > sleep 0 > acwake 1 > halfdim 1 > sms 1 > lessbright 1 > disksleep 10 > AC Power: > lidwake 1 > autopoweroff 1 > autopoweroffdelay 14400 > standbydelay 18000 > standby 0 > ttyskeepawake 1 > hibernatemode 3 > gpuswitch 2 > hibernatefile /var/vm/sleepimage > womp 1 > displaysleep 3 > networkoversleep 0 > sleep 0 > acwake 0 > halfdim 1 > sms 1 > disksleep 60 > > > Many thanks for help! > Markus > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Sebastian Höffner Hansastr. 19 49090 Osnabrück Germany +49 152 22 59 23 26 -------------- next part -------------- An HTML attachment was scrubbed... URL: From markus.gschwind at gmail.com Sun Apr 9 16:54:11 2017 From: markus.gschwind at gmail.com (Markus Gschwind) Date: Sun, 9 Apr 2017 16:54:11 +0200 Subject: [FieldTrip] Problem with Matlab system commands in OS X (XTerm, Logout, crash, sleep mode) In-Reply-To: References: Message-ID: Hi Sebastian, Thanks I forgot this workaround. Yes, very useful! Best, Markus 2017-04-09 12:05 GMT+02:00 Sebastian Höffner : > Dear Markus, > > while I don't have a proper solution for your problem with matlab, I can > recommend you the little app Caffeine which you should find on the app > store. It keeps your Mac awake and should stop your matlab process from > terminating. > > http://lightheadsw.com/caffeine/ > > Best > Sebastian > > On Sun, Apr 9, 2017, 11:31 Markus Gschwind > wrote: > >> Dear all, >> >> I hope to find here an expert who knows an answer to the following >> problem: >> >> I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not >> able to run big and lengthy matlab jobs because at each logout (which >> occurs after 2h), Matlab crashes, all results are gone (if they are not >> save to the HD and XTerm closes. >> >> I start Matlab form the XTerm (and not by clicking the App Icon) in order >> to be able to run system (unix) commands within Matlab. >> >> I guess, this behaviour is proper to XTerm, and in case I could find an >> other way to run system commands from Matlab, probably this could be >> resolved. >> >> Could it be that the running matlab job is not visible to the system >> which goes to sleep?? >> >> For info here the power management info: >> >> $ pmset -g custom >> Battery Power: >> lidwake 1 >> autopoweroff 1 >> autopoweroffdelay 14400 >> standbydelay 18000 >> standby 1 >> ttyskeepawake 0 >> hibernatemode 3 >> gpuswitch 2 >> hibernatefile /var/vm/sleepimage >> displaysleep 2 >> sleep 0 >> acwake 1 >> halfdim 1 >> sms 1 >> lessbright 1 >> disksleep 10 >> AC Power: >> lidwake 1 >> autopoweroff 1 >> autopoweroffdelay 14400 >> standbydelay 18000 >> standby 0 >> ttyskeepawake 1 >> hibernatemode 3 >> gpuswitch 2 >> hibernatefile /var/vm/sleepimage >> womp 1 >> displaysleep 3 >> networkoversleep 0 >> sleep 0 >> acwake 0 >> halfdim 1 >> sms 1 >> disksleep 60 >> >> >> Many thanks for help! >> Markus >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- > > Sebastian Höffner > Hansastr. 19 > 49090 Osnabrück > Germany > > +49 152 22 59 23 26 <+49%201522%202592326> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From seymourr at aston.ac.uk Mon Apr 10 13:14:10 2017 From: seymourr at aston.ac.uk (Seymour, Robert (Research Student)) Date: Mon, 10 Apr 2017 11:14:10 +0000 Subject: [FieldTrip] error in source parcellation and source connectivity analysis Message-ID: Hi Velmurugan, You might want to look at this tutorial: http://www.fieldtriptoolbox.org/tutorial/networkanalysis?s[]=ft&s[]=networkanalysis I might be wrong but I think the AAL atlas currently implemented in Fieldtrip does not yet contain a .parcellation field, which is why you might be running into problems. You could try to reverse engineer this using the tissuelabel field I guess. For more info on the full label names use wb_command -file-information from the HCP toolbox, or look at the supplementary materials on the Glasser paper. Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From Oleksiy.Bobrov at uni-konstanz.de Mon Apr 10 13:24:08 2017 From: Oleksiy.Bobrov at uni-konstanz.de (Oleksiy Bobrov) Date: Mon, 10 Apr 2017 13:24:08 +0200 Subject: [FieldTrip] ft_artifact_threshold + ft_rejectartifact issue? Message-ID: <40c0c482-714a-7b33-8120-e3e72d15054b@uni-konstanz.de> Hi everyone, I try automatically reject segment from my EEG-Data withamplitudes out of the range 200µV. I use the following function for it: function [fnData, conf] = rejectForRange(inData) cfg = []; cfg.continuous = 'no'; cfg.artfctdef.threshold.bpfilter = 'no'; cfg.artfctdef.threshold.range = 200; %in uV/T, default inf % cfg.artfctdef.threshold.min = -100; %in uV/T, default -inf % cfg.artfctdef.threshold.max = 100; %in uV/T, default inf [conf, artData] = ft_artifact_threshold(cfg, inData); cfg = []; cfg.artfctdef.xxx.artifact = artData; cfg.artfctdef.reject = 'complete'; fnData = ft_rejectartifact(cfg, inData); The function is evaluated with no errors. But the output is not correct. Indeed, a lot of artifact-segments are deleted. But there are still a lot of segments with amplitudes far out of the range of 200µV (visual controlled with ft_rejectvisual()). If try the rejectForRange()-function once more (on the output-data from the first run), so it founds no artifacts at all. But they are in the data. Thank you for any help in advance. Best regards Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: From beese at cbs.mpg.de Mon Apr 10 14:50:13 2017 From: beese at cbs.mpg.de (Caroline Beese) Date: Mon, 10 Apr 2017 14:50:13 +0200 (CEST) Subject: [FieldTrip] cluster-based statistics with one covariate Message-ID: <1329277450.115066.1491828613491.JavaMail.zimbra@cbs.mpg.de> Dear all, I'm trying to take age as a covariate into my cluster-based statistics comparing two dependent measures. I have read about two options: A) to use ft_regressconfound before I do the stats or B) to create a design with a third row using the .cvar field in the 'depsamplesregrT' statfun. I understand that for correcting head motions ft_regressconfound is a great option but for taking age into account as a covariate, it doesn't seem intuitive to me to do this within-subject on a trial-by-trial basis having only one number per person. Or can you use this function differently? However, for option B) the subfunction 'unitselvec' is missing and this seems to be an issue for several years. So I was wondering whether anyone has ever tried to fix this problem themselves and wouldn't mind sharing? More generally, if anyone has successfully implemented a cluster-based statistics with one or more covariates, please share your experience, it would be greatly appreciated. Best Regards, Caroline -- Caroline Beese PhD student Max-Planck Institute for Human Cognitive and Brain Sciences Department of Neuropsychology Stephanstr. 1a 04103 Leipzig office phone: +49 (0) 341 9940 129 www.cbs.mpg.de/staff/beese-11586 From m.papen at uni-koeln.de Tue Apr 11 10:34:21 2017 From: m.papen at uni-koeln.de (Michael von Papen) Date: Tue, 11 Apr 2017 10:34:21 +0200 Subject: [FieldTrip] Conference: Coupling & Causality in Complex Systems Message-ID: ============================================================== CALL FOR PAPERS (Deadline: June 01, 2017) http://c3s.uni-koeln.de ============================================================== INTERNATIONAL CONFERENCE: *Coupling and Causality in Complex Systems* September 25-27, 2017, Cologne, Germany -------------------------------------------------------------- The interdisciplinary conference Coupling and Causality in Complex Systems (C3S) is hosted by the Competence Area 3: Quantitative Modeling of Complex Systems of the University of Cologne (UoC), Germany. It is organized by the Institute of Geophysics & Meteorology, UoC, the Institute of Clinical Neuroscience and Psychology, Heinrich-Heine University Düsseldorf and the Department of Cognitive Neuroscience at the Research Center Juelich. -------------------------------------------------------------- *Abstract* Complex systems such as the human brain, Earth’s climate and economy are characterized by a multitude of coupled processes on different spatial and temporal scales. In order to better understand the dynamics of the system at hand each scientific area has developed specific tools to identify, model and quantify these processes. The conference Coupling and Causality in Complex Systems (C3S) will present a collection of these approaches with the aim to provide scientists with new analysis strategies for their field. The conference focuses on how to characterize a complex system and on the methods for estimating and modeling of statistical coupling (e.g. network coherence, creation and modulation of small networks and local or long-range synchronization by cross frequency phase-phase and phase-amplitude coupling) and causality (e.g. Granger causality, transfer entropy). Therefore, data analysts from different study fields including neuroscience, mathematics, physics, biology, and economy will present their approaches with a particular focus on the methods they use. The aim of this conference is to foster discussions and the transdisciplinary exchange of advanced techniques, methods, and algorithms, thereby stimulating potential future collaborations. -------------------------------------------------- *Invited Speakers* Elissa Aminoff - Department of Psychology, Carnegie Mellon University, Pittsburgh, USA Jörg Breitung - Macroeconomic Policy Institute, University of Cologne, Germany David Gross - Institute of Theoretical Physics, University of Cologne, Germany Philip Holmes - Mechanical and Aerospace Engineering / Princeton Neuroscience Institute, Princeton, USA Ankit Khambhati - Department of Bioengineering, University of Pennsylvania, USA Laura Marzetti - Department of Neuroscience, Università degli Studi "G. d'Annunzio" Chieti - Pescara Arkady Pikovsky - Institute of Physics and Astronomy, University Potsdam, Germany Michael Rosenblum - Institute of Physics and Astronomy, University Potsdam, Germany Jakob Runge - The Grantham Institute for Climate Change, Imperial College London -------------------------------------------------- *Preliminary Session Program* We will have different sessions with differing topics and each session will be opened by one of the invited speakers. Here is a preliminary version of our program: Session 1 Synchronization I Arkady Pikovsky Session 2 Synchronization II Silvia Daun Session 3 Coupled oscillators I Phil Holmes Session 4 Coupled oscillators II Michael Rosenblum Session 5 Phase coupling Laura Marzetti Session 6 Network structures I Elissa Aminoff Session 7 Network structures II Ankit Khambati Session 8 Bayesian networks David Gross Session 9 Granger causality I Jörg Breitung Session 10 Granger causality II Esther Florin Session 11 Causal network measures Jakob Runge Further topics of interest for the conference include, amongst others, research and methods development on: functional connectivity, (partial directed) coherence, network topology, graph-theoretic measures, directed graphs, nonlinear dynamics of complex systems, complex spatio-temporal systems, mutual information and transfer entropy. -------------------------------------------------------------- *Scientific Organizing Committee* Silvia Daun - Institute of Zoology, University of Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany Esther Florin - Institute of Clinical Neuroscience and Psychology, Düsseldorf, Germany Joachim Gross - Center for Cognitive Neuroimaging, Glasgow, UK Michael von Papen - Institute of Geophysics & Meteorology, Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany -------------------------------------------------------------- PAPER SUBMISSION AND REGISTRATION Authors are invited to submit conference abstracts with up to 400 words. Authors of exceptional abstracts will be given the opportunity to present their research in a talk. However, poster sessions will be provided with ample time for discussions. For your submission, please use the conference website c3s.uni-koeln.de. To register, please send an email with the subject "registration" to c3s-conference at uni-koeln.de. Please be sure to include your full name, your affiliation and whether you qualify as student (also PhD candidates) or not. The registration fee will cover snacks and refreshments during coffee breaks, lunch and a dinner with all participants. Early-bird registration is available until July 10 with a reduced fee of 120 EUR (60 EUR for students), after July 10 the registration fee will be 240 EUR (120 EUR for students). -------------------------------------------------------------- IMPORTANT DATES Paper Submission deadline: June 01, 2017 Author Notification: mid June, 2017 Early-bird registration: July 10, 2017 Conference: September 25-27, 2017 ============================================================== Please find the call for papers and more information at the conference website: http://c3s.uni-koeln.de. For questions regarding the conference feel free to contact us via c3s-conference at uni-koeln.de. -- ------------------------------------------ UNIVERSITY OF COLOGNE Institute of Geophysics & Meteorology Coordinator of Competence Area III: Quantitative Modeling of Complex Systems Dr. Michael von Papen Email: m.papen at uni-koeln.de http://www.uni-koeln.de/~vpapenm http://complexsystems.uni-koeln.de From jose.uriguen at deusto.es Tue Apr 11 12:08:44 2017 From: jose.uriguen at deusto.es (=?UTF-8?Q?Jos=C3=A9_Antonio_Uriguen_Garaizabal?=) Date: Tue, 11 Apr 2017 12:08:44 +0200 Subject: [FieldTrip] Need help with cluster-based permutation test with 3 groups of subjects Message-ID: Dear all My name is Toni and I am working on EEG signal processing at University of Deusto, Bilbao, Spain. More specifically, right now trying to apply cluster-based permutation testing to determine whether there exist differences among 3 groups of subjects. So, for my testing, subject groups are E, EN and N, the 2 former being different types of patients and the latter being a control group. I am forming clusters based on proximity (in space) and each subject is characterized by a matrix of values that vary in 2D (per channel and another variable related but not equal to frequency). By means of a T-statistic (indepsamplesT) I can find differences in between E and EN, but I find no clusters/differences in between E and N or EN and N, even though hypothetically (I think) they should exist. By means of an F-statistic (indepsamplesF) I can find differences among the 3 groups at the same time, then also between E and EN and no differences between E and N or EN and N... Am I missing something? I do not understand why the might exist a significant cluster when comparing all 3 groups that does not exist in the 1vs1 comparisons, even though the cluster is not the same I obtain when I compare E vs EN... For additional information, I attach how I run the test: cfg.method = 'distance'; cfg.neighbourdist = 1; cfg.elec = ft_datatype_sens(subjEN{1}.elec); neighbours = ft_prepare_neighbours(cfg); cfg = []; cfg.channel = {'EEG'}; cfg.latency = 'all'; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.neighbours = neighbours; % same as defined for the between-trials experiment cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 5000; nsubj = size(subjE,2)+size(subjEN,2); design = zeros(2,nsubj); design(1,:) = [1:nsubj/2 1:nsubj/2]; design(2,1:size(subjE,2)) = 1; design(2,size(subjE,2)+1:nsubj) = 2; cfg.design = design; cfg.ivar = 2; [stat] = ft_timelockstatistics(cfg, subjEN{:}, subjE{:}); When I compare the 3 groups cfg.method = 'distance'; cfg.neighbourdist = 1; cfg.elec = ft_datatype_sens(subjEN{1}.elec); neighbours = ft_prepare_neighbours(cfg); cfg = []; cfg.channel = {'EEG'}; cfg.latency = 'all'; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesF'; %F-statistic cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.neighbours = neighbours; % same as defined for the between-trials experiment cfg.tail = 1; %One sided cfg.clustertail = 1; cfg.alpha = 0.025; cfg.numrandomization = 5000; nsubj1 = size(subjE,2); nsubj2 = size(subjEN,2); nsubj3 = size(subjN,2); nsubj = nsubj1+nsubj2+nsubj3; design = zeros(2,nsubj); design(1,:) = [1:nsubj1 1:nsubj2 1:nsubj3]; design(2,1:nsubj1) = 1; design(2,nsubj1+1:nsubj1+nsubj2) = 2; design(2,nsubj1+nsubj2+1:nsubj) = 3; cfg.design = design; cfg.ivar = 2; %2nd row is independent var [stat] = ft_timelockstatistics(cfg, subjE{:}, subjEN{:}, subjN{:}); Then, subjE, subjN and subjEN are like this: Eall = subjE{:} Eall = struct with fields: label: {1×18 cell} fsample: 200 elec: [1×1 struct] trial: {[18×115 double]} time: {[1×115 double]} cfg: [1×1 struct] Thanks in advance -- *Jose Antonio Urigüen* PostDoc at Deustotech-LIFE (eVIDA Research Group) [image: Deusto] Universidad de Deusto / Deustuko Unibertsitatea / University of Deusto Facultad de Ingeniería, 4ª Planta Avda. Universidades 24. 48007 Bilbao Tel. +34 94 413 90 00 / Mov. +34 656 711 643 Ext. 2980 jose.uriguen at deusto.es Web: evida.deusto.es *www.deusto.es * -------------- next part -------------- An HTML attachment was scrubbed... URL: From icelandhouse at gmail.com Tue Apr 11 12:13:42 2017 From: icelandhouse at gmail.com (Maris Skujevskis) Date: Tue, 11 Apr 2017 12:13:42 +0200 Subject: [FieldTrip] Error when running ft_sourceanalysis with stats across two conditions Message-ID: Dear Fieldtrip developers/source localizing experts, I get an error when running ft_sourceanalysis on two EEG conditions with the statistical testing (permutation) enabled (no issues with single condition and no statistics). As far as I can see, I am doing everything right (as per ft_sourceanalysis reference page; my fieldtrip version: fieldtrip-20161122). Please correct me where I am wrong or ask for more information in case what I paste/explain below is not sufficient. CODE INPUT: cfg = []; cfg.method = 'dics'; cfg.frequency = 10; cfg.grid = leadfield; cfg.keepleadfield = 'no'; cfg.headmodel = vol; cfg.dics.keepfilter = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.fixedori = 'yes'; cfg.dics.keepmom = 'yes'; cfg.dics.realfilter = 'yes'; cfg.grid.filter = source_cmb.avg.filter; cfg.permutation = 'yes'; cfg.numpermutation = 500; sourceStatsAB = ft_sourceanalysis(cfg, condA, condB); COMMAND WINDOW OUTPUT: the input is freq data with 128 channels, 1 frequencybins and no timebins the input is freq data with 128 channels, 1 frequencybins and no timebins the call to "ft_selectdata" took 0 seconds converting the linearly indexed channelcombinations into a square CSD-matrix using electrodes specified in the data converting units from 'cm' to 'mm' determining source compartment (3) projecting electrodes on skin surface combining electrode transfer and system matrix creating dipole grid based on user specified dipole positions using gradiometers specified in the configuration 5124 dipoles inside, 0 dipoles outside brain the call to "ft_prepare_sourcemodel" took 0 seconds the call to "ft_selectdata" took 0 seconds the call to "ft_selectdata" took 0 seconds 2 conditions, each with 3 data objects averaging 182 replications for one condition averaging 182 replications for one condition 2 conditions, each with 3 data objects <<<<<<<<<<<<<---------- what are the "3 data objects"? creating 100 random permutations from total 6.129982e+54 HERE COMES THE ERROR: Error using prepare_resampled_data (line 381) the dimensions should be the same for every condition Error in ft_sourceanalysis (line 561) [dum, rnd_aCf, rnd_aCr, rnd_aPr, rnd_bCf, rnd_bCr, rnd_bPr] = prepare_resampled_data(cfg, aCf, aCr, aPr, bCf, bCr, bPr); When checking the function prepare_resampled_data, it turns out that it requires a cell named "datain" to have the same size matrices column-wise (whatever the columns may represent) : datain = [182x128x128 double] [182x128 double] [182x1 double] [182x128x128 double] [ 1x128 double] [ NaN] My input data condA and condB have identical dimensions, so I have no idea what has gone wrong here: condA = label: {128x1 cell} dimord: 'rpt_chan_freq' freq: 9.8462 powspctrm: [182x128 double] labelcmb: {8128x2 cell} crsspctrm: [182x8128 double] cumsumcnt: [182x1 double] cumtapcnt: [182x1 double] elec: [1x1 struct] trialinfo: [182x22 double] cfg: [1x1 struct] condB = label: {128x1 cell} dimord: 'rpt_chan_freq' freq: 9.8462 powspctrm: [182x128 double] labelcmb: {8128x2 cell} crsspctrm: [182x8128 double] cumsumcnt: [182x1 double] cumtapcnt: [182x1 double] elec: [1x1 struct] trialinfo: [182x22 double] cfg: [1x1 struct] Thanks for your input! Best wishes, Maris On Sun, Apr 9, 2017 at 12:00 PM, wrote: > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. error in source parcellation and source connectivity analysis > (velmurugan jayabal) > 2. Problem with Matlab system commands in OS X (XTerm, Logout, > crash, sleep mode) (Markus Gschwind) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 8 Apr 2017 17:54:43 -0700 > From: velmurugan jayabal > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] error in source parcellation and source > connectivity analysis > Message-ID: > mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Field-trip community, > > I am having the following errors when computing connectivity > analysis. Please any help in this regard would be highly appreciated. > Thanks in advance. > > 1. How to compute atlas based source model grid, from MMP atlas?. Since MMP > atlas doesn't contain the *dim *field, the ft_volumelookup function doesn't > work prompting me the same error. > > > 2. Alternatively, I had created AAL atlas based source model grid and used > to compute source connectivity (img.coh) from PCC beamformer source output. > But, I am unable to compute the connectivity value for each parcel using > ft_sourceparcellate. I am writing the codes used to derive the same. > > 3. Is there any acronym or a clear explanation for the parcellation label?. > I had read Glasser et al 2016 paper and their resource site. But, I > couldn't get complete names or explanation for all the ROIs. > > > CODE: > %source is the output of pcc beamformer results. > cfg = []; > cfg.method ='coh'; > cfg.complex = 'absimag'; > source_conn_imcoh = ft_connectivityanalysis(cfg, source); > > atlas =ft_read_atlas ('ROI_MNI_V5.nii'); > atlas.pos =source_conn_imcoh.pos; > cfg =[]; > cfg.method ='mean' > cfg.parameter ='cohspctrm'; > cfg.parcellation = 'tissue'; > parc_conn= ft_sourceparcellate(cfg,source_conn, atlas); > > I had even tried computing source connectivity interpolation on the atlas > before parcellation. But, I am getting a huge array > 50 GB, which exceeds > my MATLAB and system limit. > > > -- > - sincerely, > *Velmurugan Jayabal,* > *Magnetoencephalography (MEG) research centre,* > *Department of Clinical Neurosciences,* > > *National Institute of Mental Health and Neurosciences (NIMHANS),* > *Bangalore - 560029, Karnataka, India* > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170408/ede3c3c1/attachment-0001.html> > > ------------------------------ > > Message: 2 > Date: Sun, 9 Apr 2017 11:18:21 +0200 > From: Markus Gschwind > To: FieldTrip discussion list > Subject: [FieldTrip] Problem with Matlab system commands in OS X > (XTerm, Logout, crash, sleep mode) > Message-ID: > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I hope to find here an expert who knows an answer to the following problem: > > I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not able > to run big and lengthy matlab jobs because at each logout (which occurs > after 2h), Matlab crashes, all results are gone (if they are not save to > the HD and XTerm closes. > > I start Matlab form the XTerm (and not by clicking the App Icon) in order > to be able to run system (unix) commands within Matlab. > > I guess, this behaviour is proper to XTerm, and in case I could find an > other way to run system commands from Matlab, probably this could be > resolved. > > Could it be that the running matlab job is not visible to the system which > goes to sleep?? > > For info here the power management info: > > $ pmset -g custom > Battery Power: > lidwake 1 > autopoweroff 1 > autopoweroffdelay 14400 > standbydelay 18000 > standby 1 > ttyskeepawake 0 > hibernatemode 3 > gpuswitch 2 > hibernatefile /var/vm/sleepimage > displaysleep 2 > sleep 0 > acwake 1 > halfdim 1 > sms 1 > lessbright 1 > disksleep 10 > AC Power: > lidwake 1 > autopoweroff 1 > autopoweroffdelay 14400 > standbydelay 18000 > standby 0 > ttyskeepawake 1 > hibernatemode 3 > gpuswitch 2 > hibernatefile /var/vm/sleepimage > womp 1 > displaysleep 3 > networkoversleep 0 > sleep 0 > acwake 0 > halfdim 1 > sms 1 > disksleep 60 > > > Many thanks for help! > Markus > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170409/ce9b8000/attachment-0001.html> > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 77, Issue 6 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Wed Apr 12 04:35:29 2017 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Wed, 12 Apr 2017 10:35:29 +0800 Subject: [FieldTrip] cluster-based statistics with one covariate Message-ID: Dear Caroline, If your conditions are within-subject, then I think the best way to do this is to construct a dataset representing the conditionA - conditionB difference for each subject, and then using ft_statfun_indepsamplesregrT to regress the subject-wise difference on age. See e.g. https://mailman.science.ru.nl/pipermail/fieldtrip/2016-May/010528.html for a thread discussing a similar approach. Best, Steve --- Stephen Politzer-Ahles The Hong Kong Polytechnic University Department of Chinese and Bilingual Studies http://www.mypolyuweb.hk/~sjpolit/ > Message: 3 > Date: Mon, 10 Apr 2017 14:50:13 +0200 (CEST) > From: Caroline Beese > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] cluster-based statistics with one covariate > Message-ID: > <1329277450.115066.1491828613491.JavaMail.zimbra at cbs.mpg.de> > Content-Type: text/plain; charset=utf-8 > > Dear all, > > I'm trying to take age as a covariate into my cluster-based statistics > comparing two dependent measures. > > I have read about two options: > > A) to use ft_regressconfound before I do the stats or > B) to create a design with a third row using the .cvar field in the > 'depsamplesregrT' statfun. > > I understand that for correcting head motions ft_regressconfound is a > great option but for taking age into account as a covariate, it doesn't > seem intuitive to me to do this within-subject on a trial-by-trial basis > having only one number per person. Or can you use this function differently? > > However, for option B) the subfunction 'unitselvec' is missing and this > seems to be an issue for several years. So I was wondering whether anyone > has ever tried to fix this problem themselves and wouldn't mind sharing? > > More generally, if anyone has successfully implemented a cluster-based > statistics with one or more covariates, please share your experience, it > would be greatly appreciated. > > Best Regards, > Caroline > > -- > Caroline Beese > PhD student > > Max-Planck Institute for Human Cognitive and Brain Sciences > Department of Neuropsychology > Stephanstr. 1a > 04103 Leipzig > > office phone: +49 (0) 341 9940 129 > > www.cbs.mpg.de/staff/beese-11586 > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From robin.kampe at liu.se Wed Apr 12 11:01:14 2017 From: robin.kampe at liu.se (=?iso-8859-1?Q?Robin_K=E4mpe?=) Date: Wed, 12 Apr 2017 09:01:14 +0000 Subject: [FieldTrip] Installing gui_streamer Message-ID: Hi! We want to, from scratch, set up a real time fMRI capabilities. Your documentation covers this quite well. I do, however, get stuck on point 1 which is to launch the gui_streamer from the console. How does one obtain/install this program on our Siemens Prisma? Best, Robin Kämpe Research Engineer [Linköping University] CSAN, Center for Social and Affective Neuroscience Department of Clinical and Experimental Medicine, IKE Mobile: +46 (0)73 8005561 Please visit us at www.liu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From laxmi.shaw22 at gmail.com Thu Apr 13 08:07:37 2017 From: laxmi.shaw22 at gmail.com (Laxmi Shaw) Date: Thu, 13 Apr 2017 11:37:37 +0530 Subject: [FieldTrip] fieldtrip Digest, Vol 77, Issue 9 In-Reply-To: References: Message-ID: Dear Fieldtrip user, Can anybody have EEG 64 channel head model or anyother web source where i can get the 64 channel head model then please share with me . On Wed, Apr 12, 2017 at 3:30 PM, wrote: > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Need help with cluster-based permutation test with 3 groups > of subjects (Jos? Antonio Uriguen Garaizabal) > 2. Error when running ft_sourceanalysis with stats across two > conditions (Maris Skujevskis) > 3. Re: cluster-based statistics with one covariate > (Stephen Politzer-Ahles) > 4. Installing gui_streamer (Robin K?mpe) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 11 Apr 2017 12:08:44 +0200 > From: Jos? Antonio Uriguen Garaizabal > To: FieldTrip discussion list > Subject: [FieldTrip] Need help with cluster-based permutation test > with 3 groups of subjects > Message-ID: > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all > > > My name is Toni and I am working on EEG signal processing at University of > Deusto, Bilbao, Spain. More specifically, right now trying to > apply cluster-based permutation testing to determine whether there exist > differences among 3 groups of subjects. > > > So, for my testing, subject groups are E, EN and N, the 2 former being > different types of patients and the latter being a control group. I am > forming clusters based on proximity (in space) and each subject is > characterized by a matrix of values that vary in 2D (per channel and > another variable related but not equal to frequency). > > By means of a T-statistic (indepsamplesT) I can find differences in between > E and EN, but I find no clusters/differences in between E and N or EN and > N, even though hypothetically (I think) they should exist. By means of an > F-statistic (indepsamplesF) I can find differences among the 3 groups at > the same time, then also between E and EN and no differences between E and > N or EN and N... > > Am I missing something? I do not understand why the might exist a > significant cluster when comparing all 3 groups that does not exist in the > 1vs1 comparisons, even though the cluster is not the same I obtain when I > compare E vs EN... > > > For additional information, I attach how I run the test: > > cfg.method = 'distance'; > cfg.neighbourdist = 1; > cfg.elec = ft_datatype_sens(subjEN{1}.elec); > neighbours = ft_prepare_neighbours(cfg); > > cfg = []; > cfg.channel = {'EEG'}; > cfg.latency = 'all'; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.neighbours = neighbours; % same as defined for the > between-trials experiment > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 5000; > > nsubj = size(subjE,2)+size(subjEN,2); > design = zeros(2,nsubj); > design(1,:) = [1:nsubj/2 1:nsubj/2]; > design(2,1:size(subjE,2)) = 1; > design(2,size(subjE,2)+1:nsubj) = 2; > > cfg.design = design; > cfg.ivar = 2; > > [stat] = ft_timelockstatistics(cfg, subjEN{:}, subjE{:}); > > > When I compare the 3 groups > > cfg.method = 'distance'; > cfg.neighbourdist = 1; > cfg.elec = ft_datatype_sens(subjEN{1}.elec); > neighbours = ft_prepare_neighbours(cfg); > > cfg = []; > cfg.channel = {'EEG'}; > cfg.latency = 'all'; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesF'; %F-statistic > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.neighbours = neighbours; % same as defined for the > between-trials experiment > cfg.tail = 1; %One sided > cfg.clustertail = 1; > cfg.alpha = 0.025; > cfg.numrandomization = 5000; > > nsubj1 = size(subjE,2); > nsubj2 = size(subjEN,2); > nsubj3 = size(subjN,2); > nsubj = nsubj1+nsubj2+nsubj3; > > design = zeros(2,nsubj); > design(1,:) = [1:nsubj1 1:nsubj2 1:nsubj3]; > design(2,1:nsubj1) = 1; > design(2,nsubj1+1:nsubj1+nsubj2) = 2; > design(2,nsubj1+nsubj2+1:nsubj) = 3; > > cfg.design = design; > cfg.ivar = 2; %2nd row is independent var > > [stat] = ft_timelockstatistics(cfg, subjE{:}, subjEN{:}, subjN{:}); > > > Then, subjE, subjN and subjEN are like this: > > Eall = subjE{:} > > Eall = > > struct with fields: > > label: {1?18 cell} > fsample: 200 > elec: [1?1 struct] > trial: {[18?115 double]} > time: {[1?115 double]} > cfg: [1?1 struct] > > > Thanks in advance > > -- > *Jose Antonio Urig?en* > PostDoc at Deustotech-LIFE (eVIDA Research Group) > [image: Deusto] > Universidad de Deusto / Deustuko Unibertsitatea / University of Deusto > Facultad de Ingenier?a, 4? Planta > Avda. Universidades 24. 48007 Bilbao > Tel. +34 94 413 90 00 / Mov. +34 656 711 643 > Ext. 2980 > jose.uriguen at deusto.es > Web: evida.deusto.es > *www.deusto.es * > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170411/7a169976/attachment-0001.html> > > ------------------------------ > > Message: 2 > Date: Tue, 11 Apr 2017 12:13:42 +0200 > From: Maris Skujevskis > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Error when running ft_sourceanalysis with stats > across two conditions > Message-ID: > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Fieldtrip developers/source localizing experts, > > I get an error when running ft_sourceanalysis on two EEG conditions with > the statistical testing (permutation) enabled (no issues with single > condition and no statistics). > As far as I can see, I am doing everything right (as per ft_sourceanalysis > reference page; my fieldtrip version: fieldtrip-20161122). Please correct > me where I am wrong or ask for more information in case what I > paste/explain below is not sufficient. > > CODE INPUT: > > cfg = []; > cfg.method = 'dics'; > cfg.frequency = 10; > cfg.grid = leadfield; > cfg.keepleadfield = 'no'; > cfg.headmodel = vol; > cfg.dics.keepfilter = 'yes'; > cfg.dics.lambda = '5%'; > cfg.dics.fixedori = 'yes'; > cfg.dics.keepmom = 'yes'; > cfg.dics.realfilter = 'yes'; > cfg.grid.filter = source_cmb.avg.filter; > cfg.permutation = 'yes'; > cfg.numpermutation = 500; > > sourceStatsAB = ft_sourceanalysis(cfg, condA, condB); > > COMMAND WINDOW OUTPUT: > > the input is freq data with 128 channels, 1 frequencybins and no timebins > the input is freq data with 128 channels, 1 frequencybins and no timebins > the call to "ft_selectdata" took 0 seconds > converting the linearly indexed channelcombinations into a square > CSD-matrix > using electrodes specified in the data > converting units from 'cm' to 'mm' > determining source compartment (3) > projecting electrodes on skin surface > combining electrode transfer and system matrix > creating dipole grid based on user specified dipole positions > using gradiometers specified in the configuration > 5124 dipoles inside, 0 dipoles outside brain > the call to "ft_prepare_sourcemodel" took 0 seconds > the call to "ft_selectdata" took 0 seconds > the call to "ft_selectdata" took 0 seconds > 2 conditions, each with 3 data objects > averaging 182 replications for one condition > averaging 182 replications for one condition > 2 conditions, each with 3 data objects > <<<<<<<<<<<<<---------- what are the "3 data objects"? > creating 100 random permutations from total 6.129982e+54 > > HERE COMES THE ERROR: > > Error using prepare_resampled_data (line 381) > the dimensions should be the same for every condition > > Error in ft_sourceanalysis (line 561) > [dum, rnd_aCf, rnd_aCr, rnd_aPr, rnd_bCf, rnd_bCr, rnd_bPr] = > prepare_resampled_data(cfg, aCf, aCr, aPr, bCf, bCr, bPr); > > > When checking the function prepare_resampled_data, it turns out that it > requires a cell named "datain" to have the same size matrices column-wise > (whatever the columns may represent) : > > datain = > > [182x128x128 double] [182x128 double] [182x1 double] > [182x128x128 double] [ 1x128 double] [ NaN] > > > My input data condA and condB have identical dimensions, so I have no idea > what has gone wrong here: > > condA = > > label: {128x1 cell} > dimord: 'rpt_chan_freq' > freq: 9.8462 > powspctrm: [182x128 double] > labelcmb: {8128x2 cell} > crsspctrm: [182x8128 double] > cumsumcnt: [182x1 double] > cumtapcnt: [182x1 double] > elec: [1x1 struct] > trialinfo: [182x22 double] > cfg: [1x1 struct] > > condB = > > label: {128x1 cell} > dimord: 'rpt_chan_freq' > freq: 9.8462 > powspctrm: [182x128 double] > labelcmb: {8128x2 cell} > crsspctrm: [182x8128 double] > cumsumcnt: [182x1 double] > cumtapcnt: [182x1 double] > elec: [1x1 struct] > trialinfo: [182x22 double] > cfg: [1x1 struct] > > > > > Thanks for your input! > > Best wishes, > Maris > > > > > > On Sun, Apr 9, 2017 at 12:00 PM, wrote: > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. error in source parcellation and source connectivity analysis > > (velmurugan jayabal) > > 2. Problem with Matlab system commands in OS X (XTerm, Logout, > > crash, sleep mode) (Markus Gschwind) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sat, 8 Apr 2017 17:54:43 -0700 > > From: velmurugan jayabal > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] error in source parcellation and source > > connectivity analysis > > Message-ID: > > > mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Dear Field-trip community, > > > > I am having the following errors when computing connectivity > > analysis. Please any help in this regard would be highly appreciated. > > Thanks in advance. > > > > 1. How to compute atlas based source model grid, from MMP atlas?. Since > MMP > > atlas doesn't contain the *dim *field, the ft_volumelookup function > doesn't > > work prompting me the same error. > > > > > > 2. Alternatively, I had created AAL atlas based source model grid and > used > > to compute source connectivity (img.coh) from PCC beamformer source > output. > > But, I am unable to compute the connectivity value for each parcel using > > ft_sourceparcellate. I am writing the codes used to derive the same. > > > > 3. Is there any acronym or a clear explanation for the parcellation > label?. > > I had read Glasser et al 2016 paper and their resource site. But, I > > couldn't get complete names or explanation for all the ROIs. > > > > > > CODE: > > %source is the output of pcc beamformer results. > > cfg = []; > > cfg.method ='coh'; > > cfg.complex = 'absimag'; > > source_conn_imcoh = ft_connectivityanalysis(cfg, source); > > > > atlas =ft_read_atlas ('ROI_MNI_V5.nii'); > > atlas.pos =source_conn_imcoh.pos; > > cfg =[]; > > cfg.method ='mean' > > cfg.parameter ='cohspctrm'; > > cfg.parcellation = 'tissue'; > > parc_conn= ft_sourceparcellate(cfg,source_conn, atlas); > > > > I had even tried computing source connectivity interpolation on the atlas > > before parcellation. But, I am getting a huge array > 50 GB, which > exceeds > > my MATLAB and system limit. > > > > > > -- > > - sincerely, > > *Velmurugan Jayabal,* > > *Magnetoencephalography (MEG) research centre,* > > *Department of Clinical Neurosciences,* > > > > *National Institute of Mental Health and Neurosciences (NIMHANS),* > > *Bangalore - 560029, Karnataka, India* > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > attachments/20170408/ede3c3c1/attachment-0001.html> > > > > ------------------------------ > > > > Message: 2 > > Date: Sun, 9 Apr 2017 11:18:21 +0200 > > From: Markus Gschwind > > To: FieldTrip discussion list > > Subject: [FieldTrip] Problem with Matlab system commands in OS X > > (XTerm, Logout, crash, sleep mode) > > Message-ID: > > > gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Dear all, > > > > I hope to find here an expert who knows an answer to the following > problem: > > > > I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not > able > > to run big and lengthy matlab jobs because at each logout (which occurs > > after 2h), Matlab crashes, all results are gone (if they are not save to > > the HD and XTerm closes. > > > > I start Matlab form the XTerm (and not by clicking the App Icon) in order > > to be able to run system (unix) commands within Matlab. > > > > I guess, this behaviour is proper to XTerm, and in case I could find an > > other way to run system commands from Matlab, probably this could be > > resolved. > > > > Could it be that the running matlab job is not visible to the system > which > > goes to sleep?? > > > > For info here the power management info: > > > > $ pmset -g custom > > Battery Power: > > lidwake 1 > > autopoweroff 1 > > autopoweroffdelay 14400 > > standbydelay 18000 > > standby 1 > > ttyskeepawake 0 > > hibernatemode 3 > > gpuswitch 2 > > hibernatefile /var/vm/sleepimage > > displaysleep 2 > > sleep 0 > > acwake 1 > > halfdim 1 > > sms 1 > > lessbright 1 > > disksleep 10 > > AC Power: > > lidwake 1 > > autopoweroff 1 > > autopoweroffdelay 14400 > > standbydelay 18000 > > standby 0 > > ttyskeepawake 1 > > hibernatemode 3 > > gpuswitch 2 > > hibernatefile /var/vm/sleepimage > > womp 1 > > displaysleep 3 > > networkoversleep 0 > > sleep 0 > > acwake 0 > > halfdim 1 > > sms 1 > > disksleep 60 > > > > > > Many thanks for help! > > Markus > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > attachments/20170409/ce9b8000/attachment-0001.html> > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 77, Issue 6 > > **************************************** > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170411/3d323db9/attachment-0001.html> > > ------------------------------ > > Message: 3 > Date: Wed, 12 Apr 2017 10:35:29 +0800 > From: Stephen Politzer-Ahles > To: fieldtrip at science.ru.nl > Subject: Re: [FieldTrip] cluster-based statistics with one covariate > Message-ID: > A at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Caroline, > > If your conditions are within-subject, then I think the best way to do this > is to construct a dataset representing the conditionA - conditionB > difference for each subject, and then using ft_statfun_indepsamplesregrT to > regress the subject-wise difference on age. See e.g. > https://mailman.science.ru.nl/pipermail/fieldtrip/2016-May/010528.html for > a thread discussing a similar approach. > > Best, > Steve > > > --- > Stephen Politzer-Ahles > The Hong Kong Polytechnic University > Department of Chinese and Bilingual Studies > http://www.mypolyuweb.hk/~sjpolit/ > > > > > > Message: 3 > > Date: Mon, 10 Apr 2017 14:50:13 +0200 (CEST) > > From: Caroline Beese > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] cluster-based statistics with one covariate > > Message-ID: > > <1329277450.115066.1491828613491.JavaMail.zimbra at cbs.mpg.de> > > Content-Type: text/plain; charset=utf-8 > > > > Dear all, > > > > I'm trying to take age as a covariate into my cluster-based statistics > > comparing two dependent measures. > > > > I have read about two options: > > > > A) to use ft_regressconfound before I do the stats or > > B) to create a design with a third row using the .cvar field in the > > 'depsamplesregrT' statfun. > > > > I understand that for correcting head motions ft_regressconfound is a > > great option but for taking age into account as a covariate, it doesn't > > seem intuitive to me to do this within-subject on a trial-by-trial basis > > having only one number per person. Or can you use this function > differently? > > > > However, for option B) the subfunction 'unitselvec' is missing and this > > seems to be an issue for several years. So I was wondering whether anyone > > has ever tried to fix this problem themselves and wouldn't mind sharing? > > > > More generally, if anyone has successfully implemented a cluster-based > > statistics with one or more covariates, please share your experience, it > > would be greatly appreciated. > > > > Best Regards, > > Caroline > > > > -- > > Caroline Beese > > PhD student > > > > Max-Planck Institute for Human Cognitive and Brain Sciences > > Department of Neuropsychology > > Stephanstr. 1a > > 04103 Leipzig > > > > office phone: +49 (0) 341 9940 129 > > > > www.cbs.mpg.de/staff/beese-11586 > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170412/af43a0d6/attachment-0001.html> > > ------------------------------ > > Message: 4 > Date: Wed, 12 Apr 2017 09:01:14 +0000 > From: Robin K?mpe > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Installing gui_streamer > Message-ID: > eurprd06.prod.outlook.com> > > Content-Type: text/plain; charset="iso-8859-1" > > Hi! > > We want to, from scratch, set up a real time fMRI capabilities. Your > documentation covers this quite well. I do, however, get stuck on point 1 > which is to launch the gui_streamer from the console. How does one > obtain/install this program on our Siemens Prisma? > > Best, > > > Robin K?mpe > Research Engineer > > [Link?ping University] > > CSAN, Center for Social and Affective Neuroscience > Department of Clinical and Experimental Medicine, IKE > Mobile: +46 (0)73 8005561 > Please visit us at www.liu.se > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170412/cf35fa04/attachment-0001.html> > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 77, Issue 9 > **************************************** > -- Laxmi Shaw Research Scholar(PhD) IIT Kharagpur West Bengal Ph no-08388837821 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Apr 13 09:24:37 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 13 Apr 2017 07:24:37 +0000 Subject: [FieldTrip] Inquiry about Field-Trip usage for multi-channel sources In-Reply-To: References: Message-ID: <534C6190-9193-43EB-A363-8A7D84FC6F39@donders.ru.nl> Joe, You may want to have a look here: http://www.fieldtriptoolbox.org/example/compute_forward_simulated_data_and_apply_a_dipole_fit?s[]=ft&s[]=dipolesimulation to get started. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 07 Apr 2017, at 20:23, Joseph Lee > wrote: Dear Field Trip Community I am Joe from the Computational Unit of the Center for Consciousness Science, University of Michigan. We are somewhat new to forward modelling and are currently undertaking a project to generate 128 scalp-level channel signals from the 78 source-level signals. We are using the "ft_compute_leadfield" function of FieldTrip in order to accomplish that goal. Is this a valid approach for our goal or were those functions designed for a different purpose? Any comments on this will be helpful for us. Thank you very much. Best, Joe Research Assistant Center for Consciousness Science, University of Michigan Medical School, Ann Arbor, USA _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From son.ta.dinh at tum.de Thu Apr 13 14:57:45 2017 From: son.ta.dinh at tum.de (Ta Dinh, Son) Date: Thu, 13 Apr 2017 12:57:45 +0000 Subject: [FieldTrip] Functional connectivity analysis with powcorr_ortho Message-ID: Dear FieldTrip list, I am trying to do a functional connectivity analysis using the power envelope correlation introduced by Hipp et al. (Nat Neuroscience 2012) as implemented in the ft_connectivity_powcorr_ortho function. My data consists of 5 minutes of eyes-closed resting-state data and my schematic pipeline is as follows: 1. I use LCMV beamforming to source reconstruct my bandpassed and preprocessed data 2. Using the resulting spatial filter I get a projected time series for every voxel (virtual channel) 3. I do a frequency analysis on these time series 4. The results of this frequency analysis (the Fourier coefficients) are used for the connectivity analysis using powcorr_ortho To check the results of this analysis, I plotted the results of a seed-based connectivity analysis with a voxel in the left visual cortex (-20, -80, 20) as seed. In the alpha band, I expect to see a strong local connectivity pattern in the occipital region extending partially into the contralateral hemisphere, similar to what Siems et al. NeuroImage 2016 find. However, I get a basically random connectivity pattern. When using this pipeline with the debiased weighted phase lag index, I get exactly what I am expecting. I looked into the source code of the ft_connectivity_powcorr_ortho function and saw a few disconcerting comments (Fix-Me's and the like) and now I am wondering whether my pipeline is simply not suited to the connectivity analysis with powcorr_ortho as implemented in FieldTrip or if the function is simply not fully implemented yet. Has anyone used it successfully before? I use the following FieldTrip (pseudo-) code: %% LCMV source reconstruction cfg = []; cfg.method = 'lcmv'; cfg.keeptrials = 'yes'; cfg.elec = elec; cfg.grid = lf; % regular grid of 1 cm resolution cfg.headmodel = vol % standard_bem.mat cfg.lcmv.keepfilter = 'yes'; cfg.lcmv.lambda = '5%'; cfg.lcmv.projectnoise = 'yes'; source = ft_sourceanalysis(cfg, tlock_data); %% pseudo-code for the computation of the virtual channel time series virtChan_data = tlock_data; virtChan_data.label = [source.pos(:, 1), source.pos(:,2), source.pos(:,3)]; virtChan_data.trial = source.avg.filter * tlock_data.trial; %% frequency analysis of the virtual channels cfg = []; cfg.method = 'mtmfft'; cfg.output = 'fourier'; cfg.keeptrials = 'yes'; cfg.foi = 10; % alpha band cfg.taper = 'hanning' % I originally used 3 tapers but source code in ft_connectivity_powcorr_ortho implies that multitaper is not compatible virtFreq = ft_freqanalysis(cfg, virtChan_data); %% connectivity analysis cfg = []; cfg.method = 'powcorr_ortho'; conn = ft_connectivityanalysis(cfg,virtFreq); Any suggestions and/or comments would be immensely helpful! Thanks in advance. Best, Son Son Ta Dinh, M.Sc. PhD student in Human Pain Research Klinikum rechts der Isar Technische Universität München Munich, Germany Phone: +49 89 4140 7664 http://www.painlabmunich.de/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Fri Apr 14 03:27:24 2017 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Fri, 14 Apr 2017 09:27:24 +0800 Subject: [FieldTrip] Need help with cluster-based permutation test with 3 groups of subjects Message-ID: Hello Jose, I haven't looked closely at your code, but it sounds like this is working exactly as intended. A significant F-test doesn't mean that there must be significant differences between all pairs of groups; hypothetically, an F-test comparing 100 groups could be significant even if only 99 and 100 are significantly different from each other. This isn't something specific to the cluster-based permutation test, this is just how F-tests work in general. As for getting different cluster extents with the 3-level F-test vs. the pairwise t-test, this is also normal; you're comparing different things so it's natural that the test statistics will come out slightly different. Best, Steve --- Stephen Politzer-Ahles The Hong Kong Polytechnic University Department of Chinese and Bilingual Studies http://www.mypolyuweb.hk/~sjpolit/ > > > Message: 1 > Date: Tue, 11 Apr 2017 12:08:44 +0200 > From: Jos? Antonio Uriguen Garaizabal > To: FieldTrip discussion list > Subject: [FieldTrip] Need help with cluster-based permutation test > with 3 groups of subjects > Message-ID: > < CAMMf7X15byC6p3gqaie6wEuKekV2krZ0++keLLUPZ3pn2h-PAA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all > > > My name is Toni and I am working on EEG signal processing at University of > Deusto, Bilbao, Spain. More specifically, right now trying to > apply cluster-based permutation testing to determine whether there exist > differences among 3 groups of subjects. > > > So, for my testing, subject groups are E, EN and N, the 2 former being > different types of patients and the latter being a control group. I am > forming clusters based on proximity (in space) and each subject is > characterized by a matrix of values that vary in 2D (per channel and > another variable related but not equal to frequency). > > By means of a T-statistic (indepsamplesT) I can find differences in between > E and EN, but I find no clusters/differences in between E and N or EN and > N, even though hypothetically (I think) they should exist. By means of an > F-statistic (indepsamplesF) I can find differences among the 3 groups at > the same time, then also between E and EN and no differences between E and > N or EN and N... > > Am I missing something? I do not understand why the might exist a > significant cluster when comparing all 3 groups that does not exist in the > 1vs1 comparisons, even though the cluster is not the same I obtain when I > compare E vs EN... > > > For additional information, I attach how I run the test: > > cfg.method = 'distance'; > cfg.neighbourdist = 1; > cfg.elec = ft_datatype_sens(subjEN{1}.elec); > neighbours = ft_prepare_neighbours(cfg); > > cfg = []; > cfg.channel = {'EEG'}; > cfg.latency = 'all'; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.neighbours = neighbours; % same as defined for the > between-trials experiment > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 5000; > > nsubj = size(subjE,2)+size(subjEN,2); > design = zeros(2,nsubj); > design(1,:) = [1:nsubj/2 1:nsubj/2]; > design(2,1:size(subjE,2)) = 1; > design(2,size(subjE,2)+1:nsubj) = 2; > > cfg.design = design; > cfg.ivar = 2; > > [stat] = ft_timelockstatistics(cfg, subjEN{:}, subjE{:}); > > > When I compare the 3 groups > > cfg.method = 'distance'; > cfg.neighbourdist = 1; > cfg.elec = ft_datatype_sens(subjEN{1}.elec); > neighbours = ft_prepare_neighbours(cfg); > > cfg = []; > cfg.channel = {'EEG'}; > cfg.latency = 'all'; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesF'; %F-statistic > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.neighbours = neighbours; % same as defined for the > between-trials experiment > cfg.tail = 1; %One sided > cfg.clustertail = 1; > cfg.alpha = 0.025; > cfg.numrandomization = 5000; > > nsubj1 = size(subjE,2); > nsubj2 = size(subjEN,2); > nsubj3 = size(subjN,2); > nsubj = nsubj1+nsubj2+nsubj3; > > design = zeros(2,nsubj); > design(1,:) = [1:nsubj1 1:nsubj2 1:nsubj3]; > design(2,1:nsubj1) = 1; > design(2,nsubj1+1:nsubj1+nsubj2) = 2; > design(2,nsubj1+nsubj2+1:nsubj) = 3; > > cfg.design = design; > cfg.ivar = 2; %2nd row is independent var > > [stat] = ft_timelockstatistics(cfg, subjE{:}, subjEN{:}, subjN{:}); > > > Then, subjE, subjN and subjEN are like this: > > Eall = subjE{:} > > Eall = > > struct with fields: > > label: {1?18 cell} > fsample: 200 > elec: [1?1 struct] > trial: {[18?115 double]} > time: {[1?115 double]} > cfg: [1?1 struct] > > > Thanks in advance > > -- > *Jose Antonio Urig?en* > PostDoc at Deustotech-LIFE (eVIDA Research Group) > [image: Deusto] > Universidad de Deusto / Deustuko Unibertsitatea / University of Deusto > Facultad de Ingenier?a, 4? Planta > Avda. Universidades 24. 