From jan.schoffelen at donders.ru.nl Tue May 1 10:49:44 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 1 May 2018 08:49:44 +0000 Subject: [FieldTrip] ft_freqanalysis fourier rpttap to rpt conversion? In-Reply-To: References: Message-ID: <92BEAED0-FD4D-44E5-80A3-81F63803596D@donders.ru.nl> Hi John, Yes, it is forced as a preventive measure. Averaging Fourier coefficients across tapers is not allowed. Best wishes, Jan-Mathijs On 27 Apr 2018, at 05:13, John Nguyen > wrote: Hi, I noticed that it's not an option to remove the tapers if the output is "fourier". Is this because the resulting output won't be a true Fourier if the tapers are removed, and is forced as a preventive measure? I was looking to reduce my fourier size by removing the tapers but not the trials, is there a danger to this? Thank you! John Nguyen _______________________________________________ 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 bioeng.yoosofzadeh at gmail.com Wed May 2 00:00:51 2018 From: bioeng.yoosofzadeh at gmail.com (bioeng.yoosofzadeh at gmail.com) Date: Tue, 1 May 2018 17:00:51 -0500 Subject: [FieldTrip] Issue in realigning MRI Message-ID: <038601d3e197$decb8ef0$9c62acd0$@gmail.com> Dear FT experts, I am not able to realign a T1 scan using the fiducial points and headshapes of a 4D/BTI system, can anyone help me on this? The "interactive" realignment helped a lot, but the end result was not perfect! Here's what I have tried,: individual_mri = ft_read_mri(mripath); % ..\MEG_4D\C-101_T1.nii ft_sourceplot([], individual_mri); cfg = []; cfg.method = 'flip'; mri.coordsys = '4d'; individual_mri = ft_volumereslice(cfg, individual_mri); ft_sourceplot([], individual_mri); individual_mri = ft_convert_units(individual_mri, 'm'); headshape = ft_read_headshape(headpath); % ..\MEG_4D\hs_file mri_fids = headshape.fid.pos; cfg = []; cfg.fiducial.nas = mri_fids(1,:); cfg.fiducial.lpa = mri_fids(2,:); cfg.fiducial.rpa = mri_fids(3,:); cfg.coordsys = '4d'; cfg.method = 'fiducial'; mri_realigned = ft_volumerealign(cfg, individual_mri); cfg = []; cfg.coordsys = '4d'; cfg.headshape = headshape; cfg.method = 'headshape'; mri_realigned = ft_volumerealign(cfg, individual_mri); % check that the MRI is consistent after realignment ft_determine_coordsys(mri_realigned, 'interactive', 'no'); hold on; drawnow; ft_plot_headshape(headshape); Data can be found at, https://www.dropbox.com/sh/e74pt2uc08q6z4q/AAB3fkp_9gvJxi-YtO0muRSca?dl=0 Best, Vahab -------------- next part -------------- An HTML attachment was scrubbed... URL: From acskwara at ucdavis.edu Wed May 2 04:05:21 2018 From: acskwara at ucdavis.edu (Alea Skwara) Date: Tue, 1 May 2018 19:05:21 -0700 Subject: [FieldTrip] Outputting band averages with ft_freqanalysis Message-ID: Hi All, I am attempting to output averages within frequency bands using ft_freqanalysis. I have implemented the two-step solution provided in this discussion https://mailman.science.ru.nl/pipermail/fieldtrip/2016-October/010984.html resulting in the following code: cfg =[]; cfg.method = 'mtmfft'; cfg.output = 'pow'; cfg.taper = 'hanning'; cfg.channel = 'all'; cfg.foilim = [fio1 foi2]; cfg.trials = 'all'; cfg.keeptrials = 'no'; freq_avg = ft_freqanalysis(cfg, data_segmented); cfg = []; cfg.avgoverfreq = 'yes'; freq_avg = ft_freqanalysis(cfg, freq_avg); However, when I run this, I get the following error: the input is freq data with 73 channels, 41 frequencybins and no timebins Error using ft_checkdata>freq2raw (line 1315) not supported for dimord chan_freq Error in ft_checkdata (line 432) data = freq2raw(data); Error in ft_freqanalysis (line 217) data = ft_checkdata(data, 'datatype', {'raw', 'raw+comp', 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); Is there a different way I need to format my data beyond providing the function with the output of the first iteration of ft_freqanalysis? Thank you! Alea -- Alea C. Skwara, M.A. PhD Candidate | Saron Lab http://saronlab.ucdavis.edu/ Center for Mind and Brain | University of California, Davis 267 Cousteau Place | Davis CA 95616 Cell: (828) 273-8595 -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Wed May 2 04:33:05 2018 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Tue, 1 May 2018 19:33:05 -0700 Subject: [FieldTrip] Outputting band averages with ft_freqanalysis In-Reply-To: References: Message-ID: Hi Alea, Have a look at ft_selectdata, which can do this operation for you. Arjen On Tue, May 1, 2018 at 7:05 PM, Alea Skwara wrote: > Hi All, > > I am attempting to output averages within frequency bands using > ft_freqanalysis. I have implemented the two-step solution provided in this > discussion https://mailman.science.ru.nl/pipermail/ > fieldtrip/2016-October/010984.html > resulting in the following code: > > cfg =[]; > cfg.method = 'mtmfft'; > cfg.output = 'pow'; > cfg.taper = 'hanning'; > cfg.channel = 'all'; > cfg.foilim = [fio1 foi2]; > cfg.trials = 'all'; > cfg.keeptrials = 'no'; > freq_avg = ft_freqanalysis(cfg, data_segmented); > > cfg = []; > cfg.avgoverfreq = 'yes'; > freq_avg = ft_freqanalysis(cfg, freq_avg); > > However, when I run this, I get the following error: > > the input is freq data with 73 channels, 41 frequencybins and no timebins > Error using ft_checkdata>freq2raw (line 1315) > not supported for dimord chan_freq > > Error in ft_checkdata (line 432) > data = freq2raw(data); > > Error in ft_freqanalysis (line 217) > data = ft_checkdata(data, 'datatype', {'raw', 'raw+comp', 'mvar'}, > 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); > > > Is there a different way I need to format my data beyond providing the > function with the output of the first iteration of ft_freqanalysis? > > Thank you! > Alea > > -- > Alea C. Skwara, M.A. > PhD Candidate | Saron Lab > http://saronlab.ucdavis.edu/ > > Center for Mind and Brain | University of California, Davis > 267 Cousteau Place | Davis CA 95616 > Cell: (828) 273-8595 > > > > _______________________________________________ > 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 acskwara at ucdavis.edu Wed May 2 19:35:47 2018 From: acskwara at ucdavis.edu (Alea Skwara) Date: Wed, 2 May 2018 10:35:47 -0700 Subject: [FieldTrip] Outputting band averages with ft_freqanalysis In-Reply-To: References: Message-ID: Hi Arjen, Thank you, following ft_freqanalysis with ft_selectdata (and using the .avgoverfreq = 'yes') works. Alea On Tue, May 1, 2018 at 7:33 PM, Arjen Stolk wrote: > Hi Alea, > > Have a look at ft_selectdata, which can do this operation for you. > > Arjen > > > On Tue, May 1, 2018 at 7:05 PM, Alea Skwara wrote: > >> Hi All, >> >> I am attempting to output averages within frequency bands using >> ft_freqanalysis. I have implemented the two-step solution provided in this >> discussion https://mailman.science.ru.nl/pipermail/fieldtrip >> /2016-October/010984.html >> resulting in the following code: >> >> cfg =[]; >> cfg.method = 'mtmfft'; >> cfg.output = 'pow'; >> cfg.taper = 'hanning'; >> cfg.channel = 'all'; >> cfg.foilim = [fio1 foi2]; >> cfg.trials = 'all'; >> cfg.keeptrials = 'no'; >> freq_avg = ft_freqanalysis(cfg, data_segmented); >> >> cfg = []; >> cfg.avgoverfreq = 'yes'; >> freq_avg = ft_freqanalysis(cfg, freq_avg); >> >> However, when I run this, I get the following error: >> >> the input is freq data with 73 channels, 41 frequencybins and no timebins >> Error using ft_checkdata>freq2raw (line 1315) >> not supported for dimord chan_freq >> >> Error in ft_checkdata (line 432) >> data = freq2raw(data); >> >> Error in ft_freqanalysis (line 217) >> data = ft_checkdata(data, 'datatype', {'raw', 'raw+comp', 'mvar'}, >> 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); >> >> >> Is there a different way I need to format my data beyond providing the >> function with the output of the first iteration of ft_freqanalysis? >> >> Thank you! >> Alea >> >> -- >> Alea C. Skwara, M.A. >> PhD Candidate | Saron Lab >> http://saronlab.ucdavis.edu/ >> >> Center for Mind and Brain | University of California, Davis >> 267 Cousteau Place | Davis CA 95616 >> Cell: (828) 273-8595 >> >> >> >> _______________________________________________ >> 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 > -- Alea C. Skwara, M.A. PhD Candidate | Saron Lab http://saronlab.ucdavis.edu/ Center for Mind and Brain | University of California, Davis 267 Cousteau Place | Davis CA 95616 Cell: (828) 273-8595 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcarlapiastra at gmail.com Thu May 3 15:29:22 2018 From: mcarlapiastra at gmail.com (Maria Carla Piastra) Date: Thu, 3 May 2018 15:29:22 +0200 Subject: [FieldTrip] openMEEG path Ubuntu16.04 Message-ID: <874cead0-9c9b-6c0f-7430-554f9af9863d@gmail.com> Dear all, I would like to use openMEEG for computing EEG and MEG forward model solutions on Ubuntu 16.04. I installed following https://github.com/openmeeg/openmeeg. As "/whereis om_assemble/" is giving me /usr/bin. I therefore did "/setenv('PATH', '/usr/bin')/". /W/hen I am launching: /cfg = [];// //cfg.method = 'openmeeg';// //cfg.conductivity = [0.33 0.01 0.33];// //headmodel_bem = ft_prepare_headmodel(cfg, mesh_bem)/ This is the output: /the input is mesh data with multiple surfaces// //reordering the boundaries to: 3 2 1 // ///bin/bash: chmod: command not found// ///bin/bash: ./tp2279842c_636c_485a_ac62_6c2e3c4e7b25.sh: Permission denied// //Warning: an error ocurred while running OpenMEEG // //Error using fread// //Invalid file identifier. Use fopen to generate a valid file identifier.