48007 Bilbao > Tel. +34 94 413 90 00 / Mov. +34 656 711 643 > Ext. 2980 > jose.uriguen at deusto.es > Web: evida.deusto.es > *www.deusto.es * > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20170411/7a169976/attachment-0001.html > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joeboe at umich.edu Fri Apr 14 19:48:38 2017 From: joeboe at umich.edu (Joseph Lee) Date: Fri, 14 Apr 2017 13:48:38 -0400 Subject: [FieldTrip] Inquiry about Field-Trip usage for multi-channel sources In-Reply-To: <534C6190-9193-43EB-A363-8A7D84FC6F39@donders.ru.nl> References: <534C6190-9193-43EB-A363-8A7D84FC6F39@donders.ru.nl> Message-ID: Thank you for your reply Jan-Marthijs, May I ask then what the main difference between using 'ft_compute_leadfield' to calculate leadfield and generate a signal vs using 'ft_dipole_simulation'. Thanks! -Joe On Thu, Apr 13, 2017 at 3:24 AM, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Joe, > > You may want to have a look here: http://www.fieldtriptoolbox.org/example/ > compute_forward_simulated_data_and_apply_a_dipole_fit?s[ > ]=ft&s[]=dipolesimulation to get started. > > Best wishes, > Jan-Mathijs > > > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 <+31%2024%20361%204793> > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > On 07 Apr 2017, at 20:23, Joseph Lee wrote: > > Dear Field Trip Community > > I am Joe from the Computational Unit of the Center for Consciousness > Science, University of Michigan. > > We are somewhat new to forward modelling and are currently undertaking a > project to generate 128 scalp-level channel signals from the 78 > source-level signals. We are using the "ft_compute_leadfield" function of > FieldTrip in order to accomplish that goal. > > Is this a valid approach for our goal or were those functions designed for > a different purpose? > > Any comments on this will be helpful for us. Thank you very much. > > Best, > > Joe > > Research Assistant > Center for Consciousness Science, > University of Michigan Medical School, > Ann Arbor, USA > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Apr 14 21:19:15 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 14 Apr 2017 19:19:15 +0000 Subject: [FieldTrip] Inquiry about Field-Trip usage for multi-channel sources In-Reply-To: References: <534C6190-9193-43EB-A363-8A7D84FC6F39@donders.ru.nl> Message-ID: <2EC9613C-10A2-4F8F-86FE-A985C77DA2B8@donders.ru.nl> Please read the documentation. I think it should be sufficiently clear. Jan-Mathijs function [simulated] = ft_dipolesimulation(cfg) % FT_DIPOLESIMULATION computes the field or potential of a simulated dipole % and returns a datastructure identical to the FT_PREPROCESSING function. % % Use as % data = ft_dipolesimulation(cfg) % % The dipoles position and orientation have to be specified with % cfg.dip.pos = [Rx Ry Rz] (size Nx3) % cfg.dip.mom = [Qx Qy Qz] (size 3xN) % % The timecourse of the dipole activity is given as a single vector or as a % cell-array with one vectors per trial % cfg.dip.signal % or by specifying a sine-wave signal % cfg.dip.frequency in Hz % cfg.dip.phase in radians % cfg.dip.amplitude per dipole % cfg.ntrials number of trials % cfg.triallength time in seconds % cfg.fsample sampling frequency in Hz % % Random white noise can be added to the data in each trial, either by % specifying an absolute or a relative noise level % cfg.relnoise = add noise with level relative to simulated signal % cfg.absnoise = add noise with absolute level % cfg.randomseed = 'yes' or a number or vector with the seed value (default = 'yes') % % Optional input arguments are % cfg.channel = Nx1 cell-array with selection of channels (default = 'all'), % see FT_CHANNELSELECTION for details % cfg.dipoleunit = units for dipole amplitude (default nA*m) % cfg.chanunit = units for the channel data % % The volume conduction model of the head should be specified as % cfg.headmodel = structure with volume conduction model, see FT_PREPARE_HEADMODEL % % The EEG or MEG sensor positions should be specified as % cfg.elec = structure with electrode positions, see FT_DATATYPE_SENS % cfg.grad = structure with gradiometer definition, see FT_DATATYPE_SENS % cfg.elecfile = name of file containing the electrode positions, see FT_READ_SENS % cfg.gradfile = name of file containing the gradiometer definition, see FT_READ_SENS % % See also FT_SOURCEANALYSIS, FT_DIPOLEFITTING, FT_TIMELOCKSIMULATION, % FT_FREQSIMULATION, FT_CONNECTIVITYSIMULATION function [lf] = ft_compute_leadfield(dippos, sens, headmodel, varargin) % FT_COMPUTE_LEADFIELD computes a forward solution for a dipole in a a volume % conductor model. The forward solution is expressed as the leadfield % matrix (Nchan*3), where each column corresponds with the potential or field % distributions on all sensors for one of the x,y,z-orientations of the % dipole. % % Use as % [lf] = ft_compute_leadfield(dippos, sens, headmodel, ...) % with input arguments % dippos = position dipole (1*3 or Ndip*3) % sens = structure with gradiometer or electrode definition % headmodel = structure with volume conductor definition % % The headmodel represents a volume conductor model, its contents % depend on the type of model. The sens structure represents a sensor % array, i.e. EEG electrodes or MEG gradiometers. % % It is possible to compute a simultaneous forward solution for EEG and MEG % by specifying sens and grad as two cell-arrays, e.g. % sens = {senseeg, sensmeg} % headmodel = {voleeg, volmeg} % This results in the computation of the leadfield of the first element of % sens and headmodel, followed by the second, etc. The leadfields of the % different imaging modalities are subsequently concatenated. % % Additional input arguments can be specified as key-value pairs, supported % optional arguments are % 'reducerank' = 'no' or number % 'normalize' = 'no', 'yes' or 'column' % 'normalizeparam' = parameter for depth normalization (default = 0.5) % 'weight' = number or 1xN vector, weight for each dipole position (default = 1) % 'backproject' = 'yes' (default) or 'no', in the case of a rank reduction % this parameter determines whether the result will be % backprojected onto the original subspace % % The leadfield weight may be used to specify a (normalized) % corresponding surface area for each dipole, e.g. when the dipoles % represent a folded cortical surface with varying triangle size. % % Depending on the specific input arguments for the sensor and volume, this % function will select the appropriate low-level EEG or MEG forward model. % The leadfield matrix for EEG will have an average reference over all the % electrodes. % % The supported forward solutions for MEG are % single sphere (Cuffin and Cohen, 1977) % multiple spheres with one sphere per channel (Huang et al, 1999) % realistic single shell using superposition of basis functions (Nolte, 2003) % leadfield interpolation using a precomputed grid % boundary element method (BEM) % % The supported forward solutions for EEG are % single sphere % multiple concentric spheres (up to 4 spheres) % leadfield interpolation using a precomputed grid % boundary element method (BEM) % % See also FT_PREPARE_VOL_SENS, FT_HEADMODEL_ASA, FT_HEADMODEL_BEMCP, % FT_HEADMODEL_CONCENTRICSPHERES, FT_HEADMODEL_DIPOLI, FT_HEADMODEL_HALFSPACE, % FT_HEADMODEL_INFINITE, FT_HEADMODEL_LOCALSPHERES, FT_HEADMODEL_OPENMEEG, % FT_HEADMODEL_SINGLESHELL, FT_HEADMODEL_SINGLESPHERE, % FT_HEADMODEL_HALFSPACE On 14 Apr 2017, at 19:48, Joseph Lee > wrote: Thank you for your reply Jan-Marthijs, May I ask then what the main difference between using 'ft_compute_leadfield' to calculate leadfield and generate a signal vs using 'ft_dipole_simulation'. Thanks! -Joe On Thu, Apr 13, 2017 at 3:24 AM, Schoffelen, J.M. (Jan Mathijs) > wrote: Joe, You may want to have a look here: http://www.fieldtriptoolbox.org/example/compute_forward_simulated_data_and_apply_a_dipole_fit?s[]=ft&s[]=dipolesimulation to get started. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 07 Apr 2017, at 20:23, Joseph Lee > wrote: Dear Field Trip Community I am Joe from the Computational Unit of the Center for Consciousness Science, University of Michigan. We are somewhat new to forward modelling and are currently undertaking a project to generate 128 scalp-level channel signals from the 78 source-level signals. We are using the "ft_compute_leadfield" function of FieldTrip in order to accomplish that goal. Is this a valid approach for our goal or were those functions designed for a different purpose? Any comments on this will be helpful for us. Thank you very much. Best, Joe Research Assistant Center for Consciousness Science, University of Michigan Medical School, Ann Arbor, USA _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From cmuehl at gmail.com Tue Apr 18 09:28:57 2017 From: cmuehl at gmail.com (Christian Muehl) Date: Tue, 18 Apr 2017 07:28:57 +0000 Subject: [FieldTrip] CfP - reminder - Brain and physiological signals for multi-user modeling @ ACII Message-ID: ** Call for papers ** Special session in ACII 2017 (Affective Computing and Intelligent Interaction) Topic: Brain and physiological signals for multi-user modeling http://www.affective-sciences.org/en/bps-mum ** Description ** Emotional cues, generated subconsciously by the human body, have always been a crucial part of affective computing. Machines can learn about a person's affective state by analyzing measurements such as autonomic nervous system responses, neurophysiological measurements and gaze behavior. They can then act on the inferred information, adapting their own behavior, response or service based on the user's affective state. Although emotions can be viewed as a social phenomenon, current physiological computing research is focused on emotions which are triggered by non-social stimuli. In the case of group interactions, emotions do not only develop in one’s mind but rather unfold according to the emotional expressions of the others. Consequently, the behavior, expressions and physiology of interacting people are known to be in synchrony during interactions. This inter-dependency of behavior and emotional expressions can in turn predict several properties of the social interaction such as grounding, mutual understanding, conflict, or social presence. Similarly, researchers in social neuro-science perform hyper-scanning to measure joint brain activities of people interacting with each other. The objective being to uncover brain areas and neural mechanisms supporting social processes. With this special session we would like to develop research on multi-user modeling from neural and physiological sources. Here the concept of user modeling is defined broadly, including emotional, cognitive and social aspects which can be used for intelligent interactions. This special session targets researchers from computer science, neuro-science and psycho-physiology who are interested in the following research questions: - What information about the user state and the quality of the interaction between users can be gained from (neuro-)physiological signals? - How can that information, combined from several users, be used to interact adaptively with a machine? - What is the effect of sharing physiological information with others? - Which methods can be developed to reduce inter-user variability and improve user modeling? The special session topics include but are not limited to: - Collaborative brain-computer interfaces - Tangible / social display of physiological and neural cues - Social bio-feedback - Assessment of social processes (conflict, empathy, relationship etc.) - Assessment of the quality of interaction and collaboration - Social neuroscience and psycho-physiology - Emotion assessment, particularly social emotions - Domain and transfer learning for building cross-participant models - Methods for multiple user modeling (e.g. synchrony measures, dynamic multi-user models, etc.) - Applications of multi-user physiological computing To facilitate the research on physiological signal classification, several databases are publicly available. Contributions on the physiological data available in such databases are welcome but not obliged. Example databases include: EATMINT: https://eatmint.unige.ch RECOLA: https://diuf.unifr.ch/diva/recola MMDB: http://www.cbi.gatech.edu/mmdb/ Those databases are only examples and work on self-collected or other data are welcome. ** Important dates ** Conference Dates: October 23-26, 2017 Paper Submission Deadline: May 2, 2017 Reviews Provided to Authors: June 16, 2017 Author Rebuttals Due: June 23, 2017 Notification of Acceptance: July 14, 2017 Camera Ready Papers Due: August 18, 2017 Full paper authors should register By: August 7, 2017 Early registration deadline: September 1, 2017 ** Submission procedure ** Papers submitted to this Special Sessions have to be submitted following the same schedule and procedure as regular ACII papers (ACII paper submission). When submitting your paper please check the corresponding box for the Special Session on "Brain and physiological signals for multi-user modeling" in the ACII submission system. The papers will undergo the same review process by anonymous and independent reviewers as the remaining ACII submissions. ** Organizers ** Guillaume Chanel, Swiss Center for Affective Sciences, Switzerland guillaume.chanel[at]unige.ch http://cvml.unige.ch/guillaumechanel Christian Mühl, German Aerospace Center, Germany cmuehl[at]gmail.com https://www.linkedin.com/in/cmuhl Jérémy Frey, Ullo, France jfrey[at]ullo.fr http://phd.jfrey.info Anton Nijholt, University of Twente, The Netherlands anijholt[at]cs.utwente.nl http://wwwhome.cs.utwente.nl/~anijholt/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at me.com Wed Apr 19 09:14:34 2017 From: nathanweisz at me.com (Nathan Weisz) Date: Wed, 19 Apr 2017 09:14:34 +0200 Subject: [FieldTrip] PhD position Salzburg MEG lab Message-ID: <1590B171-5153-4788-A372-9233442AA22E@me.com> Dear colleagues, sorry in advance for cross-postings. Starting September 2017 a PhD position will be available in our group. See attached pdf. Please forward to potentially interested students. Best, Nathan -------------- next part -------------- A non-text attachment was scrubbed... Name: ESIT_Call_Salzburg.pdf Type: application/pdf Size: 341931 bytes Desc: not available URL: From r.oostenveld at donders.ru.nl Wed Apr 19 16:02:04 2017 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 19 Apr 2017 16:02:04 +0200 Subject: [FieldTrip] FiledTrip - Python compatibility? In-Reply-To: References: Message-ID: <327AADB7-8D61-4646-9C16-C5AF2B479946@donders.ru.nl> Hi Greydon, Let me also CC this to the FieldTrip list, as I know there are more people thinking about this. Although I am using Python for other projects (e.g. EEGsynth , we don’t have concrete plans for improving the compatibility between FieldTrip and Python, or to port parts of FieldTrip over to Python. Personally (*) I also feel that Python is not the optimal language and/or data analysis environment for the goals of the FieldTrip project. It would for sure attract more computer scientists and people that like programming, but for (non-technical) cognitive neuroscientists and people that are just able to do scripting I suspect it to become more like an application rather than a toolbox where you can look under the hood and mix it in with ones own code. (*) Other people might feel different of course MNE-Python is of course a project that I am following. The occasional improvements on the FieldTrip side are primarily focussed on making the transition between MNE-Python and FieldTrip more smooth (both ways). A complicating feature in Python is that data handling is different than in MATLAB, where we only use native built-in data structures. Saving data from Python requires a well-established file format (which does not exist) or a stable object definition (which is hard in science). Also for (open access) data sharing I hope that we can do more work on representing analysis results in a format that allows them to be reused in another pipeline. That is for exampel something that we attempted in the MEG section of the human connectome project, where the use cifti files (i.e. nifti-2 with a header extension), text files and - where needed - matlab files in a format that works well with Python. If you have ideas for improving the interoperability, you are welcome to contribute . best Robert PS Thanks for the nice remarks about FieldTrip! > On 16 Apr 2017, at 18:17, Greydon Gilmore wrote: > > Hi Robert, > > I recently stumbled across FieldTrip and I have been in love ever since. I love that I can incorporate the functions into my own scripts. > > I am curious o know if there is any work being done to make FieldTrip compatible with Python? > > Thank you for all the work your team put into FieldTrip, it's streamlined my workflow greatly. > > Greydon > > -- > Greydon Gilmore, B.Sc., M.Sc. (Neuroscience) > Ph.D. candidate in Biomedical Engineering > Movement Disorder Centre, University Hospital > University of Western Ontario > 339 Windermere Road, BLL-250 > 519-685-8500 ext. 76708 > London, Ontario > Canada, N6A 5A5 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ella.weik at gmail.com Thu Apr 20 01:12:24 2017 From: ella.weik at gmail.com (Ella Weik) Date: Wed, 19 Apr 2017 16:12:24 -0700 Subject: [FieldTrip] Problems with plotting time-frequency analysis results Message-ID: Hi Fieldtrip Community, We are currently trying to run a wavelet time frequency analysis. Our EEG data is already preprocessed and epoched with EEGlab. We are able to read in the data, define trials, and output values for TFR.powspctrm. However, we do not see any of these values plotted on our figure with ft_singleplot. This is the code we are using: cfg = []; cfg.dataset = dsname; cfg.continuous = 'no'; cfg.trialfun = 'wm_trialfun'; cfg.binNumber = 13; cfg.epochBaseInt = -0.5; cfg.epochInt = 1.5; cfg.trialdef.prestim = cfg.epochBaseInt - 0.01; cfg.trialdef.poststim = cfg.epochInt - 0.01 ; cfg = ft_definetrial(cfg); dataFIC = ft_preprocessing(cfg); save dataFIC_DirCue dataFIC; dataFIC_condX cfg = []; cfg.channel = 'EEG'; cfg.trials = 'all' cfg.keeptrials = 'no'; cfg.output = 'pow'; cfg.foi = 2:0.5:50; cfg.toi = -0.4:0.01:1.4; % cfg.method = 'wavelet'; cfg.width = 7; cfg.length = 2; TFR = ft_freqanalysis(cfg, dataFIC); save TFRwave_DirCue TFR % plot the results cfg = []; cfg.parameter = 'powspctrm'; cfg.baseline = [-0.4 0]; cfg.baselinetype = 'relative'; cfg.zlim = [-3e-10 3e-10]; cfg.showlabels = 'yes'; figure; ft_singleplotTFR(cfg,TFR); And this is our trial_function: function [trl, event] = wm_trialfun(cfg); hdr = ft_read_header(cfg.dataset); event = ft_read_event(cfg.dataset); indx=[]; if cfg.binNumber for i = 1:size(event,2) if ismember(cfg.binNumber,event(i).bini) indx=[indx;1]; else indx=[indx;0]; end end ind = find(indx); sample = [event(ind).sample]'; else sample = [event(find(strcmp(cfg.codeLabel, {event.codelabel}))).sample]'; end epochBaseSamples = -1*cfg.epochBaseInt*hdr.Fs; epochSamples = cfg.epochInt*hdr.Fs; epochTotal = epochBaseSamples + epochSamples; epochStarts = [1:epochTotal:sample(end)]; eventStarts = epochStarts + epochBaseSamples; sampleGood = intersect(sample,eventStarts); pretrig = -round(cfg.trialdef.prestim * hdr.Fs); posttrig = round(cfg.trialdef.poststim * hdr.Fs); trl = []; trl(:,1) = sampleGood + pretrig; trl(:,2) = sampleGood + posttrig; trl(:,3) = pretrig; And this is the cfg: channel: {128x1 cell} trials: 'all' keeptrials: 'no' output: 'pow' foi: [1x15 double] toi: [1x28 double] method: 'wavelet' width: 7 length: 3 outputfilepresent: 'overwrite' callinfo: [1x1 struct] version: [1x1 struct] feedback: 'text' inputlock: [] outputlock: [] gwidth: 3 pad: 0.9820 padtype: 'zero' calcdof: 'no' precision: 'double' correctt_ftimwin: 'no' polyremoval: 0 keeptapers: 'no' previous: [1x1 struct] Any insights would be greatly appreciated with regards to why we cannot see any values in our single plot figure. Also, we are not sure if the problem rests in our plotting configuration or the data itself. Best regards, Ella -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.litvak at ucl.ac.uk Thu Apr 20 18:27:36 2017 From: v.litvak at ucl.ac.uk (Vladimir Litvak) Date: Thu, 20 Apr 2017 17:27:36 +0100 Subject: [FieldTrip] Last chance: SPM course for MEG/EEG in London: May 8-10, 2017 Message-ID: Dear all, We are pleased to announce that our annual SPM course for MEG/EEG will take place this year from Monday May 8 to Wednesday May 10 2017. Hosted by University College London, the course will be held at Queen Square, a very central location in London (UK). The course will present instruction on the analysis of MEG and EEG data. The first two days will combine theoretical presentations with practical demonstrations of the different data analysis methods implemented in SPM. On the last day participants will have the opportunity to work on SPM tutorial data sets under the supervision of the course faculty. We also invite students to bring their own data for analysis. The course is suitable for both beginners and more advanced users. The topics that will be covered range from pre-processing and statistical analysis to source localization and dynamic causal modelling. The program is listed below. Registration is now open. For full details see http://www.fil.ion.ucl.ac.uk/spm/course/london/ where you can also register. Available places are limited so please register as early as possible if you would like to attend! ---------------------- Monday May 8th (33 Queen square, basement) 9.00 - 9.30 Registration 9.30 - 9.45 SPM introduction and resources Guillaume Flandin 9.45 - 10.30 What are we measuring with M/EEG? Saskia Heibling 10.30 - 11.15 Data pre-processing Hayriye Cagnan Coffee 11.45 - 12.30 Data pre-processing – demo Sofie Meyer, Misun Kim 12.30 - 13.15 General linear model and classical inference Christophe Phillips Lunch 14.15 - 15.00 Multiple comparisons problem and solutions Guillaume Flandin 15.00 - 15.45 Bayesian inference Christophe Mathys Coffee 16.15 - 17.45 Group M/EEG dataset analysis - demo Jason Taylor, Martin Dietz 17.45 - 18.30 Advanced applications of the GLM Ashwani Jha, Bernadette van Wijk Tuesday May 9th (33 Queen square, basement) 9.30 - 10.15 M/EEG source analysis Gareth Barnes 10.15 - 11.15 M/EEG source analysis – demo Jose Lopez, Leonardo Duque Coffee 11.45 - 12.30 The principles of dynamic causal modelling Bernadette van Wijk 12.30 - 13.15 DCM for evoked responses Ryszard Auksztulewicz Lunch 14.15 - 15.00 DCM for steady state responses Rosalyn Moran 15.00 - 15.45 DCM - demo Richard Rosch, Tim West Coffee 16.15 - 17.00 Bayesian model selection and averaging Peter Zeidman 17.00 - 18.30 Clinic - questions & answers Karl Friston 19.00 - ... Social Event Wednesday May 10th 9.30 - 17.00 Practical hands-on session in UCL computer class rooms. Participants can either work on SPM tutorial datasets or on their own data with the help of the faculty. There will also be an opportunity to ask questions in small tutorial groups for further discussions on the topics of the lectures. -------------- next part -------------- An HTML attachment was scrubbed... URL: From gio at gpiantoni.com Fri Apr 21 16:21:38 2017 From: gio at gpiantoni.com (Gio Piantoni) Date: Fri, 21 Apr 2017 16:21:38 +0200 Subject: [FieldTrip] FiledTrip - Python compatibility? Message-ID: I looked into creating a python wrapper around matlab for Fieldtrip. Mathworks officially supports a Matlab engine for python (pretty neat), but the bottleneck for me is that it does not convert matlab cells to python objects: https://www.mathworks.com/help/matlab/matlab_external/handle-data-returned-from-matlab-to-python.html so it's impossible to pass fieldtrip structures to python. Hopefully they'll get around to support the cell conversion in the near future. Also I don't remember how sophisticated the memory management in the engine is. Projects like python-matlab-bridge usually don't share the memory between processes (like rpy2 does), so you end up with duplicated objects (which gets unwieldy when working with large EEG datasets) -g > Date: Wed, 19 Apr 2017 16:02:04 +0200 > From: Robert Oostenveld > To: Greydon Gilmore > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] FiledTrip - Python compatibility? > Message-ID: <327AADB7-8D61-4646-9C16-C5AF2B479946 at donders.ru.nl> > Content-Type: text/plain; charset="utf-8" > > Hi Greydon, > > Let me also CC this to the FieldTrip list, as I know there are more people thinking about this. > > Although I am using Python for other projects (e.g. EEGsynth , we don?t have concrete plans for improving the compatibility between FieldTrip and Python, or to port parts of FieldTrip over to Python. Personally (*) I also feel that Python is not the optimal language and/or data analysis environment for the goals of the FieldTrip project. It would for sure attract more computer scientists and people that like programming, but for (non-technical) cognitive neuroscientists and people that are just able to do scripting I suspect it to become more like an application rather than a toolbox where you can look under the hood and mix it in with ones own code. > > (*) Other people might feel different of course > > MNE-Python is of course a project that I am following. The occasional improvements on the FieldTrip side are primarily focussed on making the transition between MNE-Python and FieldTrip more smooth (both ways). > > A complicating feature in Python is that data handling is different than in MATLAB, where we only use native built-in data structures. Saving data from Python requires a well-established file format (which does not exist) or a stable object definition (which is hard in science). Also for (open access) data sharing I hope that we can do more work on representing analysis results in a format that allows them to be reused in another pipeline. That is for exampel something that we attempted in the MEG section of the human connectome project, where the use cifti files (i.e. nifti-2 with a header extension), text files and - where needed - matlab files in a format that works well with Python. > > If you have ideas for improving the interoperability, you are welcome to contribute . > > best > Robert > > PS Thanks for the nice remarks about FieldTrip! > > >> On 16 Apr 2017, at 18:17, Greydon Gilmore wrote: >> >> Hi Robert, >> >> I recently stumbled across FieldTrip and I have been in love ever since. I love that I can incorporate the functions into my own scripts. >> >> I am curious o know if there is any work being done to make FieldTrip compatible with Python? >> >> Thank you for all the work your team put into FieldTrip, it's streamlined my workflow greatly. >> >> Greydon >> >> -- >> Greydon Gilmore, B.Sc., M.Sc. (Neuroscience) >> Ph.D. candidate in Biomedical Engineering >> Movement Disorder Centre, University Hospital >> University of Western Ontario >> 339 Windermere Road, BLL-250 >> 519-685-8500 ext. 76708 >> London, Ontario >> Canada, N6A 5A5 From tomh at kurage.nimh.nih.gov Fri Apr 21 16:54:56 2017 From: tomh at kurage.nimh.nih.gov (Tom Holroyd) Date: Fri, 21 Apr 2017 10:54:56 -0400 Subject: [FieldTrip] FiledTrip - Python compatibility? In-Reply-To: References: Message-ID: <20170421105456.5341782f@kurage.nimh.nih.gov> You might want to look at this: -- https://pypi.python.org/pypi/oct2py Oct2Py allows you to seamlessly call M-files and Octave functions from Python. It manages the Octave session for you, sharing data behind the scenes using MAT files. -- I've used FieldTrip under Octave in the past (3.0). It doesn't take too much work to get most of the important stuff ported. There's a saying, "Octave is as compatible with Matlab as Matlab is with itself." Once ported, cluster concerns vanish, just run 128 copies of Octave ... They have a nice IDE now too. Because it's open source, integration with Python is much better, see oct2py, which also has a cool name. On Fri, 21 Apr 2017 16:21:38 +0200 Gio Piantoni wrote: > I looked into creating a python wrapper around matlab for Fieldtrip. > > Mathworks officially supports a Matlab engine for python (pretty > neat), but the bottleneck for me is that it does not convert matlab > cells to python objects: > https://www.mathworks.com/help/matlab/matlab_external/handle-data-returned-from-matlab-to-python.html > so it's impossible to pass fieldtrip structures to python. > > Hopefully they'll get around to support the cell conversion in the near future. > > Also I don't remember how sophisticated the memory management in the > engine is. Projects like python-matlab-bridge usually don't share the > memory between processes (like rpy2 does), so you end up with > duplicated objects (which gets unwieldy when working with large EEG > datasets) > > -g > > > > Date: Wed, 19 Apr 2017 16:02:04 +0200 > > From: Robert Oostenveld > > To: Greydon Gilmore > > Cc: FieldTrip discussion list > > Subject: Re: [FieldTrip] FiledTrip - Python compatibility? > > Message-ID: <327AADB7-8D61-4646-9C16-C5AF2B479946 at donders.ru.nl> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Greydon, > > > > Let me also CC this to the FieldTrip list, as I know there are more people thinking about this. > > > > Although I am using Python for other projects (e.g. EEGsynth , we don?t have concrete plans for improving the compatibility between FieldTrip and Python, or to port parts of FieldTrip over to Python. Personally (*) I also feel that Python is not the optimal language and/or data analysis environment for the goals of the FieldTrip project. It would for sure attract more computer scientists and people that like programming, but for (non-technical) cognitive neuroscientists and people that are just able to do scripting I suspect it to become more like an application rather than a toolbox where you can look under the hood and mix it in with ones own code. > > > > (*) Other people might feel different of course > > > > MNE-Python is of course a project that I am following. The occasional improvements on the FieldTrip side are primarily focussed on making the transition between MNE-Python and FieldTrip more smooth (both ways). > > > > A complicating feature in Python is that data handling is different than in MATLAB, where we only use native built-in data structures. Saving data from Python requires a well-established file format (which does not exist) or a stable object definition (which is hard in science). Also for (open access) data sharing I hope that we can do more work on representing analysis results in a format that allows them to be reused in another pipeline. That is for exampel something that we attempted in the MEG section of the human connectome project, where the use cifti files (i.e. nifti-2 with a header extension), text files and - where needed - matlab files in a format that works well with Python. > > > > If you have ideas for improving the interoperability, you are welcome to contribute . > > > > best > > Robert > > > > PS Thanks for the nice remarks about FieldTrip! > > > > > >> On 16 Apr 2017, at 18:17, Greydon Gilmore wrote: > >> > >> Hi Robert, > >> > >> I recently stumbled across FieldTrip and I have been in love ever since. I love that I can incorporate the functions into my own scripts. > >> > >> I am curious o know if there is any work being done to make FieldTrip compatible with Python? > >> > >> Thank you for all the work your team put into FieldTrip, it's streamlined my workflow greatly. > >> > >> Greydon > >> > >> -- > >> Greydon Gilmore, B.Sc., M.Sc. (Neuroscience) > >> Ph.D. candidate in Biomedical Engineering > >> Movement Disorder Centre, University Hospital > >> University of Western Ontario > >> 339 Windermere Road, BLL-250 > >> 519-685-8500 ext. 76708 > >> London, Ontario > >> Canada, N6A 5A5 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Dr. Tom -- I would dance and be merry, Life would be a ding-a-derry, If I only had a brain. -- The Scarecrow From J.Verhoef at donders.ru.nl Mon Apr 24 20:25:50 2017 From: J.Verhoef at donders.ru.nl (Verhoef, J.P. (Julia)) Date: Mon, 24 Apr 2017 18:25:50 +0000 Subject: [FieldTrip] Nine Research Positions in the Dutch Consortium "Language in Interaction" (1.0 FTE) In-Reply-To: <11E9E0B371DBAE4EB859A9CC30606A04023F601E@exprd04.hosting.ru.nl> References: <11E9E0B371DBAE4EB859A9CC30606A04023F5FBE@exprd04.hosting.ru.nl>, <11E9E0B371DBAE4EB859A9CC30606A04023F601E@exprd04.hosting.ru.nl> Message-ID: <11E9E0B371DBAE4EB859A9CC30606A04023F602A@exprd04.hosting.ru.nl> Nine Research Positions in the Dutch Consortium 'Language in Interaction' (1.0 FTE) Dutch Research Consortium 'Language in Interaction' Vacancy number: 30.02.17 Application deadline: 21 May 2017 Responsibilities We are looking for highly motivated candidates to enrich a unique research consortium aiming to unravel the neurocognitive mechanisms of language at multiple levels. The goal is to understand both the universality and the variability of the human language faculty from genes to behaviour. Currently, our consortium advertises 4 Postdoc and 5 PhD positions. These positions provide the opportunity for conducting world-class research as a member of an interdisciplinary team. Each position has its own requirements and profile. Click here for more information on the advertised positions. www.languageininteraction.nl/jobs/BQsecond.html Work environment The Netherlands has an outstanding track record in the language sciences. The Language in Interaction research consortium, sponsored by a large grant from the Netherlands Organisation for Scientific Research (NWO), brings together many of the excellent research groups in the Netherlands with a research programme on the foundations of language. In addition to excellence in the domain of language and related relevant fields of cognition, our consortium provides state-of-the-art research facilities and a research team with ample experience in the complex research methods that will be invoked to address the scientific questions at the highest level of methodological sophistication. These include methods from genetics, neuroimaging, computational modelling, and patient-related research. This consortium realises both quality and critical mass for studying human language at a scale not easily found anywhere else. We have identified five Big Questions (BQ) that are central to our understanding of the human language faculty. These questions are interrelated at multiple levels. Teams of researchers will collaborate to collectively address these key questions of our field. Our five Big Questions are: BQ1: The nature of the mental lexicon: How to bridge neurobiology and psycholinguistic theory by computational modelling? BQ2: What are the characteristics and consequences of internal brain organization for language? BQ3: Creating a shared cognitive space: How is language grounded in and shaped by communicative settings of interacting people? BQ4: Variability in language processing and in language learning: Why does the ability to learn language change with age? How can we characterise and map individual language skills in relation to the population distribution? BQ5: How are other cognitive systems shaped by the presence of a language system in humans? Successful candidates will be appointed at one of the consortium’s home institutions, depending on the position applied for. All successful candidates will become members of our Big Question teams. The research is conducted in an international setting at all participating institutions. English is the lingua franca. What we expect from you Each position has its own requirements and profile. Detailed information on: www.languageininteraction.nl/jobs/BQsecond.html  General requirements for all positions are: • a degree in one of the fields indicated for the positions; • strong motivation; • excellent proficiency in written and spoken English. What we have to offer • employment: 1.0 FTE; • you will be appointed at one of the consortium’s home institutions, depending on the position applied for; • terms of employment depend on the embedding institution; • the institutes involved have regulations in place that enable their staff to create a good work-life balance. Other Information All institutes involved are equal opportunity employers, committed to building a culturally diverse intellectual community, and as such encourage applications from women and minorities. Would you like to know more? Further information on LiI consortium: http://www.languageininteraction.nl/ Further information on the different positions, including terms of employment and contacts: www.languageininteraction.nl/jobs/BQsecond.html Are you interested? You should upload your application (attn. of Prof. P. Hagoort) exclusively via: http://www.ru.nl/applyonline?tk=uk&recid=597242 Your application should include (and be limited to) the following attachment(s): • a cover letter quoting at the top the number of the position you apply for; • your curriculum vitae, including a list of publications and the names of at least two persons who can provide references. Please apply before 21 May 2017, 23:59 CET. You may apply for more than one position. No commercial propositions please. -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrea.brovelli at univ-amu.fr Mon Apr 24 21:35:26 2017 From: andrea.brovelli at univ-amu.fr (Andrea Brovelli) Date: Mon, 24 Apr 2017 21:35:26 +0200 Subject: [FieldTrip] 3 PhD scholarships in Integrative and Clinical Neurosciences at Aix-Marseille University (France) Message-ID: <8eb6aa69-e3d2-04f3-71d9-e2bfa937bbac@univ-amu.fr> In 2017, the PhD program in Integrative and Clinical Neurosciences at the Aix-Marseille University (France) will grant *three* *PhD scholarships* to excellent Master students that graduated from non-French top ranked universities. The selection process will include the following steps. 1. CALL FOR APPLICANTS (Master graduated students) * The scholarships are open to Master students that graduated from top rankenon-French universities. * Applicants must select and rank two of the proposed research projects * A guideline for student application and templates for recommendation letters must be downloaded on the following site: http://neuro-marseille.org/en/phdprogram-en/call-for-applicants/ * Applications should be sent *before May 21st, 2017 *at midnight (French time). 2. INTERVIEW * The selection committee will shortlist 10 students that will be individually interviewed in June. The students are encouraged to prepare their interviews with the project leaders they have selected. * The final decision will be known shortly after the interviews and the three successful candidates will start their PhD studies between October and December 2017. Contact Nadia Pittet nadejda.pittet at univ-amu.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.blume at sbg.ac.at Tue Apr 25 17:33:53 2017 From: christine.blume at sbg.ac.at (Blume Christine) Date: Tue, 25 Apr 2017 15:33:53 +0000 Subject: [FieldTrip] ft_definetrial on result from ft_appenddata? Message-ID: Dear FT community, I have data with overlapping segments, wherefore I need to do the raw data inspection using ft_databrowser on continuous data (unless ft_databrowser can handle overlapping segments now?). So far so good, but I have 5 different raw data files per person as our machine closes and files automatically and starts a new one as soon as they exceed 2GB. The most convenient thing would obviously be to append all 5, run ft_databrowser on the appended data and then do the segmentation. This is particularly the case because it is data from sleep and thus important to see how the EEG/MEG changes across time. However, I am wondering whether there is any way to apply ft_definetrial and ft_redefinetrial to appended datasets (as it obviously goes back to the underlying raw files, of which I have 5). Any suggestions are more than welcome :). Thanks, Christine -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandra.bendixen at physik.tu-chemnitz.de Tue Apr 25 23:00:40 2017 From: alexandra.bendixen at physik.tu-chemnitz.de (Alexandra Bendixen) Date: Tue, 25 Apr 2017 23:00:40 +0200 Subject: [FieldTrip] PhD and Postdoc positions in multimodal perception and cognition at TU Chemnitz, Germany Message-ID: <9AABDCBE-073E-4DEA-8943-1F89C3474B21@physik.tu-chemnitz.de> Dear colleagues, The Cognitive Systems Lab (Alexandra Bendixen) and the Physics of Cognition Group (Wolfgang Einhäuser) at Chemnitz University of Technology (TU Chemnitz) invite applications for 2 PhD student positions 2 postdoctoral researcher positions starting October 1st, 2017. The application deadline for all positions is May 31st, 2017. PhD positions Two PhD positions are funded by the German Research Foundation (DFG) within the project "Multistable perception across modalities: Resolving sensory ambiguity in vision and audition". The PhD projects will concern multistable perceptual phenomena (e.g., binocular rivalry, auditory streaming) with a focus on objective methods to assess observers’ perception. Methods include advanced psychophysical methods, eye tracking and pupillometry, peripheral physiology, electroencephalography (EEG) as well as theoretical and computational modelling. Experience in one or more of these fields is a plus. Salary for the PhD positions is according to the German salary scale (E13 TV-L) at 65%. Positions are contingent on funding availability and limited to 3 years in accordance with the applicable regulations. Applicants for the PhD positions must hold a M.Sc. degree or equivalent in psychology, physics, cognitive science, neuroscience or a related field. If the M.Sc. degree is not completed at the time of application, a statement by the thesis supervisor must be included that confirms that the degree will be completed before October 2017. Application documents for PhD positions must include a complete CV, copies of transcripts of all academic institutions, a letter of motivation for the specific position, as well as the names and contact information of at least 1 and up to 3 references that could be contacted for information about the applicant. Postdoctoral positions We are looking for postdocs who are prepared to develop their own research profile in interaction with the groups’ research foci in visual, auditory and/or multimodal perception and cognition. The groups operate laboratories equipped with sound-attenuated measurement rooms, state-of-the-art devices for visual and auditory psychophysics, for high-precision and mobile eye tracking, for peripheral physiology and for EEG as well as ample computational resources. Salary for the postdoc positions is according to the German salary scale (E13 TV-L) at 100%. The positions are contingent on funding availability. The initial contract will be limited to 3 years. An extension is possible depending on funding availability, personal qualification and applicable regulatory restrictions. Successful applicants are expected to engage in teaching in the "Sensors and Cognitive Psychology" study program at TU Chemnitz. Non-German-speaking applicants are expected to acquire sufficient proficiency in German for teaching these courses within the first two years. Applicants for the postdoctoral positions must hold a PhD or equivalent in psychology, physics, cognitive science, neuroscience or a related field. If the PhD is not completed at the time of application, a statement by the thesis supervisor must be included that confirms that the degree will be awarded before October 2017. Applications must have a strong background (as demonstrated by peer-reviewed publications) in at least one of the following fields: advanced psychophysics, vision research, auditory research, eye tracking, peripheral physiology, or EEG. Good programming skills and good command of English are mandatory. Application documents for postdoctoral positions must include a complete CV, a list of publications, copies of transcripts of all academic institutions, a letter stating the motivation for the specific position, the plans and objectives for future research, as well as plans for teaching and career development. The applications should also include the names and contact information of at least 2 and up to 5 references that could be contacted for information about the applicant. More information and application process More information about the research of the two groups can be found at https://www.tu-chemnitz.de/physik/SFKS/index.html.en and https://www.tu-chemnitz.de/physik/PHKP/index.html.en For more information on the positions and on how to apply, please visit the legally binding German version of the job advertisements: postdoc positions: https://www.tu-chemnitz.de/verwaltung/personal/stellen/212066_1_Kae.php PhD positions: https://www.tu-chemnitz.de/verwaltung/personal/stellen/212066_2_Kae.php TU Chemnitz is an equal opportunity employer and aims at increasing the number of female scientists; qualified women are therefore especially encouraged to apply. Application documents should be sent as single pdf-file to bewerbung_sfks_phkp at tu-chemnitz.de no later than May 31st, 2017. For the PhD positions, the subject line must include the keyword MultMod2017, for postdoctoral positions subject line must include the keyword SFKSPHKP2017. Please feel free to contact us (alexandra.bendixen at physik.tu-chemnitz.de, wolfgang.einhaeuser-treyer at physik.tu-chemnitz.de) for further information. We would be grateful if you could distribute this e-mail to suitable candidates. With best regards, Wolfgang Einhäuser-Treyer & Alexandra Bendixen -- Prof. Dr. Alexandra Bendixen TU Chemnitz - Cognitive Systems Lab http://www.tu-chemnitz.de/physik/SFKS/ Prof. Dr. Wolfgang Einhäuser-Treyer TU Chemnitz - Physics of Cognition Group http://www.tu-chemnitz.de/physik/PHKP/ From delucia.marzia at gmail.com Wed Apr 26 11:49:06 2017 From: delucia.marzia at gmail.com (Marzia De Lucia) Date: Wed, 26 Apr 2017 09:49:06 +0000 Subject: [FieldTrip] postdoctoral position in Lausanne Message-ID: <243dc9ccd6b64680a285e41adb4ca0b2@EXPRD01.hosting.ru.nl> Dear all, Applications are invited for a postdoc position at the Laboratoire de Recherche en Neuroimagerie (LREN) financed by the Eurostars project ‘ComAlert’ in collaboration with g.tec (http://www.gtec.at/). The position is under the supervision of Dr Marzia De Lucia and in close collaboration with the Neurology service and the Department of Intensive Care Medicine at the Lausanne University Hospital (CHUV). The project aims at developing EEG based tests for outcome prediction in comatose patients and to assess the degree of preserved cognitive functions during acute coma and during later stages of disorders of consciousness. This project takes advantage of sophisticated software and hardware solution provided by gtec and specifically targeted for their application in the intensive care environment. The LREN (https://www.unil.ch/lren/en/home.html) provides an excellent multidisciplinary and interactive research environment combining expertise in functional magnetic resonance imaging, electroencephalography and neuroimaging methods development. The ideal candidate should have a PhD in Neuroscience, Life Science, Biomedical Engineering or related areas. Prior experience with EEG, programming skills and proficiency in English and in French are advantageous. The position is available from the 1st of July 2017 till June 2019. The salaries are in accordance with the Swiss Public service regulations. Applications including a CV, a statement of research interests and the name and full contact details of two referees should be sent to : delucia.marzia at gmail.com Best Regards, Marzia De Lucia ------------------------------------ Marzia DE LUCIA, MER PD Laboratoire de recherche en Neuroimagerie - LREN Département des Neurosciences Cliniques Centre Hospitalier Universitaire Vaudois MP16 05 559, Chemin de Mont-Paisible 16 , 1011 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: From tim.bardouille at Dal.Ca Thu Apr 27 00:33:58 2017 From: tim.bardouille at Dal.Ca (Timothy Bardouille) Date: Wed, 26 Apr 2017 22:33:58 +0000 Subject: [FieldTrip] Position in Halifax, NS, Canada: MEG Scientist Message-ID: Please distribute widely: MEG Scientist @ IWK Health Centre, Halifax, NS, Canada The MEG lab at the Biomedical Translational Imaging Centre (BIOTIC) in the IWK Health Centre, Halifax, NS, Canada is hiring for the position of MEG Scientist. The MEG Scientist will implement a neuroimaging research program and support our existing clinical program in MEG. You will be part of the growing BIOTIC team, will be supported by an Imaging Technician, and will work with collaborators in the region and abroad. Applicants will be expected to describe an independent research plan involving MEG and neuroimaging more broadly, and be committed to supporting our clinical program. The BIOTIC MEG lab, located in the region's leading research and teaching women and children's hospital, maintains research and clinical programs in both pediatric and adult populations. These ongoing commitments occur in collaboration with researchers at the regions' universities and clinicians in Neurology and Neurosurgery. The BIOTIC MEG lab also works with industry partners in the medical technology space to achieve their strategic goals through collaborative projects. Many researchers at BIOTIC maintain professional affiliation with Dalhousie University. Qualifications • PhD degree in Physics, Biomedical Engineering, Neuroscience or a research related field • Publication track record in neuroimaging • Literacy with MATLAB and/or Python based MEG analysis packages is required • Interested in multi-modal imaging is a plus • Strong technical ability with MEG hardware/software is a plus Start Date: ASAP Salary commensurate with experience BIOTIC is a multi-site imaging centre that is embedded in the two leading research and teaching hospitals in Nova Scotia. Our advanced pre-clinical and clinical imaging equipment are housed in three labs, in two health centres encompassing over 12,000 square feet of lab space. BIOTIC operates at the intersection of research, clinical care, and industry collaboration, offering a dynamic and multifaceted work experience. The team co-develops medical technologies and creates new imaging techniques and methods for diagnosing and monitoring treatment. With a population of over 400,000 people, Halifax is the capital city of Nova Scotia, Canada. Greater Halifax boasts 5 universities and the two largest academic health centres in Atlantic Canada. Founded in the mid-1700s as a British naval fortress, Halifax balances a vibrant downtown filled with museums, theatres and pubs, with beaches, hiking trails and parks (the IWK itself is a mere 600 meters from the ocean!), and also has daily flights to London-Heathrow, NYC, Chicago etc. For more information on Halifax, please see www.destinationhalifax.ca For more information, please contact Dr. Tim Bardouille at tim.bardouille at iwk.nshealth.ca. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Halifax MEG Scientist.pdf Type: application/pdf Size: 134587 bytes Desc: Halifax MEG Scientist.pdf URL: From elam4hcp at gmail.com Thu Apr 27 19:17:04 2017 From: elam4hcp at gmail.com (Jennifer Elam) Date: Thu, 27 Apr 2017 12:17:04 -0500 Subject: [FieldTrip] Last weeks to register for HCP Course 2017 Message-ID: It's not too late to register for the 2017 HCP Course: "Exploring the Human Connectome" , to be held June 19-23 at the Djavad Mowafagian Centre for Brain Health at University of British Columbia (UBC) in Vancouver, BC, Canada! Fieldtrip tools play a major part of the HCP MEG processing pipelines and have been critical to the high quality processing of the project's 95 released MEG/MRI imaging datasets. Spaces for the course are limited and registration is on a first come, first served basis. May 17, 2017 is the deadline to reserve discounted UBC accommodations within walking distance to the course venue: https://reserve.ubcconferences.com/vancouver/availability.asp?hotelCode=%2A&startDate=06%2F16%2F2017&endDate=06%2F24%2F2017&adults=1&children=&rooms=1&requesttype=invBlockCode&code=G170618A The 5-day intensive HCP course is a great opportunity to learn directly from HCP investigators and designed for those interested in: - using data collected and distributed from the HCP young adult study - acquiring and analyzing HCP-style imaging and behavioral data at your own institution - processing your own non-HCP data using HCP pipelines and methods - using Connectome Workbench tools and sharing data using the BALSA imaging database - learning HCP multimodal neuroimaging analysis methods, including those that combine MEG and MRI data - exploring the HCP MMP 1.0 multimodal parcellation brain map and learning about how it can be used in your analyses - positioning yourself to capitalize on HCP-style data being distributed by the Connectome Coordinating Facility (CCF) from HCP development (healthy subjects ages 5-21) and aging (healthy subjects ages 35-90+) and Connectomes Related to Human Disease projects See https://store.humanconnectome.org/courses/2017/exploring-the-human-connectome.php for more info. If you have any questions, please contact us at: hcpcourse at humanconnectome.org We look forward to seeing you in Vancouver! Best, 2017 HCP Course Staff -------------- next part -------------- An HTML attachment was scrubbed... URL: From tim.bardouille at Dal.Ca Thu Apr 27 23:31:21 2017 From: tim.bardouille at Dal.Ca (Timothy Bardouille) Date: Thu, 27 Apr 2017 21:31:21 +0000 Subject: [FieldTrip] Position in Halifax, NS, Canada: MEG Scientist - application link added Message-ID: <72288243-FDB2-4D9F-A1EA-F3890D37937C@dal.ca> Hi all, Sorry for the second e-mail. I’m including the link to apply online this time. If interested in a primary position at the MEG lab in Halifax, please apply at this link: https://jobs.nshealth.ca/job/Halifax-MEG-Scientist-Nova-B3K-6R8/354454217/?locale=en_US Best regards, Tim. From: Timothy Bardouille Date: Wednesday, April 26, 2017 at 3:16 PM To: Discussion list for international MEG community Subject: Position in Halifax, NS: MEG Scientist Please distribute widely: MEG Scientist @ IWK Health Centre, Halifax, NS, Canada The MEG lab at the Biomedical Translational Imaging Centre (BIOTIC) in the IWK Health Centre, Halifax, NS, Canada is hiring for the position of MEG Scientist. The MEG Scientist will implement a neuroimaging research program and support our existing clinical program in MEG. You will be part of the growing BIOTIC team, will be supported by an Imaging Technician, and will work with collaborators in the region and abroad. Applicants will be expected to describe an independent research plan involving MEG and neuroimaging more broadly, and be committed to supporting our clinical program. The BIOTIC MEG lab, located in the region's leading research and teaching women and children's hospital, maintains research and clinical programs in both pediatric and adult populations. These ongoing commitments occur in collaboration with researchers at the regions' universities and clinicians in Neurology and Neurosurgery. The BIOTIC MEG lab also works with industry partners in the medical technology space to achieve their strategic goals through collaborative projects. Many researchers at BIOTIC maintain professional affiliation with Dalhousie University. Qualifications • PhD degree in Physics, Biomedical Engineering, Neuroscience or a research related field • Publication track record in neuroimaging • Literacy with MATLAB and/or Python based MEG analysis packages is required • Interested in multi-modal imaging is a plus • Strong technical ability with MEG hardware/software is a plus Start Date: ASAP Salary commensurate with experience BIOTIC is a multi-site imaging centre that is embedded in the two leading research and teaching hospitals in Nova Scotia. Our advanced pre-clinical and clinical imaging equipment are housed in three labs, in two health centres encompassing over 12,000 square feet of lab space. BIOTIC operates at the intersection of research, clinical care, and industry collaboration, offering a dynamic and multifaceted work experience. The team co-develops medical technologies and creates new imaging techniques and methods for diagnosing and monitoring treatment. With a population of over 400,000 people, Halifax is the capital city of Nova Scotia, Canada. Greater Halifax boasts 5 universities and the two largest academic health centres in Atlantic Canada. Founded in the mid-1700s as a British naval fortress, Halifax balances a vibrant downtown filled with museums, theatres and pubs, with beaches, hiking trails and parks (the IWK itself is a mere 600 meters from the ocean!), and also has daily flights to London-Heathrow, NYC, Chicago etc. For more information on Halifax, please see www.destinationhalifax.ca For more information, please contact Dr. Tim Bardouille at tim.bardouille at iwk.nshealth.ca. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.flandin at ucl.ac.uk Mon Apr 3 18:36:42 2017 From: g.flandin at ucl.ac.uk (Guillaume Flandin) Date: Mon, 3 Apr 2017 17:36:42 +0100 Subject: [FieldTrip] compiling ft_volumenormalise In-Reply-To: References: Message-ID: <58E27A1A.7080307@ucl.ac.uk> Dear Anne, The way we compile SPM is to use the '-a' flag as you did but with a directory instead of individual files (e.g. '-a', '~/Documents/fieldtrip/'); by doing so, all the files from the specified directory as well as all the files from subdirectories will be included so that you don't have to rely on the automatic file dependency analysis mcc performs. Best regards, Guillaume. On 15/03/17 12:29, Anne Urai wrote: > If anyone encounters the same problem, compilation works if I manually > add a bunch of spm functions (which are not recognised by mcc, probably > because they are in a class definition folder). > > Specifically, including > > '-a', '~/Documents/fieldtrip/external/spm8/spm.m', ... > '-a', '~/Documents/fieldtrip/external/spm8/templates/T1.nii', ... > '-a', '~/Documents/fieldtrip/external/freesurfer/MRIread', ... > '-a', '~/code/Tools/spmbug/dim.m', ... > '-a', '~/code/Tools/spmbug/dtype.m', ... > '-a', '~/code/Tools/spmbug/fname.m', ... > '-a', '~/code/Tools/spmbug/offset.m', ... > '-a', '~/code/Tools/spmbug/scl_slope.m', ... > '-a', '~/code/Tools/spmbug/scl_inter.m', ... > '-a', '~/code/Tools/spmbug/permission.m', ... > '-a', '~/code/Tools/spmbug/niftistruc.m', ... > '-a', '~/code/Tools/spmbug/read_hdr.m', ... > '-a', '~/code/Tools/spmbug/getdict.m', ... > '-a', '~/code/Tools/spmbug/read_extras.m', ... > '-a', '~/code/Tools/spmbug/read_hdr_raw.m', ... > > does the trick. > > Happy compiling, > Anne > > On 1 March 2017 at 19:38, Anne Urai > wrote: > > Hi FieldTrippers, > > I compile my code to run on the supercomputer cluster (without many > matlab licenses), which usually works fine when I do something like: > > /addpath('~/Documents/fieldtrip');/ > /ft_defaults; / > /addpath('~/Documents/fieldtrip/external/spm8');/ > /mcc('-mv', '-N', '-p', 'stats', '-p', 'images', '-p', 'signal', .../ > / '-R', '-nodisplay', '-R', '-singleCompThread', fname);/ > > However, compiling the ft_volumenormalise function gives me some > problems. Specifically, if source is the result of my beamformer > analysis, this code > > / cfg = [];/ > / cfg.parameter = 'pow';/ > / cfg.nonlinear = 'no'; % can warp back to individual/ > / cfg.template = > '/home/aeurai/Documents/fieldtrip/external/spm8/templates/T1.nii';/ > / cfg.write = 'no';/ > / cfg.keepinside = 'no'; % otherwise, > ft_sourcegrandaverage will bug/ > / source = ft_volumenormalise(cfg, source);/ > > works fine when running it within Matlab. However, when I run the > executable after compiling (which completes without error), a > low-level spm function throws the following error: > > /the input is source data with 16777216 brainordinates on a [256 256 > 256] grid/ > /Warning: could not reshape "freq" to the expected dimensions/ > /> In ft_datatype_volume (line 136)/ > /In ft_checkdata (line 350)/ > /In ft_volumenormalise (line 98)/ > /In B6b_sourceContrast_volNormalise (line 57)/ > /Converting the coordinate system from ctf to spm/ > /Undefined function 'fname' for input arguments of type 'struct'/ > /Error in file_array (line 32)/ > /Error in spm_create_vol>create_vol (line 77)/ > /Error in spm_create_vol (line 16)/ > /Error in volumewrite_spm (line 71)/ > /Error in ft_write_mri (line 65)/ > /Error in align_ctf2spm (line 168)/ > /Error in ft_convert_coordsys (line 95)/ > /Error in ft_volumenormalise (line 124)/ > /Error in B6b_sourceContrast_volNormalise (line 57)/ > /MATLAB:UndefinedFunction/ > > I'd be very grateful for hints from anyone who's successfully > compiled the ft_normalise function! Adding the template T1.nii file, > spm8 or freesurfer at compilation does not solve the problem. > Thanks, > > — > Anne E. Urai, MSc > PhD student | Institut für Neurophysiologie und Pathophysiologie > Universitätsklinikum Hamburg-Eppendorf | Martinistrasse 52, 20246 | > Hamburg, Germany > www.anneurai.net / @AnneEUrai > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Guillaume Flandin, PhD Wellcome Trust Centre for Neuroimaging University College London 12 Queen Square London WC1N 3BG From d.painter1 at uq.edu.au Tue Apr 4 03:41:09 2017 From: d.painter1 at uq.edu.au (David Painter) Date: Tue, 4 Apr 2017 01:41:09 +0000 Subject: [FieldTrip] Realtime buffer - possible to spawn multiple buffer threads using non-default values for host and port? In-Reply-To: <1491269842991.43690@uq.edu.au> References: <1491269842991.43690@uq.edu.au> Message-ID: <1491270069170.592@uq.edu.au> Dear Fieldtrippers, I've been using Fieldtrip's buffer.exe in conjunction with biosemi2ft.exe to read EEG data in realtime. I'd like to use buffer.exe to communicate EEG analysis results between Matlab sessions. I was wondering whether it's possible to spawn multiple buffer threads on separate ports? Host 'localhost' and port 1972 are already occupied by reading data from the amplifier. I'd like to use a separate port for additional communication during neurofeedback, but the only value for "port" that seems to work is 1972. "Host" accepts the values of 'localhost' and the current ip4 config address of the computer but can't seem to allow remote connections. Does anyone know if host and port can accept values other than "localhost" and "1972"? I couldn't many explicit examples on this procedure online, so I've posted my code for future reference. David University of Queensland Windows 7 & 10, 64-bit - Matlab R2016b 64-bit % matlab code % direct.realtime ---> where buffer.exe and related files are located: % buffer.exe % pthreadGC2-w64.dll % buffer.mexw32 % pthreadGC2.dll % Labview_DLL.dll % buffer.mexw64 % biosemi2ft.exe % libgcc_s_dw2-1.dll % biosemi_config.txt % libstdc++-6.dll !taskkill /F /IM cmd.exe /T !taskkill /F /IM buffer.exe /T system( ['e: -& cd "' direct.realtime '" & buffer.exe -&'] ); % start buffer.exe cfg.host = 'localhost'; % <---- CAN THESE VALUES CHANGE? cfg.port = uint32( 1972 ); % <----- CAN THESE VALUES CHANGE? cfg.nchans = uint32( 1 ); dat.nchans = uint32( 32 ); dat.nsamples = uint32( 200 ); dat.nevents = uint32( 0 ); dat.fsample = uint32( 200 ); dat.data_type = uint32( 9 ); % single precision data dat.bufsize = uint32( dat.nsamples * dat.nchans * 4 ); dat.buf = single( rand(dat.nsamples,dat.nchans ) ); buffer('put_hdr', dat, cfg.host, cfg.port); % hdr = buffer('get_hdr', [], cfg.host, cfg.port); % ----- read header buffer('put_dat', dat, cfg.host, cfg.port); % hdr = buffer('get_hdr', [], cfg.host, cfg.port); % ----- read header begsample = 1; endsample = 200; dat = buffer('get_dat', [begsample-1 endsample-1], cfg.host, cfg.port); -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarang at cfin.au.dk Tue Apr 4 14:21:00 2017 From: sarang at cfin.au.dk (Sarang S. Dalal) Date: Tue, 4 Apr 2017 12:21:00 +0000 Subject: [FieldTrip] April 10 deadline for MEG Nord conference (Aarhus, May 9-10 2017) Message-ID: <51C59DAA-ECA6-45B1-8EEF-501485EF59BE@cfin.au.dk> Dear all, The abstract submission and registration deadline is coming up on April 10 for the MEG Nord conference at Aarhus University, Denmark, to be held on May 9-10 (+ satellite on May 8). The preliminary program and a link to the registration/submission page can be found at: http://cfin.au.dk/meg-nord-2017/ Please feel free to advertise and forward this information to your colleagues and mailing lists. Note that you can choose between three submission types: poster (default), blitz talk (3 min – to be evaluated) and site symposium (restricted to participating Nordic MEG sites). The latter is to be agreed within each site prior to submission, and the designated individuals should submit their details individually; other submission types are open to all. Note that we do not have the capacity to book accommodation, so please use your favorite booking system. While there are no hotels on-site, any centrally located accommodation in Aarhus would be within easy reach from the AU Lakeside auditorium. For flights, in addition to Aarhus airport (connected mainly to Nordic capitals and London), please consider Billund and Aalborg as well (many direct connections throughout Europe). There are also train connections from Copenhagen and Hamburg. We look forward to welcoming you at MEG Nord 2017! On behalf of the organising committee: Yury Shtyrov, Sarang Dalal, Christopher Bailey From sarang at cfin.au.dk Thu Apr 6 16:13:18 2017 From: sarang at cfin.au.dk (Sarang S. Dalal) Date: Thu, 6 Apr 2017 14:13:18 +0000 Subject: [FieldTrip] OpenMEEG binaries are not correctly installed In-Reply-To: References: Message-ID: Hi Rachel, Contrary to what the message says, you might actually have the OpenMEEG binaries properly installed. :-) You do get the expected output when you ran system('om_assemble’)… The problem is that the program that checks for it (om_checkombin.m) simply doesn’t know how to check for it on Windows. Have a look in om_checkombin.m … maybe you can figure out how to properly check on Windows, or otherwise simply force status = 0 as a temporary hack. Cheers, Sarang On 31 Mar 2017, at 17:40, Rachel S > wrote: Hello fieldtrip community, My name is Rachel and I am a Master student working on a project on Ecog. I am trying to use ft_prepare_headmodel with cfg = 'openmeeg' and I get the error "OpenMEEG binaries are not correctly installed". I use a Windows machine and I already add the openmeeg install folder to 'PATH'. When I ran system('om_assemble'), the output is: om_assemble version 2.1.0 (799) compiled at Aug 17 2011 19:50:41 Not enough arguments Please try "om_assemble -h" or "om_assemble --help " ans = 0 Any suggestions? Thanks in advance. Best wishes, Rachel _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Apr 7 09:10:29 2017 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 7 Apr 2017 09:10:29 +0200 Subject: [FieldTrip] Realtime buffer - possible to spawn multiple buffer threads using non-default values for host and port? In-Reply-To: <1491270069170.592@uq.edu.au> References: <1491269842991.43690@uq.edu.au> <1491270069170.592@uq.edu.au> Message-ID: <6759BA3E-A2E1-456E-8847-73190BE4FF63@donders.ru.nl> Hi David, The buffer mex allows you to start a buffer server within MATLAB. However, the low-level C code does not allow multiple (posix) threads to be started to support multiple buffers in a single executable (i.e. in MATLAB), since the threads would all be reading/writing at the same piece of memory. So the only way to go is to start multiple executables. The way that I usually do this is by starting multiple instances of buffer.exe, specifying for each which port it should listen to. If you start a command line prompt, you can cd to the fieldtrip/realtime/bin/win32 directory and start buffer.exe where you specify the port number. Repeat that (in multiple command windows) for each of the buffers, each with a separate port. The buffer always runs on the computer where you start it. So the answer to the question “can the buffer run on another computer than localhost?” is no. But the code that reads and/or writes to the buffer can connect to another computer. Please note that the firewall settings have to allow for this. On http://www.fieldtriptoolbox.org/development/realtime/fmri you can find an example for a pipeline that involves two buffers. Furthermore I recommend that you do not use the buffer.mex file (it is in private for a good reason!), but rather that you use ft_read_data and ft_write_data. At that level you can also find plenty of examples, e.g. starting at http://www.fieldtriptoolbox.org/getting_started/realtime and looking at the code in fieldtrip/realtime/example. best Robert > On 04 Apr 2017, at 03:41, David Painter wrote: > > Dear Fieldtrippers, > > I've been using Fieldtrip's buffer.exe in conjunction with biosemi2ft.exe to read EEG data in realtime. > > I'd like to use buffer.exe to communicate EEG analysis results between Matlab sessions. I was wondering whether it's possible to spawn multiple buffer threads on separate ports? Host 'localhost' and port 1972 are already occupied by reading data from the amplifier. I'd like to use a separate port for additional communication during neurofeedback, but the only value for "port" that seems to work is 1972. "Host" accepts the values of 'localhost' and the current ip4 config address of the computer but can't seem to allow remote connections. > > Does anyone know if host and port can accept values other than "localhost" and "1972"? > > I couldn't many explicit examples on this procedure online, so I've posted my code for future reference. > > David > University of Queensland > Windows 7 & 10, 64-bit - Matlab R2016b 64-bit > > % matlab code > > % direct.realtime ---> where buffer.exe and related files are located: > % buffer.exe > % pthreadGC2-w64.dll > % buffer.mexw32 > % pthreadGC2.dll > % Labview_DLL.dll > % buffer.mexw64 > % biosemi2ft.exe > % libgcc_s_dw2-1.dll > % biosemi_config.txt > % libstdc++-6.dll > > !taskkill /F /IM cmd.exe /T > !taskkill /F /IM buffer.exe /T > system( ['e: -& cd "' direct.realtime '" & buffer.exe -&'] ); % start buffer.exe > > cfg.host = 'localhost'; % <---- CAN THESE VALUES CHANGE? > cfg.port = uint32( 1972 ); % <----- CAN THESE VALUES CHANGE? > > cfg.nchans = uint32( 1 ); > dat.nchans = uint32( 32 ); > dat.nsamples = uint32( 200 ); > dat.nevents = uint32( 0 ); > dat.fsample = uint32( 200 ); > dat.data_type = uint32( 9 ); % single precision data > dat.bufsize = uint32( dat.nsamples * dat.nchans * 4 ); > dat.buf = single( rand(dat.nsamples,dat.nchans ) ); > > buffer('put_hdr', dat, cfg.host, cfg.port); > % hdr = buffer('get_hdr', [], cfg.host, cfg.port); % ----- read header > buffer('put_dat', dat, cfg.host, cfg.port); > % hdr = buffer('get_hdr', [], cfg.host, cfg.port); % ----- read header > > begsample = 1; > endsample = 200; > > dat = buffer('get_dat', [begsample-1 endsample-1], cfg.host, cfg.port); > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Apr 7 09:21:07 2017 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 7 Apr 2017 09:21:07 +0200 Subject: [FieldTrip] compiling ft_volumenormalise In-Reply-To: References: Message-ID: <0F4760EF-55E7-4C00-8106-6A16CD4F70CD@donders.ru.nl> Hi Anne I opened this feature request http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2787 some time back. I made an initial implementation in a separate branch at https://github.com/robertoostenveld/fieldtrip/tree/bug2787-standalone If you look at https://github.com/fieldtrip/fieldtrip/compare/master...robertoostenveld:bug2787-standalone you can see the changes. It follows the strategy that we used for the compiled megconnectome application for the human connectome project (see https://www.humanconnectome.org/documentation/HCP-pipelines/meg-pipeline.html ), i.e. it compiles into an application which can take a script as argument and which “evals” that script. This allows for the flexibility of making changes to the pipeline and cfg settings without having to recompile. best Robert PS If you can use a single interactive MATLAB session on a head node or compute node from the cluster, you can also look into using the ‘compile’ option in qsubcellfun. See http://www.fieldtriptoolbox.org/faq#distributed_computing > On 15 Mar 2017, at 13:29, Anne Urai wrote: > > If anyone encounters the same problem, compilation works if I manually add a bunch of spm functions (which are not recognised by mcc, probably because they are in a class definition folder). > > Specifically, including > > '-a', '~/Documents/fieldtrip/external/spm8/spm.m', ... > '-a', '~/Documents/fieldtrip/external/spm8/templates/T1.nii', ... > '-a', '~/Documents/fieldtrip/external/freesurfer/MRIread', ... > '-a', '~/code/Tools/spmbug/dim.m', ... > '-a', '~/code/Tools/spmbug/dtype.m', ... > '-a', '~/code/Tools/spmbug/fname.m', ... > '-a', '~/code/Tools/spmbug/offset.m', ... > '-a', '~/code/Tools/spmbug/scl_slope.m', ... > '-a', '~/code/Tools/spmbug/scl_inter.m', ... > '-a', '~/code/Tools/spmbug/permission.m', ... > '-a', '~/code/Tools/spmbug/niftistruc.m', ... > '-a', '~/code/Tools/spmbug/read_hdr.m', ... > '-a', '~/code/Tools/spmbug/getdict.m', ... > '-a', '~/code/Tools/spmbug/read_extras.m', ... > '-a', '~/code/Tools/spmbug/read_hdr_raw.m', ... > > does the trick. > > Happy compiling, > Anne > > On 1 March 2017 at 19:38, Anne Urai > wrote: > Hi FieldTrippers, > > I compile my code to run on the supercomputer cluster (without many matlab licenses), which usually works fine when I do something like: > > addpath('~/Documents/fieldtrip'); > ft_defaults; > addpath('~/Documents/fieldtrip/external/spm8'); > mcc('-mv', '-N', '-p', 'stats', '-p', 'images', '-p', 'signal', ... > '-R', '-nodisplay', '-R', '-singleCompThread', fname); > > However, compiling the ft_volumenormalise function gives me some problems. Specifically, if source is the result of my beamformer analysis, this code > > cfg = []; > cfg.parameter = 'pow'; > cfg.nonlinear = 'no'; % can warp back to individual > cfg.template = '/home/aeurai/Documents/fieldtrip/external/spm8/templates/T1.nii'; > cfg.write = 'no'; > cfg.keepinside = 'no'; % otherwise, ft_sourcegrandaverage will bug > source = ft_volumenormalise(cfg, source); > > works fine when running it within Matlab. However, when I run the executable after compiling (which completes without error), a low-level spm function throws the following error: > > the input is source data with 16777216 brainordinates on a [256 256 256] grid > Warning: could not reshape "freq" to the expected dimensions > > In ft_datatype_volume (line 136) > In ft_checkdata (line 350) > In ft_volumenormalise (line 98) > In B6b_sourceContrast_volNormalise (line 57) > Converting the coordinate system from ctf to spm > Undefined function 'fname' for input arguments of type 'struct' > Error in file_array (line 32) > Error in spm_create_vol>create_vol (line 77) > Error in spm_create_vol (line 16) > Error in volumewrite_spm (line 71) > Error in ft_write_mri (line 65) > Error in align_ctf2spm (line 168) > Error in ft_convert_coordsys (line 95) > Error in ft_volumenormalise (line 124) > Error in B6b_sourceContrast_volNormalise (line 57) > MATLAB:UndefinedFunction > > I'd be very grateful for hints from anyone who's successfully compiled the ft_normalise function! Adding the template T1.nii file, spm8 or freesurfer at compilation does not solve the problem. > Thanks, > > — > Anne E. Urai, MSc > PhD student | Institut für Neurophysiologie und Pathophysiologie > Universitätsklinikum Hamburg-Eppendorf | Martinistrasse 52, 20246 | Hamburg, Germany > www.anneurai.net / @AnneEUrai > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From bart at vision.rutgers.edu Fri Apr 7 09:40:52 2017 From: bart at vision.rutgers.edu (Bart Krekelberg) Date: Fri, 07 Apr 2017 07:40:52 +0000 Subject: [FieldTrip] Postdoctoral Position at Rutgers University Message-ID: Postdoctoral Position at Rutgers University: Neural mechanisms of perception in schizophrenia and bipolar disorder using EEG and transcranial current stimulation. The Division of Schizophrenia Research and Center for Molecular and Behavioral Neuroscience at Rutgers University in New Jersey are seeking to hire a full-time postdoctoral fellow. The overall goal of the project is to use EEG and transcranial current stimulation (tDCS ,tACS) to investigate the neurobiological basis of perceptual differences in schizophrenia and bipolar disorder. The ideal candidate will have a doctoral degree in psychology, neuroscience, cognitive science, or a related field, will be proficient in designing and performing EEG experiments with human participants, and will have a strong affinity with sophisticated data analysis (for instance, using Matlab). The successful candidate will play a pivotal role in the design and further development of experimental protocols, organizing study data, analyzing data, writing up, and presenting scientific results. There will also be significant opportunity for designing and conducting original research of the candidate’s choosing. The Rutgers Newark Campus and the Center for Molecular and Behavioral Neuroscience provide a diverse and stimulating scientific environment. Collaborations are possible with investigators at other affiliated departments and institutions including Rutgers University Brain Imaging Center (http://rubic.rutgers.edu/), Rutgers Center for Cognitive Science ( http://ruccs.rutgers.edu), and Rutgers-Princeton Center for Computational Cognitive Neuropsychiatry (https://ccnp.princeton.edu/about-ccnp/). An infinite amount of cultural stimulation is only a 15 minute train ride away, in New York City. An appointment at NIH postdoctoral salary scales will be made for one year, with the possibility to renew for one or more additional years. Rutgers University is an equal opportunity, affirmative action institution; underrepresented minorities are encouraged to apply. The start date is flexible. Interested applicants should send a CV, cover letter, representative publications, and the names of three references to Caren Alexander ( alexanch at ubhc.rutgers.edu), using the subject heading “Postdoc Search 2017”. Informal inquiries regarding the position are welcome and may be directed to Brian Keane, (brian.keane at rutgers.edu; www.briankeane.org) or Bart Krekelberg (bart at vision.rutgers.edu; www.vision.rutgers.edu) -------------- next part -------------- An HTML attachment was scrubbed... URL: From M.Wimber at bham.ac.uk Fri Apr 7 12:04:43 2017 From: M.Wimber at bham.ac.uk (Maria Wimber) Date: Fri, 7 Apr 2017 10:04:43 +0000 Subject: [FieldTrip] Postdoc for human single neuron project in Birmingham Message-ID: The Memory Group in Birmingham (www.memorybham.com) currently has an open position for a postdoctoral research fellow, funded by a 5-year European Research Council (ERC) grant awarded to Dr Maria Wimber (www.memorybham.com/maria-wimber). The project aims to map the time course of remembering in the human brain, using memory-related patterns of neural activity. It uses a multimodal brain imaging approach, including intracranial EEG, EEG-fMRI, MEG, and high-field fMRI. The postdoc will mainly be involved in the iEEG aspects of the project, including LFP and single-unit recordings from the human medial temporal lobes. These are conducted in close collaboration with the Queen Elisabeth Hospital Birmingham (UK), and other members of the Birmingham Memory Group. We encourage applications from researchers with a strong background in electrophysiology - human or animal - and a general interest in memory. The post is open for applications until April 19th 2017. More details about the position and an application link can be found at www.jobs.ac.uk/job/AYA233/research-fellow For more information, please feel free to contact the PI directly by email at m.wimber at bham.ac.uk. ---------------------- Dr Maria Wimber Senior Lecturer School of Psychology University of Birmingham tel +44 121 4144659 www.memorybham.com/maria-wimber -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Apr 7 14:27:59 2017 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 7 Apr 2017 14:27:59 +0200 Subject: [FieldTrip] new look and feel for the Fieldtrip website Message-ID: Dear FieldTrip users Now that the FieldTrip toolkit course that we hosted here in Nijmegen is over, I have moved the website over to a new version of the dokuwiki content management system (i.e. the PHP code that runs underneath the website). Read on below for the motivation... The old version of the dokuwiki software was flagged by some online scanners as being sensitive to malware, and I received reports that at some universities it was blocked. Although there is no reason to asume that the FT wiki was malicious in any way (the whole site is carefully monitored and locked down), it is of course annoying if it gets flagged as such. The drawback of the new version of the website is that the old template is not compatible, so right now the wiki has a different look and feel. All content is exactly the same, and we will try to get the original appearance back. For those of you for whom the website was blocked: it will take some time before it gets scanned once more (which I suppose happens automatically, as I never requested for it). That means that www.fieldtriptoolbox.org might remain in some blacklist database for some time. You can use new.fieldtriptoolbox.org as a temporary alternative. It points to exactly the same site, but operates over a different web address and proxy server. best regards, Robert PS we could use some help with the website. If you know a bit of PHP/HTML/CSS - or possibly even have dokuwiki experience - and want to help us out, please send me a personal message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tfkustermann at gmail.com Fri Apr 7 17:45:09 2017 From: tfkustermann at gmail.com (Thomas Kustermann) Date: Fri, 7 Apr 2017 17:45:09 +0200 Subject: [FieldTrip] how to make the cfg.selectfeature work in ft_databrowser? In-Reply-To: References: Message-ID: Hello Diego, taking a look at the underlying code it seems that while multiple input arguments to cfg.selectfeature are accepted and passed on to artfctdef.xxx.artifact (line 403), the function then attempts to select the current artifact from cfg.selectfeature even when multiple arguments are entered. opt.ftsel = find(strcmp(artlabel,cfg.selectfeature)); % current artifact/feature being selected (line 629) You could either change this line to: opt.ftsel = find(strcmp(artlabel,cfg.selectfeature{1})); % current artifact/feature being selected automatically selecting the first input argument to cfg.selectfeature as default selection in ft_databrowser or you could write them to the cfg.artfctdef.xxx.artifact manually: cfg.selectfeature = 'a'; cfg.artfctdef.a.artifact = zeros(0,2); cfg.artfctdef.b.artifact = zeros(0,2); ... Best, Thomas On Fri, Mar 31, 2017 at 4:40 PM, Diego Lozano-Soldevilla < dlozanosoldevilla at gmail.com> wrote: > Hi all, > > I'm using ft_databrowser to inspect sleep data and I want to visually mark > different events (spindles, k-complexes, artifacts, so forth) and asign > them to different cfg.artfctdef.xxx.artifact substructures. Could somebody > help me to mark different artifact trial types using the cfg.selectfeature > option? Please find below the code and data to reproduce the error I got. > I'm using the very last fieldtrip version on windows with matlab 7.9b. > > Thanks beforehand, > > Diego > > > > data = []; > data.label = {'Fpz';'F7';'F3';'Fz';'F4';'F8';'C3';'Cz';'C4';'P3';'Pz';' > P4';'O1';'Oz';'O2'}; > data.fsample = 250; > data.trial{1} = rand(size(data.label,1),data.fsample*30); > data.time{1} = (1:data.fsample*30)./data.fsample; > > cfg = []; > cfg.length = 2; > cfg.overlap = 0; > trl = ft_redefinetrial(cfg,data); > > > cfg = []; > cfg.channel = 'all'; > cfg.blocksize = 2; > cfg.selectfeature = {'a';'b'}; > cfg.viewmode = 'vertical'; > events = ft_databrowser(cfg,trl); > > > the input is raw data with 15 channels and 15 trials > detected 0 a artifacts > detected 0 b artifacts > ??? Error using ==> plus > Matrix dimensions must agree. > > Error in ==> ft_databrowser at 745 > hsel = [1 2 3] + (opt.ftsel-1) .*3; > > ??? Reference to non-existent field 'trlvis'. > > Error in ==> ft_databrowser>redraw_cb at 1639 > begsample = opt.trlvis(opt.trlop, 1); > > Error in ==> ft_databrowser>winresize_cb at 2250 > redraw_cb(h,eventdata); > > ??? Error while evaluating figure ResizeFcn > > > > Virus-free. > www.avast.com > > <#m_-281810346689554922_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joeboe at umich.edu Fri Apr 7 20:23:32 2017 From: joeboe at umich.edu (Joseph Lee) Date: Fri, 7 Apr 2017 14:23:32 -0400 Subject: [FieldTrip] Inquiry about Field-Trip usage for multi-channel sources Message-ID: Dear Field Trip Community I am Joe from the Computational Unit of the Center for Consciousness Science, University of Michigan. We are somewhat new to forward modelling and are currently undertaking a project to generate 128 scalp-level channel signals from the 78 source-level signals. We are using the "ft_compute_leadfield" function of FieldTrip in order to accomplish that goal. Is this a valid approach for our goal or were those functions designed for a different purpose? Any comments on this will be helpful for us. Thank you very much. Best, Joe Research Assistant Center for Consciousness Science, University of Michigan Medical School, Ann Arbor, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: From timeehan at gmail.com Fri Apr 7 20:32:49 2017 From: timeehan at gmail.com (Tim Meehan) Date: Fri, 7 Apr 2017 14:32:49 -0400 Subject: [FieldTrip] iEEG square wave 'notch' artifact Message-ID: Dear FieldTrippers, I have a recurring artifact in my iEEG data, a very brief (10-15 ms) square-wave-like 'notch' that occurs intermittently and across many channels. It also varies in polarity and amplitude, seemingly randomly. Here's a link showing an example trial containing many of these artifacts: https://drive.google.com/open?id=0B4m5PGO25j3mYkVPUEI5aDZERDA As of now I've been advised to throw out trials in which these occur, but they are very frequent during some sessions. I wonder if alternatively there is some way to selectively remove these? My guess is one could do some sort of template matching to identify when they occur and interpolate across, but I have no idea how to do that or if it's feasible. Does anyone have any insight? Thank you, Tim -------------- next part -------------- An HTML attachment was scrubbed... URL: From dlozanosoldevilla at gmail.com Fri Apr 7 20:34:52 2017 From: dlozanosoldevilla at gmail.com (Diego Lozano-Soldevilla) Date: Fri, 7 Apr 2017 20:34:52 +0200 Subject: [FieldTrip] how to make the cfg.selectfeature work in ft_databrowser? In-Reply-To: References: Message-ID: Hi Thomas, Thank you for your response. It seems is not working well so I'll file a bug and figure out how to fix it. best, Diego On 7 April 2017 at 17:45, Thomas Kustermann wrote: > Hello Diego, > > taking a look at the underlying code it seems that while multiple input > arguments to cfg.selectfeature are accepted and passed on to > artfctdef.xxx.artifact (line 403), the function then attempts to select the > current artifact from cfg.selectfeature even when multiple arguments are > entered. > opt.ftsel = find(strcmp(artlabel,cfg.selectfeature)); % current > artifact/feature being selected (line 629) > > You could either change this line to: > opt.ftsel = find(strcmp(artlabel,cfg.selectfeature{1})); % current > artifact/feature being selected > > automatically selecting the first input argument to cfg.selectfeature as > default selection in ft_databrowser or you could write them to the cfg.artfctdef.xxx.artifact > manually: > > cfg.selectfeature = 'a'; > cfg.artfctdef.a.artifact = zeros(0,2); > cfg.artfctdef.b.artifact = zeros(0,2); > ... > > Best, > Thomas > > > > On Fri, Mar 31, 2017 at 4:40 PM, Diego Lozano-Soldevilla < > dlozanosoldevilla at gmail.com> wrote: > >> Hi all, >> >> I'm using ft_databrowser to inspect sleep data and I want to visually >> mark different events (spindles, k-complexes, artifacts, so forth) and >> asign them to different cfg.artfctdef.xxx.artifact substructures. Could >> somebody help me to mark different artifact trial types using the >> cfg.selectfeature option? Please find below the code and data to reproduce >> the error I got. I'm using the very last fieldtrip version on windows with >> matlab 7.9b. >> >> Thanks beforehand, >> >> Diego >> >> >> >> data = []; >> data.label = {'Fpz';'F7';'F3';'Fz';'F4';'F8';'C3';'Cz';'C4';'P3';'Pz';'P4 >> ';'O1';'Oz';'O2'}; >> data.fsample = 250; >> data.trial{1} = rand(size(data.label,1),data.fsample*30); >> data.time{1} = (1:data.fsample*30)./data.fsample; >> >> cfg = []; >> cfg.length = 2; >> cfg.overlap = 0; >> trl = ft_redefinetrial(cfg,data); >> >> >> cfg = []; >> cfg.channel = 'all'; >> cfg.blocksize = 2; >> cfg.selectfeature = {'a';'b'}; >> cfg.viewmode = 'vertical'; >> events = ft_databrowser(cfg,trl); >> >> >> the input is raw data with 15 channels and 15 trials >> detected 0 a artifacts >> detected 0 b artifacts >> ??? Error using ==> plus >> Matrix dimensions must agree. >> >> Error in ==> ft_databrowser at 745 >> hsel = [1 2 3] + (opt.ftsel-1) .*3; >> >> ??? Reference to non-existent field 'trlvis'. >> >> Error in ==> ft_databrowser>redraw_cb at 1639 >> begsample = opt.trlvis(opt.trlop, 1); >> >> Error in ==> ft_databrowser>winresize_cb at 2250 >> redraw_cb(h,eventdata); >> >> ??? Error while evaluating figure ResizeFcn >> >> >> >> Virus-free. >> www.avast.com >> >> <#m_3369054593448223812_m_-281810346689554922_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Fri Apr 7 20:56:37 2017 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Fri, 7 Apr 2017 11:56:37 -0700 Subject: [FieldTrip] iEEG square wave 'notch' artifact In-Reply-To: References: Message-ID: Hi Tim, Those may be due to wire tugs, possibly as a result of the subject making (abrupt) movements (of the head). Logically, they are artifacts and need to be dealt with. Hopefully, someone here has found a way to do so effectively. Best, Arjen 2017-04-07 11:32 GMT-07:00 Tim Meehan : > Dear FieldTrippers, > > I have a recurring artifact in my iEEG data, a very brief (10-15 ms) > square-wave-like 'notch' that occurs intermittently and across many > channels. It also varies in polarity and amplitude, seemingly randomly. > Here's a link showing an example trial containing many of these artifacts: > > https://drive.google.com/open?id=0B4m5PGO25j3mYkVPUEI5aDZERDA > > As of now I've been advised to throw out trials in which these occur, but > they are very frequent during some sessions. I wonder if alternatively > there is some way to selectively remove these? My guess is one could do > some sort of template matching to identify when they occur and interpolate > across, but I have no idea how to do that or if it's feasible. Does anyone > have any insight? > > Thank you, > Tim > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From A_Lofts at hotmail.ca Fri Apr 7 23:01:27 2017 From: A_Lofts at hotmail.ca (Andrew Lofts) Date: Fri, 7 Apr 2017 21:01:27 +0000 Subject: [FieldTrip] Fieldtrip Octave MEX files - help Message-ID: Hello Readers, I am attempting to preform dipole fitting using fieldtrip in Octave. I am having trouble whenever the code uses one of the functions that require MEX to work. I have installed liboctave-dev in order for mkoctave to work. Whenever a function such as solid_angle is called it needs to be compiled to a .mex, as preformed in the solid_angle.m file. The call can not find the .c files that are needed. "error: no such file, '/home/jad/EAndrew_Lofts/EyesTest/eeg_pipe_asr_amica/analysis/support/dependencies/eeglab_asr_amica/plugins/Fieldtrip-lite141209/forward/private/solid_angle.m' error: called from bounding_mesh at line 74 column 12 find_outermost_boundary at line 45 column 17 ft_prepare_vol_sens at line 85 column 24 prepare_headmodel at line 94 column 11 ft_dipolefitting at line 233 column 15 dipfit_gridsearch at line 106 column 8 pop_dipfit_gridsearch at line 135 column 10 pop_multifit at line 133 column 13" It appears as if these .c file do no exist. There are plenty of .mex* files in the folder but none of them are recognised by "which solid_angle" except for the one .m file. Can someone help me find the .c files to compile, or help with getting Octave to recognise and run one of the other .mex* variants. Thanks, Andrew Lofts -------------- next part -------------- An HTML attachment was scrubbed... URL: From velmurugan.nimhans at gmail.com Sun Apr 9 02:54:43 2017 From: velmurugan.nimhans at gmail.com (velmurugan jayabal) Date: Sat, 8 Apr 2017 17:54:43 -0700 Subject: [FieldTrip] error in source parcellation and source connectivity analysis Message-ID: Dear Field-trip community, I am having the following errors when computing connectivity analysis. Please any help in this regard would be highly appreciated. Thanks in advance. 1. How to compute atlas based source model grid, from MMP atlas?. Since MMP atlas doesn't contain the *dim *field, the ft_volumelookup function doesn't work prompting me the same error. 2. Alternatively, I had created AAL atlas based source model grid and used to compute source connectivity (img.coh) from PCC beamformer source output. But, I am unable to compute the connectivity value for each parcel using ft_sourceparcellate. I am writing the codes used to derive the same. 3. Is there any acronym or a clear explanation for the parcellation label?. I had read Glasser et al 2016 paper and their resource site. But, I couldn't get complete names or explanation for all the ROIs. CODE: %source is the output of pcc beamformer results. cfg = []; cfg.method ='coh'; cfg.complex = 'absimag'; source_conn_imcoh = ft_connectivityanalysis(cfg, source); atlas =ft_read_atlas ('ROI_MNI_V5.nii'); atlas.pos =source_conn_imcoh.pos; cfg =[]; cfg.method ='mean' cfg.parameter ='cohspctrm'; cfg.parcellation = 'tissue'; parc_conn= ft_sourceparcellate(cfg,source_conn, atlas); I had even tried computing source connectivity interpolation on the atlas before parcellation. But, I am getting a huge array > 50 GB, which exceeds my MATLAB and system limit. -- - sincerely, *Velmurugan Jayabal,* *Magnetoencephalography (MEG) research centre,* *Department of Clinical Neurosciences,* *National Institute of Mental Health and Neurosciences (NIMHANS),* *Bangalore - 560029, Karnataka, India* -------------- next part -------------- An HTML attachment was scrubbed... URL: From Markus.Gschwind at unige.ch Sun Apr 9 11:18:21 2017 From: Markus.Gschwind at unige.ch (Markus Gschwind) Date: Sun, 9 Apr 2017 11:18:21 +0200 Subject: [FieldTrip] Problem with Matlab system commands in OS X (XTerm, Logout, crash, sleep mode) Message-ID: Dear all, I hope to find here an expert who knows an answer to the following problem: I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not able to run big and lengthy matlab jobs because at each logout (which occurs after 2h), Matlab crashes, all results are gone (if they are not save to the HD and XTerm closes. I start Matlab form the XTerm (and not by clicking the App Icon) in order to be able to run system (unix) commands within Matlab. I guess, this behaviour is proper to XTerm, and in case I could find an other way to run system commands from Matlab, probably this could be resolved. Could it be that the running matlab job is not visible to the system which goes to sleep?? For info here the power management info: $ pmset -g custom Battery Power: lidwake 1 autopoweroff 1 autopoweroffdelay 14400 standbydelay 18000 standby 1 ttyskeepawake 0 hibernatemode 3 gpuswitch 2 hibernatefile /var/vm/sleepimage displaysleep 2 sleep 0 acwake 1 halfdim 1 sms 1 lessbright 1 disksleep 10 AC Power: lidwake 1 autopoweroff 1 autopoweroffdelay 14400 standbydelay 18000 standby 0 ttyskeepawake 1 hibernatemode 3 gpuswitch 2 hibernatefile /var/vm/sleepimage womp 1 displaysleep 3 networkoversleep 0 sleep 0 acwake 0 halfdim 1 sms 1 disksleep 60 Many thanks for help! Markus -------------- next part -------------- An HTML attachment was scrubbed... URL: From shoeffner at uos.de Sun Apr 9 12:05:12 2017 From: shoeffner at uos.de (=?UTF-8?Q?Sebastian_H=C3=B6ffner?=) Date: Sun, 09 Apr 2017 10:05:12 +0000 Subject: [FieldTrip] Problem with Matlab system commands in OS X (XTerm, Logout, crash, sleep mode) In-Reply-To: References: Message-ID: Dear Markus, while I don't have a proper solution for your problem with matlab, I can recommend you the little app Caffeine which you should find on the app store. It keeps your Mac awake and should stop your matlab process from terminating. http://lightheadsw.com/caffeine/ Best Sebastian On Sun, Apr 9, 2017, 11:31 Markus Gschwind wrote: > Dear all, > > I hope to find here an expert who knows an answer to the following problem: > > I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not > able to run big and lengthy matlab jobs because at each logout (which > occurs after 2h), Matlab crashes, all results are gone (if they are not > save to the HD and XTerm closes. > > I start Matlab form the XTerm (and not by clicking the App Icon) in order > to be able to run system (unix) commands within Matlab. > > I guess, this behaviour is proper to XTerm, and in case I could find an > other way to run system commands from Matlab, probably this could be > resolved. > > Could it be that the running matlab job is not visible to the system which > goes to sleep?? > > For info here the power management info: > > $ pmset -g custom > Battery Power: > lidwake 1 > autopoweroff 1 > autopoweroffdelay 14400 > standbydelay 18000 > standby 1 > ttyskeepawake 0 > hibernatemode 3 > gpuswitch 2 > hibernatefile /var/vm/sleepimage > displaysleep 2 > sleep 0 > acwake 1 > halfdim 1 > sms 1 > lessbright 1 > disksleep 10 > AC Power: > lidwake 1 > autopoweroff 1 > autopoweroffdelay 14400 > standbydelay 18000 > standby 0 > ttyskeepawake 1 > hibernatemode 3 > gpuswitch 2 > hibernatefile /var/vm/sleepimage > womp 1 > displaysleep 3 > networkoversleep 0 > sleep 0 > acwake 0 > halfdim 1 > sms 1 > disksleep 60 > > > Many thanks for help! > Markus > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Sebastian Höffner Hansastr. 19 49090 Osnabrück Germany +49 152 22 59 23 26 -------------- next part -------------- An HTML attachment was scrubbed... URL: From markus.gschwind at gmail.com Sun Apr 9 16:54:11 2017 From: markus.gschwind at gmail.com (Markus Gschwind) Date: Sun, 9 Apr 2017 16:54:11 +0200 Subject: [FieldTrip] Problem with Matlab system commands in OS X (XTerm, Logout, crash, sleep mode) In-Reply-To: References: Message-ID: Hi Sebastian, Thanks I forgot this workaround. Yes, very useful! Best, Markus 2017-04-09 12:05 GMT+02:00 Sebastian Höffner : > Dear Markus, > > while I don't have a proper solution for your problem with matlab, I can > recommend you the little app Caffeine which you should find on the app > store. It keeps your Mac awake and should stop your matlab process from > terminating. > > http://lightheadsw.com/caffeine/ > > Best > Sebastian > > On Sun, Apr 9, 2017, 11:31 Markus Gschwind > wrote: > >> Dear all, >> >> I hope to find here an expert who knows an answer to the following >> problem: >> >> I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not >> able to run big and lengthy matlab jobs because at each logout (which >> occurs after 2h), Matlab crashes, all results are gone (if they are not >> save to the HD and XTerm closes. >> >> I start Matlab form the XTerm (and not by clicking the App Icon) in order >> to be able to run system (unix) commands within Matlab. >> >> I guess, this behaviour is proper to XTerm, and in case I could find an >> other way to run system commands from Matlab, probably this could be >> resolved. >> >> Could it be that the running matlab job is not visible to the system >> which goes to sleep?? >> >> For info here the power management info: >> >> $ pmset -g custom >> Battery Power: >> lidwake 1 >> autopoweroff 1 >> autopoweroffdelay 14400 >> standbydelay 18000 >> standby 1 >> ttyskeepawake 0 >> hibernatemode 3 >> gpuswitch 2 >> hibernatefile /var/vm/sleepimage >> displaysleep 2 >> sleep 0 >> acwake 1 >> halfdim 1 >> sms 1 >> lessbright 1 >> disksleep 10 >> AC Power: >> lidwake 1 >> autopoweroff 1 >> autopoweroffdelay 14400 >> standbydelay 18000 >> standby 0 >> ttyskeepawake 1 >> hibernatemode 3 >> gpuswitch 2 >> hibernatefile /var/vm/sleepimage >> womp 1 >> displaysleep 3 >> networkoversleep 0 >> sleep 0 >> acwake 0 >> halfdim 1 >> sms 1 >> disksleep 60 >> >> >> Many thanks for help! >> Markus >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- > > Sebastian Höffner > Hansastr. 19 > 49090 Osnabrück > Germany > > +49 152 22 59 23 26 <+49%201522%202592326> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From seymourr at aston.ac.uk Mon Apr 10 13:14:10 2017 From: seymourr at aston.ac.uk (Seymour, Robert (Research Student)) Date: Mon, 10 Apr 2017 11:14:10 +0000 Subject: [FieldTrip] error in source parcellation and source connectivity analysis Message-ID: Hi Velmurugan, You might want to look at this tutorial: http://www.fieldtriptoolbox.org/tutorial/networkanalysis?s[]=ft&s[]=networkanalysis I might be wrong but I think the AAL atlas currently implemented in Fieldtrip does not yet contain a .parcellation field, which is why you might be running into problems. You could try to reverse engineer this using the tissuelabel field I guess. For more info on the full label names use wb_command -file-information from the HCP toolbox, or look at the supplementary materials on the Glasser paper. Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From Oleksiy.Bobrov at uni-konstanz.de Mon Apr 10 13:24:08 2017 From: Oleksiy.Bobrov at uni-konstanz.de (Oleksiy Bobrov) Date: Mon, 10 Apr 2017 13:24:08 +0200 Subject: [FieldTrip] ft_artifact_threshold + ft_rejectartifact issue? Message-ID: <40c0c482-714a-7b33-8120-e3e72d15054b@uni-konstanz.de> Hi everyone, I try automatically reject segment from my EEG-Data withamplitudes out of the range 200µV. I use the following function for it: function [fnData, conf] = rejectForRange(inData) cfg = []; cfg.continuous = 'no'; cfg.artfctdef.threshold.bpfilter = 'no'; cfg.artfctdef.threshold.range = 200; %in uV/T, default inf % cfg.artfctdef.threshold.min = -100; %in uV/T, default -inf % cfg.artfctdef.threshold.max = 100; %in uV/T, default inf [conf, artData] = ft_artifact_threshold(cfg, inData); cfg = []; cfg.artfctdef.xxx.artifact = artData; cfg.artfctdef.reject = 'complete'; fnData = ft_rejectartifact(cfg, inData); The function is evaluated with no errors. But the output is not correct. Indeed, a lot of artifact-segments are deleted. But there are still a lot of segments with amplitudes far out of the range of 200µV (visual controlled with ft_rejectvisual()). If try the rejectForRange()-function once more (on the output-data from the first run), so it founds no artifacts at all. But they are in the data. Thank you for any help in advance. Best regards Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: From beese at cbs.mpg.de Mon Apr 10 14:50:13 2017 From: beese at cbs.mpg.de (Caroline Beese) Date: Mon, 10 Apr 2017 14:50:13 +0200 (CEST) Subject: [FieldTrip] cluster-based statistics with one covariate Message-ID: <1329277450.115066.1491828613491.JavaMail.zimbra@cbs.mpg.de> Dear all, I'm trying to take age as a covariate into my cluster-based statistics comparing two dependent measures. I have read about two options: A) to use ft_regressconfound before I do the stats or B) to create a design with a third row using the .cvar field in the 'depsamplesregrT' statfun. I understand that for correcting head motions ft_regressconfound is a great option but for taking age into account as a covariate, it doesn't seem intuitive to me to do this within-subject on a trial-by-trial basis having only one number per person. Or can you use this function differently? However, for option B) the subfunction 'unitselvec' is missing and this seems to be an issue for several years. So I was wondering whether anyone has ever tried to fix this problem themselves and wouldn't mind sharing? More generally, if anyone has successfully implemented a cluster-based statistics with one or more covariates, please share your experience, it would be greatly appreciated. Best Regards, Caroline -- Caroline Beese PhD student Max-Planck Institute for Human Cognitive and Brain Sciences Department of Neuropsychology Stephanstr. 1a 04103 Leipzig office phone: +49 (0) 341 9940 129 www.cbs.mpg.de/staff/beese-11586 From m.papen at uni-koeln.de Tue Apr 11 10:34:21 2017 From: m.papen at uni-koeln.de (Michael von Papen) Date: Tue, 11 Apr 2017 10:34:21 +0200 Subject: [FieldTrip] Conference: Coupling & Causality in Complex Systems Message-ID: ============================================================== CALL FOR PAPERS (Deadline: June 01, 2017) http://c3s.uni-koeln.de ============================================================== INTERNATIONAL CONFERENCE: *Coupling and Causality in Complex Systems* September 25-27, 2017, Cologne, Germany -------------------------------------------------------------- The interdisciplinary conference Coupling and Causality in Complex Systems (C3S) is hosted by the Competence Area 3: Quantitative Modeling of Complex Systems of the University of Cologne (UoC), Germany. It is organized by the Institute of Geophysics & Meteorology, UoC, the Institute of Clinical Neuroscience and Psychology, Heinrich-Heine University Düsseldorf and the Department of Cognitive Neuroscience at the Research Center Juelich. -------------------------------------------------------------- *Abstract* Complex systems such as the human brain, Earth’s climate and economy are characterized by a multitude of coupled processes on different spatial and temporal scales. In order to better understand the dynamics of the system at hand each scientific area has developed specific tools to identify, model and quantify these processes. The conference Coupling and Causality in Complex Systems (C3S) will present a collection of these approaches with the aim to provide scientists with new analysis strategies for their field. The conference focuses on how to characterize a complex system and on the methods for estimating and modeling of statistical coupling (e.g. network coherence, creation and modulation of small networks and local or long-range synchronization by cross frequency phase-phase and phase-amplitude coupling) and causality (e.g. Granger causality, transfer entropy). Therefore, data analysts from different study fields including neuroscience, mathematics, physics, biology, and economy will present their approaches with a particular focus on the methods they use. The aim of this conference is to foster discussions and the transdisciplinary exchange of advanced techniques, methods, and algorithms, thereby stimulating potential future collaborations. -------------------------------------------------- *Invited Speakers* Elissa Aminoff - Department of Psychology, Carnegie Mellon University, Pittsburgh, USA Jörg Breitung - Macroeconomic Policy Institute, University of Cologne, Germany David Gross - Institute of Theoretical Physics, University of Cologne, Germany Philip Holmes - Mechanical and Aerospace Engineering / Princeton Neuroscience Institute, Princeton, USA Ankit Khambhati - Department of Bioengineering, University of Pennsylvania, USA Laura Marzetti - Department of Neuroscience, Università degli Studi "G. d'Annunzio" Chieti - Pescara Arkady Pikovsky - Institute of Physics and Astronomy, University Potsdam, Germany Michael Rosenblum - Institute of Physics and Astronomy, University Potsdam, Germany Jakob Runge - The Grantham Institute for Climate Change, Imperial College London -------------------------------------------------- *Preliminary Session Program* We will have different sessions with differing topics and each session will be opened by one of the invited speakers. Here is a preliminary version of our program: Session 1 Synchronization I Arkady Pikovsky Session 2 Synchronization II Silvia Daun Session 3 Coupled oscillators I Phil Holmes Session 4 Coupled oscillators II Michael Rosenblum Session 5 Phase coupling Laura Marzetti Session 6 Network structures I Elissa Aminoff Session 7 Network structures II Ankit Khambati Session 8 Bayesian networks David Gross Session 9 Granger causality I Jörg Breitung Session 10 Granger causality II Esther Florin Session 11 Causal network measures Jakob Runge Further topics of interest for the conference include, amongst others, research and methods development on: functional connectivity, (partial directed) coherence, network topology, graph-theoretic measures, directed graphs, nonlinear dynamics of complex systems, complex spatio-temporal systems, mutual information and transfer entropy. -------------------------------------------------------------- *Scientific Organizing Committee* Silvia Daun - Institute of Zoology, University of Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany Esther Florin - Institute of Clinical Neuroscience and Psychology, Düsseldorf, Germany Joachim Gross - Center for Cognitive Neuroimaging, Glasgow, UK Michael von Papen - Institute of Geophysics & Meteorology, Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany -------------------------------------------------------------- PAPER SUBMISSION AND REGISTRATION Authors are invited to submit conference abstracts with up to 400 words. Authors of exceptional abstracts will be given the opportunity to present their research in a talk. However, poster sessions will be provided with ample time for discussions. For your submission, please use the conference website c3s.uni-koeln.de. To register, please send an email with the subject "registration" to c3s-conference at uni-koeln.de. Please be sure to include your full name, your affiliation and whether you qualify as student (also PhD candidates) or not. The registration fee will cover snacks and refreshments during coffee breaks, lunch and a dinner with all participants. Early-bird registration is available until July 10 with a reduced fee of 120 EUR (60 EUR for students), after July 10 the registration fee will be 240 EUR (120 EUR for students). -------------------------------------------------------------- IMPORTANT DATES Paper Submission deadline: June 01, 2017 Author Notification: mid June, 2017 Early-bird registration: July 10, 2017 Conference: September 25-27, 2017 ============================================================== Please find the call for papers and more information at the conference website: http://c3s.uni-koeln.de. For questions regarding the conference feel free to contact us via c3s-conference at uni-koeln.de. -- ------------------------------------------ UNIVERSITY OF COLOGNE Institute of Geophysics & Meteorology Coordinator of Competence Area III: Quantitative Modeling of Complex Systems Dr. Michael von Papen Email: m.papen at uni-koeln.de http://www.uni-koeln.de/~vpapenm http://complexsystems.uni-koeln.de From jose.uriguen at deusto.es Tue Apr 11 12:08:44 2017 From: jose.uriguen at deusto.es (=?UTF-8?Q?Jos=C3=A9_Antonio_Uriguen_Garaizabal?=) Date: Tue, 11 Apr 2017 12:08:44 +0200 Subject: [FieldTrip] Need help with cluster-based permutation test with 3 groups of subjects Message-ID: Dear all My name is Toni and I am working on EEG signal processing at University of Deusto, Bilbao, Spain. More specifically, right now trying to apply cluster-based permutation testing to determine whether there exist differences among 3 groups of subjects. So, for my testing, subject groups are E, EN and N, the 2 former being different types of patients and the latter being a control group. I am forming clusters based on proximity (in space) and each subject is characterized by a matrix of values that vary in 2D (per channel and another variable related but not equal to frequency). By means of a T-statistic (indepsamplesT) I can find differences in between E and EN, but I find no clusters/differences in between E and N or EN and N, even though hypothetically (I think) they should exist. By means of an F-statistic (indepsamplesF) I can find differences among the 3 groups at the same time, then also between E and EN and no differences between E and N or EN and N... Am I missing something? I do not understand why the might exist a significant cluster when comparing all 3 groups that does not exist in the 1vs1 comparisons, even though the cluster is not the same I obtain when I compare E vs EN... For additional information, I attach how I run the test: cfg.method = 'distance'; cfg.neighbourdist = 1; cfg.elec = ft_datatype_sens(subjEN{1}.elec); neighbours = ft_prepare_neighbours(cfg); cfg = []; cfg.channel = {'EEG'}; cfg.latency = 'all'; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.neighbours = neighbours; % same as defined for the between-trials experiment cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 5000; nsubj = size(subjE,2)+size(subjEN,2); design = zeros(2,nsubj); design(1,:) = [1:nsubj/2 1:nsubj/2]; design(2,1:size(subjE,2)) = 1; design(2,size(subjE,2)+1:nsubj) = 2; cfg.design = design; cfg.ivar = 2; [stat] = ft_timelockstatistics(cfg, subjEN{:}, subjE{:}); When I compare the 3 groups cfg.method = 'distance'; cfg.neighbourdist = 1; cfg.elec = ft_datatype_sens(subjEN{1}.elec); neighbours = ft_prepare_neighbours(cfg); cfg = []; cfg.channel = {'EEG'}; cfg.latency = 'all'; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesF'; %F-statistic cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.neighbours = neighbours; % same as defined for the between-trials experiment cfg.tail = 1; %One sided cfg.clustertail = 1; cfg.alpha = 0.025; cfg.numrandomization = 5000; nsubj1 = size(subjE,2); nsubj2 = size(subjEN,2); nsubj3 = size(subjN,2); nsubj = nsubj1+nsubj2+nsubj3; design = zeros(2,nsubj); design(1,:) = [1:nsubj1 1:nsubj2 1:nsubj3]; design(2,1:nsubj1) = 1; design(2,nsubj1+1:nsubj1+nsubj2) = 2; design(2,nsubj1+nsubj2+1:nsubj) = 3; cfg.design = design; cfg.ivar = 2; %2nd row is independent var [stat] = ft_timelockstatistics(cfg, subjE{:}, subjEN{:}, subjN{:}); Then, subjE, subjN and subjEN are like this: Eall = subjE{:} Eall = struct with fields: label: {1×18 cell} fsample: 200 elec: [1×1 struct] trial: {[18×115 double]} time: {[1×115 double]} cfg: [1×1 struct] Thanks in advance -- *Jose Antonio Urigüen* PostDoc at Deustotech-LIFE (eVIDA Research Group) [image: Deusto] Universidad de Deusto / Deustuko Unibertsitatea / University of Deusto Facultad de Ingeniería, 4ª Planta Avda. Universidades 24. 48007 Bilbao Tel. +34 94 413 90 00 / Mov. +34 656 711 643 Ext. 2980 jose.uriguen at deusto.es Web: evida.deusto.es *www.deusto.es * -------------- next part -------------- An HTML attachment was scrubbed... URL: From icelandhouse at gmail.com Tue Apr 11 12:13:42 2017 From: icelandhouse at gmail.com (Maris Skujevskis) Date: Tue, 11 Apr 2017 12:13:42 +0200 Subject: [FieldTrip] Error when running ft_sourceanalysis with stats across two conditions Message-ID: Dear Fieldtrip developers/source localizing experts, I get an error when running ft_sourceanalysis on two EEG conditions with the statistical testing (permutation) enabled (no issues with single condition and no statistics). As far as I can see, I am doing everything right (as per ft_sourceanalysis reference page; my fieldtrip version: fieldtrip-20161122). Please correct me where I am wrong or ask for more information in case what I paste/explain below is not sufficient. CODE INPUT: cfg = []; cfg.method = 'dics'; cfg.frequency = 10; cfg.grid = leadfield; cfg.keepleadfield = 'no'; cfg.headmodel = vol; cfg.dics.keepfilter = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.fixedori = 'yes'; cfg.dics.keepmom = 'yes'; cfg.dics.realfilter = 'yes'; cfg.grid.filter = source_cmb.avg.filter; cfg.permutation = 'yes'; cfg.numpermutation = 500; sourceStatsAB = ft_sourceanalysis(cfg, condA, condB); COMMAND WINDOW OUTPUT: the input is freq data with 128 channels, 1 frequencybins and no timebins the input is freq data with 128 channels, 1 frequencybins and no timebins the call to "ft_selectdata" took 0 seconds converting the linearly indexed channelcombinations into a square CSD-matrix using electrodes specified in the data converting units from 'cm' to 'mm' determining source compartment (3) projecting electrodes on skin surface combining electrode transfer and system matrix creating dipole grid based on user specified dipole positions using gradiometers specified in the configuration 5124 dipoles inside, 0 dipoles outside brain the call to "ft_prepare_sourcemodel" took 0 seconds the call to "ft_selectdata" took 0 seconds the call to "ft_selectdata" took 0 seconds 2 conditions, each with 3 data objects averaging 182 replications for one condition averaging 182 replications for one condition 2 conditions, each with 3 data objects <<<<<<<<<<<<<---------- what are the "3 data objects"? creating 100 random permutations from total 6.129982e+54 HERE COMES THE ERROR: Error using prepare_resampled_data (line 381) the dimensions should be the same for every condition Error in ft_sourceanalysis (line 561) [dum, rnd_aCf, rnd_aCr, rnd_aPr, rnd_bCf, rnd_bCr, rnd_bPr] = prepare_resampled_data(cfg, aCf, aCr, aPr, bCf, bCr, bPr); When checking the function prepare_resampled_data, it turns out that it requires a cell named "datain" to have the same size matrices column-wise (whatever the columns may represent) : datain = [182x128x128 double] [182x128 double] [182x1 double] [182x128x128 double] [ 1x128 double] [ NaN] My input data condA and condB have identical dimensions, so I have no idea what has gone wrong here: condA = label: {128x1 cell} dimord: 'rpt_chan_freq' freq: 9.8462 powspctrm: [182x128 double] labelcmb: {8128x2 cell} crsspctrm: [182x8128 double] cumsumcnt: [182x1 double] cumtapcnt: [182x1 double] elec: [1x1 struct] trialinfo: [182x22 double] cfg: [1x1 struct] condB = label: {128x1 cell} dimord: 'rpt_chan_freq' freq: 9.8462 powspctrm: [182x128 double] labelcmb: {8128x2 cell} crsspctrm: [182x8128 double] cumsumcnt: [182x1 double] cumtapcnt: [182x1 double] elec: [1x1 struct] trialinfo: [182x22 double] cfg: [1x1 struct] Thanks for your input! Best wishes, Maris On Sun, Apr 9, 2017 at 12:00 PM, wrote: > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. error in source parcellation and source connectivity analysis > (velmurugan jayabal) > 2. Problem with Matlab system commands in OS X (XTerm, Logout, > crash, sleep mode) (Markus Gschwind) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 8 Apr 2017 17:54:43 -0700 > From: velmurugan jayabal > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] error in source parcellation and source > connectivity analysis > Message-ID: > mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Field-trip community, > > I am having the following errors when computing connectivity > analysis. Please any help in this regard would be highly appreciated. > Thanks in advance. > > 1. How to compute atlas based source model grid, from MMP atlas?. Since MMP > atlas doesn't contain the *dim *field, the ft_volumelookup function doesn't > work prompting me the same error. > > > 2. Alternatively, I had created AAL atlas based source model grid and used > to compute source connectivity (img.coh) from PCC beamformer source output. > But, I am unable to compute the connectivity value for each parcel using > ft_sourceparcellate. I am writing the codes used to derive the same. > > 3. Is there any acronym or a clear explanation for the parcellation label?. > I had read Glasser et al 2016 paper and their resource site. But, I > couldn't get complete names or explanation for all the ROIs. > > > CODE: > %source is the output of pcc beamformer results. > cfg = []; > cfg.method ='coh'; > cfg.complex = 'absimag'; > source_conn_imcoh = ft_connectivityanalysis(cfg, source); > > atlas =ft_read_atlas ('ROI_MNI_V5.nii'); > atlas.pos =source_conn_imcoh.pos; > cfg =[]; > cfg.method ='mean' > cfg.parameter ='cohspctrm'; > cfg.parcellation = 'tissue'; > parc_conn= ft_sourceparcellate(cfg,source_conn, atlas); > > I had even tried computing source connectivity interpolation on the atlas > before parcellation. But, I am getting a huge array > 50 GB, which exceeds > my MATLAB and system limit. > > > -- > - sincerely, > *Velmurugan Jayabal,* > *Magnetoencephalography (MEG) research centre,* > *Department of Clinical Neurosciences,* > > *National Institute of Mental Health and Neurosciences (NIMHANS),* > *Bangalore - 560029, Karnataka, India* > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170408/ede3c3c1/attachment-0001.html> > > ------------------------------ > > Message: 2 > Date: Sun, 9 Apr 2017 11:18:21 +0200 > From: Markus Gschwind > To: FieldTrip discussion list > Subject: [FieldTrip] Problem with Matlab system commands in OS X > (XTerm, Logout, crash, sleep mode) > Message-ID: > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I hope to find here an expert who knows an answer to the following problem: > > I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not able > to run big and lengthy matlab jobs because at each logout (which occurs > after 2h), Matlab crashes, all results are gone (if they are not save to > the HD and XTerm closes. > > I start Matlab form the XTerm (and not by clicking the App Icon) in order > to be able to run system (unix) commands within Matlab. > > I guess, this behaviour is proper to XTerm, and in case I could find an > other way to run system commands from Matlab, probably this could be > resolved. > > Could it be that the running matlab job is not visible to the system which > goes to sleep?? > > For info here the power management info: > > $ pmset -g custom > Battery Power: > lidwake 1 > autopoweroff 1 > autopoweroffdelay 14400 > standbydelay 18000 > standby 1 > ttyskeepawake 0 > hibernatemode 3 > gpuswitch 2 > hibernatefile /var/vm/sleepimage > displaysleep 2 > sleep 0 > acwake 1 > halfdim 1 > sms 1 > lessbright 1 > disksleep 10 > AC Power: > lidwake 1 > autopoweroff 1 > autopoweroffdelay 14400 > standbydelay 18000 > standby 0 > ttyskeepawake 1 > hibernatemode 3 > gpuswitch 2 > hibernatefile /var/vm/sleepimage > womp 1 > displaysleep 3 > networkoversleep 0 > sleep 0 > acwake 0 > halfdim 1 > sms 1 > disksleep 60 > > > Many thanks for help! > Markus > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170409/ce9b8000/attachment-0001.html> > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 77, Issue 6 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Wed Apr 12 04:35:29 2017 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Wed, 12 Apr 2017 10:35:29 +0800 Subject: [FieldTrip] cluster-based statistics with one covariate Message-ID: Dear Caroline, If your conditions are within-subject, then I think the best way to do this is to construct a dataset representing the conditionA - conditionB difference for each subject, and then using ft_statfun_indepsamplesregrT to regress the subject-wise difference on age. See e.g. https://mailman.science.ru.nl/pipermail/fieldtrip/2016-May/010528.html for a thread discussing a similar approach. Best, Steve --- Stephen Politzer-Ahles The Hong Kong Polytechnic University Department of Chinese and Bilingual Studies http://www.mypolyuweb.hk/~sjpolit/ > Message: 3 > Date: Mon, 10 Apr 2017 14:50:13 +0200 (CEST) > From: Caroline Beese > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] cluster-based statistics with one covariate > Message-ID: > <1329277450.115066.1491828613491.JavaMail.zimbra at cbs.mpg.de> > Content-Type: text/plain; charset=utf-8 > > Dear all, > > I'm trying to take age as a covariate into my cluster-based statistics > comparing two dependent measures. > > I have read about two options: > > A) to use ft_regressconfound before I do the stats or > B) to create a design with a third row using the .cvar field in the > 'depsamplesregrT' statfun. > > I understand that for correcting head motions ft_regressconfound is a > great option but for taking age into account as a covariate, it doesn't > seem intuitive to me to do this within-subject on a trial-by-trial basis > having only one number per person. Or can you use this function differently? > > However, for option B) the subfunction 'unitselvec' is missing and this > seems to be an issue for several years. So I was wondering whether anyone > has ever tried to fix this problem themselves and wouldn't mind sharing? > > More generally, if anyone has successfully implemented a cluster-based > statistics with one or more covariates, please share your experience, it > would be greatly appreciated. > > Best Regards, > Caroline > > -- > Caroline Beese > PhD student > > Max-Planck Institute for Human Cognitive and Brain Sciences > Department of Neuropsychology > Stephanstr. 1a > 04103 Leipzig > > office phone: +49 (0) 341 9940 129 > > www.cbs.mpg.de/staff/beese-11586 > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From robin.kampe at liu.se Wed Apr 12 11:01:14 2017 From: robin.kampe at liu.se (=?iso-8859-1?Q?Robin_K=E4mpe?=) Date: Wed, 12 Apr 2017 09:01:14 +0000 Subject: [FieldTrip] Installing gui_streamer Message-ID: Hi! We want to, from scratch, set up a real time fMRI capabilities. Your documentation covers this quite well. I do, however, get stuck on point 1 which is to launch the gui_streamer from the console. How does one obtain/install this program on our Siemens Prisma? Best, Robin Kämpe Research Engineer [Linköping University] CSAN, Center for Social and Affective Neuroscience Department of Clinical and Experimental Medicine, IKE Mobile: +46 (0)73 8005561 Please visit us at www.liu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From laxmi.shaw22 at gmail.com Thu Apr 13 08:07:37 2017 From: laxmi.shaw22 at gmail.com (Laxmi Shaw) Date: Thu, 13 Apr 2017 11:37:37 +0530 Subject: [FieldTrip] fieldtrip Digest, Vol 77, Issue 9 In-Reply-To: References: Message-ID: Dear Fieldtrip user, Can anybody have EEG 64 channel head model or anyother web source where i can get the 64 channel head model then please share with me . On Wed, Apr 12, 2017 at 3:30 PM, wrote: > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Need help with cluster-based permutation test with 3 groups > of subjects (Jos? Antonio Uriguen Garaizabal) > 2. Error when running ft_sourceanalysis with stats across two > conditions (Maris Skujevskis) > 3. Re: cluster-based statistics with one covariate > (Stephen Politzer-Ahles) > 4. Installing gui_streamer (Robin K?mpe) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 11 Apr 2017 12:08:44 +0200 > From: Jos? Antonio Uriguen Garaizabal > To: FieldTrip discussion list > Subject: [FieldTrip] Need help with cluster-based permutation test > with 3 groups of subjects > Message-ID: > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all > > > My name is Toni and I am working on EEG signal processing at University of > Deusto, Bilbao, Spain. More specifically, right now trying to > apply cluster-based permutation testing to determine whether there exist > differences among 3 groups of subjects. > > > So, for my testing, subject groups are E, EN and N, the 2 former being > different types of patients and the latter being a control group. I am > forming clusters based on proximity (in space) and each subject is > characterized by a matrix of values that vary in 2D (per channel and > another variable related but not equal to frequency). > > By means of a T-statistic (indepsamplesT) I can find differences in between > E and EN, but I find no clusters/differences in between E and N or EN and > N, even though hypothetically (I think) they should exist. By means of an > F-statistic (indepsamplesF) I can find differences among the 3 groups at > the same time, then also between E and EN and no differences between E and > N or EN and N... > > Am I missing something? I do not understand why the might exist a > significant cluster when comparing all 3 groups that does not exist in the > 1vs1 comparisons, even though the cluster is not the same I obtain when I > compare E vs EN... > > > For additional information, I attach how I run the test: > > cfg.method = 'distance'; > cfg.neighbourdist = 1; > cfg.elec = ft_datatype_sens(subjEN{1}.elec); > neighbours = ft_prepare_neighbours(cfg); > > cfg = []; > cfg.channel = {'EEG'}; > cfg.latency = 'all'; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.neighbours = neighbours; % same as defined for the > between-trials experiment > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 5000; > > nsubj = size(subjE,2)+size(subjEN,2); > design = zeros(2,nsubj); > design(1,:) = [1:nsubj/2 1:nsubj/2]; > design(2,1:size(subjE,2)) = 1; > design(2,size(subjE,2)+1:nsubj) = 2; > > cfg.design = design; > cfg.ivar = 2; > > [stat] = ft_timelockstatistics(cfg, subjEN{:}, subjE{:}); > > > When I compare the 3 groups > > cfg.method = 'distance'; > cfg.neighbourdist = 1; > cfg.elec = ft_datatype_sens(subjEN{1}.elec); > neighbours = ft_prepare_neighbours(cfg); > > cfg = []; > cfg.channel = {'EEG'}; > cfg.latency = 'all'; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesF'; %F-statistic > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.neighbours = neighbours; % same as defined for the > between-trials experiment > cfg.tail = 1; %One sided > cfg.clustertail = 1; > cfg.alpha = 0.025; > cfg.numrandomization = 5000; > > nsubj1 = size(subjE,2); > nsubj2 = size(subjEN,2); > nsubj3 = size(subjN,2); > nsubj = nsubj1+nsubj2+nsubj3; > > design = zeros(2,nsubj); > design(1,:) = [1:nsubj1 1:nsubj2 1:nsubj3]; > design(2,1:nsubj1) = 1; > design(2,nsubj1+1:nsubj1+nsubj2) = 2; > design(2,nsubj1+nsubj2+1:nsubj) = 3; > > cfg.design = design; > cfg.ivar = 2; %2nd row is independent var > > [stat] = ft_timelockstatistics(cfg, subjE{:}, subjEN{:}, subjN{:}); > > > Then, subjE, subjN and subjEN are like this: > > Eall = subjE{:} > > Eall = > > struct with fields: > > label: {1?18 cell} > fsample: 200 > elec: [1?1 struct] > trial: {[18?115 double]} > time: {[1?115 double]} > cfg: [1?1 struct] > > > Thanks in advance > > -- > *Jose Antonio Urig?en* > PostDoc at Deustotech-LIFE (eVIDA Research Group) > [image: Deusto] > Universidad de Deusto / Deustuko Unibertsitatea / University of Deusto > Facultad de Ingenier?a, 4? Planta > Avda. Universidades 24. 48007 Bilbao > Tel. +34 94 413 90 00 / Mov. +34 656 711 643 > Ext. 2980 > jose.uriguen at deusto.es > Web: evida.deusto.es > *www.deusto.es * > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170411/7a169976/attachment-0001.html> > > ------------------------------ > > Message: 2 > Date: Tue, 11 Apr 2017 12:13:42 +0200 > From: Maris Skujevskis > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Error when running ft_sourceanalysis with stats > across two conditions > Message-ID: > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Fieldtrip developers/source localizing experts, > > I get an error when running ft_sourceanalysis on two EEG conditions with > the statistical testing (permutation) enabled (no issues with single > condition and no statistics). > As far as I can see, I am doing everything right (as per ft_sourceanalysis > reference page; my fieldtrip version: fieldtrip-20161122). Please correct > me where I am wrong or ask for more information in case what I > paste/explain below is not sufficient. > > CODE INPUT: > > cfg = []; > cfg.method = 'dics'; > cfg.frequency = 10; > cfg.grid = leadfield; > cfg.keepleadfield = 'no'; > cfg.headmodel = vol; > cfg.dics.keepfilter = 'yes'; > cfg.dics.lambda = '5%'; > cfg.dics.fixedori = 'yes'; > cfg.dics.keepmom = 'yes'; > cfg.dics.realfilter = 'yes'; > cfg.grid.filter = source_cmb.avg.filter; > cfg.permutation = 'yes'; > cfg.numpermutation = 500; > > sourceStatsAB = ft_sourceanalysis(cfg, condA, condB); > > COMMAND WINDOW OUTPUT: > > the input is freq data with 128 channels, 1 frequencybins and no timebins > the input is freq data with 128 channels, 1 frequencybins and no timebins > the call to "ft_selectdata" took 0 seconds > converting the linearly indexed channelcombinations into a square > CSD-matrix > using electrodes specified in the data > converting units from 'cm' to 'mm' > determining source compartment (3) > projecting electrodes on skin surface > combining electrode transfer and system matrix > creating dipole grid based on user specified dipole positions > using gradiometers specified in the configuration > 5124 dipoles inside, 0 dipoles outside brain > the call to "ft_prepare_sourcemodel" took 0 seconds > the call to "ft_selectdata" took 0 seconds > the call to "ft_selectdata" took 0 seconds > 2 conditions, each with 3 data objects > averaging 182 replications for one condition > averaging 182 replications for one condition > 2 conditions, each with 3 data objects > <<<<<<<<<<<<<---------- what are the "3 data objects"? > creating 100 random permutations from total 6.129982e+54 > > HERE COMES THE ERROR: > > Error using prepare_resampled_data (line 381) > the dimensions should be the same for every condition > > Error in ft_sourceanalysis (line 561) > [dum, rnd_aCf, rnd_aCr, rnd_aPr, rnd_bCf, rnd_bCr, rnd_bPr] = > prepare_resampled_data(cfg, aCf, aCr, aPr, bCf, bCr, bPr); > > > When checking the function prepare_resampled_data, it turns out that it > requires a cell named "datain" to have the same size matrices column-wise > (whatever the columns may represent) : > > datain = > > [182x128x128 double] [182x128 double] [182x1 double] > [182x128x128 double] [ 1x128 double] [ NaN] > > > My input data condA and condB have identical dimensions, so I have no idea > what has gone wrong here: > > condA = > > label: {128x1 cell} > dimord: 'rpt_chan_freq' > freq: 9.8462 > powspctrm: [182x128 double] > labelcmb: {8128x2 cell} > crsspctrm: [182x8128 double] > cumsumcnt: [182x1 double] > cumtapcnt: [182x1 double] > elec: [1x1 struct] > trialinfo: [182x22 double] > cfg: [1x1 struct] > > condB = > > label: {128x1 cell} > dimord: 'rpt_chan_freq' > freq: 9.8462 > powspctrm: [182x128 double] > labelcmb: {8128x2 cell} > crsspctrm: [182x8128 double] > cumsumcnt: [182x1 double] > cumtapcnt: [182x1 double] > elec: [1x1 struct] > trialinfo: [182x22 double] > cfg: [1x1 struct] > > > > > Thanks for your input! > > Best wishes, > Maris > > > > > > On Sun, Apr 9, 2017 at 12:00 PM, wrote: > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. error in source parcellation and source connectivity analysis > > (velmurugan jayabal) > > 2. Problem with Matlab system commands in OS X (XTerm, Logout, > > crash, sleep mode) (Markus Gschwind) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sat, 8 Apr 2017 17:54:43 -0700 > > From: velmurugan jayabal > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] error in source parcellation and source > > connectivity analysis > > Message-ID: > > > mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Dear Field-trip community, > > > > I am having the following errors when computing connectivity > > analysis. Please any help in this regard would be highly appreciated. > > Thanks in advance. > > > > 1. How to compute atlas based source model grid, from MMP atlas?. Since > MMP > > atlas doesn't contain the *dim *field, the ft_volumelookup function > doesn't > > work prompting me the same error. > > > > > > 2. Alternatively, I had created AAL atlas based source model grid and > used > > to compute source connectivity (img.coh) from PCC beamformer source > output. > > But, I am unable to compute the connectivity value for each parcel using > > ft_sourceparcellate. I am writing the codes used to derive the same. > > > > 3. Is there any acronym or a clear explanation for the parcellation > label?. > > I had read Glasser et al 2016 paper and their resource site. But, I > > couldn't get complete names or explanation for all the ROIs. > > > > > > CODE: > > %source is the output of pcc beamformer results. > > cfg = []; > > cfg.method ='coh'; > > cfg.complex = 'absimag'; > > source_conn_imcoh = ft_connectivityanalysis(cfg, source); > > > > atlas =ft_read_atlas ('ROI_MNI_V5.nii'); > > atlas.pos =source_conn_imcoh.pos; > > cfg =[]; > > cfg.method ='mean' > > cfg.parameter ='cohspctrm'; > > cfg.parcellation = 'tissue'; > > parc_conn= ft_sourceparcellate(cfg,source_conn, atlas); > > > > I had even tried computing source connectivity interpolation on the atlas > > before parcellation. But, I am getting a huge array > 50 GB, which > exceeds > > my MATLAB and system limit. > > > > > > -- > > - sincerely, > > *Velmurugan Jayabal,* > > *Magnetoencephalography (MEG) research centre,* > > *Department of Clinical Neurosciences,* > > > > *National Institute of Mental Health and Neurosciences (NIMHANS),* > > *Bangalore - 560029, Karnataka, India* > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > attachments/20170408/ede3c3c1/attachment-0001.html> > > > > ------------------------------ > > > > Message: 2 > > Date: Sun, 9 Apr 2017 11:18:21 +0200 > > From: Markus Gschwind > > To: FieldTrip discussion list > > Subject: [FieldTrip] Problem with Matlab system commands in OS X > > (XTerm, Logout, crash, sleep mode) > > Message-ID: > > > gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Dear all, > > > > I hope to find here an expert who knows an answer to the following > problem: > > > > I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not > able > > to run big and lengthy matlab jobs because at each logout (which occurs > > after 2h), Matlab crashes, all results are gone (if they are not save to > > the HD and XTerm closes. > > > > I start Matlab form the XTerm (and not by clicking the App Icon) in order > > to be able to run system (unix) commands within Matlab. > > > > I guess, this behaviour is proper to XTerm, and in case I could find an > > other way to run system commands from Matlab, probably this could be > > resolved. > > > > Could it be that the running matlab job is not visible to the system > which > > goes to sleep?? > > > > For info here the power management info: > > > > $ pmset -g custom > > Battery Power: > > lidwake 1 > > autopoweroff 1 > > autopoweroffdelay 14400 > > standbydelay 18000 > > standby 1 > > ttyskeepawake 0 > > hibernatemode 3 > > gpuswitch 2 > > hibernatefile /var/vm/sleepimage > > displaysleep 2 > > sleep 0 > > acwake 1 > > halfdim 1 > > sms 1 > > lessbright 1 > > disksleep 10 > > AC Power: > > lidwake 1 > > autopoweroff 1 > > autopoweroffdelay 14400 > > standbydelay 18000 > > standby 0 > > ttyskeepawake 1 > > hibernatemode 3 > > gpuswitch 2 > > hibernatefile /var/vm/sleepimage > > womp 1 > > displaysleep 3 > > networkoversleep 0 > > sleep 0 > > acwake 0 > > halfdim 1 > > sms 1 > > disksleep 60 > > > > > > Many thanks for help! > > Markus > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > attachments/20170409/ce9b8000/attachment-0001.html> > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 77, Issue 6 > > **************************************** > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170411/3d323db9/attachment-0001.html> > > ------------------------------ > > Message: 3 > Date: Wed, 12 Apr 2017 10:35:29 +0800 > From: Stephen Politzer-Ahles > To: fieldtrip at science.ru.nl > Subject: Re: [FieldTrip] cluster-based statistics with one covariate > Message-ID: > A at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Caroline, > > If your conditions are within-subject, then I think the best way to do this > is to construct a dataset representing the conditionA - conditionB > difference for each subject, and then using ft_statfun_indepsamplesregrT to > regress the subject-wise difference on age. See e.g. > https://mailman.science.ru.nl/pipermail/fieldtrip/2016-May/010528.html for > a thread discussing a similar approach. > > Best, > Steve > > > --- > Stephen Politzer-Ahles > The Hong Kong Polytechnic University > Department of Chinese and Bilingual Studies > http://www.mypolyuweb.hk/~sjpolit/ > > > > > > Message: 3 > > Date: Mon, 10 Apr 2017 14:50:13 +0200 (CEST) > > From: Caroline Beese > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] cluster-based statistics with one covariate > > Message-ID: > > <1329277450.115066.1491828613491.JavaMail.zimbra at cbs.mpg.de> > > Content-Type: text/plain; charset=utf-8 > > > > Dear all, > > > > I'm trying to take age as a covariate into my cluster-based statistics > > comparing two dependent measures. > > > > I have read about two options: > > > > A) to use ft_regressconfound before I do the stats or > > B) to create a design with a third row using the .cvar field in the > > 'depsamplesregrT' statfun. > > > > I understand that for correcting head motions ft_regressconfound is a > > great option but for taking age into account as a covariate, it doesn't > > seem intuitive to me to do this within-subject on a trial-by-trial basis > > having only one number per person. Or can you use this function > differently? > > > > However, for option B) the subfunction 'unitselvec' is missing and this > > seems to be an issue for several years. So I was wondering whether anyone > > has ever tried to fix this problem themselves and wouldn't mind sharing? > > > > More generally, if anyone has successfully implemented a cluster-based > > statistics with one or more covariates, please share your experience, it > > would be greatly appreciated. > > > > Best Regards, > > Caroline > > > > -- > > Caroline Beese > > PhD student > > > > Max-Planck Institute for Human Cognitive and Brain Sciences > > Department of Neuropsychology > > Stephanstr. 1a > > 04103 Leipzig > > > > office phone: +49 (0) 341 9940 129 > > > > www.cbs.mpg.de/staff/beese-11586 > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170412/af43a0d6/attachment-0001.html> > > ------------------------------ > > Message: 4 > Date: Wed, 12 Apr 2017 09:01:14 +0000 > From: Robin K?mpe > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Installing gui_streamer > Message-ID: > eurprd06.prod.outlook.com> > > Content-Type: text/plain; charset="iso-8859-1" > > Hi! > > We want to, from scratch, set up a real time fMRI capabilities. Your > documentation covers this quite well. I do, however, get stuck on point 1 > which is to launch the gui_streamer from the console. How does one > obtain/install this program on our Siemens Prisma? > > Best, > > > Robin K?mpe > Research Engineer > > [Link?ping University] > > CSAN, Center for Social and Affective Neuroscience > Department of Clinical and Experimental Medicine, IKE > Mobile: +46 (0)73 8005561 > Please visit us at www.liu.se > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170412/cf35fa04/attachment-0001.html> > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 77, Issue 9 > **************************************** > -- Laxmi Shaw Research Scholar(PhD) IIT Kharagpur West Bengal Ph no-08388837821 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Apr 13 09:24:37 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 13 Apr 2017 07:24:37 +0000 Subject: [FieldTrip] Inquiry about Field-Trip usage for multi-channel sources In-Reply-To: References: Message-ID: <534C6190-9193-43EB-A363-8A7D84FC6F39@donders.ru.nl> Joe, You may want to have a look here: http://www.fieldtriptoolbox.org/example/compute_forward_simulated_data_and_apply_a_dipole_fit?s[]=ft&s[]=dipolesimulation to get started. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 07 Apr 2017, at 20:23, Joseph Lee > wrote: Dear Field Trip Community I am Joe from the Computational Unit of the Center for Consciousness Science, University of Michigan. We are somewhat new to forward modelling and are currently undertaking a project to generate 128 scalp-level channel signals from the 78 source-level signals. We are using the "ft_compute_leadfield" function of FieldTrip in order to accomplish that goal. Is this a valid approach for our goal or were those functions designed for a different purpose? Any comments on this will be helpful for us. Thank you very much. Best, Joe Research Assistant Center for Consciousness Science, University of Michigan Medical School, Ann Arbor, USA _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From son.ta.dinh at tum.de Thu Apr 13 14:57:45 2017 From: son.ta.dinh at tum.de (Ta Dinh, Son) Date: Thu, 13 Apr 2017 12:57:45 +0000 Subject: [FieldTrip] Functional connectivity analysis with powcorr_ortho Message-ID: Dear FieldTrip list, I am trying to do a functional connectivity analysis using the power envelope correlation introduced by Hipp et al. (Nat Neuroscience 2012) as implemented in the ft_connectivity_powcorr_ortho function. My data consists of 5 minutes of eyes-closed resting-state data and my schematic pipeline is as follows: 1. I use LCMV beamforming to source reconstruct my bandpassed and preprocessed data 2. Using the resulting spatial filter I get a projected time series for every voxel (virtual channel) 3. I do a frequency analysis on these time series 4. The results of this frequency analysis (the Fourier coefficients) are used for the connectivity analysis using powcorr_ortho To check the results of this analysis, I plotted the results of a seed-based connectivity analysis with a voxel in the left visual cortex (-20, -80, 20) as seed. In the alpha band, I expect to see a strong local connectivity pattern in the occipital region extending partially into the contralateral hemisphere, similar to what Siems et al. NeuroImage 2016 find. However, I get a basically random connectivity pattern. When using this pipeline with the debiased weighted phase lag index, I get exactly what I am expecting. I looked into the source code of the ft_connectivity_powcorr_ortho function and saw a few disconcerting comments (Fix-Me's and the like) and now I am wondering whether my pipeline is simply not suited to the connectivity analysis with powcorr_ortho as implemented in FieldTrip or if the function is simply not fully implemented yet. Has anyone used it successfully before? I use the following FieldTrip (pseudo-) code: %% LCMV source reconstruction cfg = []; cfg.method = 'lcmv'; cfg.keeptrials = 'yes'; cfg.elec = elec; cfg.grid = lf; % regular grid of 1 cm resolution cfg.headmodel = vol % standard_bem.mat cfg.lcmv.keepfilter = 'yes'; cfg.lcmv.lambda = '5%'; cfg.lcmv.projectnoise = 'yes'; source = ft_sourceanalysis(cfg, tlock_data); %% pseudo-code for the computation of the virtual channel time series virtChan_data = tlock_data; virtChan_data.label = [source.pos(:, 1), source.pos(:,2), source.pos(:,3)]; virtChan_data.trial = source.avg.filter * tlock_data.trial; %% frequency analysis of the virtual channels cfg = []; cfg.method = 'mtmfft'; cfg.output = 'fourier'; cfg.keeptrials = 'yes'; cfg.foi = 10; % alpha band cfg.taper = 'hanning' % I originally used 3 tapers but source code in ft_connectivity_powcorr_ortho implies that multitaper is not compatible virtFreq = ft_freqanalysis(cfg, virtChan_data); %% connectivity analysis cfg = []; cfg.method = 'powcorr_ortho'; conn = ft_connectivityanalysis(cfg,virtFreq); Any suggestions and/or comments would be immensely helpful! Thanks in advance. Best, Son Son Ta Dinh, M.Sc. PhD student in Human Pain Research Klinikum rechts der Isar Technische Universität München Munich, Germany Phone: +49 89 4140 7664 http://www.painlabmunich.de/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Fri Apr 14 03:27:24 2017 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Fri, 14 Apr 2017 09:27:24 +0800 Subject: [FieldTrip] Need help with cluster-based permutation test with 3 groups of subjects Message-ID: Hello Jose, I haven't looked closely at your code, but it sounds like this is working exactly as intended. A significant F-test doesn't mean that there must be significant differences between all pairs of groups; hypothetically, an F-test comparing 100 groups could be significant even if only 99 and 100 are significantly different from each other. This isn't something specific to the cluster-based permutation test, this is just how F-tests work in general. As for getting different cluster extents with the 3-level F-test vs. the pairwise t-test, this is also normal; you're comparing different things so it's natural that the test statistics will come out slightly different. Best, Steve --- Stephen Politzer-Ahles The Hong Kong Polytechnic University Department of Chinese and Bilingual Studies http://www.mypolyuweb.hk/~sjpolit/ > > > Message: 1 > Date: Tue, 11 Apr 2017 12:08:44 +0200 > From: Jos? Antonio Uriguen Garaizabal > To: FieldTrip discussion list > Subject: [FieldTrip] Need help with cluster-based permutation test > with 3 groups of subjects > Message-ID: > < CAMMf7X15byC6p3gqaie6wEuKekV2krZ0++keLLUPZ3pn2h-PAA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all > > > My name is Toni and I am working on EEG signal processing at University of > Deusto, Bilbao, Spain. More specifically, right now trying to > apply cluster-based permutation testing to determine whether there exist > differences among 3 groups of subjects. > > > So, for my testing, subject groups are E, EN and N, the 2 former being > different types of patients and the latter being a control group. I am > forming clusters based on proximity (in space) and each subject is > characterized by a matrix of values that vary in 2D (per channel and > another variable related but not equal to frequency). > > By means of a T-statistic (indepsamplesT) I can find differences in between > E and EN, but I find no clusters/differences in between E and N or EN and > N, even though hypothetically (I think) they should exist. By means of an > F-statistic (indepsamplesF) I can find differences among the 3 groups at > the same time, then also between E and EN and no differences between E and > N or EN and N... > > Am I missing something? I do not understand why the might exist a > significant cluster when comparing all 3 groups that does not exist in the > 1vs1 comparisons, even though the cluster is not the same I obtain when I > compare E vs EN... > > > For additional information, I attach how I run the test: > > cfg.method = 'distance'; > cfg.neighbourdist = 1; > cfg.elec = ft_datatype_sens(subjEN{1}.elec); > neighbours = ft_prepare_neighbours(cfg); > > cfg = []; > cfg.channel = {'EEG'}; > cfg.latency = 'all'; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.neighbours = neighbours; % same as defined for the > between-trials experiment > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 5000; > > nsubj = size(subjE,2)+size(subjEN,2); > design = zeros(2,nsubj); > design(1,:) = [1:nsubj/2 1:nsubj/2]; > design(2,1:size(subjE,2)) = 1; > design(2,size(subjE,2)+1:nsubj) = 2; > > cfg.design = design; > cfg.ivar = 2; > > [stat] = ft_timelockstatistics(cfg, subjEN{:}, subjE{:}); > > > When I compare the 3 groups > > cfg.method = 'distance'; > cfg.neighbourdist = 1; > cfg.elec = ft_datatype_sens(subjEN{1}.elec); > neighbours = ft_prepare_neighbours(cfg); > > cfg = []; > cfg.channel = {'EEG'}; > cfg.latency = 'all'; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesF'; %F-statistic > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.neighbours = neighbours; % same as defined for the > between-trials experiment > cfg.tail = 1; %One sided > cfg.clustertail = 1; > cfg.alpha = 0.025; > cfg.numrandomization = 5000; > > nsubj1 = size(subjE,2); > nsubj2 = size(subjEN,2); > nsubj3 = size(subjN,2); > nsubj = nsubj1+nsubj2+nsubj3; > > design = zeros(2,nsubj); > design(1,:) = [1:nsubj1 1:nsubj2 1:nsubj3]; > design(2,1:nsubj1) = 1; > design(2,nsubj1+1:nsubj1+nsubj2) = 2; > design(2,nsubj1+nsubj2+1:nsubj) = 3; > > cfg.design = design; > cfg.ivar = 2; %2nd row is independent var > > [stat] = ft_timelockstatistics(cfg, subjE{:}, subjEN{:}, subjN{:}); > > > Then, subjE, subjN and subjEN are like this: > > Eall = subjE{:} > > Eall = > > struct with fields: > > label: {1?18 cell} > fsample: 200 > elec: [1?1 struct] > trial: {[18?115 double]} > time: {[1?115 double]} > cfg: [1?1 struct] > > > Thanks in advance > > -- > *Jose Antonio Urig?en* > PostDoc at Deustotech-LIFE (eVIDA Research Group) > [image: Deusto] > Universidad de Deusto / Deustuko Unibertsitatea / University of Deusto > Facultad de Ingenier?a, 4? Planta > Avda. Universidades 24. 48007 Bilbao > Tel. +34 94 413 90 00 / Mov. +34 656 711 643 > Ext. 2980 > jose.uriguen at deusto.es > Web: evida.deusto.es > *www.deusto.es * > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20170411/7a169976/attachment-0001.html > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joeboe at umich.edu Fri Apr 14 19:48:38 2017 From: joeboe at umich.edu (Joseph Lee) Date: Fri, 14 Apr 2017 13:48:38 -0400 Subject: [FieldTrip] Inquiry about Field-Trip usage for multi-channel sources In-Reply-To: <534C6190-9193-43EB-A363-8A7D84FC6F39@donders.ru.nl> References: <534C6190-9193-43EB-A363-8A7D84FC6F39@donders.ru.nl> Message-ID: Thank you for your reply Jan-Marthijs, May I ask then what the main difference between using 'ft_compute_leadfield' to calculate leadfield and generate a signal vs using 'ft_dipole_simulation'. Thanks! -Joe On Thu, Apr 13, 2017 at 3:24 AM, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Joe, > > You may want to have a look here: http://www.fieldtriptoolbox.org/example/ > compute_forward_simulated_data_and_apply_a_dipole_fit?s[ > ]=ft&s[]=dipolesimulation to get started. > > Best wishes, > Jan-Mathijs > > > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 <+31%2024%20361%204793> > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > On 07 Apr 2017, at 20:23, Joseph Lee wrote: > > Dear Field Trip Community > > I am Joe from the Computational Unit of the Center for Consciousness > Science, University of Michigan. > > We are somewhat new to forward modelling and are currently undertaking a > project to generate 128 scalp-level channel signals from the 78 > source-level signals. We are using the "ft_compute_leadfield" function of > FieldTrip in order to accomplish that goal. > > Is this a valid approach for our goal or were those functions designed for > a different purpose? > > Any comments on this will be helpful for us. Thank you very much. > > Best, > > Joe > > Research Assistant > Center for Consciousness Science, > University of Michigan Medical School, > Ann Arbor, USA > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Apr 14 21:19:15 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 14 Apr 2017 19:19:15 +0000 Subject: [FieldTrip] Inquiry about Field-Trip usage for multi-channel sources In-Reply-To: References: <534C6190-9193-43EB-A363-8A7D84FC6F39@donders.ru.nl> Message-ID: <2EC9613C-10A2-4F8F-86FE-A985C77DA2B8@donders.ru.nl> Please read the documentation. I think it should be sufficiently clear. Jan-Mathijs function [simulated] = ft_dipolesimulation(cfg) % FT_DIPOLESIMULATION computes the field or potential of a simulated dipole % and returns a datastructure identical to the FT_PREPROCESSING function. % % Use as % data = ft_dipolesimulation(cfg) % % The dipoles position and orientation have to be specified with % cfg.dip.pos = [Rx Ry Rz] (size Nx3) % cfg.dip.mom = [Qx Qy Qz] (size 3xN) % % The timecourse of the dipole activity is given as a single vector or as a % cell-array with one vectors per trial % cfg.dip.signal % or by specifying a sine-wave signal % cfg.dip.frequency in Hz % cfg.dip.phase in radians % cfg.dip.amplitude per dipole % cfg.ntrials number of trials % cfg.triallength time in seconds % cfg.fsample sampling frequency in Hz % % Random white noise can be added to the data in each trial, either by % specifying an absolute or a relative noise level % cfg.relnoise = add noise with level relative to simulated signal % cfg.absnoise = add noise with absolute level % cfg.randomseed = 'yes' or a number or vector with the seed value (default = 'yes') % % Optional input arguments are % cfg.channel = Nx1 cell-array with selection of channels (default = 'all'), % see FT_CHANNELSELECTION for details % cfg.dipoleunit = units for dipole amplitude (default nA*m) % cfg.chanunit = units for the channel data % % The volume conduction model of the head should be specified as % cfg.headmodel = structure with volume conduction model, see FT_PREPARE_HEADMODEL % % The EEG or MEG sensor positions should be specified as % cfg.elec = structure with electrode positions, see FT_DATATYPE_SENS % cfg.grad = structure with gradiometer definition, see FT_DATATYPE_SENS % cfg.elecfile = name of file containing the electrode positions, see FT_READ_SENS % cfg.gradfile = name of file containing the gradiometer definition, see FT_READ_SENS % % See also FT_SOURCEANALYSIS, FT_DIPOLEFITTING, FT_TIMELOCKSIMULATION, % FT_FREQSIMULATION, FT_CONNECTIVITYSIMULATION function [lf] = ft_compute_leadfield(dippos, sens, headmodel, varargin) % FT_COMPUTE_LEADFIELD computes a forward solution for a dipole in a a volume % conductor model. The forward solution is expressed as the leadfield % matrix (Nchan*3), where each column corresponds with the potential or field % distributions on all sensors for one of the x,y,z-orientations of the % dipole. % % Use as % [lf] = ft_compute_leadfield(dippos, sens, headmodel, ...) % with input arguments % dippos = position dipole (1*3 or Ndip*3) % sens = structure with gradiometer or electrode definition % headmodel = structure with volume conductor definition % % The headmodel represents a volume conductor model, its contents % depend on the type of model. The sens structure represents a sensor % array, i.e. EEG electrodes or MEG gradiometers. % % It is possible to compute a simultaneous forward solution for EEG and MEG % by specifying sens and grad as two cell-arrays, e.g. % sens = {senseeg, sensmeg} % headmodel = {voleeg, volmeg} % This results in the computation of the leadfield of the first element of % sens and headmodel, followed by the second, etc. The leadfields of the % different imaging modalities are subsequently concatenated. % % Additional input arguments can be specified as key-value pairs, supported % optional arguments are % 'reducerank' = 'no' or number % 'normalize' = 'no', 'yes' or 'column' % 'normalizeparam' = parameter for depth normalization (default = 0.5) % 'weight' = number or 1xN vector, weight for each dipole position (default = 1) % 'backproject' = 'yes' (default) or 'no', in the case of a rank reduction % this parameter determines whether the result will be % backprojected onto the original subspace % % The leadfield weight may be used to specify a (normalized) % corresponding surface area for each dipole, e.g. when the dipoles % represent a folded cortical surface with varying triangle size. % % Depending on the specific input arguments for the sensor and volume, this % function will select the appropriate low-level EEG or MEG forward model. % The leadfield matrix for EEG will have an average reference over all the % electrodes. % % The supported forward solutions for MEG are % single sphere (Cuffin and Cohen, 1977) % multiple spheres with one sphere per channel (Huang et al, 1999) % realistic single shell using superposition of basis functions (Nolte, 2003) % leadfield interpolation using a precomputed grid % boundary element method (BEM) % % The supported forward solutions for EEG are % single sphere % multiple concentric spheres (up to 4 spheres) % leadfield interpolation using a precomputed grid % boundary element method (BEM) % % See also FT_PREPARE_VOL_SENS, FT_HEADMODEL_ASA, FT_HEADMODEL_BEMCP, % FT_HEADMODEL_CONCENTRICSPHERES, FT_HEADMODEL_DIPOLI, FT_HEADMODEL_HALFSPACE, % FT_HEADMODEL_INFINITE, FT_HEADMODEL_LOCALSPHERES, FT_HEADMODEL_OPENMEEG, % FT_HEADMODEL_SINGLESHELL, FT_HEADMODEL_SINGLESPHERE, % FT_HEADMODEL_HALFSPACE On 14 Apr 2017, at 19:48, Joseph Lee > wrote: Thank you for your reply Jan-Marthijs, May I ask then what the main difference between using 'ft_compute_leadfield' to calculate leadfield and generate a signal vs using 'ft_dipole_simulation'. Thanks! -Joe On Thu, Apr 13, 2017 at 3:24 AM, Schoffelen, J.M. (Jan Mathijs) > wrote: Joe, You may want to have a look here: http://www.fieldtriptoolbox.org/example/compute_forward_simulated_data_and_apply_a_dipole_fit?s[]=ft&s[]=dipolesimulation to get started. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 07 Apr 2017, at 20:23, Joseph Lee > wrote: Dear Field Trip Community I am Joe from the Computational Unit of the Center for Consciousness Science, University of Michigan. We are somewhat new to forward modelling and are currently undertaking a project to generate 128 scalp-level channel signals from the 78 source-level signals. We are using the "ft_compute_leadfield" function of FieldTrip in order to accomplish that goal. Is this a valid approach for our goal or were those functions designed for a different purpose? Any comments on this will be helpful for us. Thank you very much. Best, Joe Research Assistant Center for Consciousness Science, University of Michigan Medical School, Ann Arbor, USA _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From cmuehl at gmail.com Tue Apr 18 09:28:57 2017 From: cmuehl at gmail.com (Christian Muehl) Date: Tue, 18 Apr 2017 07:28:57 +0000 Subject: [FieldTrip] CfP - reminder - Brain and physiological signals for multi-user modeling @ ACII Message-ID: ** Call for papers ** Special session in ACII 2017 (Affective Computing and Intelligent Interaction) Topic: Brain and physiological signals for multi-user modeling http://www.affective-sciences.org/en/bps-mum ** Description ** Emotional cues, generated subconsciously by the human body, have always been a crucial part of affective computing. Machines can learn about a person's affective state by analyzing measurements such as autonomic nervous system responses, neurophysiological measurements and gaze behavior. They can then act on the inferred information, adapting their own behavior, response or service based on the user's affective state. Although emotions can be viewed as a social phenomenon, current physiological computing research is focused on emotions which are triggered by non-social stimuli. In the case of group interactions, emotions do not only develop in one’s mind but rather unfold according to the emotional expressions of the others. Consequently, the behavior, expressions and physiology of interacting people are known to be in synchrony during interactions. This inter-dependency of behavior and emotional expressions can in turn predict several properties of the social interaction such as grounding, mutual understanding, conflict, or social presence. Similarly, researchers in social neuro-science perform hyper-scanning to measure joint brain activities of people interacting with each other. The objective being to uncover brain areas and neural mechanisms supporting social processes. With this special session we would like to develop research on multi-user modeling from neural and physiological sources. Here the concept of user modeling is defined broadly, including emotional, cognitive and social aspects which can be used for intelligent interactions. This special session targets researchers from computer science, neuro-science and psycho-physiology who are interested in the following research questions: - What information about the user state and the quality of the interaction between users can be gained from (neuro-)physiological signals? - How can that information, combined from several users, be used to interact adaptively with a machine? - What is the effect of sharing physiological information with others? - Which methods can be developed to reduce inter-user variability and improve user modeling? The special session topics include but are not limited to: - Collaborative brain-computer interfaces - Tangible / social display of physiological and neural cues - Social bio-feedback - Assessment of social processes (conflict, empathy, relationship etc.) - Assessment of the quality of interaction and collaboration - Social neuroscience and psycho-physiology - Emotion assessment, particularly social emotions - Domain and transfer learning for building cross-participant models - Methods for multiple user modeling (e.g. synchrony measures, dynamic multi-user models, etc.) - Applications of multi-user physiological computing To facilitate the research on physiological signal classification, several databases are publicly available. Contributions on the physiological data available in such databases are welcome but not obliged. Example databases include: EATMINT: https://eatmint.unige.ch RECOLA: https://diuf.unifr.ch/diva/recola MMDB: http://www.cbi.gatech.edu/mmdb/ Those databases are only examples and work on self-collected or other data are welcome. ** Important dates ** Conference Dates: October 23-26, 2017 Paper Submission Deadline: May 2, 2017 Reviews Provided to Authors: June 16, 2017 Author Rebuttals Due: June 23, 2017 Notification of Acceptance: July 14, 2017 Camera Ready Papers Due: August 18, 2017 Full paper authors should register By: August 7, 2017 Early registration deadline: September 1, 2017 ** Submission procedure ** Papers submitted to this Special Sessions have to be submitted following the same schedule and procedure as regular ACII papers (ACII paper submission). When submitting your paper please check the corresponding box for the Special Session on "Brain and physiological signals for multi-user modeling" in the ACII submission system. The papers will undergo the same review process by anonymous and independent reviewers as the remaining ACII submissions. ** Organizers ** Guillaume Chanel, Swiss Center for Affective Sciences, Switzerland guillaume.chanel[at]unige.ch http://cvml.unige.ch/guillaumechanel Christian Mühl, German Aerospace Center, Germany cmuehl[at]gmail.com https://www.linkedin.com/in/cmuhl Jérémy Frey, Ullo, France jfrey[at]ullo.fr http://phd.jfrey.info Anton Nijholt, University of Twente, The Netherlands anijholt[at]cs.utwente.nl http://wwwhome.cs.utwente.nl/~anijholt/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at me.com Wed Apr 19 09:14:34 2017 From: nathanweisz at me.com (Nathan Weisz) Date: Wed, 19 Apr 2017 09:14:34 +0200 Subject: [FieldTrip] PhD position Salzburg MEG lab Message-ID: <1590B171-5153-4788-A372-9233442AA22E@me.com> Dear colleagues, sorry in advance for cross-postings. Starting September 2017 a PhD position will be available in our group. See attached pdf. Please forward to potentially interested students. Best, Nathan -------------- next part -------------- A non-text attachment was scrubbed... Name: ESIT_Call_Salzburg.pdf Type: application/pdf Size: 341931 bytes Desc: not available URL: From r.oostenveld at donders.ru.nl Wed Apr 19 16:02:04 2017 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 19 Apr 2017 16:02:04 +0200 Subject: [FieldTrip] FiledTrip - Python compatibility? In-Reply-To: References: Message-ID: <327AADB7-8D61-4646-9C16-C5AF2B479946@donders.ru.nl> Hi Greydon, Let me also CC this to the FieldTrip list, as I know there are more people thinking about this. Although I am using Python for other projects (e.g. EEGsynth , we don’t have concrete plans for improving the compatibility between FieldTrip and Python, or to port parts of FieldTrip over to Python. Personally (*) I also feel that Python is not the optimal language and/or data analysis environment for the goals of the FieldTrip project. It would for sure attract more computer scientists and people that like programming, but for (non-technical) cognitive neuroscientists and people that are just able to do scripting I suspect it to become more like an application rather than a toolbox where you can look under the hood and mix it in with ones own code. (*) Other people might feel different of course MNE-Python is of course a project that I am following. The occasional improvements on the FieldTrip side are primarily focussed on making the transition between MNE-Python and FieldTrip more smooth (both ways). A complicating feature in Python is that data handling is different than in MATLAB, where we only use native built-in data structures. Saving data from Python requires a well-established file format (which does not exist) or a stable object definition (which is hard in science). Also for (open access) data sharing I hope that we can do more work on representing analysis results in a format that allows them to be reused in another pipeline. That is for exampel something that we attempted in the MEG section of the human connectome project, where the use cifti files (i.e. nifti-2 with a header extension), text files and - where needed - matlab files in a format that works well with Python. If you have ideas for improving the interoperability, you are welcome to contribute . best Robert PS Thanks for the nice remarks about FieldTrip! > On 16 Apr 2017, at 18:17, Greydon Gilmore wrote: > > Hi Robert, > > I recently stumbled across FieldTrip and I have been in love ever since. I love that I can incorporate the functions into my own scripts. > > I am curious o know if there is any work being done to make FieldTrip compatible with Python? > > Thank you for all the work your team put into FieldTrip, it's streamlined my workflow greatly. > > Greydon > > -- > Greydon Gilmore, B.Sc., M.Sc. (Neuroscience) > Ph.D. candidate in Biomedical Engineering > Movement Disorder Centre, University Hospital > University of Western Ontario > 339 Windermere Road, BLL-250 > 519-685-8500 ext. 76708 > London, Ontario > Canada, N6A 5A5 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ella.weik at gmail.com Thu Apr 20 01:12:24 2017 From: ella.weik at gmail.com (Ella Weik) Date: Wed, 19 Apr 2017 16:12:24 -0700 Subject: [FieldTrip] Problems with plotting time-frequency analysis results Message-ID: Hi Fieldtrip Community, We are currently trying to run a wavelet time frequency analysis. Our EEG data is already preprocessed and epoched with EEGlab. We are able to read in the data, define trials, and output values for TFR.powspctrm. However, we do not see any of these values plotted on our figure with ft_singleplot. This is the code we are using: cfg = []; cfg.dataset = dsname; cfg.continuous = 'no'; cfg.trialfun = 'wm_trialfun'; cfg.binNumber = 13; cfg.epochBaseInt = -0.5; cfg.epochInt = 1.5; cfg.trialdef.prestim = cfg.epochBaseInt - 0.01; cfg.trialdef.poststim = cfg.epochInt - 0.01 ; cfg = ft_definetrial(cfg); dataFIC = ft_preprocessing(cfg); save dataFIC_DirCue dataFIC; dataFIC_condX cfg = []; cfg.channel = 'EEG'; cfg.trials = 'all' cfg.keeptrials = 'no'; cfg.output = 'pow'; cfg.foi = 2:0.5:50; cfg.toi = -0.4:0.01:1.4; % cfg.method = 'wavelet'; cfg.width = 7; cfg.length = 2; TFR = ft_freqanalysis(cfg, dataFIC); save TFRwave_DirCue TFR % plot the results cfg = []; cfg.parameter = 'powspctrm'; cfg.baseline = [-0.4 0]; cfg.baselinetype = 'relative'; cfg.zlim = [-3e-10 3e-10]; cfg.showlabels = 'yes'; figure; ft_singleplotTFR(cfg,TFR); And this is our trial_function: function [trl, event] = wm_trialfun(cfg); hdr = ft_read_header(cfg.dataset); event = ft_read_event(cfg.dataset); indx=[]; if cfg.binNumber for i = 1:size(event,2) if ismember(cfg.binNumber,event(i).bini) indx=[indx;1]; else indx=[indx;0]; end end ind = find(indx); sample = [event(ind).sample]'; else sample = [event(find(strcmp(cfg.codeLabel, {event.codelabel}))).sample]'; end epochBaseSamples = -1*cfg.epochBaseInt*hdr.Fs; epochSamples = cfg.epochInt*hdr.Fs; epochTotal = epochBaseSamples + epochSamples; epochStarts = [1:epochTotal:sample(end)]; eventStarts = epochStarts + epochBaseSamples; sampleGood = intersect(sample,eventStarts); pretrig = -round(cfg.trialdef.prestim * hdr.Fs); posttrig = round(cfg.trialdef.poststim * hdr.Fs); trl = []; trl(:,1) = sampleGood + pretrig; trl(:,2) = sampleGood + posttrig; trl(:,3) = pretrig; And this is the cfg: channel: {128x1 cell} trials: 'all' keeptrials: 'no' output: 'pow' foi: [1x15 double] toi: [1x28 double] method: 'wavelet' width: 7 length: 3 outputfilepresent: 'overwrite' callinfo: [1x1 struct] version: [1x1 struct] feedback: 'text' inputlock: [] outputlock: [] gwidth: 3 pad: 0.9820 padtype: 'zero' calcdof: 'no' precision: 'double' correctt_ftimwin: 'no' polyremoval: 0 keeptapers: 'no' previous: [1x1 struct] Any insights would be greatly appreciated with regards to why we cannot see any values in our single plot figure. Also, we are not sure if the problem rests in our plotting configuration or the data itself. Best regards, Ella -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.litvak at ucl.ac.uk Thu Apr 20 18:27:36 2017 From: v.litvak at ucl.ac.uk (Vladimir Litvak) Date: Thu, 20 Apr 2017 17:27:36 +0100 Subject: [FieldTrip] Last chance: SPM course for MEG/EEG in London: May 8-10, 2017 Message-ID: Dear all, We are pleased to announce that our annual SPM course for MEG/EEG will take place this year from Monday May 8 to Wednesday May 10 2017. Hosted by University College London, the course will be held at Queen Square, a very central location in London (UK). The course will present instruction on the analysis of MEG and EEG data. The first two days will combine theoretical presentations with practical demonstrations of the different data analysis methods implemented in SPM. On the last day participants will have the opportunity to work on SPM tutorial data sets under the supervision of the course faculty. We also invite students to bring their own data for analysis. The course is suitable for both beginners and more advanced users. The topics that will be covered range from pre-processing and statistical analysis to source localization and dynamic causal modelling. The program is listed below. Registration is now open. For full details see http://www.fil.ion.ucl.ac.uk/spm/course/london/ where you can also register. Available places are limited so please register as early as possible if you would like to attend! ---------------------- Monday May 8th (33 Queen square, basement) 9.00 - 9.30 Registration 9.30 - 9.45 SPM introduction and resources Guillaume Flandin 9.45 - 10.30 What are we measuring with M/EEG? Saskia Heibling 10.30 - 11.15 Data pre-processing Hayriye Cagnan Coffee 11.45 - 12.30 Data pre-processing – demo Sofie Meyer, Misun Kim 12.30 - 13.15 General linear model and classical inference Christophe Phillips Lunch 14.15 - 15.00 Multiple comparisons problem and solutions Guillaume Flandin 15.00 - 15.45 Bayesian inference Christophe Mathys Coffee 16.15 - 17.45 Group M/EEG dataset analysis - demo Jason Taylor, Martin Dietz 17.45 - 18.30 Advanced applications of the GLM Ashwani Jha, Bernadette van Wijk Tuesday May 9th (33 Queen square, basement) 9.30 - 10.15 M/EEG source analysis Gareth Barnes 10.15 - 11.15 M/EEG source analysis – demo Jose Lopez, Leonardo Duque Coffee 11.45 - 12.30 The principles of dynamic causal modelling Bernadette van Wijk 12.30 - 13.15 DCM for evoked responses Ryszard Auksztulewicz Lunch 14.15 - 15.00 DCM for steady state responses Rosalyn Moran 15.00 - 15.45 DCM - demo Richard Rosch, Tim West Coffee 16.15 - 17.00 Bayesian model selection and averaging Peter Zeidman 17.00 - 18.30 Clinic - questions & answers Karl Friston 19.00 - ... Social Event Wednesday May 10th 9.30 - 17.00 Practical hands-on session in UCL computer class rooms. Participants can either work on SPM tutorial datasets or on their own data with the help of the faculty. There will also be an opportunity to ask questions in small tutorial groups for further discussions on the topics of the lectures. -------------- next part -------------- An HTML attachment was scrubbed... URL: From gio at gpiantoni.com Fri Apr 21 16:21:38 2017 From: gio at gpiantoni.com (Gio Piantoni) Date: Fri, 21 Apr 2017 16:21:38 +0200 Subject: [FieldTrip] FiledTrip - Python compatibility? Message-ID: I looked into creating a python wrapper around matlab for Fieldtrip. Mathworks officially supports a Matlab engine for python (pretty neat), but the bottleneck for me is that it does not convert matlab cells to python objects: https://www.mathworks.com/help/matlab/matlab_external/handle-data-returned-from-matlab-to-python.html so it's impossible to pass fieldtrip structures to python. Hopefully they'll get around to support the cell conversion in the near future. Also I don't remember how sophisticated the memory management in the engine is. Projects like python-matlab-bridge usually don't share the memory between processes (like rpy2 does), so you end up with duplicated objects (which gets unwieldy when working with large EEG datasets) -g > Date: Wed, 19 Apr 2017 16:02:04 +0200 > From: Robert Oostenveld > To: Greydon Gilmore > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] FiledTrip - Python compatibility? > Message-ID: <327AADB7-8D61-4646-9C16-C5AF2B479946 at donders.ru.nl> > Content-Type: text/plain; charset="utf-8" > > Hi Greydon, > > Let me also CC this to the FieldTrip list, as I know there are more people thinking about this. > > Although I am using Python for other projects (e.g. EEGsynth , we don?t have concrete plans for improving the compatibility between FieldTrip and Python, or to port parts of FieldTrip over to Python. Personally (*) I also feel that Python is not the optimal language and/or data analysis environment for the goals of the FieldTrip project. It would for sure attract more computer scientists and people that like programming, but for (non-technical) cognitive neuroscientists and people that are just able to do scripting I suspect it to become more like an application rather than a toolbox where you can look under the hood and mix it in with ones own code. > > (*) Other people might feel different of course > > MNE-Python is of course a project that I am following. The occasional improvements on the FieldTrip side are primarily focussed on making the transition between MNE-Python and FieldTrip more smooth (both ways). > > A complicating feature in Python is that data handling is different than in MATLAB, where we only use native built-in data structures. Saving data from Python requires a well-established file format (which does not exist) or a stable object definition (which is hard in science). Also for (open access) data sharing I hope that we can do more work on representing analysis results in a format that allows them to be reused in another pipeline. That is for exampel something that we attempted in the MEG section of the human connectome project, where the use cifti files (i.e. nifti-2 with a header extension), text files and - where needed - matlab files in a format that works well with Python. > > If you have ideas for improving the interoperability, you are welcome to contribute . > > best > Robert > > PS Thanks for the nice remarks about FieldTrip! > > >> On 16 Apr 2017, at 18:17, Greydon Gilmore wrote: >> >> Hi Robert, >> >> I recently stumbled across FieldTrip and I have been in love ever since. I love that I can incorporate the functions into my own scripts. >> >> I am curious o know if there is any work being done to make FieldTrip compatible with Python? >> >> Thank you for all the work your team put into FieldTrip, it's streamlined my workflow greatly. >> >> Greydon >> >> -- >> Greydon Gilmore, B.Sc., M.Sc. (Neuroscience) >> Ph.D. candidate in Biomedical Engineering >> Movement Disorder Centre, University Hospital >> University of Western Ontario >> 339 Windermere Road, BLL-250 >> 519-685-8500 ext. 76708 >> London, Ontario >> Canada, N6A 5A5 From tomh at kurage.nimh.nih.gov Fri Apr 21 16:54:56 2017 From: tomh at kurage.nimh.nih.gov (Tom Holroyd) Date: Fri, 21 Apr 2017 10:54:56 -0400 Subject: [FieldTrip] FiledTrip - Python compatibility? In-Reply-To: References: Message-ID: <20170421105456.5341782f@kurage.nimh.nih.gov> You might want to look at this: -- https://pypi.python.org/pypi/oct2py Oct2Py allows you to seamlessly call M-files and Octave functions from Python. It manages the Octave session for you, sharing data behind the scenes using MAT files. -- I've used FieldTrip under Octave in the past (3.0). It doesn't take too much work to get most of the important stuff ported. There's a saying, "Octave is as compatible with Matlab as Matlab is with itself." Once ported, cluster concerns vanish, just run 128 copies of Octave ... They have a nice IDE now too. Because it's open source, integration with Python is much better, see oct2py, which also has a cool name. On Fri, 21 Apr 2017 16:21:38 +0200 Gio Piantoni wrote: > I looked into creating a python wrapper around matlab for Fieldtrip. > > Mathworks officially supports a Matlab engine for python (pretty > neat), but the bottleneck for me is that it does not convert matlab > cells to python objects: > https://www.mathworks.com/help/matlab/matlab_external/handle-data-returned-from-matlab-to-python.html > so it's impossible to pass fieldtrip structures to python. > > Hopefully they'll get around to support the cell conversion in the near future. > > Also I don't remember how sophisticated the memory management in the > engine is. Projects like python-matlab-bridge usually don't share the > memory between processes (like rpy2 does), so you end up with > duplicated objects (which gets unwieldy when working with large EEG > datasets) > > -g > > > > Date: Wed, 19 Apr 2017 16:02:04 +0200 > > From: Robert Oostenveld > > To: Greydon Gilmore > > Cc: FieldTrip discussion list > > Subject: Re: [FieldTrip] FiledTrip - Python compatibility? > > Message-ID: <327AADB7-8D61-4646-9C16-C5AF2B479946 at donders.ru.nl> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Greydon, > > > > Let me also CC this to the FieldTrip list, as I know there are more people thinking about this. > > > > Although I am using Python for other projects (e.g. EEGsynth , we don?t have concrete plans for improving the compatibility between FieldTrip and Python, or to port parts of FieldTrip over to Python. Personally (*) I also feel that Python is not the optimal language and/or data analysis environment for the goals of the FieldTrip project. It would for sure attract more computer scientists and people that like programming, but for (non-technical) cognitive neuroscientists and people that are just able to do scripting I suspect it to become more like an application rather than a toolbox where you can look under the hood and mix it in with ones own code. > > > > (*) Other people might feel different of course > > > > MNE-Python is of course a project that I am following. The occasional improvements on the FieldTrip side are primarily focussed on making the transition between MNE-Python and FieldTrip more smooth (both ways). > > > > A complicating feature in Python is that data handling is different than in MATLAB, where we only use native built-in data structures. Saving data from Python requires a well-established file format (which does not exist) or a stable object definition (which is hard in science). Also for (open access) data sharing I hope that we can do more work on representing analysis results in a format that allows them to be reused in another pipeline. That is for exampel something that we attempted in the MEG section of the human connectome project, where the use cifti files (i.e. nifti-2 with a header extension), text files and - where needed - matlab files in a format that works well with Python. > > > > If you have ideas for improving the interoperability, you are welcome to contribute . > > > > best > > Robert > > > > PS Thanks for the nice remarks about FieldTrip! > > > > > >> On 16 Apr 2017, at 18:17, Greydon Gilmore wrote: > >> > >> Hi Robert, > >> > >> I recently stumbled across FieldTrip and I have been in love ever since. I love that I can incorporate the functions into my own scripts. > >> > >> I am curious o know if there is any work being done to make FieldTrip compatible with Python? > >> > >> Thank you for all the work your team put into FieldTrip, it's streamlined my workflow greatly. > >> > >> Greydon > >> > >> -- > >> Greydon Gilmore, B.Sc., M.Sc. (Neuroscience) > >> Ph.D. candidate in Biomedical Engineering > >> Movement Disorder Centre, University Hospital > >> University of Western Ontario > >> 339 Windermere Road, BLL-250 > >> 519-685-8500 ext. 76708 > >> London, Ontario > >> Canada, N6A 5A5 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Dr. Tom -- I would dance and be merry, Life would be a ding-a-derry, If I only had a brain. -- The Scarecrow From J.Verhoef at donders.ru.nl Mon Apr 24 20:25:50 2017 From: J.Verhoef at donders.ru.nl (Verhoef, J.P. (Julia)) Date: Mon, 24 Apr 2017 18:25:50 +0000 Subject: [FieldTrip] Nine Research Positions in the Dutch Consortium "Language in Interaction" (1.0 FTE) In-Reply-To: <11E9E0B371DBAE4EB859A9CC30606A04023F601E@exprd04.hosting.ru.nl> References: <11E9E0B371DBAE4EB859A9CC30606A04023F5FBE@exprd04.hosting.ru.nl>, <11E9E0B371DBAE4EB859A9CC30606A04023F601E@exprd04.hosting.ru.nl> Message-ID: <11E9E0B371DBAE4EB859A9CC30606A04023F602A@exprd04.hosting.ru.nl> Nine Research Positions in the Dutch Consortium 'Language in Interaction' (1.0 FTE) Dutch Research Consortium 'Language in Interaction' Vacancy number: 30.02.17 Application deadline: 21 May 2017 Responsibilities We are looking for highly motivated candidates to enrich a unique research consortium aiming to unravel the neurocognitive mechanisms of language at multiple levels. The goal is to understand both the universality and the variability of the human language faculty from genes to behaviour. Currently, our consortium advertises 4 Postdoc and 5 PhD positions. These positions provide the opportunity for conducting world-class research as a member of an interdisciplinary team. Each position has its own requirements and profile. Click here for more information on the advertised positions. www.languageininteraction.nl/jobs/BQsecond.html Work environment The Netherlands has an outstanding track record in the language sciences. The Language in Interaction research consortium, sponsored by a large grant from the Netherlands Organisation for Scientific Research (NWO), brings together many of the excellent research groups in the Netherlands with a research programme on the foundations of language. In addition to excellence in the domain of language and related relevant fields of cognition, our consortium provides state-of-the-art research facilities and a research team with ample experience in the complex research methods that will be invoked to address the scientific questions at the highest level of methodological sophistication. These include methods from genetics, neuroimaging, computational modelling, and patient-related research. This consortium realises both quality and critical mass for studying human language at a scale not easily found anywhere else. We have identified five Big Questions (BQ) that are central to our understanding of the human language faculty. These questions are interrelated at multiple levels. Teams of researchers will collaborate to collectively address these key questions of our field. Our five Big Questions are: BQ1: The nature of the mental lexicon: How to bridge neurobiology and psycholinguistic theory by computational modelling? BQ2: What are the characteristics and consequences of internal brain organization for language? BQ3: Creating a shared cognitive space: How is language grounded in and shaped by communicative settings of interacting people? BQ4: Variability in language processing and in language learning: Why does the ability to learn language change with age? How can we characterise and map individual language skills in relation to the population distribution? BQ5: How are other cognitive systems shaped by the presence of a language system in humans? Successful candidates will be appointed at one of the consortium’s home institutions, depending on the position applied for. All successful candidates will become members of our Big Question teams. The research is conducted in an international setting at all participating institutions. English is the lingua franca. What we expect from you Each position has its own requirements and profile. Detailed information on: www.languageininteraction.nl/jobs/BQsecond.html  General requirements for all positions are: • a degree in one of the fields indicated for the positions; • strong motivation; • excellent proficiency in written and spoken English. What we have to offer • employment: 1.0 FTE; • you will be appointed at one of the consortium’s home institutions, depending on the position applied for; • terms of employment depend on the embedding institution; • the institutes involved have regulations in place that enable their staff to create a good work-life balance. Other Information All institutes involved are equal opportunity employers, committed to building a culturally diverse intellectual community, and as such encourage applications from women and minorities. Would you like to know more? Further information on LiI consortium: http://www.languageininteraction.nl/ Further information on the different positions, including terms of employment and contacts: www.languageininteraction.nl/jobs/BQsecond.html Are you interested? You should upload your application (attn. of Prof. P. Hagoort) exclusively via: http://www.ru.nl/applyonline?tk=uk&recid=597242 Your application should include (and be limited to) the following attachment(s): • a cover letter quoting at the top the number of the position you apply for; • your curriculum vitae, including a list of publications and the names of at least two persons who can provide references. Please apply before 21 May 2017, 23:59 CET. You may apply for more than one position. No commercial propositions please. -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrea.brovelli at univ-amu.fr Mon Apr 24 21:35:26 2017 From: andrea.brovelli at univ-amu.fr (Andrea Brovelli) Date: Mon, 24 Apr 2017 21:35:26 +0200 Subject: [FieldTrip] 3 PhD scholarships in Integrative and Clinical Neurosciences at Aix-Marseille University (France) Message-ID: <8eb6aa69-e3d2-04f3-71d9-e2bfa937bbac@univ-amu.fr> In 2017, the PhD program in Integrative and Clinical Neurosciences at the Aix-Marseille University (France) will grant *three* *PhD scholarships* to excellent Master students that graduated from non-French top ranked universities. The selection process will include the following steps. 1. CALL FOR APPLICANTS (Master graduated students) * The scholarships are open to Master students that graduated from top rankenon-French universities. * Applicants must select and rank two of the proposed research projects * A guideline for student application and templates for recommendation letters must be downloaded on the following site: http://neuro-marseille.org/en/phdprogram-en/call-for-applicants/ * Applications should be sent *before May 21st, 2017 *at midnight (French time). 2. INTERVIEW * The selection committee will shortlist 10 students that will be individually interviewed in June. The students are encouraged to prepare their interviews with the project leaders they have selected. * The final decision will be known shortly after the interviews and the three successful candidates will start their PhD studies between October and December 2017. Contact Nadia Pittet nadejda.pittet at univ-amu.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.blume at sbg.ac.at Tue Apr 25 17:33:53 2017 From: christine.blume at sbg.ac.at (Blume Christine) Date: Tue, 25 Apr 2017 15:33:53 +0000 Subject: [FieldTrip] ft_definetrial on result from ft_appenddata? Message-ID: Dear FT community, I have data with overlapping segments, wherefore I need to do the raw data inspection using ft_databrowser on continuous data (unless ft_databrowser can handle overlapping segments now?). So far so good, but I have 5 different raw data files per person as our machine closes and files automatically and starts a new one as soon as they exceed 2GB. The most convenient thing would obviously be to append all 5, run ft_databrowser on the appended data and then do the segmentation. This is particularly the case because it is data from sleep and thus important to see how the EEG/MEG changes across time. However, I am wondering whether there is any way to apply ft_definetrial and ft_redefinetrial to appended datasets (as it obviously goes back to the underlying raw files, of which I have 5). Any suggestions are more than welcome :). Thanks, Christine -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandra.bendixen at physik.tu-chemnitz.de Tue Apr 25 23:00:40 2017 From: alexandra.bendixen at physik.tu-chemnitz.de (Alexandra Bendixen) Date: Tue, 25 Apr 2017 23:00:40 +0200 Subject: [FieldTrip] PhD and Postdoc positions in multimodal perception and cognition at TU Chemnitz, Germany Message-ID: <9AABDCBE-073E-4DEA-8943-1F89C3474B21@physik.tu-chemnitz.de> Dear colleagues, The Cognitive Systems Lab (Alexandra Bendixen) and the Physics of Cognition Group (Wolfgang Einhäuser) at Chemnitz University of Technology (TU Chemnitz) invite applications for 2 PhD student positions 2 postdoctoral researcher positions starting October 1st, 2017. The application deadline for all positions is May 31st, 2017. PhD positions Two PhD positions are funded by the German Research Foundation (DFG) within the project "Multistable perception across modalities: Resolving sensory ambiguity in vision and audition". The PhD projects will concern multistable perceptual phenomena (e.g., binocular rivalry, auditory streaming) with a focus on objective methods to assess observers’ perception. Methods include advanced psychophysical methods, eye tracking and pupillometry, peripheral physiology, electroencephalography (EEG) as well as theoretical and computational modelling. Experience in one or more of these fields is a plus. Salary for the PhD positions is according to the German salary scale (E13 TV-L) at 65%. Positions are contingent on funding availability and limited to 3 years in accordance with the applicable regulations. Applicants for the PhD positions must hold a M.Sc. degree or equivalent in psychology, physics, cognitive science, neuroscience or a related field. If the M.Sc. degree is not completed at the time of application, a statement by the thesis supervisor must be included that confirms that the degree will be completed before October 2017. Application documents for PhD positions must include a complete CV, copies of transcripts of all academic institutions, a letter of motivation for the specific position, as well as the names and contact information of at least 1 and up to 3 references that could be contacted for information about the applicant. Postdoctoral positions We are looking for postdocs who are prepared to develop their own research profile in interaction with the groups’ research foci in visual, auditory and/or multimodal perception and cognition. The groups operate laboratories equipped with sound-attenuated measurement rooms, state-of-the-art devices for visual and auditory psychophysics, for high-precision and mobile eye tracking, for peripheral physiology and for EEG as well as ample computational resources. Salary for the postdoc positions is according to the German salary scale (E13 TV-L) at 100%. The positions are contingent on funding availability. The initial contract will be limited to 3 years. An extension is possible depending on funding availability, personal qualification and applicable regulatory restrictions. Successful applicants are expected to engage in teaching in the "Sensors and Cognitive Psychology" study program at TU Chemnitz. Non-German-speaking applicants are expected to acquire sufficient proficiency in German for teaching these courses within the first two years. Applicants for the postdoctoral positions must hold a PhD or equivalent in psychology, physics, cognitive science, neuroscience or a related field. If the PhD is not completed at the time of application, a statement by the thesis supervisor must be included that confirms that the degree will be awarded before October 2017. Applications must have a strong background (as demonstrated by peer-reviewed publications) in at least one of the following fields: advanced psychophysics, vision research, auditory research, eye tracking, peripheral physiology, or EEG. Good programming skills and good command of English are mandatory. Application documents for postdoctoral positions must include a complete CV, a list of publications, copies of transcripts of all academic institutions, a letter stating the motivation for the specific position, the plans and objectives for future research, as well as plans for teaching and career development. The applications should also include the names and contact information of at least 2 and up to 5 references that could be contacted for information about the applicant. More information and application process More information about the research of the two groups can be found at https://www.tu-chemnitz.de/physik/SFKS/index.html.en and https://www.tu-chemnitz.de/physik/PHKP/index.html.en For more information on the positions and on how to apply, please visit the legally binding German version of the job advertisements: postdoc positions: https://www.tu-chemnitz.de/verwaltung/personal/stellen/212066_1_Kae.php PhD positions: https://www.tu-chemnitz.de/verwaltung/personal/stellen/212066_2_Kae.php TU Chemnitz is an equal opportunity employer and aims at increasing the number of female scientists; qualified women are therefore especially encouraged to apply. Application documents should be sent as single pdf-file to bewerbung_sfks_phkp at tu-chemnitz.de no later than May 31st, 2017. For the PhD positions, the subject line must include the keyword MultMod2017, for postdoctoral positions subject line must include the keyword SFKSPHKP2017. Please feel free to contact us (alexandra.bendixen at physik.tu-chemnitz.de, wolfgang.einhaeuser-treyer at physik.tu-chemnitz.de) for further information. We would be grateful if you could distribute this e-mail to suitable candidates. With best regards, Wolfgang Einhäuser-Treyer & Alexandra Bendixen -- Prof. Dr. Alexandra Bendixen TU Chemnitz - Cognitive Systems Lab http://www.tu-chemnitz.de/physik/SFKS/ Prof. Dr. Wolfgang Einhäuser-Treyer TU Chemnitz - Physics of Cognition Group http://www.tu-chemnitz.de/physik/PHKP/ From delucia.marzia at gmail.com Wed Apr 26 11:49:06 2017 From: delucia.marzia at gmail.com (Marzia De Lucia) Date: Wed, 26 Apr 2017 09:49:06 +0000 Subject: [FieldTrip] postdoctoral position in Lausanne Message-ID: <243dc9ccd6b64680a285e41adb4ca0b2@EXPRD01.hosting.ru.nl> Dear all, Applications are invited for a postdoc position at the Laboratoire de Recherche en Neuroimagerie (LREN) financed by the Eurostars project ‘ComAlert’ in collaboration with g.tec (http://www.gtec.at/). The position is under the supervision of Dr Marzia De Lucia and in close collaboration with the Neurology service and the Department of Intensive Care Medicine at the Lausanne University Hospital (CHUV). The project aims at developing EEG based tests for outcome prediction in comatose patients and to assess the degree of preserved cognitive functions during acute coma and during later stages of disorders of consciousness. This project takes advantage of sophisticated software and hardware solution provided by gtec and specifically targeted for their application in the intensive care environment. The LREN (https://www.unil.ch/lren/en/home.html) provides an excellent multidisciplinary and interactive research environment combining expertise in functional magnetic resonance imaging, electroencephalography and neuroimaging methods development. The ideal candidate should have a PhD in Neuroscience, Life Science, Biomedical Engineering or related areas. Prior experience with EEG, programming skills and proficiency in English and in French are advantageous. The position is available from the 1st of July 2017 till June 2019. The salaries are in accordance with the Swiss Public service regulations. Applications including a CV, a statement of research interests and the name and full contact details of two referees should be sent to : delucia.marzia at gmail.com Best Regards, Marzia De Lucia ------------------------------------ Marzia DE LUCIA, MER PD Laboratoire de recherche en Neuroimagerie - LREN Département des Neurosciences Cliniques Centre Hospitalier Universitaire Vaudois MP16 05 559, Chemin de Mont-Paisible 16 , 1011 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: From tim.bardouille at Dal.Ca Thu Apr 27 00:33:58 2017 From: tim.bardouille at Dal.Ca (Timothy Bardouille) Date: Wed, 26 Apr 2017 22:33:58 +0000 Subject: [FieldTrip] Position in Halifax, NS, Canada: MEG Scientist Message-ID: Please distribute widely: MEG Scientist @ IWK Health Centre, Halifax, NS, Canada The MEG lab at the Biomedical Translational Imaging Centre (BIOTIC) in the IWK Health Centre, Halifax, NS, Canada is hiring for the position of MEG Scientist. The MEG Scientist will implement a neuroimaging research program and support our existing clinical program in MEG. You will be part of the growing BIOTIC team, will be supported by an Imaging Technician, and will work with collaborators in the region and abroad. Applicants will be expected to describe an independent research plan involving MEG and neuroimaging more broadly, and be committed to supporting our clinical program. The BIOTIC MEG lab, located in the region's leading research and teaching women and children's hospital, maintains research and clinical programs in both pediatric and adult populations. These ongoing commitments occur in collaboration with researchers at the regions' universities and clinicians in Neurology and Neurosurgery. The BIOTIC MEG lab also works with industry partners in the medical technology space to achieve their strategic goals through collaborative projects. Many researchers at BIOTIC maintain professional affiliation with Dalhousie University. Qualifications • PhD degree in Physics, Biomedical Engineering, Neuroscience or a research related field • Publication track record in neuroimaging • Literacy with MATLAB and/or Python based MEG analysis packages is required • Interested in multi-modal imaging is a plus • Strong technical ability with MEG hardware/software is a plus Start Date: ASAP Salary commensurate with experience BIOTIC is a multi-site imaging centre that is embedded in the two leading research and teaching hospitals in Nova Scotia. Our advanced pre-clinical and clinical imaging equipment are housed in three labs, in two health centres encompassing over 12,000 square feet of lab space. BIOTIC operates at the intersection of research, clinical care, and industry collaboration, offering a dynamic and multifaceted work experience. The team co-develops medical technologies and creates new imaging techniques and methods for diagnosing and monitoring treatment. With a population of over 400,000 people, Halifax is the capital city of Nova Scotia, Canada. Greater Halifax boasts 5 universities and the two largest academic health centres in Atlantic Canada. Founded in the mid-1700s as a British naval fortress, Halifax balances a vibrant downtown filled with museums, theatres and pubs, with beaches, hiking trails and parks (the IWK itself is a mere 600 meters from the ocean!), and also has daily flights to London-Heathrow, NYC, Chicago etc. For more information on Halifax, please see www.destinationhalifax.ca For more information, please contact Dr. Tim Bardouille at tim.bardouille at iwk.nshealth.ca. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Halifax MEG Scientist.pdf Type: application/pdf Size: 134587 bytes Desc: Halifax MEG Scientist.pdf URL: From elam4hcp at gmail.com Thu Apr 27 19:17:04 2017 From: elam4hcp at gmail.com (Jennifer Elam) Date: Thu, 27 Apr 2017 12:17:04 -0500 Subject: [FieldTrip] Last weeks to register for HCP Course 2017 Message-ID: It's not too late to register for the 2017 HCP Course: "Exploring the Human Connectome" , to be held June 19-23 at the Djavad Mowafagian Centre for Brain Health at University of British Columbia (UBC) in Vancouver, BC, Canada! Fieldtrip tools play a major part of the HCP MEG processing pipelines and have been critical to the high quality processing of the project's 95 released MEG/MRI imaging datasets. Spaces for the course are limited and registration is on a first come, first served basis. May 17, 2017 is the deadline to reserve discounted UBC accommodations within walking distance to the course venue: https://reserve.ubcconferences.com/vancouver/availability.asp?hotelCode=%2A&startDate=06%2F16%2F2017&endDate=06%2F24%2F2017&adults=1&children=&rooms=1&requesttype=invBlockCode&code=G170618A The 5-day intensive HCP course is a great opportunity to learn directly from HCP investigators and designed for those interested in: - using data collected and distributed from the HCP young adult study - acquiring and analyzing HCP-style imaging and behavioral data at your own institution - processing your own non-HCP data using HCP pipelines and methods - using Connectome Workbench tools and sharing data using the BALSA imaging database - learning HCP multimodal neuroimaging analysis methods, including those that combine MEG and MRI data - exploring the HCP MMP 1.0 multimodal parcellation brain map and learning about how it can be used in your analyses - positioning yourself to capitalize on HCP-style data being distributed by the Connectome Coordinating Facility (CCF) from HCP development (healthy subjects ages 5-21) and aging (healthy subjects ages 35-90+) and Connectomes Related to Human Disease projects See https://store.humanconnectome.org/courses/2017/exploring-the-human-connectome.php for more info. If you have any questions, please contact us at: hcpcourse at humanconnectome.org We look forward to seeing you in Vancouver! Best, 2017 HCP Course Staff -------------- next part -------------- An HTML attachment was scrubbed... URL: From tim.bardouille at Dal.Ca Thu Apr 27 23:31:21 2017 From: tim.bardouille at Dal.Ca (Timothy Bardouille) Date: Thu, 27 Apr 2017 21:31:21 +0000 Subject: [FieldTrip] Position in Halifax, NS, Canada: MEG Scientist - application link added Message-ID: <72288243-FDB2-4D9F-A1EA-F3890D37937C@dal.ca> Hi all, Sorry for the second e-mail. I’m including the link to apply online this time. If interested in a primary position at the MEG lab in Halifax, please apply at this link: https://jobs.nshealth.ca/job/Halifax-MEG-Scientist-Nova-B3K-6R8/354454217/?locale=en_US Best regards, Tim. From: Timothy Bardouille Date: Wednesday, April 26, 2017 at 3:16 PM To: Discussion list for international MEG community Subject: Position in Halifax, NS: MEG Scientist Please distribute widely: MEG Scientist @ IWK Health Centre, Halifax, NS, Canada The MEG lab at the Biomedical Translational Imaging Centre (BIOTIC) in the IWK Health Centre, Halifax, NS, Canada is hiring for the position of MEG Scientist. The MEG Scientist will implement a neuroimaging research program and support our existing clinical program in MEG. You will be part of the growing BIOTIC team, will be supported by an Imaging Technician, and will work with collaborators in the region and abroad. Applicants will be expected to describe an independent research plan involving MEG and neuroimaging more broadly, and be committed to supporting our clinical program. The BIOTIC MEG lab, located in the region's leading research and teaching women and children's hospital, maintains research and clinical programs in both pediatric and adult populations. These ongoing commitments occur in collaboration with researchers at the regions' universities and clinicians in Neurology and Neurosurgery. The BIOTIC MEG lab also works with industry partners in the medical technology space to achieve their strategic goals through collaborative projects. Many researchers at BIOTIC maintain professional affiliation with Dalhousie University. Qualifications • PhD degree in Physics, Biomedical Engineering, Neuroscience or a research related field • Publication track record in neuroimaging • Literacy with MATLAB and/or Python based MEG analysis packages is required • Interested in multi-modal imaging is a plus • Strong technical ability with MEG hardware/software is a plus Start Date: ASAP Salary commensurate with experience BIOTIC is a multi-site imaging centre that is embedded in the two leading research and teaching hospitals in Nova Scotia. Our advanced pre-clinical and clinical imaging equipment are housed in three labs, in two health centres encompassing over 12,000 square feet of lab space. BIOTIC operates at the intersection of research, clinical care, and industry collaboration, offering a dynamic and multifaceted work experience. The team co-develops medical technologies and creates new imaging techniques and methods for diagnosing and monitoring treatment. With a population of over 400,000 people, Halifax is the capital city of Nova Scotia, Canada. Greater Halifax boasts 5 universities and the two largest academic health centres in Atlantic Canada. Founded in the mid-1700s as a British naval fortress, Halifax balances a vibrant downtown filled with museums, theatres and pubs, with beaches, hiking trails and parks (the IWK itself is a mere 600 meters from the ocean!), and also has daily flights to London-Heathrow, NYC, Chicago etc. For more information on Halifax, please see www.destinationhalifax.ca For more information, please contact Dr. Tim Bardouille at tim.bardouille at iwk.nshealth.ca. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.flandin at ucl.ac.uk Mon Apr 3 18:36:42 2017 From: g.flandin at ucl.ac.uk (Guillaume Flandin) Date: Mon, 3 Apr 2017 17:36:42 +0100 Subject: [FieldTrip] compiling ft_volumenormalise In-Reply-To: References: Message-ID: <58E27A1A.7080307@ucl.ac.uk> Dear Anne, The way we compile SPM is to use the '-a' flag as you did but with a directory instead of individual files (e.g. '-a', '~/Documents/fieldtrip/'); by doing so, all the files from the specified directory as well as all the files from subdirectories will be included so that you don't have to rely on the automatic file dependency analysis mcc performs. Best regards, Guillaume. On 15/03/17 12:29, Anne Urai wrote: > If anyone encounters the same problem, compilation works if I manually > add a bunch of spm functions (which are not recognised by mcc, probably > because they are in a class definition folder). > > Specifically, including > > '-a', '~/Documents/fieldtrip/external/spm8/spm.m', ... > '-a', '~/Documents/fieldtrip/external/spm8/templates/T1.nii', ... > '-a', '~/Documents/fieldtrip/external/freesurfer/MRIread', ... > '-a', '~/code/Tools/spmbug/dim.m', ... > '-a', '~/code/Tools/spmbug/dtype.m', ... > '-a', '~/code/Tools/spmbug/fname.m', ... > '-a', '~/code/Tools/spmbug/offset.m', ... > '-a', '~/code/Tools/spmbug/scl_slope.m', ... > '-a', '~/code/Tools/spmbug/scl_inter.m', ... > '-a', '~/code/Tools/spmbug/permission.m', ... > '-a', '~/code/Tools/spmbug/niftistruc.m', ... > '-a', '~/code/Tools/spmbug/read_hdr.m', ... > '-a', '~/code/Tools/spmbug/getdict.m', ... > '-a', '~/code/Tools/spmbug/read_extras.m', ... > '-a', '~/code/Tools/spmbug/read_hdr_raw.m', ... > > does the trick. > > Happy compiling, > Anne > > On 1 March 2017 at 19:38, Anne Urai > wrote: > > Hi FieldTrippers, > > I compile my code to run on the supercomputer cluster (without many > matlab licenses), which usually works fine when I do something like: > > /addpath('~/Documents/fieldtrip');/ > /ft_defaults; / > /addpath('~/Documents/fieldtrip/external/spm8');/ > /mcc('-mv', '-N', '-p', 'stats', '-p', 'images', '-p', 'signal', .../ > / '-R', '-nodisplay', '-R', '-singleCompThread', fname);/ > > However, compiling the ft_volumenormalise function gives me some > problems. Specifically, if source is the result of my beamformer > analysis, this code > > / cfg = [];/ > / cfg.parameter = 'pow';/ > / cfg.nonlinear = 'no'; % can warp back to individual/ > / cfg.template = > '/home/aeurai/Documents/fieldtrip/external/spm8/templates/T1.nii';/ > / cfg.write = 'no';/ > / cfg.keepinside = 'no'; % otherwise, > ft_sourcegrandaverage will bug/ > / source = ft_volumenormalise(cfg, source);/ > > works fine when running it within Matlab. However, when I run the > executable after compiling (which completes without error), a > low-level spm function throws the following error: > > /the input is source data with 16777216 brainordinates on a [256 256 > 256] grid/ > /Warning: could not reshape "freq" to the expected dimensions/ > /> In ft_datatype_volume (line 136)/ > /In ft_checkdata (line 350)/ > /In ft_volumenormalise (line 98)/ > /In B6b_sourceContrast_volNormalise (line 57)/ > /Converting the coordinate system from ctf to spm/ > /Undefined function 'fname' for input arguments of type 'struct'/ > /Error in file_array (line 32)/ > /Error in spm_create_vol>create_vol (line 77)/ > /Error in spm_create_vol (line 16)/ > /Error in volumewrite_spm (line 71)/ > /Error in ft_write_mri (line 65)/ > /Error in align_ctf2spm (line 168)/ > /Error in ft_convert_coordsys (line 95)/ > /Error in ft_volumenormalise (line 124)/ > /Error in B6b_sourceContrast_volNormalise (line 57)/ > /MATLAB:UndefinedFunction/ > > I'd be very grateful for hints from anyone who's successfully > compiled the ft_normalise function! Adding the template T1.nii file, > spm8 or freesurfer at compilation does not solve the problem. > Thanks, > > — > Anne E. Urai, MSc > PhD student | Institut für Neurophysiologie und Pathophysiologie > Universitätsklinikum Hamburg-Eppendorf | Martinistrasse 52, 20246 | > Hamburg, Germany > www.anneurai.net / @AnneEUrai > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Guillaume Flandin, PhD Wellcome Trust Centre for Neuroimaging University College London 12 Queen Square London WC1N 3BG From d.painter1 at uq.edu.au Tue Apr 4 03:41:09 2017 From: d.painter1 at uq.edu.au (David Painter) Date: Tue, 4 Apr 2017 01:41:09 +0000 Subject: [FieldTrip] Realtime buffer - possible to spawn multiple buffer threads using non-default values for host and port? In-Reply-To: <1491269842991.43690@uq.edu.au> References: <1491269842991.43690@uq.edu.au> Message-ID: <1491270069170.592@uq.edu.au> Dear Fieldtrippers, I've been using Fieldtrip's buffer.exe in conjunction with biosemi2ft.exe to read EEG data in realtime. I'd like to use buffer.exe to communicate EEG analysis results between Matlab sessions. I was wondering whether it's possible to spawn multiple buffer threads on separate ports? Host 'localhost' and port 1972 are already occupied by reading data from the amplifier. I'd like to use a separate port for additional communication during neurofeedback, but the only value for "port" that seems to work is 1972. "Host" accepts the values of 'localhost' and the current ip4 config address of the computer but can't seem to allow remote connections. Does anyone know if host and port can accept values other than "localhost" and "1972"? I couldn't many explicit examples on this procedure online, so I've posted my code for future reference. David University of Queensland Windows 7 & 10, 64-bit - Matlab R2016b 64-bit % matlab code % direct.realtime ---> where buffer.exe and related files are located: % buffer.exe % pthreadGC2-w64.dll % buffer.mexw32 % pthreadGC2.dll % Labview_DLL.dll % buffer.mexw64 % biosemi2ft.exe % libgcc_s_dw2-1.dll % biosemi_config.txt % libstdc++-6.dll !taskkill /F /IM cmd.exe /T !taskkill /F /IM buffer.exe /T system( ['e: -& cd "' direct.realtime '" & buffer.exe -&'] ); % start buffer.exe cfg.host = 'localhost'; % <---- CAN THESE VALUES CHANGE? cfg.port = uint32( 1972 ); % <----- CAN THESE VALUES CHANGE? cfg.nchans = uint32( 1 ); dat.nchans = uint32( 32 ); dat.nsamples = uint32( 200 ); dat.nevents = uint32( 0 ); dat.fsample = uint32( 200 ); dat.data_type = uint32( 9 ); % single precision data dat.bufsize = uint32( dat.nsamples * dat.nchans * 4 ); dat.buf = single( rand(dat.nsamples,dat.nchans ) ); buffer('put_hdr', dat, cfg.host, cfg.port); % hdr = buffer('get_hdr', [], cfg.host, cfg.port); % ----- read header buffer('put_dat', dat, cfg.host, cfg.port); % hdr = buffer('get_hdr', [], cfg.host, cfg.port); % ----- read header begsample = 1; endsample = 200; dat = buffer('get_dat', [begsample-1 endsample-1], cfg.host, cfg.port); -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarang at cfin.au.dk Tue Apr 4 14:21:00 2017 From: sarang at cfin.au.dk (Sarang S. Dalal) Date: Tue, 4 Apr 2017 12:21:00 +0000 Subject: [FieldTrip] April 10 deadline for MEG Nord conference (Aarhus, May 9-10 2017) Message-ID: <51C59DAA-ECA6-45B1-8EEF-501485EF59BE@cfin.au.dk> Dear all, The abstract submission and registration deadline is coming up on April 10 for the MEG Nord conference at Aarhus University, Denmark, to be held on May 9-10 (+ satellite on May 8). The preliminary program and a link to the registration/submission page can be found at: http://cfin.au.dk/meg-nord-2017/ Please feel free to advertise and forward this information to your colleagues and mailing lists. Note that you can choose between three submission types: poster (default), blitz talk (3 min – to be evaluated) and site symposium (restricted to participating Nordic MEG sites). The latter is to be agreed within each site prior to submission, and the designated individuals should submit their details individually; other submission types are open to all. Note that we do not have the capacity to book accommodation, so please use your favorite booking system. While there are no hotels on-site, any centrally located accommodation in Aarhus would be within easy reach from the AU Lakeside auditorium. For flights, in addition to Aarhus airport (connected mainly to Nordic capitals and London), please consider Billund and Aalborg as well (many direct connections throughout Europe). There are also train connections from Copenhagen and Hamburg. We look forward to welcoming you at MEG Nord 2017! On behalf of the organising committee: Yury Shtyrov, Sarang Dalal, Christopher Bailey From sarang at cfin.au.dk Thu Apr 6 16:13:18 2017 From: sarang at cfin.au.dk (Sarang S. Dalal) Date: Thu, 6 Apr 2017 14:13:18 +0000 Subject: [FieldTrip] OpenMEEG binaries are not correctly installed In-Reply-To: References: Message-ID: Hi Rachel, Contrary to what the message says, you might actually have the OpenMEEG binaries properly installed. :-) You do get the expected output when you ran system('om_assemble’)… The problem is that the program that checks for it (om_checkombin.m) simply doesn’t know how to check for it on Windows. Have a look in om_checkombin.m … maybe you can figure out how to properly check on Windows, or otherwise simply force status = 0 as a temporary hack. Cheers, Sarang On 31 Mar 2017, at 17:40, Rachel S > wrote: Hello fieldtrip community, My name is Rachel and I am a Master student working on a project on Ecog. I am trying to use ft_prepare_headmodel with cfg = 'openmeeg' and I get the error "OpenMEEG binaries are not correctly installed". I use a Windows machine and I already add the openmeeg install folder to 'PATH'. When I ran system('om_assemble'), the output is: om_assemble version 2.1.0 (799) compiled at Aug 17 2011 19:50:41 Not enough arguments Please try "om_assemble -h" or "om_assemble --help " ans = 0 Any suggestions? Thanks in advance. Best wishes, Rachel _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Apr 7 09:10:29 2017 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 7 Apr 2017 09:10:29 +0200 Subject: [FieldTrip] Realtime buffer - possible to spawn multiple buffer threads using non-default values for host and port? In-Reply-To: <1491270069170.592@uq.edu.au> References: <1491269842991.43690@uq.edu.au> <1491270069170.592@uq.edu.au> Message-ID: <6759BA3E-A2E1-456E-8847-73190BE4FF63@donders.ru.nl> Hi David, The buffer mex allows you to start a buffer server within MATLAB. However, the low-level C code does not allow multiple (posix) threads to be started to support multiple buffers in a single executable (i.e. in MATLAB), since the threads would all be reading/writing at the same piece of memory. So the only way to go is to start multiple executables. The way that I usually do this is by starting multiple instances of buffer.exe, specifying for each which port it should listen to. If you start a command line prompt, you can cd to the fieldtrip/realtime/bin/win32 directory and start buffer.exe where you specify the port number. Repeat that (in multiple command windows) for each of the buffers, each with a separate port. The buffer always runs on the computer where you start it. So the answer to the question “can the buffer run on another computer than localhost?” is no. But the code that reads and/or writes to the buffer can connect to another computer. Please note that the firewall settings have to allow for this. On http://www.fieldtriptoolbox.org/development/realtime/fmri you can find an example for a pipeline that involves two buffers. Furthermore I recommend that you do not use the buffer.mex file (it is in private for a good reason!), but rather that you use ft_read_data and ft_write_data. At that level you can also find plenty of examples, e.g. starting at http://www.fieldtriptoolbox.org/getting_started/realtime and looking at the code in fieldtrip/realtime/example. best Robert > On 04 Apr 2017, at 03:41, David Painter wrote: > > Dear Fieldtrippers, > > I've been using Fieldtrip's buffer.exe in conjunction with biosemi2ft.exe to read EEG data in realtime. > > I'd like to use buffer.exe to communicate EEG analysis results between Matlab sessions. I was wondering whether it's possible to spawn multiple buffer threads on separate ports? Host 'localhost' and port 1972 are already occupied by reading data from the amplifier. I'd like to use a separate port for additional communication during neurofeedback, but the only value for "port" that seems to work is 1972. "Host" accepts the values of 'localhost' and the current ip4 config address of the computer but can't seem to allow remote connections. > > Does anyone know if host and port can accept values other than "localhost" and "1972"? > > I couldn't many explicit examples on this procedure online, so I've posted my code for future reference. > > David > University of Queensland > Windows 7 & 10, 64-bit - Matlab R2016b 64-bit > > % matlab code > > % direct.realtime ---> where buffer.exe and related files are located: > % buffer.exe > % pthreadGC2-w64.dll > % buffer.mexw32 > % pthreadGC2.dll > % Labview_DLL.dll > % buffer.mexw64 > % biosemi2ft.exe > % libgcc_s_dw2-1.dll > % biosemi_config.txt > % libstdc++-6.dll > > !taskkill /F /IM cmd.exe /T > !taskkill /F /IM buffer.exe /T > system( ['e: -& cd "' direct.realtime '" & buffer.exe -&'] ); % start buffer.exe > > cfg.host = 'localhost'; % <---- CAN THESE VALUES CHANGE? > cfg.port = uint32( 1972 ); % <----- CAN THESE VALUES CHANGE? > > cfg.nchans = uint32( 1 ); > dat.nchans = uint32( 32 ); > dat.nsamples = uint32( 200 ); > dat.nevents = uint32( 0 ); > dat.fsample = uint32( 200 ); > dat.data_type = uint32( 9 ); % single precision data > dat.bufsize = uint32( dat.nsamples * dat.nchans * 4 ); > dat.buf = single( rand(dat.nsamples,dat.nchans ) ); > > buffer('put_hdr', dat, cfg.host, cfg.port); > % hdr = buffer('get_hdr', [], cfg.host, cfg.port); % ----- read header > buffer('put_dat', dat, cfg.host, cfg.port); > % hdr = buffer('get_hdr', [], cfg.host, cfg.port); % ----- read header > > begsample = 1; > endsample = 200; > > dat = buffer('get_dat', [begsample-1 endsample-1], cfg.host, cfg.port); > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Apr 7 09:21:07 2017 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 7 Apr 2017 09:21:07 +0200 Subject: [FieldTrip] compiling ft_volumenormalise In-Reply-To: References: Message-ID: <0F4760EF-55E7-4C00-8106-6A16CD4F70CD@donders.ru.nl> Hi Anne I opened this feature request http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2787 some time back. I made an initial implementation in a separate branch at https://github.com/robertoostenveld/fieldtrip/tree/bug2787-standalone If you look at https://github.com/fieldtrip/fieldtrip/compare/master...robertoostenveld:bug2787-standalone you can see the changes. It follows the strategy that we used for the compiled megconnectome application for the human connectome project (see https://www.humanconnectome.org/documentation/HCP-pipelines/meg-pipeline.html ), i.e. it compiles into an application which can take a script as argument and which “evals” that script. This allows for the flexibility of making changes to the pipeline and cfg settings without having to recompile. best Robert PS If you can use a single interactive MATLAB session on a head node or compute node from the cluster, you can also look into using the ‘compile’ option in qsubcellfun. See http://www.fieldtriptoolbox.org/faq#distributed_computing > On 15 Mar 2017, at 13:29, Anne Urai wrote: > > If anyone encounters the same problem, compilation works if I manually add a bunch of spm functions (which are not recognised by mcc, probably because they are in a class definition folder). > > Specifically, including > > '-a', '~/Documents/fieldtrip/external/spm8/spm.m', ... > '-a', '~/Documents/fieldtrip/external/spm8/templates/T1.nii', ... > '-a', '~/Documents/fieldtrip/external/freesurfer/MRIread', ... > '-a', '~/code/Tools/spmbug/dim.m', ... > '-a', '~/code/Tools/spmbug/dtype.m', ... > '-a', '~/code/Tools/spmbug/fname.m', ... > '-a', '~/code/Tools/spmbug/offset.m', ... > '-a', '~/code/Tools/spmbug/scl_slope.m', ... > '-a', '~/code/Tools/spmbug/scl_inter.m', ... > '-a', '~/code/Tools/spmbug/permission.m', ... > '-a', '~/code/Tools/spmbug/niftistruc.m', ... > '-a', '~/code/Tools/spmbug/read_hdr.m', ... > '-a', '~/code/Tools/spmbug/getdict.m', ... > '-a', '~/code/Tools/spmbug/read_extras.m', ... > '-a', '~/code/Tools/spmbug/read_hdr_raw.m', ... > > does the trick. > > Happy compiling, > Anne > > On 1 March 2017 at 19:38, Anne Urai > wrote: > Hi FieldTrippers, > > I compile my code to run on the supercomputer cluster (without many matlab licenses), which usually works fine when I do something like: > > addpath('~/Documents/fieldtrip'); > ft_defaults; > addpath('~/Documents/fieldtrip/external/spm8'); > mcc('-mv', '-N', '-p', 'stats', '-p', 'images', '-p', 'signal', ... > '-R', '-nodisplay', '-R', '-singleCompThread', fname); > > However, compiling the ft_volumenormalise function gives me some problems. Specifically, if source is the result of my beamformer analysis, this code > > cfg = []; > cfg.parameter = 'pow'; > cfg.nonlinear = 'no'; % can warp back to individual > cfg.template = '/home/aeurai/Documents/fieldtrip/external/spm8/templates/T1.nii'; > cfg.write = 'no'; > cfg.keepinside = 'no'; % otherwise, ft_sourcegrandaverage will bug > source = ft_volumenormalise(cfg, source); > > works fine when running it within Matlab. However, when I run the executable after compiling (which completes without error), a low-level spm function throws the following error: > > the input is source data with 16777216 brainordinates on a [256 256 256] grid > Warning: could not reshape "freq" to the expected dimensions > > In ft_datatype_volume (line 136) > In ft_checkdata (line 350) > In ft_volumenormalise (line 98) > In B6b_sourceContrast_volNormalise (line 57) > Converting the coordinate system from ctf to spm > Undefined function 'fname' for input arguments of type 'struct' > Error in file_array (line 32) > Error in spm_create_vol>create_vol (line 77) > Error in spm_create_vol (line 16) > Error in volumewrite_spm (line 71) > Error in ft_write_mri (line 65) > Error in align_ctf2spm (line 168) > Error in ft_convert_coordsys (line 95) > Error in ft_volumenormalise (line 124) > Error in B6b_sourceContrast_volNormalise (line 57) > MATLAB:UndefinedFunction > > I'd be very grateful for hints from anyone who's successfully compiled the ft_normalise function! Adding the template T1.nii file, spm8 or freesurfer at compilation does not solve the problem. > Thanks, > > — > Anne E. Urai, MSc > PhD student | Institut für Neurophysiologie und Pathophysiologie > Universitätsklinikum Hamburg-Eppendorf | Martinistrasse 52, 20246 | Hamburg, Germany > www.anneurai.net / @AnneEUrai > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From bart at vision.rutgers.edu Fri Apr 7 09:40:52 2017 From: bart at vision.rutgers.edu (Bart Krekelberg) Date: Fri, 07 Apr 2017 07:40:52 +0000 Subject: [FieldTrip] Postdoctoral Position at Rutgers University Message-ID: Postdoctoral Position at Rutgers University: Neural mechanisms of perception in schizophrenia and bipolar disorder using EEG and transcranial current stimulation. The Division of Schizophrenia Research and Center for Molecular and Behavioral Neuroscience at Rutgers University in New Jersey are seeking to hire a full-time postdoctoral fellow. The overall goal of the project is to use EEG and transcranial current stimulation (tDCS ,tACS) to investigate the neurobiological basis of perceptual differences in schizophrenia and bipolar disorder. The ideal candidate will have a doctoral degree in psychology, neuroscience, cognitive science, or a related field, will be proficient in designing and performing EEG experiments with human participants, and will have a strong affinity with sophisticated data analysis (for instance, using Matlab). The successful candidate will play a pivotal role in the design and further development of experimental protocols, organizing study data, analyzing data, writing up, and presenting scientific results. There will also be significant opportunity for designing and conducting original research of the candidate’s choosing. The Rutgers Newark Campus and the Center for Molecular and Behavioral Neuroscience provide a diverse and stimulating scientific environment. Collaborations are possible with investigators at other affiliated departments and institutions including Rutgers University Brain Imaging Center (http://rubic.rutgers.edu/), Rutgers Center for Cognitive Science ( http://ruccs.rutgers.edu), and Rutgers-Princeton Center for Computational Cognitive Neuropsychiatry (https://ccnp.princeton.edu/about-ccnp/). An infinite amount of cultural stimulation is only a 15 minute train ride away, in New York City. An appointment at NIH postdoctoral salary scales will be made for one year, with the possibility to renew for one or more additional years. Rutgers University is an equal opportunity, affirmative action institution; underrepresented minorities are encouraged to apply. The start date is flexible. Interested applicants should send a CV, cover letter, representative publications, and the names of three references to Caren Alexander ( alexanch at ubhc.rutgers.edu), using the subject heading “Postdoc Search 2017”. Informal inquiries regarding the position are welcome and may be directed to Brian Keane, (brian.keane at rutgers.edu; www.briankeane.org) or Bart Krekelberg (bart at vision.rutgers.edu; www.vision.rutgers.edu) -------------- next part -------------- An HTML attachment was scrubbed... URL: From M.Wimber at bham.ac.uk Fri Apr 7 12:04:43 2017 From: M.Wimber at bham.ac.uk (Maria Wimber) Date: Fri, 7 Apr 2017 10:04:43 +0000 Subject: [FieldTrip] Postdoc for human single neuron project in Birmingham Message-ID: The Memory Group in Birmingham (www.memorybham.com) currently has an open position for a postdoctoral research fellow, funded by a 5-year European Research Council (ERC) grant awarded to Dr Maria Wimber (www.memorybham.com/maria-wimber). The project aims to map the time course of remembering in the human brain, using memory-related patterns of neural activity. It uses a multimodal brain imaging approach, including intracranial EEG, EEG-fMRI, MEG, and high-field fMRI. The postdoc will mainly be involved in the iEEG aspects of the project, including LFP and single-unit recordings from the human medial temporal lobes. These are conducted in close collaboration with the Queen Elisabeth Hospital Birmingham (UK), and other members of the Birmingham Memory Group. We encourage applications from researchers with a strong background in electrophysiology - human or animal - and a general interest in memory. The post is open for applications until April 19th 2017. More details about the position and an application link can be found at www.jobs.ac.uk/job/AYA233/research-fellow For more information, please feel free to contact the PI directly by email at m.wimber at bham.ac.uk. ---------------------- Dr Maria Wimber Senior Lecturer School of Psychology University of Birmingham tel +44 121 4144659 www.memorybham.com/maria-wimber -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Apr 7 14:27:59 2017 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 7 Apr 2017 14:27:59 +0200 Subject: [FieldTrip] new look and feel for the Fieldtrip website Message-ID: Dear FieldTrip users Now that the FieldTrip toolkit course that we hosted here in Nijmegen is over, I have moved the website over to a new version of the dokuwiki content management system (i.e. the PHP code that runs underneath the website). Read on below for the motivation... The old version of the dokuwiki software was flagged by some online scanners as being sensitive to malware, and I received reports that at some universities it was blocked. Although there is no reason to asume that the FT wiki was malicious in any way (the whole site is carefully monitored and locked down), it is of course annoying if it gets flagged as such. The drawback of the new version of the website is that the old template is not compatible, so right now the wiki has a different look and feel. All content is exactly the same, and we will try to get the original appearance back. For those of you for whom the website was blocked: it will take some time before it gets scanned once more (which I suppose happens automatically, as I never requested for it). That means that www.fieldtriptoolbox.org might remain in some blacklist database for some time. You can use new.fieldtriptoolbox.org as a temporary alternative. It points to exactly the same site, but operates over a different web address and proxy server. best regards, Robert PS we could use some help with the website. If you know a bit of PHP/HTML/CSS - or possibly even have dokuwiki experience - and want to help us out, please send me a personal message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tfkustermann at gmail.com Fri Apr 7 17:45:09 2017 From: tfkustermann at gmail.com (Thomas Kustermann) Date: Fri, 7 Apr 2017 17:45:09 +0200 Subject: [FieldTrip] how to make the cfg.selectfeature work in ft_databrowser? In-Reply-To: References: Message-ID: Hello Diego, taking a look at the underlying code it seems that while multiple input arguments to cfg.selectfeature are accepted and passed on to artfctdef.xxx.artifact (line 403), the function then attempts to select the current artifact from cfg.selectfeature even when multiple arguments are entered. opt.ftsel = find(strcmp(artlabel,cfg.selectfeature)); % current artifact/feature being selected (line 629) You could either change this line to: opt.ftsel = find(strcmp(artlabel,cfg.selectfeature{1})); % current artifact/feature being selected automatically selecting the first input argument to cfg.selectfeature as default selection in ft_databrowser or you could write them to the cfg.artfctdef.xxx.artifact manually: cfg.selectfeature = 'a'; cfg.artfctdef.a.artifact = zeros(0,2); cfg.artfctdef.b.artifact = zeros(0,2); ... Best, Thomas On Fri, Mar 31, 2017 at 4:40 PM, Diego Lozano-Soldevilla < dlozanosoldevilla at gmail.com> wrote: > Hi all, > > I'm using ft_databrowser to inspect sleep data and I want to visually mark > different events (spindles, k-complexes, artifacts, so forth) and asign > them to different cfg.artfctdef.xxx.artifact substructures. Could somebody > help me to mark different artifact trial types using the cfg.selectfeature > option? Please find below the code and data to reproduce the error I got. > I'm using the very last fieldtrip version on windows with matlab 7.9b. > > Thanks beforehand, > > Diego > > > > data = []; > data.label = {'Fpz';'F7';'F3';'Fz';'F4';'F8';'C3';'Cz';'C4';'P3';'Pz';' > P4';'O1';'Oz';'O2'}; > data.fsample = 250; > data.trial{1} = rand(size(data.label,1),data.fsample*30); > data.time{1} = (1:data.fsample*30)./data.fsample; > > cfg = []; > cfg.length = 2; > cfg.overlap = 0; > trl = ft_redefinetrial(cfg,data); > > > cfg = []; > cfg.channel = 'all'; > cfg.blocksize = 2; > cfg.selectfeature = {'a';'b'}; > cfg.viewmode = 'vertical'; > events = ft_databrowser(cfg,trl); > > > the input is raw data with 15 channels and 15 trials > detected 0 a artifacts > detected 0 b artifacts > ??? Error using ==> plus > Matrix dimensions must agree. > > Error in ==> ft_databrowser at 745 > hsel = [1 2 3] + (opt.ftsel-1) .*3; > > ??? Reference to non-existent field 'trlvis'. > > Error in ==> ft_databrowser>redraw_cb at 1639 > begsample = opt.trlvis(opt.trlop, 1); > > Error in ==> ft_databrowser>winresize_cb at 2250 > redraw_cb(h,eventdata); > > ??? Error while evaluating figure ResizeFcn > > > > Virus-free. > www.avast.com > > <#m_-281810346689554922_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joeboe at umich.edu Fri Apr 7 20:23:32 2017 From: joeboe at umich.edu (Joseph Lee) Date: Fri, 7 Apr 2017 14:23:32 -0400 Subject: [FieldTrip] Inquiry about Field-Trip usage for multi-channel sources Message-ID: Dear Field Trip Community I am Joe from the Computational Unit of the Center for Consciousness Science, University of Michigan. We are somewhat new to forward modelling and are currently undertaking a project to generate 128 scalp-level channel signals from the 78 source-level signals. We are using the "ft_compute_leadfield" function of FieldTrip in order to accomplish that goal. Is this a valid approach for our goal or were those functions designed for a different purpose? Any comments on this will be helpful for us. Thank you very much. Best, Joe Research Assistant Center for Consciousness Science, University of Michigan Medical School, Ann Arbor, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: From timeehan at gmail.com Fri Apr 7 20:32:49 2017 From: timeehan at gmail.com (Tim Meehan) Date: Fri, 7 Apr 2017 14:32:49 -0400 Subject: [FieldTrip] iEEG square wave 'notch' artifact Message-ID: Dear FieldTrippers, I have a recurring artifact in my iEEG data, a very brief (10-15 ms) square-wave-like 'notch' that occurs intermittently and across many channels. It also varies in polarity and amplitude, seemingly randomly. Here's a link showing an example trial containing many of these artifacts: https://drive.google.com/open?id=0B4m5PGO25j3mYkVPUEI5aDZERDA As of now I've been advised to throw out trials in which these occur, but they are very frequent during some sessions. I wonder if alternatively there is some way to selectively remove these? My guess is one could do some sort of template matching to identify when they occur and interpolate across, but I have no idea how to do that or if it's feasible. Does anyone have any insight? Thank you, Tim -------------- next part -------------- An HTML attachment was scrubbed... URL: From dlozanosoldevilla at gmail.com Fri Apr 7 20:34:52 2017 From: dlozanosoldevilla at gmail.com (Diego Lozano-Soldevilla) Date: Fri, 7 Apr 2017 20:34:52 +0200 Subject: [FieldTrip] how to make the cfg.selectfeature work in ft_databrowser? In-Reply-To: References: Message-ID: Hi Thomas, Thank you for your response. It seems is not working well so I'll file a bug and figure out how to fix it. best, Diego On 7 April 2017 at 17:45, Thomas Kustermann wrote: > Hello Diego, > > taking a look at the underlying code it seems that while multiple input > arguments to cfg.selectfeature are accepted and passed on to > artfctdef.xxx.artifact (line 403), the function then attempts to select the > current artifact from cfg.selectfeature even when multiple arguments are > entered. > opt.ftsel = find(strcmp(artlabel,cfg.selectfeature)); % current > artifact/feature being selected (line 629) > > You could either change this line to: > opt.ftsel = find(strcmp(artlabel,cfg.selectfeature{1})); % current > artifact/feature being selected > > automatically selecting the first input argument to cfg.selectfeature as > default selection in ft_databrowser or you could write them to the cfg.artfctdef.xxx.artifact > manually: > > cfg.selectfeature = 'a'; > cfg.artfctdef.a.artifact = zeros(0,2); > cfg.artfctdef.b.artifact = zeros(0,2); > ... > > Best, > Thomas > > > > On Fri, Mar 31, 2017 at 4:40 PM, Diego Lozano-Soldevilla < > dlozanosoldevilla at gmail.com> wrote: > >> Hi all, >> >> I'm using ft_databrowser to inspect sleep data and I want to visually >> mark different events (spindles, k-complexes, artifacts, so forth) and >> asign them to different cfg.artfctdef.xxx.artifact substructures. Could >> somebody help me to mark different artifact trial types using the >> cfg.selectfeature option? Please find below the code and data to reproduce >> the error I got. I'm using the very last fieldtrip version on windows with >> matlab 7.9b. >> >> Thanks beforehand, >> >> Diego >> >> >> >> data = []; >> data.label = {'Fpz';'F7';'F3';'Fz';'F4';'F8';'C3';'Cz';'C4';'P3';'Pz';'P4 >> ';'O1';'Oz';'O2'}; >> data.fsample = 250; >> data.trial{1} = rand(size(data.label,1),data.fsample*30); >> data.time{1} = (1:data.fsample*30)./data.fsample; >> >> cfg = []; >> cfg.length = 2; >> cfg.overlap = 0; >> trl = ft_redefinetrial(cfg,data); >> >> >> cfg = []; >> cfg.channel = 'all'; >> cfg.blocksize = 2; >> cfg.selectfeature = {'a';'b'}; >> cfg.viewmode = 'vertical'; >> events = ft_databrowser(cfg,trl); >> >> >> the input is raw data with 15 channels and 15 trials >> detected 0 a artifacts >> detected 0 b artifacts >> ??? Error using ==> plus >> Matrix dimensions must agree. >> >> Error in ==> ft_databrowser at 745 >> hsel = [1 2 3] + (opt.ftsel-1) .*3; >> >> ??? Reference to non-existent field 'trlvis'. >> >> Error in ==> ft_databrowser>redraw_cb at 1639 >> begsample = opt.trlvis(opt.trlop, 1); >> >> Error in ==> ft_databrowser>winresize_cb at 2250 >> redraw_cb(h,eventdata); >> >> ??? Error while evaluating figure ResizeFcn >> >> >> >> Virus-free. >> www.avast.com >> >> <#m_3369054593448223812_m_-281810346689554922_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Fri Apr 7 20:56:37 2017 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Fri, 7 Apr 2017 11:56:37 -0700 Subject: [FieldTrip] iEEG square wave 'notch' artifact In-Reply-To: References: Message-ID: Hi Tim, Those may be due to wire tugs, possibly as a result of the subject making (abrupt) movements (of the head). Logically, they are artifacts and need to be dealt with. Hopefully, someone here has found a way to do so effectively. Best, Arjen 2017-04-07 11:32 GMT-07:00 Tim Meehan : > Dear FieldTrippers, > > I have a recurring artifact in my iEEG data, a very brief (10-15 ms) > square-wave-like 'notch' that occurs intermittently and across many > channels. It also varies in polarity and amplitude, seemingly randomly. > Here's a link showing an example trial containing many of these artifacts: > > https://drive.google.com/open?id=0B4m5PGO25j3mYkVPUEI5aDZERDA > > As of now I've been advised to throw out trials in which these occur, but > they are very frequent during some sessions. I wonder if alternatively > there is some way to selectively remove these? My guess is one could do > some sort of template matching to identify when they occur and interpolate > across, but I have no idea how to do that or if it's feasible. Does anyone > have any insight? > > Thank you, > Tim > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From A_Lofts at hotmail.ca Fri Apr 7 23:01:27 2017 From: A_Lofts at hotmail.ca (Andrew Lofts) Date: Fri, 7 Apr 2017 21:01:27 +0000 Subject: [FieldTrip] Fieldtrip Octave MEX files - help Message-ID: Hello Readers, I am attempting to preform dipole fitting using fieldtrip in Octave. I am having trouble whenever the code uses one of the functions that require MEX to work. I have installed liboctave-dev in order for mkoctave to work. Whenever a function such as solid_angle is called it needs to be compiled to a .mex, as preformed in the solid_angle.m file. The call can not find the .c files that are needed. "error: no such file, '/home/jad/EAndrew_Lofts/EyesTest/eeg_pipe_asr_amica/analysis/support/dependencies/eeglab_asr_amica/plugins/Fieldtrip-lite141209/forward/private/solid_angle.m' error: called from bounding_mesh at line 74 column 12 find_outermost_boundary at line 45 column 17 ft_prepare_vol_sens at line 85 column 24 prepare_headmodel at line 94 column 11 ft_dipolefitting at line 233 column 15 dipfit_gridsearch at line 106 column 8 pop_dipfit_gridsearch at line 135 column 10 pop_multifit at line 133 column 13" It appears as if these .c file do no exist. There are plenty of .mex* files in the folder but none of them are recognised by "which solid_angle" except for the one .m file. Can someone help me find the .c files to compile, or help with getting Octave to recognise and run one of the other .mex* variants. Thanks, Andrew Lofts -------------- next part -------------- An HTML attachment was scrubbed... URL: From velmurugan.nimhans at gmail.com Sun Apr 9 02:54:43 2017 From: velmurugan.nimhans at gmail.com (velmurugan jayabal) Date: Sat, 8 Apr 2017 17:54:43 -0700 Subject: [FieldTrip] error in source parcellation and source connectivity analysis Message-ID: Dear Field-trip community, I am having the following errors when computing connectivity analysis. Please any help in this regard would be highly appreciated. Thanks in advance. 1. How to compute atlas based source model grid, from MMP atlas?. Since MMP atlas doesn't contain the *dim *field, the ft_volumelookup function doesn't work prompting me the same error. 2. Alternatively, I had created AAL atlas based source model grid and used to compute source connectivity (img.coh) from PCC beamformer source output. But, I am unable to compute the connectivity value for each parcel using ft_sourceparcellate. I am writing the codes used to derive the same. 3. Is there any acronym or a clear explanation for the parcellation label?. I had read Glasser et al 2016 paper and their resource site. But, I couldn't get complete names or explanation for all the ROIs. CODE: %source is the output of pcc beamformer results. cfg = []; cfg.method ='coh'; cfg.complex = 'absimag'; source_conn_imcoh = ft_connectivityanalysis(cfg, source); atlas =ft_read_atlas ('ROI_MNI_V5.nii'); atlas.pos =source_conn_imcoh.pos; cfg =[]; cfg.method ='mean' cfg.parameter ='cohspctrm'; cfg.parcellation = 'tissue'; parc_conn= ft_sourceparcellate(cfg,source_conn, atlas); I had even tried computing source connectivity interpolation on the atlas before parcellation. But, I am getting a huge array > 50 GB, which exceeds my MATLAB and system limit. -- - sincerely, *Velmurugan Jayabal,* *Magnetoencephalography (MEG) research centre,* *Department of Clinical Neurosciences,* *National Institute of Mental Health and Neurosciences (NIMHANS),* *Bangalore - 560029, Karnataka, India* -------------- next part -------------- An HTML attachment was scrubbed... URL: From Markus.Gschwind at unige.ch Sun Apr 9 11:18:21 2017 From: Markus.Gschwind at unige.ch (Markus Gschwind) Date: Sun, 9 Apr 2017 11:18:21 +0200 Subject: [FieldTrip] Problem with Matlab system commands in OS X (XTerm, Logout, crash, sleep mode) Message-ID: Dear all, I hope to find here an expert who knows an answer to the following problem: I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not able to run big and lengthy matlab jobs because at each logout (which occurs after 2h), Matlab crashes, all results are gone (if they are not save to the HD and XTerm closes. I start Matlab form the XTerm (and not by clicking the App Icon) in order to be able to run system (unix) commands within Matlab. I guess, this behaviour is proper to XTerm, and in case I could find an other way to run system commands from Matlab, probably this could be resolved. Could it be that the running matlab job is not visible to the system which goes to sleep?? For info here the power management info: $ pmset -g custom Battery Power: lidwake 1 autopoweroff 1 autopoweroffdelay 14400 standbydelay 18000 standby 1 ttyskeepawake 0 hibernatemode 3 gpuswitch 2 hibernatefile /var/vm/sleepimage displaysleep 2 sleep 0 acwake 1 halfdim 1 sms 1 lessbright 1 disksleep 10 AC Power: lidwake 1 autopoweroff 1 autopoweroffdelay 14400 standbydelay 18000 standby 0 ttyskeepawake 1 hibernatemode 3 gpuswitch 2 hibernatefile /var/vm/sleepimage womp 1 displaysleep 3 networkoversleep 0 sleep 0 acwake 0 halfdim 1 sms 1 disksleep 60 Many thanks for help! Markus -------------- next part -------------- An HTML attachment was scrubbed... URL: From shoeffner at uos.de Sun Apr 9 12:05:12 2017 From: shoeffner at uos.de (=?UTF-8?Q?Sebastian_H=C3=B6ffner?=) Date: Sun, 09 Apr 2017 10:05:12 +0000 Subject: [FieldTrip] Problem with Matlab system commands in OS X (XTerm, Logout, crash, sleep mode) In-Reply-To: References: Message-ID: Dear Markus, while I don't have a proper solution for your problem with matlab, I can recommend you the little app Caffeine which you should find on the app store. It keeps your Mac awake and should stop your matlab process from terminating. http://lightheadsw.com/caffeine/ Best Sebastian On Sun, Apr 9, 2017, 11:31 Markus Gschwind wrote: > Dear all, > > I hope to find here an expert who knows an answer to the following problem: > > I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not > able to run big and lengthy matlab jobs because at each logout (which > occurs after 2h), Matlab crashes, all results are gone (if they are not > save to the HD and XTerm closes. > > I start Matlab form the XTerm (and not by clicking the App Icon) in order > to be able to run system (unix) commands within Matlab. > > I guess, this behaviour is proper to XTerm, and in case I could find an > other way to run system commands from Matlab, probably this could be > resolved. > > Could it be that the running matlab job is not visible to the system which > goes to sleep?? > > For info here the power management info: > > $ pmset -g custom > Battery Power: > lidwake 1 > autopoweroff 1 > autopoweroffdelay 14400 > standbydelay 18000 > standby 1 > ttyskeepawake 0 > hibernatemode 3 > gpuswitch 2 > hibernatefile /var/vm/sleepimage > displaysleep 2 > sleep 0 > acwake 1 > halfdim 1 > sms 1 > lessbright 1 > disksleep 10 > AC Power: > lidwake 1 > autopoweroff 1 > autopoweroffdelay 14400 > standbydelay 18000 > standby 0 > ttyskeepawake 1 > hibernatemode 3 > gpuswitch 2 > hibernatefile /var/vm/sleepimage > womp 1 > displaysleep 3 > networkoversleep 0 > sleep 0 > acwake 0 > halfdim 1 > sms 1 > disksleep 60 > > > Many thanks for help! > Markus > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Sebastian Höffner Hansastr. 19 49090 Osnabrück Germany +49 152 22 59 23 26 -------------- next part -------------- An HTML attachment was scrubbed... URL: From markus.gschwind at gmail.com Sun Apr 9 16:54:11 2017 From: markus.gschwind at gmail.com (Markus Gschwind) Date: Sun, 9 Apr 2017 16:54:11 +0200 Subject: [FieldTrip] Problem with Matlab system commands in OS X (XTerm, Logout, crash, sleep mode) In-Reply-To: References: Message-ID: Hi Sebastian, Thanks I forgot this workaround. Yes, very useful! Best, Markus 2017-04-09 12:05 GMT+02:00 Sebastian Höffner : > Dear Markus, > > while I don't have a proper solution for your problem with matlab, I can > recommend you the little app Caffeine which you should find on the app > store. It keeps your Mac awake and should stop your matlab process from > terminating. > > http://lightheadsw.com/caffeine/ > > Best > Sebastian > > On Sun, Apr 9, 2017, 11:31 Markus Gschwind > wrote: > >> Dear all, >> >> I hope to find here an expert who knows an answer to the following >> problem: >> >> I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not >> able to run big and lengthy matlab jobs because at each logout (which >> occurs after 2h), Matlab crashes, all results are gone (if they are not >> save to the HD and XTerm closes. >> >> I start Matlab form the XTerm (and not by clicking the App Icon) in order >> to be able to run system (unix) commands within Matlab. >> >> I guess, this behaviour is proper to XTerm, and in case I could find an >> other way to run system commands from Matlab, probably this could be >> resolved. >> >> Could it be that the running matlab job is not visible to the system >> which goes to sleep?? >> >> For info here the power management info: >> >> $ pmset -g custom >> Battery Power: >> lidwake 1 >> autopoweroff 1 >> autopoweroffdelay 14400 >> standbydelay 18000 >> standby 1 >> ttyskeepawake 0 >> hibernatemode 3 >> gpuswitch 2 >> hibernatefile /var/vm/sleepimage >> displaysleep 2 >> sleep 0 >> acwake 1 >> halfdim 1 >> sms 1 >> lessbright 1 >> disksleep 10 >> AC Power: >> lidwake 1 >> autopoweroff 1 >> autopoweroffdelay 14400 >> standbydelay 18000 >> standby 0 >> ttyskeepawake 1 >> hibernatemode 3 >> gpuswitch 2 >> hibernatefile /var/vm/sleepimage >> womp 1 >> displaysleep 3 >> networkoversleep 0 >> sleep 0 >> acwake 0 >> halfdim 1 >> sms 1 >> disksleep 60 >> >> >> Many thanks for help! >> Markus >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- > > Sebastian Höffner > Hansastr. 19 > 49090 Osnabrück > Germany > > +49 152 22 59 23 26 <+49%201522%202592326> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From seymourr at aston.ac.uk Mon Apr 10 13:14:10 2017 From: seymourr at aston.ac.uk (Seymour, Robert (Research Student)) Date: Mon, 10 Apr 2017 11:14:10 +0000 Subject: [FieldTrip] error in source parcellation and source connectivity analysis Message-ID: Hi Velmurugan, You might want to look at this tutorial: http://www.fieldtriptoolbox.org/tutorial/networkanalysis?s[]=ft&s[]=networkanalysis I might be wrong but I think the AAL atlas currently implemented in Fieldtrip does not yet contain a .parcellation field, which is why you might be running into problems. You could try to reverse engineer this using the tissuelabel field I guess. For more info on the full label names use wb_command -file-information from the HCP toolbox, or look at the supplementary materials on the Glasser paper. Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From Oleksiy.Bobrov at uni-konstanz.de Mon Apr 10 13:24:08 2017 From: Oleksiy.Bobrov at uni-konstanz.de (Oleksiy Bobrov) Date: Mon, 10 Apr 2017 13:24:08 +0200 Subject: [FieldTrip] ft_artifact_threshold + ft_rejectartifact issue? Message-ID: <40c0c482-714a-7b33-8120-e3e72d15054b@uni-konstanz.de> Hi everyone, I try automatically reject segment from my EEG-Data withamplitudes out of the range 200µV. I use the following function for it: function [fnData, conf] = rejectForRange(inData) cfg = []; cfg.continuous = 'no'; cfg.artfctdef.threshold.bpfilter = 'no'; cfg.artfctdef.threshold.range = 200; %in uV/T, default inf % cfg.artfctdef.threshold.min = -100; %in uV/T, default -inf % cfg.artfctdef.threshold.max = 100; %in uV/T, default inf [conf, artData] = ft_artifact_threshold(cfg, inData); cfg = []; cfg.artfctdef.xxx.artifact = artData; cfg.artfctdef.reject = 'complete'; fnData = ft_rejectartifact(cfg, inData); The function is evaluated with no errors. But the output is not correct. Indeed, a lot of artifact-segments are deleted. But there are still a lot of segments with amplitudes far out of the range of 200µV (visual controlled with ft_rejectvisual()). If try the rejectForRange()-function once more (on the output-data from the first run), so it founds no artifacts at all. But they are in the data. Thank you for any help in advance. Best regards Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: From beese at cbs.mpg.de Mon Apr 10 14:50:13 2017 From: beese at cbs.mpg.de (Caroline Beese) Date: Mon, 10 Apr 2017 14:50:13 +0200 (CEST) Subject: [FieldTrip] cluster-based statistics with one covariate Message-ID: <1329277450.115066.1491828613491.JavaMail.zimbra@cbs.mpg.de> Dear all, I'm trying to take age as a covariate into my cluster-based statistics comparing two dependent measures. I have read about two options: A) to use ft_regressconfound before I do the stats or B) to create a design with a third row using the .cvar field in the 'depsamplesregrT' statfun. I understand that for correcting head motions ft_regressconfound is a great option but for taking age into account as a covariate, it doesn't seem intuitive to me to do this within-subject on a trial-by-trial basis having only one number per person. Or can you use this function differently? However, for option B) the subfunction 'unitselvec' is missing and this seems to be an issue for several years. So I was wondering whether anyone has ever tried to fix this problem themselves and wouldn't mind sharing? More generally, if anyone has successfully implemented a cluster-based statistics with one or more covariates, please share your experience, it would be greatly appreciated. Best Regards, Caroline -- Caroline Beese PhD student Max-Planck Institute for Human Cognitive and Brain Sciences Department of Neuropsychology Stephanstr. 