// //Warning: File 'tp54b47429_45d4_47c4_ab6f_3a02b37de78f.bin' not found. // //Warning: File 'tp692ddbba_6d12_4b31_b1ee_f70fc7680936.bin' not found. // //the call to "ft_prepare_headmodel" took 0 seconds and required the additional allocation of an estimated 0 MB// // //headmodel_bem = // // //             bnd: [1x3 struct]// //            cond: [0.3300 0.0100 0.3300]// //    skin_surface: 1// //          source: 3// //            type: 'openmeeg'// //            unit: 'mm'// //             cfg: [1x1 struct]/ Any ideas? Best, Maria Carla -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Thu May 3 17:05:12 2018 From: michelic72 at gmail.com (Cristiano Micheli) Date: Thu, 3 May 2018 17:05:12 +0200 Subject: [FieldTrip] openMEEG path Ubuntu16.04 In-Reply-To: <874cead0-9c9b-6c0f-7430-554f9af9863d@gmail.com> References: <874cead0-9c9b-6c0f-7430-554f9af9863d@gmail.com> Message-ID: Dear Maria Carla it seems that you do not have permissions to write in your temporary files folder. As a consequence the shell file which is called to execute the OpenMEEG commands is not written and cannot be executed. I hope this helps Cris Micheli @MindAffect NovioTech Campus Nijmegen The Netherlands On Thu, May 3, 2018 at 3:29 PM, Maria Carla Piastra wrote: > Dear all, > > I would like to use openMEEG for computing EEG and MEG forward model > solutions on Ubuntu 16.04. > > I installed following https://github.com/openmeeg/openmeeg. > > As "*whereis om_assemble*" is giving me /usr/bin. I therefore did "*setenv('PATH', > '/usr/bin')*". > *W*hen I am launching: > *cfg = [];* > *cfg.method = 'openmeeg';* > *cfg.conductivity = [0.33 0.01 0.33];* > *headmodel_bem = ft_prepare_headmodel(cfg, mesh_bem)* > > This is the output: > > *the input is mesh data with multiple surfaces* > *reordering the boundaries to: 3 2 1 * > */bin/bash: chmod: command not found* > */bin/bash: ./tp2279842c_636c_485a_ac62_6c2e3c4e7b25.sh: Permission denied* > *Warning: an error ocurred while running OpenMEEG * > *Error using fread* > *Invalid file identifier. Use fopen to generate a valid file identifier.* > *Warning: File 'tp54b47429_45d4_47c4_ab6f_3a02b37de78f.bin' not found. * > *Warning: File 'tp692ddbba_6d12_4b31_b1ee_f70fc7680936.bin' not found. * > *the call to "ft_prepare_headmodel" took 0 seconds and required the > additional allocation of an estimated 0 MB* > > *headmodel_bem = * > > * bnd: [1x3 struct]* > * cond: [0.3300 0.0100 0.3300]* > * skin_surface: 1* > * source: 3* > * type: 'openmeeg'* > * unit: 'mm'* > * cfg: [1x1 struct]* > > > Any ideas? > > Best, > > Maria Carla > > _______________________________________________ > 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 christoph.kayser at uni-bielefeld.de Fri May 4 08:41:22 2018 From: christoph.kayser at uni-bielefeld.de (Christoph Kayser) Date: Fri, 04 May 2018 08:41:22 +0200 Subject: [FieldTrip] PostDoc & PhD Position, Cognitive Neuroscience, Bielefeld, Germany Message-ID: <00d601d3e372$ea9b9cc0$bfd2d640$@uni-bielefeld.de> The Department of Cognitive Neuroscience at Bielefeld University, Germany, is advertising a 3-year Postdoctoral position, and a 3-year PhD position in auditory and multisensory neuroimaging studies. We are looking to fill two positions to complement our research on auditory and multisensory perception based on a combination of psychophysics, neuroimaging (EEG) and statistical modelling. The Department for Cognitive Neuroscience is dedicated to understanding the integration of sensory information in the brain. Our studies use state of the art EEG imaging, combined with eyetracking, psychophysical paradigms, and substantive quantitative data analysis to better understand when and how the brain transforms sensory information into a conscious percept. Further details about our research can be found here http://www.uni-bielefeld.de/biologie/cns/ The positions involve all aspects of study design, implementation, data collection, data analysis and the write up of results. Contributions to the supervision of student projects or the preparation of practical courses are also expected. Applicants should have a background in neuroscience, cognitive science, psychology, mathematics, or a relevant discipline. Applicants for the post-doc position should have a doctoral degree or equivalent title. We are especially interested in devotion to advanced quantitative data analysis including the capabilities to program or modify analysis code. The ideal applicant will have a strong analytical background and direct experience using MATLAB. Applicants should have enthusiasm, and a clear, demonstrable capacity for acquiring expertise in these techniques. The positions are funded for 3 years starting ideally around September 2018, at Germany salary grades TV-L E13 (100% for post-doc, 65% for PhD student). Interested candidates please contact Christoph Kayser -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.rimmele at ae.mpg.de Wed May 2 10:48:03 2018 From: johanna.rimmele at ae.mpg.de (Rimmele, Johanna Maria) Date: Wed, 2 May 2018 08:48:03 +0000 Subject: [FieldTrip] PhD position on auditory timing in speech and music at MPIEA Frankfurt Message-ID: <63B92215-CA68-49D2-8E1D-C629CF949609@ae.mpg.de> Dear all, We are currently looking for an excellent candidate for a 3 year Ph.D. position in the Neuroscience Department at the MPI for Empirical Aesthetics in Frankfurt am Main. This is a chance to work in a relentlessly interdisciplinary and exciting place. The project focuses on auditory timing in speech and music using behavioral and neurophysiological measures. For details visit our homepage: https://www.aesthetics.mpg.de/en/the-institute/jobs/phd-position-neuroscience-department.html Please forward this info to interested and skilled candidates or people that might know suitable candidates! Many thanks! All the Best, Johanna _______ Dr. Johanna Rimmele Max-Planck-Institute for Empirical Aesthetics Department of Neuroscience Grüneburgweg 14 D-60322 Frankfurt am Main Phone: +49 69 8300479 323 j.rimmele at aesthetics.mpg.de www.aesthetics.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdhami06 at gmail.com Tue May 8 11:05:54 2018 From: pdhami06 at gmail.com (Paul Dhami) Date: Tue, 8 May 2018 05:05:54 -0400 Subject: [FieldTrip] requested data segment extends over a discontinuous trial boundary Message-ID: Hi FieldTrip, my name is Paul, and I'm a student studying response inhibition in psychiatric disorders, as well as working with corresponding TMS-EEG data. I was able to go through the analysis pipeline just fine with some ERP data (preprocessed before imported to FieldTrip), but when using essentially the same steps for some TMS-EEG data (also preprocessed before being imported into FieldTrip), I ran into the following error at the ft_preprocessing(cfg) command: Error using ft_read_data (line 270) > requested data segment extends over a discontinuous trial boundary > Error in ft_preprocessing (line 582) > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', > begsample, 'endsample', > endsample, 'chanindx', rawindx, 'checkboundary', > strcmp(cfg.continuous, 'no'), > 'dataformat', cfg.dataformat); My cfg that I entered with ft_preprocessing looked like this (altered the filename just for this email): dataset: 'subject1.set' > trialdef: [1×1 struct] > trackusage: 'B8F919AB' > trackconfig: 'off' > checkconfig: 'loose' > checksize: 100000 > showcallinfo: 'yes' > debug: 'no' > outputfilepresent: 'overwrite' > trackcallinfo: 'yes' > trackdatainfo: 'no' > toolbox: [1×1 struct] > notification: [1×1 struct] > progress: [1×1 struct] > callinfo: [1×1 struct] > version: [1×1 struct] > datafile: 'subject1.set' > headerfile: 'subject1.set' > dataformat: 'eeglab_set' > headerformat: 'eeglab_set' > trialfun: @ft_trialfun_general > event: [1×151 struct] > trl: [75×4 double] > Prior code to ft_preprocessing was: cfg = []; > > % adding dataset field to configuration file > cfg.dataset = [myfilepath '/' myfilename]; > %cfg.dataset = 'filename.set' > % adding trialdef information to configuration file > cfg.trialdef.eventtype = 'trigger'; > cfg.trialdef.eventvalue = 128; % TMS trigger > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 0.999; Is there something that I am doing wrong as to why the ERP files were able to be preprocessed just fine where as I am running into this error for the TMS-EEG data? Is this likely related to the TMS-EEG data having been collected in a "pseudo-continuous" manner, and in that case, is it as easy as including the cfg.continuous = 'yes' option (which I noted in a couple similar forum posts)? Any help would be greatly appreciated. Thank you. Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue May 8 15:28:25 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 8 May 2018 15:28:25 +0200 Subject: [FieldTrip] EEG/iEEG/MEG - short survey on data formats you use Message-ID: <44D7960D-DC95-4A7D-975C-3A6F68874F37@donders.ru.nl> Dear colleagues, Several members of the electrophysiology community (EEG, MEG, iEEG) are working on an open specification for storing cognitive electrophysiology data, called the Brain Imaging Data Structure . Its goal is to make our workflows more reproducible, more sharable, and more efficient. The BIDS format is not a new data format, but is a data specification. It should accommodate pre-existing workflows in cognitive neuroscience. As such, we are investigating what data formats researchers use already, and which they'd be willing to use for sharing their data. Please respond to this short (3 question, ~2 minute) survey at the link below, in order to share with us which data formats you currently use in your electrophysiological research. https://goo.gl/forms/Ytr6UmawWvwvIB9R2 If you know of any other interested parties in the cognitive electrophysiology community, please do forward along this link so that we can get a sample from as many people as possible. Thanks very much for your time! Robert, Chris, Cyril, Dora and others -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue May 8 16:53:21 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 8 May 2018 16:53:21 +0200 Subject: [FieldTrip] plot ft_sourceplot figures into a subplot In-Reply-To: References: Message-ID: Dear Hame ft_sourceplot is a high-level function that includes interaction with the data (i.e. clicking). Furthermore, depending on method (ortho/surface/montage/glassbrain/cloud) you will get one or mutliple sub-axes within one figure. So it is not suited for use in a loop with multiple axes or subplots. I know that people are using it to export images to pdf/ps or ai format and then use external software to glue them together. I also find it convenient to save the figures to a bitmap using “print -dpng” and use external software (such as Windows picture viewer) to browse through large numbers of files. I believe this is also mentioned somewhere on http://www.fieldtriptoolbox.org/tutorial/plotting If you want closer control over the figures and different axes within one figure, I recommend you use the lower-level plotting functions that you can find in fieldtrip/plotting. E.g. ft_plot_mesh , which you can give the mesh and the colors you want on each of the vertices or triangles. See also http://www.fieldtriptoolbox.org/reference#from_the_plotting_module best regards, Robert PS please use the fieldtrip mailing list next time, there are many people on it that can help, and providing answers on the list benefits others as well > On 27 Apr 2018, at 14:20, Hame Park wrote: > > Dear Robert > > Hello! > I was trying to make a big figure with many > sourceplots, created from ft_sourceplot with the 'surface' method, > but it seems it always creates a separate figure. > > I tried something like > > h = figure; > ha = nan(length(T), 1); > for t=1:length(T) > ha(t) = subplot(1, length(T), t); > end > > for t=1:length(T) > axes(ha(t)) > ft_sourceplot(cfg, data) > end > > but it still opens up a new figure for ft_sourceplot. > I tried to look into the code, and tried disabling the line > h=figure; but this gave me errors which I couldn't comprehend. > > Any help would be much appreciated! > > Thank you. > Best wishes, > Hame -------------- next part -------------- An HTML attachment was scrubbed... URL: From hame.hame.hame at gmail.com Tue May 8 17:40:16 2018 From: hame.hame.hame at gmail.com (Hame Park) Date: Tue, 8 May 2018 17:40:16 +0200 Subject: [FieldTrip] plot ft_sourceplot figures into a subplot In-Reply-To: References: Message-ID: Dear Robert Thank you! Best regards, Hame On Tue, May 8, 2018 at 4:53 PM, Robert Oostenveld < r.oostenveld at donders.ru.nl> wrote: > Dear Hame > > ft_sourceplot is a high-level function that includes interaction with the > data (i.e. clicking). Furthermore, depending on method > (ortho/surface/montage/glassbrain/cloud) you will get one or mutliple > sub-axes within one figure. So it is not suited for use in a loop with > multiple axes or subplots. > > I know that people are using it to export images to pdf/ps or ai format > and then use external software to glue them together. I also find it > convenient to save the figures to a bitmap using “print -dpng” and use > external software (such as Windows picture viewer) to browse through large > numbers of files. I believe this is also mentioned somewhere on > http://www.fieldtriptoolbox.org/tutorial/plotting > > If you want closer control over the figures and different axes within one > figure, I recommend you use the lower-level plotting functions that you can > find in fieldtrip/plotting. E.g. ft_plot_mesh > , which you can > give the mesh and the colors you want on each of the vertices or triangles. > See also http://www.fieldtriptoolbox.org/reference#from_the_plotting_ > module > > > best regards, > Robert > > PS please use the fieldtrip mailing list next time, there are many people > on it that can help, and providing answers on the list benefits others as > well > > > On 27 Apr 2018, at 14:20, Hame Park wrote: > > Dear Robert > > Hello! > I was trying to make a big figure with many > sourceplots, created from ft_sourceplot with the 'surface' method, > but it seems it always creates a separate figure. > > I tried something like > > h = figure; > ha = nan(length(T), 1); > for t=1:length(T) > ha(t) = subplot(1, length(T), t); > end > > for t=1:length(T) > axes(ha(t)) > ft_sourceplot(cfg, data) > end > > but it still opens up a new figure for ft_sourceplot. > I tried to look into the code, and tried disabling the line > h=figure; but this gave me errors which I couldn't comprehend. > > Any help would be much appreciated! > > Thank you. > Best wishes, > Hame > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.Hanslmayr at bham.ac.uk Wed May 9 14:50:12 2018 From: S.Hanslmayr at bham.ac.uk (Simon Hanslmayr) Date: Wed, 9 May 2018 12:50:12 +0000 Subject: [FieldTrip] PhD position in Birmingham Message-ID: <257F6C65A372A04CA41056EACC0DE7CED874ABCE@EX12.adf.bham.ac.uk> To anyone looking for a PhD position, Applications are sought for a fully-funded PhD position to work with Dr Simon Hanslmayr (University of Birmingham, School of Psychology, http://www.memorybham.com/people/#/simon-hanslmayr/). The project is focussed on generating computational models to simulate single-neuron responses and neural oscillations in the service of memory processes. The work will build on a theoretical framework, termed the Synch/deSync Model which assumes that memory processes are implemented via cortical desynchronization and hippocampal synchronization processes (see Parish et al., 2018). The PhD student will have the opportunity to work with single-unit and EEG data recorded from the human hippocampus in patients suffering from epilepsy. The candidate should have a strong background in computational neuroscience or related area. Apply for this post by sending an email with your CV and a short description (100 words) outlining your skills and motivation to Sophie Watson (Sophie Watson S.Watson.2 at bham.ac.uk). https://www.findaphd.com/search/ProjectDetails.aspx?PJID=97892 Dr. Simon Hanslmayr Reader in Cognitive Neuroscience Royal Society Wolfson Research Merit Award Holder School of Psychology Hills Building 2.37 University of Birmingham Edgbaston Birmingham B15 2TT UK Tel +44 121 4146203 http://www.memorybham.com/people/#/simon-hanslmayr/ [http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 8560 bytes Desc: image001.gif URL: From SSaleh at kesslerfoundation.org Wed May 9 16:29:19 2018 From: SSaleh at kesslerfoundation.org (Soha Saleh - Research Scientist) Date: Wed, 9 May 2018 14:29:19 +0000 Subject: [FieldTrip] Postdoctoral Fellowship in Neurorehabilitation and Neuroimaging Research - Kessler Foundation Message-ID: <92143A403B96384DB97C1AF41F645AD92397BBC9@EXCHANGE.kmrrec.org> Dear all, The Kessler Foundation (West Orange, New Jersey) is recruiting postdoctoral fellows to conduct Neurorehabilitation and Neuroimaging Research. Applications are being accepted for fellowships funded by an Advanced Rehabilitation Research Training (ARRT) grant from the National Institute on Disability and Rehabilitation Research (NIDILRR), and are expected to last for a two-year term. Qualifying candidates must have an earned doctorate in engineering (e.g., biomedical, rehabilitation mechanical), neuroscience, or a related field. Strong candidates will have prior experience in performing neuroimaging research studies in human subjects, as well as some history of publication and presentation of original research. The successful candidate will work on ongoing research that uses neuroimaging to better understand motor related impairment following neurological, neuromuscular and musculoskeletal diseases and injuries, for diverse patient populations including traumatic brain injury, multiple sclerosis, spinal cord injury, cancer, and stroke. To this end, our research uses a multimodality approach that includes neuroimaging (fMRI, MRI, fNIRS, EEG) combined with eye tracking, electrophysiology analysis, and motion analysis. The Kessler Foundation has research-dedicated 3 Tesla MRI scanner, state-of-the-art mobile imaging equipment (EEG, fNIRS), instrumented treadmill with virtual reality (C-Mill), Neurocom Balance Platform, biodex, and is a leader in powered exoskeleton assisted rehabilitation therapy. The successful applicant will also be expected to develop his/her own mentored research project. He/she will work on various aspects of research projects from inception (e.g., study formulation, grant-writing, etc.), through dissemination (conference presentation and manuscript publication). Requirements include: * Background and experience in functional and/or structural MRI image processing (DTI, fMRI), and ideally connectivity analysis (resting state functional connectivity, effective connectivity, graph theory-based analysis) * Experience in programming, preferentially Matlab * Knowledge of statistical data analysis * Excellent written communication skills Preferred experience/qualifications: * Research studies in human subjects, and history of publication and presentation of original research * EEG/EMG/fNIRS data collection and analysis * Biomedical Instrumentation * Neuromuscular rehabilitation; brain and muscle electrophysiology * Image-processing software such as FSL, AFNI, SPM, EEGLAB, Brainstorm Opportunities for collaborating with clinicians on existing or future clinical research are also available. All fellows participate in an extensive training curriculum and didactic offerings. Multidisciplinary mentored training opportunities are individually tailored to achieve specific goals considering each fellow's prior background and interests. Kessler Foundation is a public charity that advances its mission of improving the lives of people with disabilities through research and grant-making programs. The Kessler Foundation is a global leader in medical rehabilitation research and affiliated with the renowned Kessler Institute for Rehabilitation in West Orange, New Jersey and enjoys collaborations with partners at the New Jersey Institute of Technology and Rutgers New Jersey Medical School (RNJMS), Rutgers University in New Jersey. Applicants are encouraged to visit the Foundation's website (http://www.kesslerfoundation.org/research/) to learn about the missions, activities, and resources of the Foundation and its laboratories. Administration of the ARRT fellowships occurs within the academic Department of Physical Medicine and Rehabilitation at RNJMS. As such, fellows enjoy the benefits and academic resources available to all post-doctoral fellows at the Medical School. Fellows may also be recommended for an academic appointment at the rank of Instructor. Initial and informal inquiries about the fellowship may be directed by email to Guang Yue, Ph.D. ARRT Project Director, Kessler Foundation, and Professor at RNJMS GYue at kesslerfoundation.org Applicants for fellowships should refer to the "Neuro-Musculoskeletal Fellowship" and forward * Letter of application * Curriculum Vitae * One-page statement of research interests by email to: career at kesslerfoundation.org or by mail to: Kessler Foundation, Attn: Human Resources 120 Eagle Rock Ave, Suite 100 East Hanover, NJ 07936 Letters of recommendation: At the time of application, candidates should request letters of recommendation from three current or former professional associates to be mailed to the Project Director (address above). Alternatively, applicants may enclose sealed letters of recommendation with mailed applications. Due to limitations in resources, we regret that only candidates whose applications are brought forward by the fellowship committee will be contacted. In addition to citizens and permanent residents of the US, non-citizen nationals, and non-immigrants are eligible to apply provided they can be lawfully employed in the U.S. Thanks, Soha -------------------------------------------------------------------------- Soha Saleh, PhD Research Scientist Human Performance and Engineering Lab Kessler Foundation 1199 Pleasant Valley Way, West Orange, NJ, 07052 Tel: (973) 324 3520 Email: ssaleh at KesslerFoundation.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From mansoureh.aghabeig at yahoo.com Wed May 9 21:19:53 2018 From: mansoureh.aghabeig at yahoo.com (Mansoureh Aghabeig) Date: Wed, 9 May 2018 19:19:53 +0000 (UTC) Subject: [FieldTrip] How can I fix the "the 1/f power spectrum effect" in fieldtrip References: <280532632.1686057.1525893593539.ref@mail.yahoo.com> Message-ID: <280532632.1686057.1525893593539@mail.yahoo.com> Dear Sir/Madam, My name is Mansoureh Aghabeig and I am working in the ICNT lab in Torun, Poland as a Ph.D. student. Currently, I am working on time-frequency analysis with fieldtrip . But I obtained very strange TFR results. Please find the attachment. It is clear in the attached plot the lower frequencies dominate the higher one. In fact, there is the 1/f power spectrum effect. I think one solution for solving this problem is normalizing over power spectrum but I do not know how can I do it in fieldtrip . I would be appreciated if you kindly guide me. Thanks in advance Mansoureh Aghabeig        منصوره آقابیگ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: E124.jpg Type: image/jpeg Size: 32087 bytes Desc: not available URL: From r.oostenveld at donders.ru.nl Thu May 10 09:43:10 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 10 May 2018 09:43:10 +0200 Subject: [FieldTrip] Donders Brain Stimulation Toolkit in Sept 2018 Message-ID: <3F30C7E2-6931-4D41-99CF-3761569196DF@donders.ru.nl> — Please disseminate to PhD students, postdoctoral researchers, and other senior researchers interested in advanced brain stimulation (TMS, TDCS) On 10-13 September 2018 we will host the "Donders Brain Stimulation Toolkit" at the Donders Institute in Nijmegen, the Netherlands. This advanced course is designed for researchers who want to learn advanced transcranial magnetic stimulation (TMS) and/or transcranial current stimulation (tDCS/tACS) techniques. Lectures by expert researchers and hands-on training sessions will provide you with the latest on experimental design, stimulation application, data acquisition and data analysis. We place a special emphasis on state-of-the-art multi-modal techniques including: TMS-EEG; tD/ACS-MEG and tD/ACS-fMRI. Our main program (September 11-13) is therefore aimed at advanced brain stimulation topics. Need a basic refresher on TMS and TD/ACS? We will go over the basics in an extra day prior to the course (September 10). More information, including a preliminary program and registration, can be found at http://www.ru.nl/donders/agenda/donders-tool-kits/vm-tool-kits/donders-brain-stimulation-tool-kit-version-2/ Looking forward to welcoming you in Nijmegen, Ian Cameron _______________________________ Ian Cameron, PhD Senior Researcher Donders Centre for Cognitive Neuroimaging visiting address: Kapittelweg 29, 6525 EN mailing address: P.O. Box 9101, NL-6500 HB Nijmegen, The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From deydhiman794 at gmail.com Thu May 10 21:08:35 2018 From: deydhiman794 at gmail.com (Dhiman Dey) Date: Fri, 11 May 2018 00:38:35 +0530 Subject: [FieldTrip] EEG/MRI dataset Message-ID: I am a final year b.tech student. My project work is Source localization using EEG/MRI signals. I am in search of dataset.If anybody can provide me the dataset,it will be helpful for me. Mailid: deydhiman794 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.kochari at uva.nl Fri May 11 10:17:25 2018 From: a.kochari at uva.nl (Arnold Kochari) Date: Fri, 11 May 2018 10:17:25 +0200 Subject: [FieldTrip] EEG/MRI dataset In-Reply-To: References: Message-ID: Hi Dhiman Dey, Perhaps you can find something suitable here: https://openfmri.org/dataset/. Kind regards, Arnold On Thu, May 10, 2018 at 9:08 PM, Dhiman Dey wrote: > I am a final year b.tech student. > My project work is Source localization using EEG/MRI signals. > I am in search of dataset.If anybody can provide me the dataset,it will be > helpful for me. > > Mailid: deydhiman794 at gmail.com > > _______________________________________________ > 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 nathanweisz at me.com Fri May 11 10:46:45 2018 From: nathanweisz at me.com (Nathan Weisz) Date: Fri, 11 May 2018 10:46:45 +0200 Subject: [FieldTrip] PhD position in Salzburg Message-ID: <6867CF09-C780-4398-8375-31E8E31ADE52@me.com> We are currently seeking a motivated PhD student to join our team to study lipreading processes in normal hearing and deaf individuals using MEG+EEG. Please forward to any potentially interested person. Thanks, Nathan -------------- next part -------------- A non-text attachment was scrubbed... Name: Call_FWF_lipreading.pdf Type: application/pdf Size: 68024 bytes Desc: not available URL: From rssundar at gmail.com Fri May 11 14:13:23 2018 From: rssundar at gmail.com (Shyam Rajagopalan) Date: Fri, 11 May 2018 17:43:23 +0530 Subject: [FieldTrip] EEG/MRI dataset In-Reply-To: References: Message-ID: Hi Dhiman Dey, You may want to check https://paris-saclay-cds.github.io/autism_challenge/ as well. Regards Shyam On Fri, May 11, 2018 at 1:47 PM, Arnold Kochari wrote: > Hi Dhiman Dey, > > Perhaps you can find something suitable here: https://openfmri.org/ > dataset/. > > > Kind regards, > Arnold > > > On Thu, May 10, 2018 at 9:08 PM, Dhiman Dey > wrote: > >> I am a final year b.tech student. >> My project work is Source localization using EEG/MRI signals. >> I am in search of dataset.If anybody can provide me the dataset,it will >> be helpful for me. >> >> Mailid: deydhiman794 at gmail.com >> >> _______________________________________________ >> 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 deydhiman794 at gmail.com Fri May 11 18:28:31 2018 From: deydhiman794 at gmail.com (Dhiman Dey) Date: Fri, 11 May 2018 21:58:31 +0530 Subject: [FieldTrip] EEG/MRI dataset In-Reply-To: References: Message-ID: Thank you Arnold On Fri 11 May, 2018 2:05 pm Arnold Kochari, wrote: > Hi Dhiman Dey, > > Perhaps you can find something suitable here: > https://openfmri.org/dataset/. > > > Kind regards, > Arnold > > > On Thu, May 10, 2018 at 9:08 PM, Dhiman Dey > wrote: > >> I am a final year b.tech student. >> My project work is Source localization using EEG/MRI signals. >> I am in search of dataset.If anybody can provide me the dataset,it will >> be helpful for me. >> >> Mailid: deydhiman794 at gmail.com >> >> _______________________________________________ >> 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 deydhiman794 at gmail.com Fri May 11 18:28:50 2018 From: deydhiman794 at gmail.com (Dhiman Dey) Date: Fri, 11 May 2018 21:58:50 +0530 Subject: [FieldTrip] EEG/MRI dataset In-Reply-To: References: Message-ID: Thank you Shyam On Fri 11 May, 2018 6:05 pm Shyam Rajagopalan, wrote: > Hi Dhiman Dey, > > You may want to check https://paris-saclay-cds.github.io/autism_challenge/ > as well. > > Regards > Shyam > > On Fri, May 11, 2018 at 1:47 PM, Arnold Kochari wrote: > >> Hi Dhiman Dey, >> >> Perhaps you can find something suitable here: >> https://openfmri.org/dataset/. >> >> >> Kind regards, >> Arnold >> >> >> On Thu, May 10, 2018 at 9:08 PM, Dhiman Dey >> wrote: >> >>> I am a final year b.tech student. >>> My project work is Source localization using EEG/MRI signals. >>> I am in search of dataset.If anybody can provide me the dataset,it will >>> be helpful for me. >>> >>> Mailid: deydhiman794 at gmail.com >>> >>> _______________________________________________ >>> 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 Matthias.Franken at UGent.be Mon May 14 14:39:28 2018 From: Matthias.Franken at UGent.be (Matthias Franken) Date: Mon, 14 May 2018 12:39:28 +0000 Subject: [FieldTrip] partial artifact rejection for time-frequency analysis Message-ID: <549818693f0c4c31acabed976edb5fea@xmail303.UGent.be> Dear all, I have an EEG dataset that consists of quite long trials (>20s). Therefore, For artifact rejection I would like to only reject the part of the trial that contains the artifact, rather than throwing away the entire trial, and thus I will use the cfg.artfctdef.method = ‘partial’; option in ft_rejectartifact. However, this leads to some trials being cut in two shorter “trials” (i.e., the part before the artifact and the part after the artifact). I’m guessing this will lead to edge artifacts in my time-frequency analysis, not only at the edges of the original trials, but also at time points where artifacts were cut out. SO I’m not sure how to deal with this. I guess one option would be to perform the time-frequency analysis first, and afterwards cut out the artifacts, although (1) that might lead to the artifact smearing into data points that were not cut out, depending on the time window width during frequency analysis, and (2) the artifacts identified visually using ft_databrowser are define din ample numbers, and the result from ft_freqanalysis downsamples the data. Did anyone face similar issues or have ideas on how to get around this? ________________________________________ Matthias Franken postdoctoral researcher Experimental Psychology Department Ghent University -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon May 14 15:55:35 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 14 May 2018 13:55:35 +0000 Subject: [FieldTrip] partial artifact rejection for time-frequency analysis In-Reply-To: <549818693f0c4c31acabed976edb5fea@xmail303.UGent.be> References: <549818693f0c4c31acabed976edb5fea@xmail303.UGent.be> Message-ID: <9CBD4CAF-5EB2-432D-907B-15E728977F97@donders.ru.nl> Dear Matthias, Don’t worry. The partial rejection method indeed cuts original trials in smaller portions, but it preserves the local time axes, relative to the original trials. Since ft_freqanalysis returns per ‘segment’ TFRs with numeric data only for those portions of data for which the time windows are entirely filled with data (and nans otheriwse, with the average across segments is computed as a nanmean) there is no worry about ‘edge artifacts’ as such. The only thing to keep in the back of your head is that different time-frequency points may end up having slightly different degrees of freedom in the average. Best wishes, Jan-Mathijs On 14 May 2018, at 14:39, Matthias Franken > wrote: Dear all, I have an EEG dataset that consists of quite long trials (>20s). Therefore, For artifact rejection I would like to only reject the part of the trial that contains the artifact, rather than throwing away the entire trial, and thus I will use the cfg.artfctdef.method = ‘partial’; option in ft_rejectartifact. However, this leads to some trials being cut in two shorter “trials” (i.e., the part before the artifact and the part after the artifact). I’m guessing this will lead to edge artifacts in my time-frequency analysis, not only at the edges of the original trials, but also at time points where artifacts were cut out. SO I’m not sure how to deal with this. I guess one option would be to perform the time-frequency analysis first, and afterwards cut out the artifacts, although (1) that might lead to the artifact smearing into data points that were not cut out, depending on the time window width during frequency analysis, and (2) the artifacts identified visually using ft_databrowser are define din ample numbers, and the result from ft_freqanalysis downsamples the data. Did anyone face similar issues or have ideas on how to get around this? ________________________________________ Matthias Franken postdoctoral researcher Experimental Psychology Department Ghent University _______________________________________________ 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 m.manahova at gmail.com Mon May 14 16:04:03 2018 From: m.manahova at gmail.com (Mariya Manahova) Date: Mon, 14 May 2018 16:04:03 +0200 Subject: [FieldTrip] partial artifact rejection for time-frequency analysis In-Reply-To: <549818693f0c4c31acabed976edb5fea@xmail303.UGent.be> References: <549818693f0c4c31acabed976edb5fea@xmail303.UGent.be> Message-ID: Hi Matthias, Perhaps you could try taking the part of the trial you want to reject and replacing the values there with NaNs? Then you'd be able to remove the artifact-related part of the data while keeping your trials of the same length. I know that some FieldTrip functions can deal with NaNs, so this may be a solution. All the best, Marisha On Mon, May 14, 2018 at 3:35 PM Matthias Franken wrote: > Dear all, > > > > I have an EEG dataset that consists of quite long trials (>20s). > Therefore, For artifact rejection I would like to only reject the part of > the trial that contains the artifact, rather than throwing away the entire > trial, and thus I will use the cfg.artfctdef.method = ‘partial’; option in > ft_rejectartifact. > > However, this leads to some trials being cut in two shorter “trials” > (i.e., the part before the artifact and the part after the artifact). I’m > guessing this will lead to edge artifacts in my time-frequency analysis, > not only at the edges of the original trials, but also at time points where > artifacts were cut out. SO I’m not sure how to deal with this. > > > > I guess one option would be to perform the time-frequency analysis first, > and afterwards cut out the artifacts, although (1) that might lead to the > artifact smearing into data points that were not cut out, depending on the > time window width during frequency analysis, and (2) the artifacts > identified visually using ft_databrowser are define din ample numbers, and > the result from ft_freqanalysis downsamples the data. > > > > Did anyone face similar issues or have ideas on how to get around this? > > > > > > > ________________________________________ > Matthias Franken > postdoctoral researcher > Experimental Psychology Department > Ghent University > > > _______________________________________________ > 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 elam4hcp at gmail.com Mon May 14 23:22:26 2018 From: elam4hcp at gmail.com (Jennifer Elam) Date: Mon, 14 May 2018 16:22:26 -0500 Subject: [FieldTrip] Reminder to Register for HCP Course 2018 Message-ID: Only a few weeks remain to register for the *2018 HCP Course: "Exploring the Human Connectome"*. For more info visit the HCP Course 2018 website . A limited number of registrations with accommodation at Worcester College included are available until filled, or May 29 at the latest. HCP Course 2018 will be held June 25 – 29 at the Blavatnik School of Government , at the University of Oxford , in Oxford, UK. The 5-day intensive course of lectures and hands-on practicals is a great opportunity to learn directly from HCP investigators and gain practical experience with the Human Connectome Project's data and approach to multimodal whole brain imaging, processing and analysis. The course is also a great way to get up to speed on HCP tools including Connectome Workbench (v1.3.0 just released!) and sharing your own analyzed imaging datasets via the BALSA database. If you have any questions, please contact us at: hcpcourse at humanconnectome.org We look forward to seeing you in Oxford! Best, 2018 HCP Course Staff -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam at wustl.edu www.humanconnectome.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From fereshte.ramezani at gmail.com Wed May 16 05:59:29 2018 From: fereshte.ramezani at gmail.com (Fereshte) Date: Wed, 16 May 2018 08:29:29 +0430 Subject: [FieldTrip] EEG average In-Reply-To: References: Message-ID: Dear all, I've solved the forward problem for a FEM head model and as a result, obtained the lead field matrix. Now I'm going to do the Dipole Fit approch in order to solve the inverse problem. How can I obtain the ' EEG-avg ' data in the script below which is a part of " http://www.fieldtriptoolbox.org/workshop/baci2017/inverseproblem" due to the forward problem once I solved? Thank you! load elecload sourcemodelload headmodel_bemload leadfield_bemload mri_reslicedload EEG_avg Then we do the dipole fit % Dipole fit cfg = []; cfg.numdipoles = 1; %number of expected cfg.headmodel = headmodel_bem; %the head model cfg.grid = leadfield_bem; %the precomputed leadfield cfg.elec = elec; %the electrode model cfg.latency = 0.025; %the latency of interest dipfit_bem = ft_dipolefitting(cfg,EEG_avg); dipfit_bem.dip ans = pos: [13.958237048680118 34.388465910583285 97.809684095994314] %dipole position mom: [3x1 double ] %dipole moment pot: [74x1 double ] %potential at the electrodes rv: 0.034549469532012 %residual variance unit: 'mm' -------------- next part -------------- An HTML attachment was scrubbed... URL: From uwe.graichen at tu-ilmenau.de Wed May 16 15:42:24 2018 From: uwe.graichen at tu-ilmenau.de (Uwe Graichen) Date: Wed, 16 May 2018 15:42:24 +0200 Subject: [FieldTrip] =?utf-8?q?8th_International_Summer_School_=E2=80=9EMu?= =?utf-8?q?ltimodal_integration_of_brain_measurements_in_research_and_clin?= =?utf-8?q?ical_practice=E2=80=9C?= Message-ID: Dear colleagues, we are pleased to announce the 8th International Summer School in Biomedical Engineering „Multimodal integration of brain measurements in research and clinical practice“, 1st – 12th October 2018 in Chengdu, China. This event stands in the tradition of a series of successful summer schools on hot themes in biomedical engineering, dedicated to intense learning in the fruitful atmosphere of tight interaction between students and world-leading specialists. This year’s summer school is devoted to EEG/MEG source reconstruction technologies in the frame work of multimodal integration of brain measurements in research and clinical practice. In particular, the 8th International Summer School on Biomedical Engineering will focus on methodological approaches and challenges, measurement devices and characteristics, types of underlying theoretic modeling, specifics of data analysis, ability to derive conclusions about neuroscientific meaning. It will cover both theoretical foundations and practical applications. We aim at a thorough understanding of the underlying mechanisms. Thus, we will develop a critical view on current applications and possible future developments. The second important aim of the summer school consists in providing contact with both leading experts in the field and other students with similar interests, thereby facilitating the exchange of ideas on latest developments in the field. Target Group: - PhD students - Advanced Master students - Researchers entering the field of brain measurement and stimulation techniques Further Information about the 7th International Summer School in Biomedical Engineering: www.bme-school.org We would be happy to receive your application. Please pass this announcement to your colleagues who might be interested. Sincerely, Jens Haueisen and Thomas Knösche From jose.herrero66 at gmail.com Wed May 16 18:17:52 2018 From: jose.herrero66 at gmail.com (Jose Herrero) Date: Wed, 16 May 2018 12:17:52 -0400 Subject: [FieldTrip] ft_connectivity_laggedcoherence Message-ID: dear Fieldtrippers, I'm comparing different coherence methods including the fieldtrip method of lagged coherence. running the code with... cfg.method = 'laggedcoherence'; lcoh = ft_connectivityanalysis(cfg, freq) results on... Error using ft_connectivityanalysis (line 375) unknown method laggedcoherence running the code with... lcoh = ft_connectivity_laggedcoherence(cfg, freq) results on: In an assignment A(:) = B, the number of elements in A and B must be the same. Error in ft_connectivity_laggedcoherence (line 213) lagwidth(lagindx) = cfg.lag*cyclelength*lagindx; as 'cfg.lag' is assigned a length equal to the length of the trial (1x15000, single trial). if this method works, is it possible to use it to compute lagged coherence between an external signal (which oscillates at a freq <0.5Hz) and the iEEG brain signal? thanks, JHerr -------------- next part -------------- An HTML attachment was scrubbed... URL: From frsantos at fpce.up.pt Wed May 16 13:16:40 2018 From: frsantos at fpce.up.pt (Fernando Ferreira-Santos) Date: Wed, 16 May 2018 11:16:40 +0000 Subject: [FieldTrip] 2018 Porto EEG/ERP Summer School Message-ID: <2BAB036A9BAEA44984A131DFCE446108021F3E3905@SRVMBX01.fpceup.psi.up.pt> Dear colleagues, The Laboratory of Neuropsychopsysiology at the University of Porto (http://www.fpce.up.pt/labpsi/) is pleased to announce the 7th edition of the International Cognitive and Affective Neurophysiology Summer School: Acquisition, processing, and analysis of EEG signal (https://sites.google.com/view/can-summerschool-porto). This summer school is focused on the application of Electroencephalography (EEG) and Event Related Potential (ERP) techniques to the study of cognitive and affective processes. This 36h course will be fully taught in English and is aimed at an introductory level, so no previous experience with EEG or ERP is required. This year we are introducing a new module on reproducibility and open science practices in EEG/ERP research. This event will take place from 3-7 of September 2018 in the lovely city of Porto. The course is generally fully booked and, as such, we recommend early registration (course places are attributed by order of registration). For additional details and instructions on how to register, please visit the website (via http://www.fpce.up.pt/labpsi/summerschool/ or directly to the course website: https://sites.google.com/view/can-summerschool-porto). Please feel free to pass this information along to students or researchers that may be potentially interested. Thanks you and best wishes, Fernando Ferreira-Santos Professor Auxiliar | Assistant Professor Laboratório de Neuropsicofisiologia | Laboratory of Neuropsychophysiology Faculdade de Psicologia e de Ciências da Educação da Universidade do Porto Faculty of Psychology and Education Sciences - University of Porto Rua Alfredo Allen, 4200-135 Porto, Portugal http://www.fpce.up.pt | frsantos at fpce.up.pt | (+351) 22 607 97 00 (ext. 409) Lab: http://www.fpce.up.pt/labpsi Personal: http://ferreira-santos.eu -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu May 17 09:26:00 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 17 May 2018 07:26:00 +0000 Subject: [FieldTrip] ft_connectivity_laggedcoherence In-Reply-To: References: Message-ID: <01302D06-30B7-40BF-A655-4D280ACC0C13@donders.ru.nl> Dear Jose, As far as I know, this code is not functional. The first author of the paper started the implementation in fieldtrip-style, but never finished it. Also, note that the method itself is not strictly speaking a ‘connectivity’ measure, but it was intended to identify rhythmicity within signals. Best wishes, Jan Mathijs J.M.Schoffelen, MD PhD Associate PI, VIDI-fellow Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 16 May 2018, at 18:17, Jose Herrero > wrote: dear Fieldtrippers, I'm comparing different coherence methods including the fieldtrip method of lagged coherence. running the code with... cfg.method = 'laggedcoherence'; lcoh = ft_connectivityanalysis(cfg, freq) results on... Error using ft_connectivityanalysis (line 375) unknown method laggedcoherence running the code with... lcoh = ft_connectivity_laggedcoherence(cfg, freq) results on: In an assignment A(:) = B, the number of elements in A and B must be the same. Error in ft_connectivity_laggedcoherence (line 213) lagwidth(lagindx) = cfg.lag*cyclelength*lagindx; as 'cfg.lag' is assigned a length equal to the length of the trial (1x15000, single trial). if this method works, is it possible to use it to compute lagged coherence between an external signal (which oscillates at a freq <0.5Hz) and the iEEG brain signal? thanks, JHerr _______________________________________________ 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 jose.herrero66 at gmail.com Thu May 17 14:31:24 2018 From: jose.herrero66 at gmail.com (Jose Herrero) Date: Thu, 17 May 2018 08:31:24 -0400 Subject: [FieldTrip] ft_connectivity_laggedcoherence In-Reply-To: <01302D06-30B7-40BF-A655-4D280ACC0C13@donders.ru.nl> References: <01302D06-30B7-40BF-A655-4D280ACC0C13@donders.ru.nl> Message-ID: thanks Jan Mathijs for your reply, yes not to blame for not finishing up ... a lot of nice work already in his paper! after reading your tutorial ( http://www.fieldtriptoolbox.org/project/guidelines/paper/connectivity_analysis?s[]=coherence&s[]=lags) still would love your thoughts on this. ideally, I'd like to find out whether a specific phase of an ultraslow (<0.5Hz rhythmic external) signal is leading/lagging the phase of the iEEG signal at the same frequency (effective connectivity). Would it be adequate here to use 'granger' over 'pdc' since I'm not interested in the freq domain (as both signals have been filtered <0.5Hz). Note that dominant frequencies between signals differs a lot. Also, interesting to know if there are consistent phase lags in some iEEG electrodes but not others (functional connectivity). which ft measures would you advice particularly if you want to compute phase lags? The Nolte (2004) paper suggested cfg.method = 'coh' & cfg.complex = 'imag' as being a superior method. Is that right for this particular case? Would it be adequate here to use cfg.method='wpli' or 'wpli_debiased' ? I've explored other methods (Guo, 2007, PLoS) but not sure they're adequate for this specific case (where dominant frequencies between signals differs a lot). thanks On Thu, May 17, 2018 at 3:26 AM, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Dear Jose, > As far as I know, this code is not functional. The first author of the > paper started the implementation in fieldtrip-style, but never finished it. > Also, note that the method itself is not strictly speaking a > ‘connectivity’ measure, but it was intended to identify rhythmicity within > signals. > > Best wishes, > Jan Mathijs > > J.M.Schoffelen, MD PhD > Associate PI, VIDI-fellow > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > > On 16 May 2018, at 18:17, Jose Herrero wrote: > > dear Fieldtrippers, > > I'm comparing different coherence methods including the fieldtrip method > of lagged coherence. > > running the code with... > cfg.method = 'laggedcoherence'; > > lcoh = ft_connectivityanalysis(cfg, freq) > results on... > Error using ft_connectivityanalysis (line 375) > > unknown method laggedcoherence > > running the code with... > lcoh = ft_connectivity_laggedcoherence(cfg, freq) > results on: > In an assignment A(:) = B, the number of elements in A and B must be the > same. > Error in ft_connectivity_laggedcoherence (line 213) > lagwidth(lagindx) = cfg.lag*cyclelength*lagindx; > as 'cfg.lag' is assigned a length equal to the length of the trial > (1x15000, single trial). > > if this method works, is it possible to use it to compute lagged coherence > between an external signal (which oscillates at a freq <0.5Hz) and the iEEG > brain signal? > > thanks, > JHerr > > > _______________________________________________ > 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 > -- Jose L Herrero, PhD Department of Neurosurgery Northwell University Hospital Feinstein Institute for Medical Research New York -------------- next part -------------- An HTML attachment was scrubbed... URL: From annekathrinweise at gmail.com Thu May 17 15:06:34 2018 From: annekathrinweise at gmail.com (Annekathrin Weise) Date: Thu, 17 May 2018 15:06:34 +0200 Subject: [FieldTrip] potential bug when using ft_icabrowser - help needed Message-ID: <1a107ce2-873f-8204-454e-a0bfe70deb2b@gmail.com> Dear all, I am interested in using the ft_icabrowser to inpsect ICA components. I run into a potential bug (see my code and the related error messages in the screenshot below). Note that I also used the ft_databrowser to inspect the independent components what worked nicely. So, there seems to be no issue with the data "ica_components' itself. In case you want to have a closer look to efficiently evaluate the problem, you can find the data here. I appreciate any help to find a workaround. Cheers, Anne -- Annekathrin Weise, Dr. Paris-Lodron Universität Salzburg Division of Physiological Psychology Hellbrunnerstraße 34 5020 Salzburg Austria e-mail: annekathrin.weise at sbg.ac.at; annekathrinweise at gmail.com web: http://www.oboblab.at/ https://sites.google.com/site/weiseannekathrin/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hagbbfcodljipehl.png Type: image/png Size: 112378 bytes Desc: not available URL: From radman.thomas at gmail.com Sat May 19 16:04:09 2018 From: radman.thomas at gmail.com (Thomas Radman) Date: Sat, 19 May 2018 10:04:09 -0400 Subject: [FieldTrip] ft_determine_coordsys does not return coordinate system Message-ID: Hello, I would like to use individual MRIs to perform source analysis on EEG data. The problem I have is when importing dicoms into fieldtrip, and then using ft_determine_coordsys, the coordinate system is not returned. How can I determine the coordinate system and align this to my EEG sensors? Also, to use ft_volumerealign in interactive mode to select fiducials I need to know which side is right and which is left. Is it possible to do this if I did not have a vitamin E marker in my scans? Thank you, Tom Radman -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Sat May 19 17:57:41 2018 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Sat, 19 May 2018 08:57:41 -0700 Subject: [FieldTrip] ft_determine_coordsys does not return coordinate system In-Reply-To: References: Message-ID: Hi Thomas, First thing that comes to my mind is step 3 of this ECoG tutorial , which demonstrates how to determine the coordinate system of an anatomical image. You'll need Box 2 from the preprint , and Video 1 . Video 2 addresses your second point, on how to use the coordinate system to find left and right. Hope that helps, Arjen On Sat, May 19, 2018 at 7:04 AM, Thomas Radman wrote: > Hello, > > > > I would like to use individual MRIs to perform source analysis on EEG > data. > > > The problem I have is when importing dicoms into fieldtrip, and then using > ft_determine_coordsys, the coordinate system is not returned. How can I > determine the coordinate system and align this to my EEG sensors? > > > Also, to use ft_volumerealign in interactive mode to select fiducials I > need to know which side is right and which is left. Is it possible to do > this if I did not have a vitamin E marker in my scans? > > > Thank you, > > Tom Radman > > > _______________________________________________ > 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 diana-hime at yandex.ru Sun May 20 17:08:44 2018 From: diana-hime at yandex.ru (=?utf-8?B?LSDQlNC40LDQvdCw?=) Date: Sun, 20 May 2018 18:08:44 +0300 Subject: [FieldTrip] Wavelet spectrum is cut strangely on low frequencies Message-ID: <3893281526828924@web25o.yandex.ru> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: singleplot_TFRwaveA10.png Type: image/png Size: 17727 bytes Desc: not available URL: From julian.keil at gmail.com Sun May 20 17:17:22 2018 From: julian.keil at gmail.com (Julian Keil) Date: Sun, 20 May 2018 17:17:22 +0200 Subject: [FieldTrip] Wavelet spectrum is cut strangely on low frequencies In-Reply-To: <3893281526828924@web25o.yandex.ru> References: <3893281526828924@web25o.yandex.ru> Message-ID: Hi Diana, That is what you would expect given your wavelet settings. The "strange" cutting off of your low frequencies is due to the length of the wavelet combined with the length of your trial. Only frequencies for which your wavelet fits into your trial will be computed. For example, 7 cycles at 1 Hz will need 7s of data to compute, 7 cycles at 10 Hz will need 0.7s. Play around with the cfg.width setting to see the effect of different taper sizes. Good luck, Julian - Диана schrieb am So. 20. Mai 2018 um 17:11: > Hello! > > My name is Diana. Currently I'm triyng to do a wavelet analysis of my > data, which is 128 (129 with reference elctrode) EEG recording. > > The problem is thatthe result looks strangely - the low frequencies are > cut off. Can't understand the reason for this, and should it be this way or > it not. Would be happy with any help) > > The script I use: > > %preprocessing > cfg = []; > cfg.dataset = FileName; > cfg.continuous = 'yes'; %считываем файл как непрерывный > data_preproc = ft_preprocessing(cfg); > > > % deftrial > cfg = []; > cfg.dataset = FileName; > cfg.trialdef.eventtype = 'trigger'; > cfg.trialdef.eventvalue = 'tim0'; > cfg.trialdef.prestim = 0.2; > cfg.trialdef.poststim = 2.2; > > cfg_deftrial = ft_definetrial(cfg); > > data_deftrialed = ft_redefinetrial(cfg_deftrial, data_preproc); > > %wavelet > > cfg = []; > cfg.channel = 'all'; > cfg.method = 'wavelet'; > cfg.width = 7; > cfg.output = 'pow'; > cfg.foi = 1:1:45; > cfg.toi = 1:0.01:2; > TFRwave = ft_freqanalysis(cfg, data_deftrialed); > > > > The wavelet I get: > > > > > > Thanks in advance, Diana. > Undergraduate Student > Department of Biology of MSU > > P.S: Sorry for my english this time... > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: singleplot_TFRwaveA10.png Type: image/png Size: 17727 bytes Desc: not available URL: From a.stolk8 at gmail.com Sun May 20 17:26:30 2018 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Sun, 20 May 2018 08:26:30 -0700 Subject: [FieldTrip] Wavelet spectrum is cut strangely on low frequencies In-Reply-To: <3893281526828924@web25o.yandex.ru> References: <3893281526828924@web25o.yandex.ru> Message-ID: Hi Diana, This is because your time points of interest are close to the boundaries of the original time series, as described here: http://www.fieldtriptoolbox.org/faq/why_does_my_tfr_contain_nans You may want to include more data from your original time series (at call to ft_definetrial / ft_preprocessing) or use smaller spectral windows / fewer wavelet cycles (at ft_frequencyanalysis, spectral resolution permitting). Best regards, Arjen On Sun, May 20, 2018 at 8:08 AM, - Диана wrote: > Hello! > > My name is Diana. Currently I'm triyng to do a wavelet analysis of my > data, which is 128 (129 with reference elctrode) EEG recording. > > The problem is thatthe result looks strangely - the low frequencies are > cut off. Can't understand the reason for this, and should it be this way or > it not. Would be happy with any help) > > The script I use: > > %preprocessing > cfg = []; > cfg.dataset = FileName; > cfg.continuous = 'yes'; %считываем файл как непрерывный > data_preproc = ft_preprocessing(cfg); > > > % deftrial > cfg = []; > cfg.dataset = FileName; > cfg.trialdef.eventtype = 'trigger'; > cfg.trialdef.eventvalue = 'tim0'; > cfg.trialdef.prestim = 0.2; > cfg.trialdef.poststim = 2.2; > > cfg_deftrial = ft_definetrial(cfg); > > data_deftrialed = ft_redefinetrial(cfg_deftrial, data_preproc); > > %wavelet > > cfg = []; > cfg.channel = 'all'; > cfg.method = 'wavelet'; > cfg.width = 7; > cfg.output = 'pow'; > cfg.foi = 1:1:45; > cfg.toi = 1:0.01:2; > TFRwave = ft_freqanalysis(cfg, data_deftrialed); > > > > The wavelet I get: > > > > > > Thanks in advance, Diana. > Undergraduate Student > Department of Biology of MSU > > P.S: Sorry for my english this time... > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: singleplot_TFRwaveA10.png Type: image/png Size: 17727 bytes Desc: not available URL: From diana-hime at yandex.ru Mon May 21 00:02:56 2018 From: diana-hime at yandex.ru (=?utf-8?B?LSDQlNC40LDQvdCw?=) Date: Mon, 21 May 2018 01:02:56 +0300 Subject: [FieldTrip] Wavelet spectrum is cut strangely on low frequencies In-Reply-To: References: <3893281526828924@web25o.yandex.ru> Message-ID: <4339051526853776@web13o.yandex.ru> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: singleplot_TFRwaveA10.png Type: image/png Size: 17727 bytes Desc: not available URL: From deydhiman794 at gmail.com Mon May 21 09:30:01 2018 From: deydhiman794 at gmail.com (Dhiman Dey) Date: Mon, 21 May 2018 13:00:01 +0530 Subject: [FieldTrip] Brain Source Localization using EEG Signals Message-ID: Hello everyone I am doing b.tech final year project on Brain Source Localization using EEG Signals. I am following the FieldTrip Toolbox for this project. The workshop http://www.fieldtriptoolbox.org/workshop/baci2017/forwardproblem provides the solution of my project but they had used MRI dataset(i.e .mri file) instead of EEG dataset(i.e .eeg file) Please provide me the solution using EEG dataset. Thank you. mailid: deydhiman794 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From fereshte.ramezani at gmail.com Mon May 21 09:50:50 2018 From: fereshte.ramezani at gmail.com (Fereshte) Date: Mon, 21 May 2018 12:20:50 +0430 Subject: [FieldTrip] Brain Source Localization using EEG Signals In-Reply-To: References: Message-ID: Hi, This tutorial explains how to create a FEM/BEM head model ( using MRI dataset) for solving forward problem ( to obtain the leadfield) . I think in your case ( using EEG signals) you need to solve the inverse problem which is explained " http://www.fieldtriptoolbox.org/workshop/baci2017/inverseproblem". Cheers On Mon, May 21, 2018 at 12:02 PM Dhiman Dey wrote: > Hello everyone > > I am doing b.tech final year project on Brain Source Localization using > EEG Signals. > I am following the FieldTrip Toolbox for this project. > > The workshop > http://www.fieldtriptoolbox.org/workshop/baci2017/forwardproblem provides > the solution of my project but they had used MRI dataset(i.e .mri file) > instead of EEG dataset(i.e .eeg file) > > Please provide me the solution using EEG dataset. > Thank you. > > mailid: deydhiman794 at gmail.com > _______________________________________________ > 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 fereshte.ramezani at gmail.com Mon May 21 10:42:16 2018 From: fereshte.ramezani at gmail.com (Fereshte) Date