1a 04103 Leipzig office phone: +49 (0) 341 9940 129 www.cbs.mpg.de/staff/beese-11586 From m.papen at uni-koeln.de Tue Apr 11 10:34:21 2017 From: m.papen at uni-koeln.de (Michael von Papen) Date: Tue, 11 Apr 2017 10:34:21 +0200 Subject: [FieldTrip] Conference: Coupling & Causality in Complex Systems Message-ID: ============================================================== CALL FOR PAPERS (Deadline: June 01, 2017) http://c3s.uni-koeln.de ============================================================== INTERNATIONAL CONFERENCE: *Coupling and Causality in Complex Systems* September 25-27, 2017, Cologne, Germany -------------------------------------------------------------- The interdisciplinary conference Coupling and Causality in Complex Systems (C3S) is hosted by the Competence Area 3: Quantitative Modeling of Complex Systems of the University of Cologne (UoC), Germany. It is organized by the Institute of Geophysics & Meteorology, UoC, the Institute of Clinical Neuroscience and Psychology, Heinrich-Heine University Düsseldorf and the Department of Cognitive Neuroscience at the Research Center Juelich. -------------------------------------------------------------- *Abstract* Complex systems such as the human brain, Earth’s climate and economy are characterized by a multitude of coupled processes on different spatial and temporal scales. In order to better understand the dynamics of the system at hand each scientific area has developed specific tools to identify, model and quantify these processes. The conference Coupling and Causality in Complex Systems (C3S) will present a collection of these approaches with the aim to provide scientists with new analysis strategies for their field. The conference focuses on how to characterize a complex system and on the methods for estimating and modeling of statistical coupling (e.g. network coherence, creation and modulation of small networks and local or long-range synchronization by cross frequency phase-phase and phase-amplitude coupling) and causality (e.g. Granger causality, transfer entropy). Therefore, data analysts from different study fields including neuroscience, mathematics, physics, biology, and economy will present their approaches with a particular focus on the methods they use. The aim of this conference is to foster discussions and the transdisciplinary exchange of advanced techniques, methods, and algorithms, thereby stimulating potential future collaborations. -------------------------------------------------- *Invited Speakers* Elissa Aminoff - Department of Psychology, Carnegie Mellon University, Pittsburgh, USA Jörg Breitung - Macroeconomic Policy Institute, University of Cologne, Germany David Gross - Institute of Theoretical Physics, University of Cologne, Germany Philip Holmes - Mechanical and Aerospace Engineering / Princeton Neuroscience Institute, Princeton, USA Ankit Khambhati - Department of Bioengineering, University of Pennsylvania, USA Laura Marzetti - Department of Neuroscience, Università degli Studi "G. d'Annunzio" Chieti - Pescara Arkady Pikovsky - Institute of Physics and Astronomy, University Potsdam, Germany Michael Rosenblum - Institute of Physics and Astronomy, University Potsdam, Germany Jakob Runge - The Grantham Institute for Climate Change, Imperial College London -------------------------------------------------- *Preliminary Session Program* We will have different sessions with differing topics and each session will be opened by one of the invited speakers. Here is a preliminary version of our program: Session 1 Synchronization I Arkady Pikovsky Session 2 Synchronization II Silvia Daun Session 3 Coupled oscillators I Phil Holmes Session 4 Coupled oscillators II Michael Rosenblum Session 5 Phase coupling Laura Marzetti Session 6 Network structures I Elissa Aminoff Session 7 Network structures II Ankit Khambati Session 8 Bayesian networks David Gross Session 9 Granger causality I Jörg Breitung Session 10 Granger causality II Esther Florin Session 11 Causal network measures Jakob Runge Further topics of interest for the conference include, amongst others, research and methods development on: functional connectivity, (partial directed) coherence, network topology, graph-theoretic measures, directed graphs, nonlinear dynamics of complex systems, complex spatio-temporal systems, mutual information and transfer entropy. -------------------------------------------------------------- *Scientific Organizing Committee* Silvia Daun - Institute of Zoology, University of Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany Esther Florin - Institute of Clinical Neuroscience and Psychology, Düsseldorf, Germany Joachim Gross - Center for Cognitive Neuroimaging, Glasgow, UK Michael von Papen - Institute of Geophysics & Meteorology, Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany -------------------------------------------------------------- PAPER SUBMISSION AND REGISTRATION Authors are invited to submit conference abstracts with up to 400 words. Authors of exceptional abstracts will be given the opportunity to present their research in a talk. However, poster sessions will be provided with ample time for discussions. For your submission, please use the conference website c3s.uni-koeln.de. To register, please send an email with the subject "registration" to c3s-conference at uni-koeln.de. Please be sure to include your full name, your affiliation and whether you qualify as student (also PhD candidates) or not. The registration fee will cover snacks and refreshments during coffee breaks, lunch and a dinner with all participants. Early-bird registration is available until July 10 with a reduced fee of 120 EUR (60 EUR for students), after July 10 the registration fee will be 240 EUR (120 EUR for students). -------------------------------------------------------------- IMPORTANT DATES Paper Submission deadline: June 01, 2017 Author Notification: mid June, 2017 Early-bird registration: July 10, 2017 Conference: September 25-27, 2017 ============================================================== Please find the call for papers and more information at the conference website: http://c3s.uni-koeln.de. For questions regarding the conference feel free to contact us via c3s-conference at uni-koeln.de. -- ------------------------------------------ UNIVERSITY OF COLOGNE Institute of Geophysics & Meteorology Coordinator of Competence Area III: Quantitative Modeling of Complex Systems Dr. Michael von Papen Email: m.papen at uni-koeln.de http://www.uni-koeln.de/~vpapenm http://complexsystems.uni-koeln.de From jose.uriguen at deusto.es Tue Apr 11 12:08:44 2017 From: jose.uriguen at deusto.es (=?UTF-8?Q?Jos=C3=A9_Antonio_Uriguen_Garaizabal?=) Date: Tue, 11 Apr 2017 12:08:44 +0200 Subject: [FieldTrip] Need help with cluster-based permutation test with 3 groups of subjects Message-ID: Dear all My name is Toni and I am working on EEG signal processing at University of Deusto, Bilbao, Spain. More specifically, right now trying to apply cluster-based permutation testing to determine whether there exist differences among 3 groups of subjects. So, for my testing, subject groups are E, EN and N, the 2 former being different types of patients and the latter being a control group. I am forming clusters based on proximity (in space) and each subject is characterized by a matrix of values that vary in 2D (per channel and another variable related but not equal to frequency). By means of a T-statistic (indepsamplesT) I can find differences in between E and EN, but I find no clusters/differences in between E and N or EN and N, even though hypothetically (I think) they should exist. By means of an F-statistic (indepsamplesF) I can find differences among the 3 groups at the same time, then also between E and EN and no differences between E and N or EN and N... Am I missing something? I do not understand why the might exist a significant cluster when comparing all 3 groups that does not exist in the 1vs1 comparisons, even though the cluster is not the same I obtain when I compare E vs EN... For additional information, I attach how I run the test: cfg.method = 'distance'; cfg.neighbourdist = 1; cfg.elec = ft_datatype_sens(subjEN{1}.elec); neighbours = ft_prepare_neighbours(cfg); cfg = []; cfg.channel = {'EEG'}; cfg.latency = 'all'; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.neighbours = neighbours; % same as defined for the between-trials experiment cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 5000; nsubj = size(subjE,2)+size(subjEN,2); design = zeros(2,nsubj); design(1,:) = [1:nsubj/2 1:nsubj/2]; design(2,1:size(subjE,2)) = 1; design(2,size(subjE,2)+1:nsubj) = 2; cfg.design = design; cfg.ivar = 2; [stat] = ft_timelockstatistics(cfg, subjEN{:}, subjE{:}); When I compare the 3 groups cfg.method = 'distance'; cfg.neighbourdist = 1; cfg.elec = ft_datatype_sens(subjEN{1}.elec); neighbours = ft_prepare_neighbours(cfg); cfg = []; cfg.channel = {'EEG'}; cfg.latency = 'all'; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesF'; %F-statistic cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.neighbours = neighbours; % same as defined for the between-trials experiment cfg.tail = 1; %One sided cfg.clustertail = 1; cfg.alpha = 0.025; cfg.numrandomization = 5000; nsubj1 = size(subjE,2); nsubj2 = size(subjEN,2); nsubj3 = size(subjN,2); nsubj = nsubj1+nsubj2+nsubj3; design = zeros(2,nsubj); design(1,:) = [1:nsubj1 1:nsubj2 1:nsubj3]; design(2,1:nsubj1) = 1; design(2,nsubj1+1:nsubj1+nsubj2) = 2; design(2,nsubj1+nsubj2+1:nsubj) = 3; cfg.design = design; cfg.ivar = 2; %2nd row is independent var [stat] = ft_timelockstatistics(cfg, subjE{:}, subjEN{:}, subjN{:}); Then, subjE, subjN and subjEN are like this: Eall = subjE{:} Eall = struct with fields: label: {1×18 cell} fsample: 200 elec: [1×1 struct] trial: {[18×115 double]} time: {[1×115 double]} cfg: [1×1 struct] Thanks in advance -- *Jose Antonio Urigüen* PostDoc at Deustotech-LIFE (eVIDA Research Group) [image: Deusto] Universidad de Deusto / Deustuko Unibertsitatea / University of Deusto Facultad de Ingeniería, 4ª Planta Avda. Universidades 24. 48007 Bilbao Tel. +34 94 413 90 00 / Mov. +34 656 711 643 Ext. 2980 jose.uriguen at deusto.es Web: evida.deusto.es *www.deusto.es * -------------- next part -------------- An HTML attachment was scrubbed... URL: From icelandhouse at gmail.com Tue Apr 11 12:13:42 2017 From: icelandhouse at gmail.com (Maris Skujevskis) Date: Tue, 11 Apr 2017 12:13:42 +0200 Subject: [FieldTrip] Error when running ft_sourceanalysis with stats across two conditions Message-ID: Dear Fieldtrip developers/source localizing experts, I get an error when running ft_sourceanalysis on two EEG conditions with the statistical testing (permutation) enabled (no issues with single condition and no statistics). As far as I can see, I am doing everything right (as per ft_sourceanalysis reference page; my fieldtrip version: fieldtrip-20161122). Please correct me where I am wrong or ask for more information in case what I paste/explain below is not sufficient. CODE INPUT: cfg = []; cfg.method = 'dics'; cfg.frequency = 10; cfg.grid = leadfield; cfg.keepleadfield = 'no'; cfg.headmodel = vol; cfg.dics.keepfilter = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.fixedori = 'yes'; cfg.dics.keepmom = 'yes'; cfg.dics.realfilter = 'yes'; cfg.grid.filter = source_cmb.avg.filter; cfg.permutation = 'yes'; cfg.numpermutation = 500; sourceStatsAB = ft_sourceanalysis(cfg, condA, condB); COMMAND WINDOW OUTPUT: the input is freq data with 128 channels, 1 frequencybins and no timebins the input is freq data with 128 channels, 1 frequencybins and no timebins the call to "ft_selectdata" took 0 seconds converting the linearly indexed channelcombinations into a square CSD-matrix using electrodes specified in the data converting units from 'cm' to 'mm' determining source compartment (3) projecting electrodes on skin surface combining electrode transfer and system matrix creating dipole grid based on user specified dipole positions using gradiometers specified in the configuration 5124 dipoles inside, 0 dipoles outside brain the call to "ft_prepare_sourcemodel" took 0 seconds the call to "ft_selectdata" took 0 seconds the call to "ft_selectdata" took 0 seconds 2 conditions, each with 3 data objects averaging 182 replications for one condition averaging 182 replications for one condition 2 conditions, each with 3 data objects <<<<<<<<<<<<<---------- what are the "3 data objects"? creating 100 random permutations from total 6.129982e+54 HERE COMES THE ERROR: Error using prepare_resampled_data (line 381) the dimensions should be the same for every condition Error in ft_sourceanalysis (line 561) [dum, rnd_aCf, rnd_aCr, rnd_aPr, rnd_bCf, rnd_bCr, rnd_bPr] = prepare_resampled_data(cfg, aCf, aCr, aPr, bCf, bCr, bPr); When checking the function prepare_resampled_data, it turns out that it requires a cell named "datain" to have the same size matrices column-wise (whatever the columns may represent) : datain = [182x128x128 double] [182x128 double] [182x1 double] [182x128x128 double] [ 1x128 double] [ NaN] My input data condA and condB have identical dimensions, so I have no idea what has gone wrong here: condA = label: {128x1 cell} dimord: 'rpt_chan_freq' freq: 9.8462 powspctrm: [182x128 double] labelcmb: {8128x2 cell} crsspctrm: [182x8128 double] cumsumcnt: [182x1 double] cumtapcnt: [182x1 double] elec: [1x1 struct] trialinfo: [182x22 double] cfg: [1x1 struct] condB = label: {128x1 cell} dimord: 'rpt_chan_freq' freq: 9.8462 powspctrm: [182x128 double] labelcmb: {8128x2 cell} crsspctrm: [182x8128 double] cumsumcnt: [182x1 double] cumtapcnt: [182x1 double] elec: [1x1 struct] trialinfo: [182x22 double] cfg: [1x1 struct] Thanks for your input! Best wishes, Maris On Sun, Apr 9, 2017 at 12:00 PM, wrote: > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. error in source parcellation and source connectivity analysis > (velmurugan jayabal) > 2. Problem with Matlab system commands in OS X (XTerm, Logout, > crash, sleep mode) (Markus Gschwind) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 8 Apr 2017 17:54:43 -0700 > From: velmurugan jayabal > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] error in source parcellation and source > connectivity analysis > Message-ID: > mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Field-trip community, > > I am having the following errors when computing connectivity > analysis. Please any help in this regard would be highly appreciated. > Thanks in advance. > > 1. How to compute atlas based source model grid, from MMP atlas?. Since MMP > atlas doesn't contain the *dim *field, the ft_volumelookup function doesn't > work prompting me the same error. > > > 2. Alternatively, I had created AAL atlas based source model grid and used > to compute source connectivity (img.coh) from PCC beamformer source output. > But, I am unable to compute the connectivity value for each parcel using > ft_sourceparcellate. I am writing the codes used to derive the same. > > 3. Is there any acronym or a clear explanation for the parcellation label?. > I had read Glasser et al 2016 paper and their resource site. But, I > couldn't get complete names or explanation for all the ROIs. > > > CODE: > %source is the output of pcc beamformer results. > cfg = []; > cfg.method ='coh'; > cfg.complex = 'absimag'; > source_conn_imcoh = ft_connectivityanalysis(cfg, source); > > atlas =ft_read_atlas ('ROI_MNI_V5.nii'); > atlas.pos =source_conn_imcoh.pos; > cfg =[]; > cfg.method ='mean' > cfg.parameter ='cohspctrm'; > cfg.parcellation = 'tissue'; > parc_conn= ft_sourceparcellate(cfg,source_conn, atlas); > > I had even tried computing source connectivity interpolation on the atlas > before parcellation. But, I am getting a huge array > 50 GB, which exceeds > my MATLAB and system limit. > > > -- > - sincerely, > *Velmurugan Jayabal,* > *Magnetoencephalography (MEG) research centre,* > *Department of Clinical Neurosciences,* > > *National Institute of Mental Health and Neurosciences (NIMHANS),* > *Bangalore - 560029, Karnataka, India* > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170408/ede3c3c1/attachment-0001.html> > > ------------------------------ > > Message: 2 > Date: Sun, 9 Apr 2017 11:18:21 +0200 > From: Markus Gschwind > To: FieldTrip discussion list > Subject: [FieldTrip] Problem with Matlab system commands in OS X > (XTerm, Logout, crash, sleep mode) > Message-ID: > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I hope to find here an expert who knows an answer to the following problem: > > I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not able > to run big and lengthy matlab jobs because at each logout (which occurs > after 2h), Matlab crashes, all results are gone (if they are not save to > the HD and XTerm closes. > > I start Matlab form the XTerm (and not by clicking the App Icon) in order > to be able to run system (unix) commands within Matlab. > > I guess, this behaviour is proper to XTerm, and in case I could find an > other way to run system commands from Matlab, probably this could be > resolved. > > Could it be that the running matlab job is not visible to the system which > goes to sleep?? > > For info here the power management info: > > $ pmset -g custom > Battery Power: > lidwake 1 > autopoweroff 1 > autopoweroffdelay 14400 > standbydelay 18000 > standby 1 > ttyskeepawake 0 > hibernatemode 3 > gpuswitch 2 > hibernatefile /var/vm/sleepimage > displaysleep 2 > sleep 0 > acwake 1 > halfdim 1 > sms 1 > lessbright 1 > disksleep 10 > AC Power: > lidwake 1 > autopoweroff 1 > autopoweroffdelay 14400 > standbydelay 18000 > standby 0 > ttyskeepawake 1 > hibernatemode 3 > gpuswitch 2 > hibernatefile /var/vm/sleepimage > womp 1 > displaysleep 3 > networkoversleep 0 > sleep 0 > acwake 0 > halfdim 1 > sms 1 > disksleep 60 > > > Many thanks for help! > Markus > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170409/ce9b8000/attachment-0001.html> > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 77, Issue 6 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Wed Apr 12 04:35:29 2017 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Wed, 12 Apr 2017 10:35:29 +0800 Subject: [FieldTrip] cluster-based statistics with one covariate Message-ID: Dear Caroline, If your conditions are within-subject, then I think the best way to do this is to construct a dataset representing the conditionA - conditionB difference for each subject, and then using ft_statfun_indepsamplesregrT to regress the subject-wise difference on age. See e.g. https://mailman.science.ru.nl/pipermail/fieldtrip/2016-May/010528.html for a thread discussing a similar approach. Best, Steve --- Stephen Politzer-Ahles The Hong Kong Polytechnic University Department of Chinese and Bilingual Studies http://www.mypolyuweb.hk/~sjpolit/ > Message: 3 > Date: Mon, 10 Apr 2017 14:50:13 +0200 (CEST) > From: Caroline Beese > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] cluster-based statistics with one covariate > Message-ID: > <1329277450.115066.1491828613491.JavaMail.zimbra at cbs.mpg.de> > Content-Type: text/plain; charset=utf-8 > > Dear all, > > I'm trying to take age as a covariate into my cluster-based statistics > comparing two dependent measures. > > I have read about two options: > > A) to use ft_regressconfound before I do the stats or > B) to create a design with a third row using the .cvar field in the > 'depsamplesregrT' statfun. > > I understand that for correcting head motions ft_regressconfound is a > great option but for taking age into account as a covariate, it doesn't > seem intuitive to me to do this within-subject on a trial-by-trial basis > having only one number per person. Or can you use this function differently? > > However, for option B) the subfunction 'unitselvec' is missing and this > seems to be an issue for several years. So I was wondering whether anyone > has ever tried to fix this problem themselves and wouldn't mind sharing? > > More generally, if anyone has successfully implemented a cluster-based > statistics with one or more covariates, please share your experience, it > would be greatly appreciated. > > Best Regards, > Caroline > > -- > Caroline Beese > PhD student > > Max-Planck Institute for Human Cognitive and Brain Sciences > Department of Neuropsychology > Stephanstr. 1a > 04103 Leipzig > > office phone: +49 (0) 341 9940 129 > > www.cbs.mpg.de/staff/beese-11586 > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From robin.kampe at liu.se Wed Apr 12 11:01:14 2017 From: robin.kampe at liu.se (=?iso-8859-1?Q?Robin_K=E4mpe?=) Date: Wed, 12 Apr 2017 09:01:14 +0000 Subject: [FieldTrip] Installing gui_streamer Message-ID: Hi! We want to, from scratch, set up a real time fMRI capabilities. Your documentation covers this quite well. I do, however, get stuck on point 1 which is to launch the gui_streamer from the console. How does one obtain/install this program on our Siemens Prisma? Best, Robin Kämpe Research Engineer [Linköping University] CSAN, Center for Social and Affective Neuroscience Department of Clinical and Experimental Medicine, IKE Mobile: +46 (0)73 8005561 Please visit us at www.liu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From laxmi.shaw22 at gmail.com Thu Apr 13 08:07:37 2017 From: laxmi.shaw22 at gmail.com (Laxmi Shaw) Date: Thu, 13 Apr 2017 11:37:37 +0530 Subject: [FieldTrip] fieldtrip Digest, Vol 77, Issue 9 In-Reply-To: References: Message-ID: Dear Fieldtrip user, Can anybody have EEG 64 channel head model or anyother web source where i can get the 64 channel head model then please share with me . On Wed, Apr 12, 2017 at 3:30 PM, wrote: > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Need help with cluster-based permutation test with 3 groups > of subjects (Jos? Antonio Uriguen Garaizabal) > 2. Error when running ft_sourceanalysis with stats across two > conditions (Maris Skujevskis) > 3. Re: cluster-based statistics with one covariate > (Stephen Politzer-Ahles) > 4. Installing gui_streamer (Robin K?mpe) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 11 Apr 2017 12:08:44 +0200 > From: Jos? Antonio Uriguen Garaizabal > To: FieldTrip discussion list > Subject: [FieldTrip] Need help with cluster-based permutation test > with 3 groups of subjects > Message-ID: > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all > > > My name is Toni and I am working on EEG signal processing at University of > Deusto, Bilbao, Spain. More specifically, right now trying to > apply cluster-based permutation testing to determine whether there exist > differences among 3 groups of subjects. > > > So, for my testing, subject groups are E, EN and N, the 2 former being > different types of patients and the latter being a control group. I am > forming clusters based on proximity (in space) and each subject is > characterized by a matrix of values that vary in 2D (per channel and > another variable related but not equal to frequency). > > By means of a T-statistic (indepsamplesT) I can find differences in between > E and EN, but I find no clusters/differences in between E and N or EN and > N, even though hypothetically (I think) they should exist. By means of an > F-statistic (indepsamplesF) I can find differences among the 3 groups at > the same time, then also between E and EN and no differences between E and > N or EN and N... > > Am I missing something? I do not understand why the might exist a > significant cluster when comparing all 3 groups that does not exist in the > 1vs1 comparisons, even though the cluster is not the same I obtain when I > compare E vs EN... > > > For additional information, I attach how I run the test: > > cfg.method = 'distance'; > cfg.neighbourdist = 1; > cfg.elec = ft_datatype_sens(subjEN{1}.elec); > neighbours = ft_prepare_neighbours(cfg); > > cfg = []; > cfg.channel = {'EEG'}; > cfg.latency = 'all'; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.neighbours = neighbours; % same as defined for the > between-trials experiment > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 5000; > > nsubj = size(subjE,2)+size(subjEN,2); > design = zeros(2,nsubj); > design(1,:) = [1:nsubj/2 1:nsubj/2]; > design(2,1:size(subjE,2)) = 1; > design(2,size(subjE,2)+1:nsubj) = 2; > > cfg.design = design; > cfg.ivar = 2; > > [stat] = ft_timelockstatistics(cfg, subjEN{:}, subjE{:}); > > > When I compare the 3 groups > > cfg.method = 'distance'; > cfg.neighbourdist = 1; > cfg.elec = ft_datatype_sens(subjEN{1}.elec); > neighbours = ft_prepare_neighbours(cfg); > > cfg = []; > cfg.channel = {'EEG'}; > cfg.latency = 'all'; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesF'; %F-statistic > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.neighbours = neighbours; % same as defined for the > between-trials experiment > cfg.tail = 1; %One sided > cfg.clustertail = 1; > cfg.alpha = 0.025; > cfg.numrandomization = 5000; > > nsubj1 = size(subjE,2); > nsubj2 = size(subjEN,2); > nsubj3 = size(subjN,2); > nsubj = nsubj1+nsubj2+nsubj3; > > design = zeros(2,nsubj); > design(1,:) = [1:nsubj1 1:nsubj2 1:nsubj3]; > design(2,1:nsubj1) = 1; > design(2,nsubj1+1:nsubj1+nsubj2) = 2; > design(2,nsubj1+nsubj2+1:nsubj) = 3; > > cfg.design = design; > cfg.ivar = 2; %2nd row is independent var > > [stat] = ft_timelockstatistics(cfg, subjE{:}, subjEN{:}, subjN{:}); > > > Then, subjE, subjN and subjEN are like this: > > Eall = subjE{:} > > Eall = > > struct with fields: > > label: {1?18 cell} > fsample: 200 > elec: [1?1 struct] > trial: {[18?115 double]} > time: {[1?115 double]} > cfg: [1?1 struct] > > > Thanks in advance > > -- > *Jose Antonio Urig?en* > PostDoc at Deustotech-LIFE (eVIDA Research Group) > [image: Deusto] > Universidad de Deusto / Deustuko Unibertsitatea / University of Deusto > Facultad de Ingenier?a, 4? Planta > Avda. Universidades 24. 48007 Bilbao > Tel. +34 94 413 90 00 / Mov. +34 656 711 643 > Ext. 2980 > jose.uriguen at deusto.es > Web: evida.deusto.es > *www.deusto.es * > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170411/7a169976/attachment-0001.html> > > ------------------------------ > > Message: 2 > Date: Tue, 11 Apr 2017 12:13:42 +0200 > From: Maris Skujevskis > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Error when running ft_sourceanalysis with stats > across two conditions > Message-ID: > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Fieldtrip developers/source localizing experts, > > I get an error when running ft_sourceanalysis on two EEG conditions with > the statistical testing (permutation) enabled (no issues with single > condition and no statistics). > As far as I can see, I am doing everything right (as per ft_sourceanalysis > reference page; my fieldtrip version: fieldtrip-20161122). Please correct > me where I am wrong or ask for more information in case what I > paste/explain below is not sufficient. > > CODE INPUT: > > cfg = []; > cfg.method = 'dics'; > cfg.frequency = 10; > cfg.grid = leadfield; > cfg.keepleadfield = 'no'; > cfg.headmodel = vol; > cfg.dics.keepfilter = 'yes'; > cfg.dics.lambda = '5%'; > cfg.dics.fixedori = 'yes'; > cfg.dics.keepmom = 'yes'; > cfg.dics.realfilter = 'yes'; > cfg.grid.filter = source_cmb.avg.filter; > cfg.permutation = 'yes'; > cfg.numpermutation = 500; > > sourceStatsAB = ft_sourceanalysis(cfg, condA, condB); > > COMMAND WINDOW OUTPUT: > > the input is freq data with 128 channels, 1 frequencybins and no timebins > the input is freq data with 128 channels, 1 frequencybins and no timebins > the call to "ft_selectdata" took 0 seconds > converting the linearly indexed channelcombinations into a square > CSD-matrix > using electrodes specified in the data > converting units from 'cm' to 'mm' > determining source compartment (3) > projecting electrodes on skin surface > combining electrode transfer and system matrix > creating dipole grid based on user specified dipole positions > using gradiometers specified in the configuration > 5124 dipoles inside, 0 dipoles outside brain > the call to "ft_prepare_sourcemodel" took 0 seconds > the call to "ft_selectdata" took 0 seconds > the call to "ft_selectdata" took 0 seconds > 2 conditions, each with 3 data objects > averaging 182 replications for one condition > averaging 182 replications for one condition > 2 conditions, each with 3 data objects > <<<<<<<<<<<<<---------- what are the "3 data objects"? > creating 100 random permutations from total 6.129982e+54 > > HERE COMES THE ERROR: > > Error using prepare_resampled_data (line 381) > the dimensions should be the same for every condition > > Error in ft_sourceanalysis (line 561) > [dum, rnd_aCf, rnd_aCr, rnd_aPr, rnd_bCf, rnd_bCr, rnd_bPr] = > prepare_resampled_data(cfg, aCf, aCr, aPr, bCf, bCr, bPr); > > > When checking the function prepare_resampled_data, it turns out that it > requires a cell named "datain" to have the same size matrices column-wise > (whatever the columns may represent) : > > datain = > > [182x128x128 double] [182x128 double] [182x1 double] > [182x128x128 double] [ 1x128 double] [ NaN] > > > My input data condA and condB have identical dimensions, so I have no idea > what has gone wrong here: > > condA = > > label: {128x1 cell} > dimord: 'rpt_chan_freq' > freq: 9.8462 > powspctrm: [182x128 double] > labelcmb: {8128x2 cell} > crsspctrm: [182x8128 double] > cumsumcnt: [182x1 double] > cumtapcnt: [182x1 double] > elec: [1x1 struct] > trialinfo: [182x22 double] > cfg: [1x1 struct] > > condB = > > label: {128x1 cell} > dimord: 'rpt_chan_freq' > freq: 9.8462 > powspctrm: [182x128 double] > labelcmb: {8128x2 cell} > crsspctrm: [182x8128 double] > cumsumcnt: [182x1 double] > cumtapcnt: [182x1 double] > elec: [1x1 struct] > trialinfo: [182x22 double] > cfg: [1x1 struct] > > > > > Thanks for your input! > > Best wishes, > Maris > > > > > > On Sun, Apr 9, 2017 at 12:00 PM, wrote: > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. error in source parcellation and source connectivity analysis > > (velmurugan jayabal) > > 2. Problem with Matlab system commands in OS X (XTerm, Logout, > > crash, sleep mode) (Markus Gschwind) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sat, 8 Apr 2017 17:54:43 -0700 > > From: velmurugan jayabal > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] error in source parcellation and source > > connectivity analysis > > Message-ID: > > > mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Dear Field-trip community, > > > > I am having the following errors when computing connectivity > > analysis. Please any help in this regard would be highly appreciated. > > Thanks in advance. > > > > 1. How to compute atlas based source model grid, from MMP atlas?. Since > MMP > > atlas doesn't contain the *dim *field, the ft_volumelookup function > doesn't > > work prompting me the same error. > > > > > > 2. Alternatively, I had created AAL atlas based source model grid and > used > > to compute source connectivity (img.coh) from PCC beamformer source > output. > > But, I am unable to compute the connectivity value for each parcel using > > ft_sourceparcellate. I am writing the codes used to derive the same. > > > > 3. Is there any acronym or a clear explanation for the parcellation > label?. > > I had read Glasser et al 2016 paper and their resource site. But, I > > couldn't get complete names or explanation for all the ROIs. > > > > > > CODE: > > %source is the output of pcc beamformer results. > > cfg = []; > > cfg.method ='coh'; > > cfg.complex = 'absimag'; > > source_conn_imcoh = ft_connectivityanalysis(cfg, source); > > > > atlas =ft_read_atlas ('ROI_MNI_V5.nii'); > > atlas.pos =source_conn_imcoh.pos; > > cfg =[]; > > cfg.method ='mean' > > cfg.parameter ='cohspctrm'; > > cfg.parcellation = 'tissue'; > > parc_conn= ft_sourceparcellate(cfg,source_conn, atlas); > > > > I had even tried computing source connectivity interpolation on the atlas > > before parcellation. But, I am getting a huge array > 50 GB, which > exceeds > > my MATLAB and system limit. > > > > > > -- > > - sincerely, > > *Velmurugan Jayabal,* > > *Magnetoencephalography (MEG) research centre,* > > *Department of Clinical Neurosciences,* > > > > *National Institute of Mental Health and Neurosciences (NIMHANS),* > > *Bangalore - 560029, Karnataka, India* > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > attachments/20170408/ede3c3c1/attachment-0001.html> > > > > ------------------------------ > > > > Message: 2 > > Date: Sun, 9 Apr 2017 11:18:21 +0200 > > From: Markus Gschwind > > To: FieldTrip discussion list > > Subject: [FieldTrip] Problem with Matlab system commands in OS X > > (XTerm, Logout, crash, sleep mode) > > Message-ID: > > > gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Dear all, > > > > I hope to find here an expert who knows an answer to the following > problem: > > > > I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not > able > > to run big and lengthy matlab jobs because at each logout (which occurs > > after 2h), Matlab crashes, all results are gone (if they are not save to > > the HD and XTerm closes. > > > > I start Matlab form the XTerm (and not by clicking the App Icon) in order > > to be able to run system (unix) commands within Matlab. > > > > I guess, this behaviour is proper to XTerm, and in case I could find an > > other way to run system commands from Matlab, probably this could be > > resolved. > > > > Could it be that the running matlab job is not visible to the system > which > > goes to sleep?? > > > > For info here the power management info: > > > > $ pmset -g custom > > Battery Power: > > lidwake 1 > > autopoweroff 1 > > autopoweroffdelay 14400 > > standbydelay 18000 > > standby 1 > > ttyskeepawake 0 > > hibernatemode 3 > > gpuswitch 2 > > hibernatefile /var/vm/sleepimage > > displaysleep 2 > > sleep 0 > > acwake 1 > > halfdim 1 > > sms 1 > > lessbright 1 > > disksleep 10 > > AC Power: > > lidwake 1 > > autopoweroff 1 > > autopoweroffdelay 14400 > > standbydelay 18000 > > standby 0 > > ttyskeepawake 1 > > hibernatemode 3 > > gpuswitch 2 > > hibernatefile /var/vm/sleepimage > > womp 1 > > displaysleep 3 > > networkoversleep 0 > > sleep 0 > > acwake 0 > > halfdim 1 > > sms 1 > > disksleep 60 > > > > > > Many thanks for help! > > Markus > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > attachments/20170409/ce9b8000/attachment-0001.html> > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 77, Issue 6 > > **************************************** > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170411/3d323db9/attachment-0001.html> > > ------------------------------ > > Message: 3 > Date: Wed, 12 Apr 2017 10:35:29 +0800 > From: Stephen Politzer-Ahles > To: fieldtrip at science.ru.nl > Subject: Re: [FieldTrip] cluster-based statistics with one covariate > Message-ID: > A at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Caroline, > > If your conditions are within-subject, then I think the best way to do this > is to construct a dataset representing the conditionA - conditionB > difference for each subject, and then using ft_statfun_indepsamplesregrT to > regress the subject-wise difference on age. See e.g. > https://mailman.science.ru.nl/pipermail/fieldtrip/2016-May/010528.html for > a thread discussing a similar approach. > > Best, > Steve > > > --- > Stephen Politzer-Ahles > The Hong Kong Polytechnic University > Department of Chinese and Bilingual Studies > http://www.mypolyuweb.hk/~sjpolit/ > > > > > > Message: 3 > > Date: Mon, 10 Apr 2017 14:50:13 +0200 (CEST) > > From: Caroline Beese > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] cluster-based statistics with one covariate > > Message-ID: > > <1329277450.115066.1491828613491.JavaMail.zimbra at cbs.mpg.de> > > Content-Type: text/plain; charset=utf-8 > > > > Dear all, > > > > I'm trying to take age as a covariate into my cluster-based statistics > > comparing two dependent measures. > > > > I have read about two options: > > > > A) to use ft_regressconfound before I do the stats or > > B) to create a design with a third row using the .cvar field in the > > 'depsamplesregrT' statfun. > > > > I understand that for correcting head motions ft_regressconfound is a > > great option but for taking age into account as a covariate, it doesn't > > seem intuitive to me to do this within-subject on a trial-by-trial basis > > having only one number per person. Or can you use this function > differently? > > > > However, for option B) the subfunction 'unitselvec' is missing and this > > seems to be an issue for several years. So I was wondering whether anyone > > has ever tried to fix this problem themselves and wouldn't mind sharing? > > > > More generally, if anyone has successfully implemented a cluster-based > > statistics with one or more covariates, please share your experience, it > > would be greatly appreciated. > > > > Best Regards, > > Caroline > > > > -- > > Caroline Beese > > PhD student > > > > Max-Planck Institute for Human Cognitive and Brain Sciences > > Department of Neuropsychology > > Stephanstr. 1a > > 04103 Leipzig > > > > office phone: +49 (0) 341 9940 129 > > > > www.cbs.mpg.de/staff/beese-11586 > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170412/af43a0d6/attachment-0001.html> > > ------------------------------ > > Message: 4 > Date: Wed, 12 Apr 2017 09:01:14 +0000 > From: Robin K?mpe > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Installing gui_streamer > Message-ID: > eurprd06.prod.outlook.com> > > Content-Type: text/plain; charset="iso-8859-1" > > Hi! > > We want to, from scratch, set up a real time fMRI capabilities. Your > documentation covers this quite well. I do, however, get stuck on point 1 > which is to launch the gui_streamer from the console. How does one > obtain/install this program on our Siemens Prisma? > > Best, > > > Robin K?mpe > Research Engineer > > [Link?ping University] > > CSAN, Center for Social and Affective Neuroscience > Department of Clinical and Experimental Medicine, IKE > Mobile: +46 (0)73 8005561 > Please visit us at www.liu.se > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170412/cf35fa04/attachment-0001.html> > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 77, Issue 9 > **************************************** > -- Laxmi Shaw Research Scholar(PhD) IIT Kharagpur West Bengal Ph no-08388837821 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Apr 13 09:24:37 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 13 Apr 2017 07:24:37 +0000 Subject: [FieldTrip] Inquiry about Field-Trip usage for multi-channel sources In-Reply-To: References: Message-ID: <534C6190-9193-43EB-A363-8A7D84FC6F39@donders.ru.nl> Joe, You may want to have a look here: http://www.fieldtriptoolbox.org/example/compute_forward_simulated_data_and_apply_a_dipole_fit?s[]=ft&s[]=dipolesimulation to get started. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 07 Apr 2017, at 20:23, Joseph Lee > wrote: Dear Field Trip Community I am Joe from the Computational Unit of the Center for Consciousness Science, University of Michigan. We are somewhat new to forward modelling and are currently undertaking a project to generate 128 scalp-level channel signals from the 78 source-level signals. We are using the "ft_compute_leadfield" function of FieldTrip in order to accomplish that goal. Is this a valid approach for our goal or were those functions designed for a different purpose? Any comments on this will be helpful for us. Thank you very much. Best, Joe Research Assistant Center for Consciousness Science, University of Michigan Medical School, Ann Arbor, USA _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From son.ta.dinh at tum.de Thu Apr 13 14:57:45 2017 From: son.ta.dinh at tum.de (Ta Dinh, Son) Date: Thu, 13 Apr 2017 12:57:45 +0000 Subject: [FieldTrip] Functional connectivity analysis with powcorr_ortho Message-ID: Dear FieldTrip list, I am trying to do a functional connectivity analysis using the power envelope correlation introduced by Hipp et al. (Nat Neuroscience 2012) as implemented in the ft_connectivity_powcorr_ortho function. My data consists of 5 minutes of eyes-closed resting-state data and my schematic pipeline is as follows: 1. I use LCMV beamforming to source reconstruct my bandpassed and preprocessed data 2. Using the resulting spatial filter I get a projected time series for every voxel (virtual channel) 3. I do a frequency analysis on these time series 4. The results of this frequency analysis (the Fourier coefficients) are used for the connectivity analysis using powcorr_ortho To check the results of this analysis, I plotted the results of a seed-based connectivity analysis with a voxel in the left visual cortex (-20, -80, 20) as seed. In the alpha band, I expect to see a strong local connectivity pattern in the occipital region extending partially into the contralateral hemisphere, similar to what Siems et al. NeuroImage 2016 find. However, I get a basically random connectivity pattern. When using this pipeline with the debiased weighted phase lag index, I get exactly what I am expecting. I looked into the source code of the ft_connectivity_powcorr_ortho function and saw a few disconcerting comments (Fix-Me's and the like) and now I am wondering whether my pipeline is simply not suited to the connectivity analysis with powcorr_ortho as implemented in FieldTrip or if the function is simply not fully implemented yet. Has anyone used it successfully before? I use the following FieldTrip (pseudo-) code: %% LCMV source reconstruction cfg = []; cfg.method = 'lcmv'; cfg.keeptrials = 'yes'; cfg.elec = elec; cfg.grid = lf; % regular grid of 1 cm resolution cfg.headmodel = vol % standard_bem.mat cfg.lcmv.keepfilter = 'yes'; cfg.lcmv.lambda = '5%'; cfg.lcmv.projectnoise = 'yes'; source = ft_sourceanalysis(cfg, tlock_data); %% pseudo-code for the computation of the virtual channel time series virtChan_data = tlock_data; virtChan_data.label = [source.pos(:, 1), source.pos(:,2), source.pos(:,3)]; virtChan_data.trial = source.avg.filter * tlock_data.trial; %% frequency analysis of the virtual channels cfg = []; cfg.method = 'mtmfft'; cfg.output = 'fourier'; cfg.keeptrials = 'yes'; cfg.foi = 10; % alpha band cfg.taper = 'hanning' % I originally used 3 tapers but source code in ft_connectivity_powcorr_ortho implies that multitaper is not compatible virtFreq = ft_freqanalysis(cfg, virtChan_data); %% connectivity analysis cfg = []; cfg.method = 'powcorr_ortho'; conn = ft_connectivityanalysis(cfg,virtFreq); Any suggestions and/or comments would be immensely helpful! Thanks in advance. Best, Son Son Ta Dinh, M.Sc. PhD student in Human Pain Research Klinikum rechts der Isar Technische Universität München Munich, Germany Phone: +49 89 4140 7664 http://www.painlabmunich.de/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Fri Apr 14 03:27:24 2017 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Fri, 14 Apr 2017 09:27:24 +0800 Subject: [FieldTrip] Need help with cluster-based permutation test with 3 groups of subjects Message-ID: Hello Jose, I haven't looked closely at your code, but it sounds like this is working exactly as intended. A significant F-test doesn't mean that there must be significant differences between all pairs of groups; hypothetically, an F-test comparing 100 groups could be significant even if only 99 and 100 are significantly different from each other. This isn't something specific to the cluster-based permutation test, this is just how F-tests work in general. As for getting different cluster extents with the 3-level F-test vs. the pairwise t-test, this is also normal; you're comparing different things so it's natural that the test statistics will come out slightly different. Best, Steve --- Stephen Politzer-Ahles The Hong Kong Polytechnic University Department of Chinese and Bilingual Studies http://www.mypolyuweb.hk/~sjpolit/ > > > Message: 1 > Date: Tue, 11 Apr 2017 12:08:44 +0200 > From: Jos? Antonio Uriguen Garaizabal > To: FieldTrip discussion list > Subject: [FieldTrip] Need help with cluster-based permutation test > with 3 groups of subjects > Message-ID: > < CAMMf7X15byC6p3gqaie6wEuKekV2krZ0++keLLUPZ3pn2h-PAA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all > > > My name is Toni and I am working on EEG signal processing at University of > Deusto, Bilbao, Spain. More specifically, right now trying to > apply cluster-based permutation testing to determine whether there exist > differences among 3 groups of subjects. > > > So, for my testing, subject groups are E, EN and N, the 2 former being > different types of patients and the latter being a control group. I am > forming clusters based on proximity (in space) and each subject is > characterized by a matrix of values that vary in 2D (per channel and > another variable related but not equal to frequency). > > By means of a T-statistic (indepsamplesT) I can find differences in between > E and EN, but I find no clusters/differences in between E and N or EN and > N, even though hypothetically (I think) they should exist. By means of an > F-statistic (indepsamplesF) I can find differences among the 3 groups at > the same time, then also between E and EN and no differences between E and > N or EN and N... > > Am I missing something? I do not understand why the might exist a > significant cluster when comparing all 3 groups that does not exist in the > 1vs1 comparisons, even though the cluster is not the same I obtain when I > compare E vs EN... > > > For additional information, I attach how I run the test: > > cfg.method = 'distance'; > cfg.neighbourdist = 1; > cfg.elec = ft_datatype_sens(subjEN{1}.elec); > neighbours = ft_prepare_neighbours(cfg); > > cfg = []; > cfg.channel = {'EEG'}; > cfg.latency = 'all'; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.neighbours = neighbours; % same as defined for the > between-trials experiment > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 5000; > > nsubj = size(subjE,2)+size(subjEN,2); > design = zeros(2,nsubj); > design(1,:) = [1:nsubj/2 1:nsubj/2]; > design(2,1:size(subjE,2)) = 1; > design(2,size(subjE,2)+1:nsubj) = 2; > > cfg.design = design; > cfg.ivar = 2; > > [stat] = ft_timelockstatistics(cfg, subjEN{:}, subjE{:}); > > > When I compare the 3 groups > > cfg.method = 'distance'; > cfg.neighbourdist = 1; > cfg.elec = ft_datatype_sens(subjEN{1}.elec); > neighbours = ft_prepare_neighbours(cfg); > > cfg = []; > cfg.channel = {'EEG'}; > cfg.latency = 'all'; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesF'; %F-statistic > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.neighbours = neighbours; % same as defined for the > between-trials experiment > cfg.tail = 1; %One sided > cfg.clustertail = 1; > cfg.alpha = 0.025; > cfg.numrandomization = 5000; > > nsubj1 = size(subjE,2); > nsubj2 = size(subjEN,2); > nsubj3 = size(subjN,2); > nsubj = nsubj1+nsubj2+nsubj3; > > design = zeros(2,nsubj); > design(1,:) = [1:nsubj1 1:nsubj2 1:nsubj3]; > design(2,1:nsubj1) = 1; > design(2,nsubj1+1:nsubj1+nsubj2) = 2; > design(2,nsubj1+nsubj2+1:nsubj) = 3; > > cfg.design = design; > cfg.ivar = 2; %2nd row is independent var > > [stat] = ft_timelockstatistics(cfg, subjE{:}, subjEN{:}, subjN{:}); > > > Then, subjE, subjN and subjEN are like this: > > Eall = subjE{:} > > Eall = > > struct with fields: > > label: {1?18 cell} > fsample: 200 > elec: [1?1 struct] > trial: {[18?115 double]} > time: {[1?115 double]} > cfg: [1?1 struct] > > > Thanks in advance > > -- > *Jose Antonio Urig?en* > PostDoc at Deustotech-LIFE (eVIDA Research Group) > [image: Deusto] > Universidad de Deusto / Deustuko Unibertsitatea / University of Deusto > Facultad de Ingenier?a, 4? Planta > Avda. Universidades 24. 48007 Bilbao > Tel. +34 94 413 90 00 / Mov. +34 656 711 643 > Ext. 2980 > jose.uriguen at deusto.es > Web: evida.deusto.es > *www.deusto.es * > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20170411/7a169976/attachment-0001.html > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joeboe at umich.edu Fri Apr 14 19:48:38 2017 From: joeboe at umich.edu (Joseph Lee) Date: Fri, 14 Apr 2017 13:48:38 -0400 Subject: [FieldTrip] Inquiry about Field-Trip usage for multi-channel sources In-Reply-To: <534C6190-9193-43EB-A363-8A7D84FC6F39@donders.ru.nl> References: <534C6190-9193-43EB-A363-8A7D84FC6F39@donders.ru.nl> Message-ID: Thank you for your reply Jan-Marthijs, May I ask then what the main difference between using 'ft_compute_leadfield' to calculate leadfield and generate a signal vs using 'ft_dipole_simulation'. Thanks! -Joe On Thu, Apr 13, 2017 at 3:24 AM, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Joe, > > You may want to have a look here: http://www.fieldtriptoolbox.org/example/ > compute_forward_simulated_data_and_apply_a_dipole_fit?s[ > ]=ft&s[]=dipolesimulation to get started. > > Best wishes, > Jan-Mathijs > > > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 <+31%2024%20361%204793> > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > On 07 Apr 2017, at 20:23, Joseph Lee wrote: > > Dear Field Trip Community > > I am Joe from the Computational Unit of the Center for Consciousness > Science, University of Michigan. > > We are somewhat new to forward modelling and are currently undertaking a > project to generate 128 scalp-level channel signals from the 78 > source-level signals. We are using the "ft_compute_leadfield" function of > FieldTrip in order to accomplish that goal. > > Is this a valid approach for our goal or were those functions designed for > a different purpose? > > Any comments on this will be helpful for us. Thank you very much. > > Best, > > Joe > > Research Assistant > Center for Consciousness Science, > University of Michigan Medical School, > Ann Arbor, USA > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Apr 14 21:19:15 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 14 Apr 2017 19:19:15 +0000 Subject: [FieldTrip] Inquiry about Field-Trip usage for multi-channel sources In-Reply-To: References: <534C6190-9193-43EB-A363-8A7D84FC6F39@donders.ru.nl> Message-ID: <2EC9613C-10A2-4F8F-86FE-A985C77DA2B8@donders.ru.nl> Please read the documentation. I think it should be sufficiently clear. Jan-Mathijs function [simulated] = ft_dipolesimulation(cfg) % FT_DIPOLESIMULATION computes the field or potential of a simulated dipole % and returns a datastructure identical to the FT_PREPROCESSING function. % % Use as % data = ft_dipolesimulation(cfg) % % The dipoles position and orientation have to be specified with % cfg.dip.pos = [Rx Ry Rz] (size Nx3) % cfg.dip.mom = [Qx Qy Qz] (size 3xN) % % The timecourse of the dipole activity is given as a single vector or as a % cell-array with one vectors per trial % cfg.dip.signal % or by specifying a sine-wave signal % cfg.dip.frequency in Hz % cfg.dip.phase in radians % cfg.dip.amplitude per dipole % cfg.ntrials number of trials % cfg.triallength time in seconds % cfg.fsample sampling frequency in Hz % % Random white noise can be added to the data in each trial, either by % specifying an absolute or a relative noise level % cfg.relnoise = add noise with level relative to simulated signal % cfg.absnoise = add noise with absolute level % cfg.randomseed = 'yes' or a number or vector with the seed value (default = 'yes') % % Optional input arguments are % cfg.channel = Nx1 cell-array with selection of channels (default = 'all'), % see FT_CHANNELSELECTION for details % cfg.dipoleunit = units for dipole amplitude (default nA*m) % cfg.chanunit = units for the channel data % % The volume conduction model of the head should be specified as % cfg.headmodel = structure with volume conduction model, see FT_PREPARE_HEADMODEL % % The EEG or MEG sensor positions should be specified as % cfg.elec = structure with electrode positions, see FT_DATATYPE_SENS % cfg.grad = structure with gradiometer definition, see FT_DATATYPE_SENS % cfg.elecfile = name of file containing the electrode positions, see FT_READ_SENS % cfg.gradfile = name of file containing the gradiometer definition, see FT_READ_SENS % % See also FT_SOURCEANALYSIS, FT_DIPOLEFITTING, FT_TIMELOCKSIMULATION, % FT_FREQSIMULATION, FT_CONNECTIVITYSIMULATION function [lf] = ft_compute_leadfield(dippos, sens, headmodel, varargin) % FT_COMPUTE_LEADFIELD computes a forward solution for a dipole in a a volume % conductor model. The forward solution is expressed as the leadfield % matrix (Nchan*3), where each column corresponds with the potential or field % distributions on all sensors for one of the x,y,z-orientations of the % dipole. % % Use as % [lf] = ft_compute_leadfield(dippos, sens, headmodel, ...) % with input arguments % dippos = position dipole (1*3 or Ndip*3) % sens = structure with gradiometer or electrode definition % headmodel = structure with volume conductor definition % % The headmodel represents a volume conductor model, its contents % depend on the type of model. The sens structure represents a sensor % array, i.e. EEG electrodes or MEG gradiometers. % % It is possible to compute a simultaneous forward solution for EEG and MEG % by specifying sens and grad as two cell-arrays, e.g. % sens = {senseeg, sensmeg} % headmodel = {voleeg, volmeg} % This results in the computation of the leadfield of the first element of % sens and headmodel, followed by the second, etc. The leadfields of the % different imaging modalities are subsequently concatenated. % % Additional input arguments can be specified as key-value pairs, supported % optional arguments are % 'reducerank' = 'no' or number % 'normalize' = 'no', 'yes' or 'column' % 'normalizeparam' = parameter for depth normalization (default = 0.5) % 'weight' = number or 1xN vector, weight for each dipole position (default = 1) % 'backproject' = 'yes' (default) or 'no', in the case of a rank reduction % this parameter determines whether the result will be % backprojected onto the original subspace % % The leadfield weight may be used to specify a (normalized) % corresponding surface area for each dipole, e.g. when the dipoles % represent a folded cortical surface with varying triangle size. % % Depending on the specific input arguments for the sensor and volume, this % function will select the appropriate low-level EEG or MEG forward model. % The leadfield matrix for EEG will have an average reference over all the % electrodes. % % The supported forward solutions for MEG are % single sphere (Cuffin and Cohen, 1977) % multiple spheres with one sphere per channel (Huang et al, 1999) % realistic single shell using superposition of basis functions (Nolte, 2003) % leadfield interpolation using a precomputed grid % boundary element method (BEM) % % The supported forward solutions for EEG are % single sphere % multiple concentric spheres (up to 4 spheres) % leadfield interpolation using a precomputed grid % boundary element method (BEM) % % See also FT_PREPARE_VOL_SENS, FT_HEADMODEL_ASA, FT_HEADMODEL_BEMCP, % FT_HEADMODEL_CONCENTRICSPHERES, FT_HEADMODEL_DIPOLI, FT_HEADMODEL_HALFSPACE, % FT_HEADMODEL_INFINITE, FT_HEADMODEL_LOCALSPHERES, FT_HEADMODEL_OPENMEEG, % FT_HEADMODEL_SINGLESHELL, FT_HEADMODEL_SINGLESPHERE, % FT_HEADMODEL_HALFSPACE On 14 Apr 2017, at 19:48, Joseph Lee > wrote: Thank you for your reply Jan-Marthijs, May I ask then what the main difference between using 'ft_compute_leadfield' to calculate leadfield and generate a signal vs using 'ft_dipole_simulation'. Thanks! -Joe On Thu, Apr 13, 2017 at 3:24 AM, Schoffelen, J.M. (Jan Mathijs) > wrote: Joe, You may want to have a look here: http://www.fieldtriptoolbox.org/example/compute_forward_simulated_data_and_apply_a_dipole_fit?s[]=ft&s[]=dipolesimulation to get started. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 07 Apr 2017, at 20:23, Joseph Lee > wrote: Dear Field Trip Community I am Joe from the Computational Unit of the Center for Consciousness Science, University of Michigan. We are somewhat new to forward modelling and are currently undertaking a project to generate 128 scalp-level channel signals from the 78 source-level signals. We are using the "ft_compute_leadfield" function of FieldTrip in order to accomplish that goal. Is this a valid approach for our goal or were those functions designed for a different purpose? Any comments on this will be helpful for us. Thank you very much. Best, Joe Research Assistant Center for Consciousness Science, University of Michigan Medical School, Ann Arbor, USA _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From cmuehl at gmail.com Tue Apr 18 09:28:57 2017 From: cmuehl at gmail.com (Christian Muehl) Date: Tue, 18 Apr 2017 07:28:57 +0000 Subject: [FieldTrip] CfP - reminder - Brain and physiological signals for multi-user modeling @ ACII Message-ID: ** Call for papers ** Special session in ACII 2017 (Affective Computing and Intelligent Interaction) Topic: Brain and physiological signals for multi-user modeling http://www.affective-sciences.org/en/bps-mum ** Description ** Emotional cues, generated subconsciously by the human body, have always been a crucial part of affective computing. Machines can learn about a person's affective state by analyzing measurements such as autonomic nervous system responses, neurophysiological measurements and gaze behavior. They can then act on the inferred information, adapting their own behavior, response or service based on the user's affective state. Although emotions can be viewed as a social phenomenon, current physiological computing research is focused on emotions which are triggered by non-social stimuli. In the case of group interactions, emotions do not only develop in one’s mind but rather unfold according to the emotional expressions of the others. Consequently, the behavior, expressions and physiology of interacting people are known to be in synchrony during interactions. This inter-dependency of behavior and emotional expressions can in turn predict several properties of the social interaction such as grounding, mutual understanding, conflict, or social presence. Similarly, researchers in social neuro-science perform hyper-scanning to measure joint brain activities of people interacting with each other. The objective being to uncover brain areas and neural mechanisms supporting social processes. With this special session we would like to develop research on multi-user modeling from neural and physiological sources. Here the concept of user modeling is defined broadly, including emotional, cognitive and social aspects which can be used for intelligent interactions. This special session targets researchers from computer science, neuro-science and psycho-physiology who are interested in the following research questions: - What information about the user state and the quality of the interaction between users can be gained from (neuro-)physiological signals? - How can that information, combined from several users, be used to interact adaptively with a machine? - What is the effect of sharing physiological information with others? - Which methods can be developed to reduce inter-user variability and improve user modeling? The special session topics include but are not limited to: - Collaborative brain-computer interfaces - Tangible / social display of physiological and neural cues - Social bio-feedback - Assessment of social processes (conflict, empathy, relationship etc.) - Assessment of the quality of interaction and collaboration - Social neuroscience and psycho-physiology - Emotion assessment, particularly social emotions - Domain and transfer learning for building cross-participant models - Methods for multiple user modeling (e.g. synchrony measures, dynamic multi-user models, etc.) - Applications of multi-user physiological computing To facilitate the research on physiological signal classification, several databases are publicly available. Contributions on the physiological data available in such databases are welcome but not obliged. Example databases include: EATMINT: https://eatmint.unige.ch RECOLA: https://diuf.unifr.ch/diva/recola MMDB: http://www.cbi.gatech.edu/mmdb/ Those databases are only examples and work on self-collected or other data are welcome. ** Important dates ** Conference Dates: October 23-26, 2017 Paper Submission Deadline: May 2, 2017 Reviews Provided to Authors: June 16, 2017 Author Rebuttals Due: June 23, 2017 Notification of Acceptance: July 14, 2017 Camera Ready Papers Due: August 18, 2017 Full paper authors should register By: August 7, 2017 Early registration deadline: September 1, 2017 ** Submission procedure ** Papers submitted to this Special Sessions have to be submitted following the same schedule and procedure as regular ACII papers (ACII paper submission). When submitting your paper please check the corresponding box for the Special Session on "Brain and physiological signals for multi-user modeling" in the ACII submission system. The papers will undergo the same review process by anonymous and independent reviewers as the remaining ACII submissions. ** Organizers ** Guillaume Chanel, Swiss Center for Affective Sciences, Switzerland guillaume.chanel[at]unige.ch http://cvml.unige.ch/guillaumechanel Christian Mühl, German Aerospace Center, Germany cmuehl[at]gmail.com https://www.linkedin.com/in/cmuhl Jérémy Frey, Ullo, France jfrey[at]ullo.fr http://phd.jfrey.info Anton Nijholt, University of Twente, The Netherlands anijholt[at]cs.utwente.nl http://wwwhome.cs.utwente.nl/~anijholt/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at me.com Wed Apr 19 09:14:34 2017 From: nathanweisz at me.com (Nathan Weisz) Date: Wed, 19 Apr 2017 09:14:34 +0200 Subject: [FieldTrip] PhD position Salzburg MEG lab Message-ID: <1590B171-5153-4788-A372-9233442AA22E@me.com> Dear colleagues, sorry in advance for cross-postings. Starting September 2017 a PhD position will be available in our group. See attached pdf. Please forward to potentially interested students. Best, Nathan -------------- next part -------------- A non-text attachment was scrubbed... Name: ESIT_Call_Salzburg.pdf Type: application/pdf Size: 341931 bytes Desc: not available URL: From r.oostenveld at donders.ru.nl Wed Apr 19 16:02:04 2017 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 19 Apr 2017 16:02:04 +0200 Subject: [FieldTrip] FiledTrip - Python compatibility? In-Reply-To: References: Message-ID: <327AADB7-8D61-4646-9C16-C5AF2B479946@donders.ru.nl> Hi Greydon, Let me also CC this to the FieldTrip list, as I know there are more people thinking about this. Although I am using Python for other projects (e.g. EEGsynth , we don’t have concrete plans for improving the compatibility between FieldTrip and Python, or to port parts of FieldTrip over to Python. Personally (*) I also feel that Python is not the optimal language and/or data analysis environment for the goals of the FieldTrip project. It would for sure attract more computer scientists and people that like programming, but for (non-technical) cognitive neuroscientists and people that are just able to do scripting I suspect it to become more like an application rather than a toolbox where you can look under the hood and mix it in with ones own code. (*) Other people might feel different of course MNE-Python is of course a project that I am following. The occasional improvements on the FieldTrip side are primarily focussed on making the transition between MNE-Python and FieldTrip more smooth (both ways). A complicating feature in Python is that data handling is different than in MATLAB, where we only use native built-in data structures. Saving data from Python requires a well-established file format (which does not exist) or a stable object definition (which is hard in science). Also for (open access) data sharing I hope that we can do more work on representing analysis results in a format that allows them to be reused in another pipeline. That is for exampel something that we attempted in the MEG section of the human connectome project, where the use cifti files (i.e. nifti-2 with a header extension), text files and - where needed - matlab files in a format that works well with Python. If you have ideas for improving the interoperability, you are welcome to contribute . best Robert PS Thanks for the nice remarks about FieldTrip! > On 16 Apr 2017, at 18:17, Greydon Gilmore wrote: > > Hi Robert, > > I recently stumbled across FieldTrip and I have been in love ever since. I love that I can incorporate the functions into my own scripts. > > I am curious o know if there is any work being done to make FieldTrip compatible with Python? > > Thank you for all the work your team put into FieldTrip, it's streamlined my workflow greatly. > > Greydon > > -- > Greydon Gilmore, B.Sc., M.Sc. (Neuroscience) > Ph.D. candidate in Biomedical Engineering > Movement Disorder Centre, University Hospital > University of Western Ontario > 339 Windermere Road, BLL-250 > 519-685-8500 ext. 76708 > London, Ontario > Canada, N6A 5A5 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ella.weik at gmail.com Thu Apr 20 01:12:24 2017 From: ella.weik at gmail.com (Ella Weik) Date: Wed, 19 Apr 2017 16:12:24 -0700 Subject: [FieldTrip] Problems with plotting time-frequency analysis results Message-ID: Hi Fieldtrip Community, We are currently trying to run a wavelet time frequency analysis. Our EEG data is already preprocessed and epoched with EEGlab. We are able to read in the data, define trials, and output values for TFR.powspctrm. However, we do not see any of these values plotted on our figure with ft_singleplot. This is the code we are using: cfg = []; cfg.dataset = dsname; cfg.continuous = 'no'; cfg.trialfun = 'wm_trialfun'; cfg.binNumber = 13; cfg.epochBaseInt = -0.5; cfg.epochInt = 1.5; cfg.trialdef.prestim = cfg.epochBaseInt - 0.01; cfg.trialdef.poststim = cfg.epochInt - 0.01 ; cfg = ft_definetrial(cfg); dataFIC = ft_preprocessing(cfg); save dataFIC_DirCue dataFIC; dataFIC_condX cfg = []; cfg.channel = 'EEG'; cfg.trials = 'all' cfg.keeptrials = 'no'; cfg.output = 'pow'; cfg.foi = 2:0.5:50; cfg.toi = -0.4:0.01:1.4; % cfg.method = 'wavelet'; cfg.width = 7; cfg.length = 2; TFR = ft_freqanalysis(cfg, dataFIC); save TFRwave_DirCue TFR % plot the results cfg = []; cfg.parameter = 'powspctrm'; cfg.baseline = [-0.4 0]; cfg.baselinetype = 'relative'; cfg.zlim = [-3e-10 3e-10]; cfg.showlabels = 'yes'; figure; ft_singleplotTFR(cfg,TFR); And this is our trial_function: function [trl, event] = wm_trialfun(cfg); hdr = ft_read_header(cfg.dataset); event = ft_read_event(cfg.dataset); indx=[]; if cfg.binNumber for i = 1:size(event,2) if ismember(cfg.binNumber,event(i).bini) indx=[indx;1]; else indx=[indx;0]; end end ind = find(indx); sample = [event(ind).sample]'; else sample = [event(find(strcmp(cfg.codeLabel, {event.codelabel}))).sample]'; end epochBaseSamples = -1*cfg.epochBaseInt*hdr.Fs; epochSamples = cfg.epochInt*hdr.Fs; epochTotal = epochBaseSamples + epochSamples; epochStarts = [1:epochTotal:sample(end)]; eventStarts = epochStarts + epochBaseSamples; sampleGood = intersect(sample,eventStarts); pretrig = -round(cfg.trialdef.prestim * hdr.Fs); posttrig = round(cfg.trialdef.poststim * hdr.Fs); trl = []; trl(:,1) = sampleGood + pretrig; trl(:,2) = sampleGood + posttrig; trl(:,3) = pretrig; And this is the cfg: channel: {128x1 cell} trials: 'all' keeptrials: 'no' output: 'pow' foi: [1x15 double] toi: [1x28 double] method: 'wavelet' width: 7 length: 3 outputfilepresent: 'overwrite' callinfo: [1x1 struct] version: [1x1 struct] feedback: 'text' inputlock: [] outputlock: [] gwidth: 3 pad: 0.9820 padtype: 'zero' calcdof: 'no' precision: 'double' correctt_ftimwin: 'no' polyremoval: 0 keeptapers: 'no' previous: [1x1 struct] Any insights would be greatly appreciated with regards to why we cannot see any values in our single plot figure. Also, we are not sure if the problem rests in our plotting configuration or the data itself. Best regards, Ella -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.litvak at ucl.ac.uk Thu Apr 20 18:27:36 2017 From: v.litvak at ucl.ac.uk (Vladimir Litvak) Date: Thu, 20 Apr 2017 17:27:36 +0100 Subject: [FieldTrip] Last chance: SPM course for MEG/EEG in London: May 8-10, 2017 Message-ID: Dear all, We are pleased to announce that our annual SPM course for MEG/EEG will take place this year from Monday May 8 to Wednesday May 10 2017. Hosted by University College London, the course will be held at Queen Square, a very central location in London (UK). The course will present instruction on the analysis of MEG and EEG data. The first two days will combine theoretical presentations with practical demonstrations of the different data analysis methods implemented in SPM. On the last day participants will have the opportunity to work on SPM tutorial data sets under the supervision of the course faculty. We also invite students to bring their own data for analysis. The course is suitable for both beginners and more advanced users. The topics that will be covered range from pre-processing and statistical analysis to source localization and dynamic causal modelling. The program is listed below. Registration is now open. For full details see http://www.fil.ion.ucl.ac.uk/spm/course/london/ where you can also register. Available places are limited so please register as early as possible if you would like to attend! ---------------------- Monday May 8th (33 Queen square, basement) 9.00 - 9.30 Registration 9.30 - 9.45 SPM introduction and resources Guillaume Flandin 9.45 - 10.30 What are we measuring with M/EEG? Saskia Heibling 10.30 - 11.15 Data pre-processing Hayriye Cagnan Coffee 11.45 - 12.30 Data pre-processing – demo Sofie Meyer, Misun Kim 12.30 - 13.15 General linear model and classical inference Christophe Phillips Lunch 14.15 - 15.00 Multiple comparisons problem and solutions Guillaume Flandin 15.00 - 15.45 Bayesian inference Christophe Mathys Coffee 16.15 - 17.45 Group M/EEG dataset analysis - demo Jason Taylor, Martin Dietz 17.45 - 18.30 Advanced applications of the GLM Ashwani Jha, Bernadette van Wijk Tuesday May 9th (33 Queen square, basement) 9.30 - 10.15 M/EEG source analysis Gareth Barnes 10.15 - 11.15 M/EEG source analysis – demo Jose Lopez, Leonardo Duque Coffee 11.45 - 12.30 The principles of dynamic causal modelling Bernadette van Wijk 12.30 - 13.15 DCM for evoked responses Ryszard Auksztulewicz Lunch 14.15 - 15.00 DCM for steady state responses Rosalyn Moran 15.00 - 15.45 DCM - demo Richard Rosch, Tim West Coffee 16.15 - 17.00 Bayesian model selection and averaging Peter Zeidman 17.00 - 18.30 Clinic - questions & answers Karl Friston 19.00 - ... Social Event Wednesday May 10th 9.30 - 17.00 Practical hands-on session in UCL computer class rooms. Participants can either work on SPM tutorial datasets or on their own data with the help of the faculty. There will also be an opportunity to ask questions in small tutorial groups for further discussions on the topics of the lectures. -------------- next part -------------- An HTML attachment was scrubbed... URL: From gio at gpiantoni.com Fri Apr 21 16:21:38 2017 From: gio at gpiantoni.com (Gio Piantoni) Date: Fri, 21 Apr 2017 16:21:38 +0200 Subject: [FieldTrip] FiledTrip - Python compatibility? Message-ID: I looked into creating a python wrapper around matlab for Fieldtrip. Mathworks officially supports a Matlab engine for python (pretty neat), but the bottleneck for me is that it does not convert matlab cells to python objects: https://www.mathworks.com/help/matlab/matlab_external/handle-data-returned-from-matlab-to-python.html so it's impossible to pass fieldtrip structures to python. Hopefully they'll get around to support the cell conversion in the near future. Also I don't remember how sophisticated the memory management in the engine is. Projects like python-matlab-bridge usually don't share the memory between processes (like rpy2 does), so you end up with duplicated objects (which gets unwieldy when working with large EEG datasets) -g > Date: Wed, 19 Apr 2017 16:02:04 +0200 > From: Robert Oostenveld > To: Greydon Gilmore > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] FiledTrip - Python compatibility? > Message-ID: <327AADB7-8D61-4646-9C16-C5AF2B479946 at donders.ru.nl> > Content-Type: text/plain; charset="utf-8" > > Hi Greydon, > > Let me also CC this to the FieldTrip list, as I know there are more people thinking about this. > > Although I am using Python for other projects (e.g. EEGsynth , we don?t have concrete plans for improving the compatibility between FieldTrip and Python, or to port parts of FieldTrip over to Python. Personally (*) I also feel that Python is not the optimal language and/or data analysis environment for the goals of the FieldTrip project. It would for sure attract more computer scientists and people that like programming, but for (non-technical) cognitive neuroscientists and people that are just able to do scripting I suspect it to become more like an application rather than a toolbox where you can look under the hood and mix it in with ones own code. > > (*) Other people might feel different of course > > MNE-Python is of course a project that I am following. The occasional improvements on the FieldTrip side are primarily focussed on making the transition between MNE-Python and FieldTrip more smooth (both ways). > > A complicating feature in Python is that data handling is different than in MATLAB, where we only use native built-in data structures. Saving data from Python requires a well-established file format (which does not exist) or a stable object definition (which is hard in science). Also for (open access) data sharing I hope that we can do more work on representing analysis results in a format that allows them to be reused in another pipeline. That is for exampel something that we attempted in the MEG section of the human connectome project, where the use cifti files (i.e. nifti-2 with a header extension), text files and - where needed - matlab files in a format that works well with Python. > > If you have ideas for improving the interoperability, you are welcome to contribute . > > best > Robert > > PS Thanks for the nice remarks about FieldTrip! > > >> On 16 Apr 2017, at 18:17, Greydon Gilmore wrote: >> >> Hi Robert, >> >> I recently stumbled across FieldTrip and I have been in love ever since. I love that I can incorporate the functions into my own scripts. >> >> I am curious o know if there is any work being done to make FieldTrip compatible with Python? >> >> Thank you for all the work your team put into FieldTrip, it's streamlined my workflow greatly. >> >> Greydon >> >> -- >> Greydon Gilmore, B.Sc., M.Sc. (Neuroscience) >> Ph.D. candidate in Biomedical Engineering >> Movement Disorder Centre, University Hospital >> University of Western Ontario >> 339 Windermere Road, BLL-250 >> 519-685-8500 ext. 76708 >> London, Ontario >> Canada, N6A 5A5 From tomh at kurage.nimh.nih.gov Fri Apr 21 16:54:56 2017 From: tomh at kurage.nimh.nih.gov (Tom Holroyd) Date: Fri, 21 Apr 2017 10:54:56 -0400 Subject: [FieldTrip] FiledTrip - Python compatibility? In-Reply-To: References: Message-ID: <20170421105456.5341782f@kurage.nimh.nih.gov> You might want to look at this: -- https://pypi.python.org/pypi/oct2py Oct2Py allows you to seamlessly call M-files and Octave functions from Python. It manages the Octave session for you, sharing data behind the scenes using MAT files. -- I've used FieldTrip under Octave in the past (3.0). It doesn't take too much work to get most of the important stuff ported. There's a saying, "Octave is as compatible with Matlab as Matlab is with itself." Once ported, cluster concerns vanish, just run 128 copies of Octave ... They have a nice IDE now too. Because it's open source, integration with Python is much better, see oct2py, which also has a cool name. On Fri, 21 Apr 2017 16:21:38 +0200 Gio Piantoni wrote: > I looked into creating a python wrapper around matlab for Fieldtrip. > > Mathworks officially supports a Matlab engine for python (pretty > neat), but the bottleneck for me is that it does not convert matlab > cells to python objects: > https://www.mathworks.com/help/matlab/matlab_external/handle-data-returned-from-matlab-to-python.html > so it's impossible to pass fieldtrip structures to python. > > Hopefully they'll get around to support the cell conversion in the near future. > > Also I don't remember how sophisticated the memory management in the > engine is. Projects like python-matlab-bridge usually don't share the > memory between processes (like rpy2 does), so you end up with > duplicated objects (which gets unwieldy when working with large EEG > datasets) > > -g > > > > Date: Wed, 19 Apr 2017 16:02:04 +0200 > > From: Robert Oostenveld > > To: Greydon Gilmore > > Cc: FieldTrip discussion list > > Subject: Re: [FieldTrip] FiledTrip - Python compatibility? > > Message-ID: <327AADB7-8D61-4646-9C16-C5AF2B479946 at donders.ru.nl> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Greydon, > > > > Let me also CC this to the FieldTrip list, as I know there are more people thinking about this. > > > > Although I am using Python for other projects (e.g. EEGsynth , we don?t have concrete plans for improving the compatibility between FieldTrip and Python, or to port parts of FieldTrip over to Python. Personally (*) I also feel that Python is not the optimal language and/or data analysis environment for the goals of the FieldTrip project. It would for sure attract more computer scientists and people that like programming, but for (non-technical) cognitive neuroscientists and people that are just able to do scripting I suspect it to become more like an application rather than a toolbox where you can look under the hood and mix it in with ones own code. > > > > (*) Other people might feel different of course > > > > MNE-Python is of course a project that I am following. The occasional improvements on the FieldTrip side are primarily focussed on making the transition between MNE-Python and FieldTrip more smooth (both ways). > > > > A complicating feature in Python is that data handling is different than in MATLAB, where we only use native built-in data structures. Saving data from Python requires a well-established file format (which does not exist) or a stable object definition (which is hard in science). Also for (open access) data sharing I hope that we can do more work on representing analysis results in a format that allows them to be reused in another pipeline. That is for exampel something that we attempted in the MEG section of the human connectome project, where the use cifti files (i.e. nifti-2 with a header extension), text files and - where needed - matlab files in a format that works well with Python. > > > > If you have ideas for improving the interoperability, you are welcome to contribute . > > > > best > > Robert > > > > PS Thanks for the nice remarks about FieldTrip! > > > > > >> On 16 Apr 2017, at 18:17, Greydon Gilmore wrote: > >> > >> Hi Robert, > >> > >> I recently stumbled across FieldTrip and I have been in love ever since. I love that I can incorporate the functions into my own scripts. > >> > >> I am curious o know if there is any work being done to make FieldTrip compatible with Python? > >> > >> Thank you for all the work your team put into FieldTrip, it's streamlined my workflow greatly. > >> > >> Greydon > >> > >> -- > >> Greydon Gilmore, B.Sc., M.Sc. (Neuroscience) > >> Ph.D. candidate in Biomedical Engineering > >> Movement Disorder Centre, University Hospital > >> University of Western Ontario > >> 339 Windermere Road, BLL-250 > >> 519-685-8500 ext. 76708 > >> London, Ontario > >> Canada, N6A 5A5 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Dr. Tom -- I would dance and be merry, Life would be a ding-a-derry, If I only had a brain. -- The Scarecrow From J.Verhoef at donders.ru.nl Mon Apr 24 20:25:50 2017 From: J.Verhoef at donders.ru.nl (Verhoef, J.P. (Julia)) Date: Mon, 24 Apr 2017 18:25:50 +0000 Subject: [FieldTrip] Nine Research Positions in the Dutch Consortium "Language in Interaction" (1.0 FTE) In-Reply-To: <11E9E0B371DBAE4EB859A9CC30606A04023F601E@exprd04.hosting.ru.nl> References: <11E9E0B371DBAE4EB859A9CC30606A04023F5FBE@exprd04.hosting.ru.nl>, <11E9E0B371DBAE4EB859A9CC30606A04023F601E@exprd04.hosting.ru.nl> Message-ID: <11E9E0B371DBAE4EB859A9CC30606A04023F602A@exprd04.hosting.ru.nl> Nine Research Positions in the Dutch Consortium 'Language in Interaction' (1.0 FTE) Dutch Research Consortium 'Language in Interaction' Vacancy number: 30.02.17 Application deadline: 21 May 2017 Responsibilities We are looking for highly motivated candidates to enrich a unique research consortium aiming to unravel the neurocognitive mechanisms of language at multiple levels. The goal is to understand both the universality and the variability of the human language faculty from genes to behaviour. Currently, our consortium advertises 4 Postdoc and 5 PhD positions. These positions provide the opportunity for conducting world-class research as a member of an interdisciplinary team. Each position has its own requirements and profile. Click here for more information on the advertised positions. www.languageininteraction.nl/jobs/BQsecond.html Work environment The Netherlands has an outstanding track record in the language sciences. The Language in Interaction research consortium, sponsored by a large grant from the Netherlands Organisation for Scientific Research (NWO), brings together many of the excellent research groups in the Netherlands with a research programme on the foundations of language. In addition to excellence in the domain of language and related relevant fields of cognition, our consortium provides state-of-the-art research facilities and a research team with ample experience in the complex research methods that will be invoked to address the scientific questions at the highest level of methodological sophistication. These include methods from genetics, neuroimaging, computational modelling, and patient-related research. This consortium realises both quality and critical mass for studying human language at a scale not easily found anywhere else. We have identified five Big Questions (BQ) that are central to our understanding of the human language faculty. These questions are interrelated at multiple levels. Teams of researchers will collaborate to collectively address these key questions of our field. Our five Big Questions are: BQ1: The nature of the mental lexicon: How to bridge neurobiology and psycholinguistic theory by computational modelling? BQ2: What are the characteristics and consequences of internal brain organization for language? BQ3: Creating a shared cognitive space: How is language grounded in and shaped by communicative settings of interacting people? BQ4: Variability in language processing and in language learning: Why does the ability to learn language change with age? How can we characterise and map individual language skills in relation to the population distribution? BQ5: How are other cognitive systems shaped by the presence of a language system in humans? Successful candidates will be appointed at one of the consortium’s home institutions, depending on the position applied for. All successful candidates will become members of our Big Question teams. The research is conducted in an international setting at all participating institutions. English is the lingua franca. What we expect from you Each position has its own requirements and profile. Detailed information on: www.languageininteraction.nl/jobs/BQsecond.html  General requirements for all positions are: • a degree in one of the fields indicated for the positions; • strong motivation; • excellent proficiency in written and spoken English. What we have to offer • employment: 1.0 FTE; • you will be appointed at one of the consortium’s home institutions, depending on the position applied for; • terms of employment depend on the embedding institution; • the institutes involved have regulations in place that enable their staff to create a good work-life balance. Other Information All institutes involved are equal opportunity employers, committed to building a culturally diverse intellectual community, and as such encourage applications from women and minorities. Would you like to know more? Further information on LiI consortium: http://www.languageininteraction.nl/ Further information on the different positions, including terms of employment and contacts: www.languageininteraction.nl/jobs/BQsecond.html Are you interested? You should upload your application (attn. of Prof. P. Hagoort) exclusively via: http://www.ru.nl/applyonline?tk=uk&recid=597242 Your application should include (and be limited to) the following attachment(s): • a cover letter quoting at the top the number of the position you apply for; • your curriculum vitae, including a list of publications and the names of at least two persons who can provide references. Please apply before 21 May 2017, 23:59 CET. You may apply for more than one position. No commercial propositions please. -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrea.brovelli at univ-amu.fr Mon Apr 24 21:35:26 2017 From: andrea.brovelli at univ-amu.fr (Andrea Brovelli) Date: Mon, 24 Apr 2017 21:35:26 +0200 Subject: [FieldTrip] 3 PhD scholarships in Integrative and Clinical Neurosciences at Aix-Marseille University (France) Message-ID: <8eb6aa69-e3d2-04f3-71d9-e2bfa937bbac@univ-amu.fr> In 2017, the PhD program in Integrative and Clinical Neurosciences at the Aix-Marseille University (France) will grant *three* *PhD scholarships* to excellent Master students that graduated from non-French top ranked universities. The selection process will include the following steps. 1. CALL FOR APPLICANTS (Master graduated students) * The scholarships are open to Master students that graduated from top rankenon-French universities. * Applicants must select and rank two of the proposed research projects * A guideline for student application and templates for recommendation letters must be downloaded on the following site: http://neuro-marseille.org/en/phdprogram-en/call-for-applicants/ * Applications should be sent *before May 21st, 2017 *at midnight (French time). 2. INTERVIEW * The selection committee will shortlist 10 students that will be individually interviewed in June. The students are encouraged to prepare their interviews with the project leaders they have selected. * The final decision will be known shortly after the interviews and the three successful candidates will start their PhD studies between October and December 2017. Contact Nadia Pittet nadejda.pittet at univ-amu.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.blume at sbg.ac.at Tue Apr 25 17:33:53 2017 From: christine.blume at sbg.ac.at (Blume Christine) Date: Tue, 25 Apr 2017 15:33:53 +0000 Subject: [FieldTrip] ft_definetrial on result from ft_appenddata? Message-ID: Dear FT community, I have data with overlapping segments, wherefore I need to do the raw data inspection using ft_databrowser on continuous data (unless ft_databrowser can handle overlapping segments now?). So far so good, but I have 5 different raw data files per person as our machine closes and files automatically and starts a new one as soon as they exceed 2GB. The most convenient thing would obviously be to append all 5, run ft_databrowser on the appended data and then do the segmentation. This is particularly the case because it is data from sleep and thus important to see how the EEG/MEG changes across time. However, I am wondering whether there is any way to apply ft_definetrial and ft_redefinetrial to appended datasets (as it obviously goes back to the underlying raw files, of which I have 5). Any suggestions are more than welcome :). Thanks, Christine -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandra.bendixen at physik.tu-chemnitz.de Tue Apr 25 23:00:40 2017 From: alexandra.bendixen at physik.tu-chemnitz.de (Alexandra Bendixen) Date: Tue, 25 Apr 2017 23:00:40 +0200 Subject: [FieldTrip] PhD and Postdoc positions in multimodal perception and cognition at TU Chemnitz, Germany Message-ID: <9AABDCBE-073E-4DEA-8943-1F89C3474B21@physik.tu-chemnitz.de> Dear colleagues, The Cognitive Systems Lab (Alexandra Bendixen) and the Physics of Cognition Group (Wolfgang Einhäuser) at Chemnitz University of Technology (TU Chemnitz) invite applications for 2 PhD student positions 2 postdoctoral researcher positions starting October 1st, 2017. The application deadline for all positions is May 31st, 2017. PhD positions Two PhD positions are funded by the German Research Foundation (DFG) within the project "Multistable perception across modalities: Resolving sensory ambiguity in vision and audition". The PhD projects will concern multistable perceptual phenomena (e.g., binocular rivalry, auditory streaming) with a focus on objective methods to assess observers’ perception. Methods include advanced psychophysical methods, eye tracking and pupillometry, peripheral physiology, electroencephalography (EEG) as well as theoretical and computational modelling. Experience in one or more of these fields is a plus. Salary for the PhD positions is according to the German salary scale (E13 TV-L) at 65%. Positions are contingent on funding availability and limited to 3 years in accordance with the applicable regulations. Applicants for the PhD positions must hold a M.Sc. degree or equivalent in psychology, physics, cognitive science, neuroscience or a related field. If the M.Sc. degree is not completed at the time of application, a statement by the thesis supervisor must be included that confirms that the degree will be completed before October 2017. Application documents for PhD positions must include a complete CV, copies of transcripts of all academic institutions, a letter of motivation for the specific position, as well as the names and contact information of at least 1 and up to 3 references that could be contacted for information about the applicant. Postdoctoral positions We are looking for postdocs who are prepared to develop their own research profile in interaction with the groups’ research foci in visual, auditory and/or multimodal perception and cognition. The groups operate laboratories equipped with sound-attenuated measurement rooms, state-of-the-art devices for visual and auditory psychophysics, for high-precision and mobile eye tracking, for peripheral physiology and for EEG as well as ample computational resources. Salary for the postdoc positions is according to the German salary scale (E13 TV-L) at 100%. The positions are contingent on funding availability. The initial contract will be limited to 3 years. An extension is possible depending on funding availability, personal qualification and applicable regulatory restrictions. Successful applicants are expected to engage in teaching in the "Sensors and Cognitive Psychology" study program at TU Chemnitz. Non-German-speaking applicants are expected to acquire sufficient proficiency in German for teaching these courses within the first two years. Applicants for the postdoctoral positions must hold a PhD or equivalent in psychology, physics, cognitive science, neuroscience or a related field. If the PhD is not completed at the time of application, a statement by the thesis supervisor must be included that confirms that the degree will be awarded before October 2017. Applications must have a strong background (as demonstrated by peer-reviewed publications) in at least one of the following fields: advanced psychophysics, vision research, auditory research, eye tracking, peripheral physiology, or EEG. Good programming skills and good command of English are mandatory. Application documents for postdoctoral positions must include a complete CV, a list of publications, copies of transcripts of all academic institutions, a letter stating the motivation for the specific position, the plans and objectives for future research, as well as plans for teaching and career development. The applications should also include the names and contact information of at least 2 and up to 5 references that could be contacted for information about the applicant. More information and application process More information about the research of the two groups can be found at https://www.tu-chemnitz.de/physik/SFKS/index.html.en and https://www.tu-chemnitz.de/physik/PHKP/index.html.en For more information on the positions and on how to apply, please visit the legally binding German version of the job advertisements: postdoc positions: https://www.tu-chemnitz.de/verwaltung/personal/stellen/212066_1_Kae.php PhD positions: https://www.tu-chemnitz.de/verwaltung/personal/stellen/212066_2_Kae.php TU Chemnitz is an equal opportunity employer and aims at increasing the number of female scientists; qualified women are therefore especially encouraged to apply. Application documents should be sent as single pdf-file to bewerbung_sfks_phkp at tu-chemnitz.de no later than May 31st, 2017. For the PhD positions, the subject line must include the keyword MultMod2017, for postdoctoral positions subject line must include the keyword SFKSPHKP2017. Please feel free to contact us (alexandra.bendixen at physik.tu-chemnitz.de, wolfgang.einhaeuser-treyer at physik.tu-chemnitz.de) for further information. We would be grateful if you could distribute this e-mail to suitable candidates. With best regards, Wolfgang Einhäuser-Treyer & Alexandra Bendixen -- Prof. Dr. Alexandra Bendixen TU Chemnitz - Cognitive Systems Lab http://www.tu-chemnitz.de/physik/SFKS/ Prof. Dr. Wolfgang Einhäuser-Treyer TU Chemnitz - Physics of Cognition Group http://www.tu-chemnitz.de/physik/PHKP/ From delucia.marzia at gmail.com Wed Apr 26 11:49:06 2017 From: delucia.marzia at gmail.com (Marzia De Lucia) Date: Wed, 26 Apr 2017 09:49:06 +0000 Subject: [FieldTrip] postdoctoral position in Lausanne Message-ID: <243dc9ccd6b64680a285e41adb4ca0b2@EXPRD01.hosting.ru.nl> Dear all, Applications are invited for a postdoc position at the Laboratoire de Recherche en Neuroimagerie (LREN) financed by the Eurostars project ‘ComAlert’ in collaboration with g.tec (http://www.gtec.at/). The position is under the supervision of Dr Marzia De Lucia and in close collaboration with the Neurology service and the Department of Intensive Care Medicine at the Lausanne University Hospital (CHUV). The project aims at developing EEG based tests for outcome prediction in comatose patients and to assess the degree of preserved cognitive functions during acute coma and during later stages of disorders of consciousness. This project takes advantage of sophisticated software and hardware solution provided by gtec and specifically targeted for their application in the intensive care environment. The LREN (https://www.unil.ch/lren/en/home.html) provides an excellent multidisciplinary and interactive research environment combining expertise in functional magnetic resonance imaging, electroencephalography and neuroimaging methods development. The ideal candidate should have a PhD in Neuroscience, Life Science, Biomedical Engineering or related areas. Prior experience with EEG, programming skills and proficiency in English and in French are advantageous. The position is available from the 1st of July 2017 till June 2019. The salaries are in accordance with the Swiss Public service regulations. Applications including a CV, a statement of research interests and the name and full contact details of two referees should be sent to : delucia.marzia at gmail.com Best Regards, Marzia De Lucia ------------------------------------ Marzia DE LUCIA, MER PD Laboratoire de recherche en Neuroimagerie - LREN Département des Neurosciences Cliniques Centre Hospitalier Universitaire Vaudois MP16 05 559, Chemin de Mont-Paisible 16 , 1011 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: From tim.bardouille at Dal.Ca Thu Apr 27 00:33:58 2017 From: tim.bardouille at Dal.Ca (Timothy Bardouille) Date: Wed, 26 Apr 2017 22:33:58 +0000 Subject: [FieldTrip] Position in Halifax, NS, Canada: MEG Scientist Message-ID: Please distribute widely: MEG Scientist @ IWK Health Centre, Halifax, NS, Canada The MEG lab at the Biomedical Translational Imaging Centre (BIOTIC) in the IWK Health Centre, Halifax, NS, Canada is hiring for the position of MEG Scientist. The MEG Scientist will implement a neuroimaging research program and support our existing clinical program in MEG. You will be part of the growing BIOTIC team, will be supported by an Imaging Technician, and will work with collaborators in the region and abroad. Applicants will be expected to describe an independent research plan involving MEG and neuroimaging more broadly, and be committed to supporting our clinical program. The BIOTIC MEG lab, located in the region's leading research and teaching women and children's hospital, maintains research and clinical programs in both pediatric and adult populations. These ongoing commitments occur in collaboration with researchers at the regions' universities and clinicians in Neurology and Neurosurgery. The BIOTIC MEG lab also works with industry partners in the medical technology space to achieve their strategic goals through collaborative projects. Many researchers at BIOTIC maintain professional affiliation with Dalhousie University. Qualifications • PhD degree in Physics, Biomedical Engineering, Neuroscience or a research related field • Publication track record in neuroimaging • Literacy with MATLAB and/or Python based MEG analysis packages is required • Interested in multi-modal imaging is a plus • Strong technical ability with MEG hardware/software is a plus Start Date: ASAP Salary commensurate with experience BIOTIC is a multi-site imaging centre that is embedded in the two leading research and teaching hospitals in Nova Scotia. Our advanced pre-clinical and clinical imaging equipment are housed in three labs, in two health centres encompassing over 12,000 square feet of lab space. BIOTIC operates at the intersection of research, clinical care, and industry collaboration, offering a dynamic and multifaceted work experience. The team co-develops medical technologies and creates new imaging techniques and methods for diagnosing and monitoring treatment. With a population of over 400,000 people, Halifax is the capital city of Nova Scotia, Canada. Greater Halifax boasts 5 universities and the two largest academic health centres in Atlantic Canada. Founded in the mid-1700s as a British naval fortress, Halifax balances a vibrant downtown filled with museums, theatres and pubs, with beaches, hiking trails and parks (the IWK itself is a mere 600 meters from the ocean!), and also has daily flights to London-Heathrow, NYC, Chicago etc. For more information on Halifax, please see www.destinationhalifax.ca For more information, please contact Dr. Tim Bardouille at tim.bardouille at iwk.nshealth.ca. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Halifax MEG Scientist.pdf Type: application/pdf Size: 134587 bytes Desc: Halifax MEG Scientist.pdf URL: From elam4hcp at gmail.com Thu Apr 27 19:17:04 2017 From: elam4hcp at gmail.com (Jennifer Elam) Date: Thu, 27 Apr 2017 12:17:04 -0500 Subject: [FieldTrip] Last weeks to register for HCP Course 2017 Message-ID: It's not too late to register for the 2017 HCP Course: "Exploring the Human Connectome" , to be held June 19-23 at the Djavad Mowafagian Centre for Brain Health at University of British Columbia (UBC) in Vancouver, BC, Canada! Fieldtrip tools play a major part of the HCP MEG processing pipelines and have been critical to the high quality processing of the project's 95 released MEG/MRI imaging datasets. Spaces for the course are limited and registration is on a first come, first served basis. May 17, 2017 is the deadline to reserve discounted UBC accommodations within walking distance to the course venue: https://reserve.ubcconferences.com/vancouver/availability.asp?hotelCode=%2A&startDate=06%2F16%2F2017&endDate=06%2F24%2F2017&adults=1&children=&rooms=1&requesttype=invBlockCode&code=G170618A The 5-day intensive HCP course is a great opportunity to learn directly from HCP investigators and designed for those interested in: - using data collected and distributed from the HCP young adult study - acquiring and analyzing HCP-style imaging and behavioral data at your own institution - processing your own non-HCP data using HCP pipelines and methods - using Connectome Workbench tools and sharing data using the BALSA imaging database - learning HCP multimodal neuroimaging analysis methods, including those that combine MEG and MRI data - exploring the HCP MMP 1.0 multimodal parcellation brain map and learning about how it can be used in your analyses - positioning yourself to capitalize on HCP-style data being distributed by the Connectome Coordinating Facility (CCF) from HCP development (healthy subjects ages 5-21) and aging (healthy subjects ages 35-90+) and Connectomes Related to Human Disease projects See https://store.humanconnectome.org/courses/2017/exploring-the-human-connectome.php for more info. If you have any questions, please contact us at: hcpcourse at humanconnectome.org We look forward to seeing you in Vancouver! Best, 2017 HCP Course Staff -------------- next part -------------- An HTML attachment was scrubbed... URL: From tim.bardouille at Dal.Ca Thu Apr 27 23:31:21 2017 From: tim.bardouille at Dal.Ca (Timothy Bardouille) Date: Thu, 27 Apr 2017 21:31:21 +0000 Subject: [FieldTrip] Position in Halifax, NS, Canada: MEG Scientist - application link added Message-ID: <72288243-FDB2-4D9F-A1EA-F3890D37937C@dal.ca> Hi all, Sorry for the second e-mail. I’m including the link to apply online this time. If interested in a primary position at the MEG lab in Halifax, please apply at this link: https://jobs.nshealth.ca/job/Halifax-MEG-Scientist-Nova-B3K-6R8/354454217/?locale=en_US Best regards, Tim. From: Timothy Bardouille Date: Wednesday, April 26, 2017 at 3:16 PM To: Discussion list for international MEG community Subject: Position in Halifax, NS: MEG Scientist Please distribute widely: MEG Scientist @ IWK Health Centre, Halifax, NS, Canada The MEG lab at the Biomedical Translational Imaging Centre (BIOTIC) in the IWK Health Centre, Halifax, NS, Canada is hiring for the position of MEG Scientist. The MEG Scientist will implement a neuroimaging research program and support our existing clinical program in MEG. You will be part of the growing BIOTIC team, will be supported by an Imaging Technician, and will work with collaborators in the region and abroad. Applicants will be expected to describe an independent research plan involving MEG and neuroimaging more broadly, and be committed to supporting our clinical program. The BIOTIC MEG lab, located in the region's leading research and teaching women and children's hospital, maintains research and clinical programs in both pediatric and adult populations. These ongoing commitments occur in collaboration with researchers at the regions' universities and clinicians in Neurology and Neurosurgery. The BIOTIC MEG lab also works with industry partners in the medical technology space to achieve their strategic goals through collaborative projects. Many researchers at BIOTIC maintain professional affiliation with Dalhousie University. Qualifications • PhD degree in Physics, Biomedical Engineering, Neuroscience or a research related field • Publication track record in neuroimaging • Literacy with MATLAB and/or Python based MEG analysis packages is required • Interested in multi-modal imaging is a plus • Strong technical ability with MEG hardware/software is a plus Start Date: ASAP Salary commensurate with experience BIOTIC is a multi-site imaging centre that is embedded in the two leading research and teaching hospitals in Nova Scotia. Our advanced pre-clinical and clinical imaging equipment are housed in three labs, in two health centres encompassing over 12,000 square feet of lab space. BIOTIC operates at the intersection of research, clinical care, and industry collaboration, offering a dynamic and multifaceted work experience. The team co-develops medical technologies and creates new imaging techniques and methods for diagnosing and monitoring treatment. With a population of over 400,000 people, Halifax is the capital city of Nova Scotia, Canada. Greater Halifax boasts 5 universities and the two largest academic health centres in Atlantic Canada. Founded in the mid-1700s as a British naval fortress, Halifax balances a vibrant downtown filled with museums, theatres and pubs, with beaches, hiking trails and parks (the IWK itself is a mere 600 meters from the ocean!), and also has daily flights to London-Heathrow, NYC, Chicago etc. For more information on Halifax, please see www.destinationhalifax.ca For more information, please contact Dr. Tim Bardouille at tim.bardouille at iwk.nshealth.ca. -------------- next part -------------- An HTML attachment was scrubbed... URL: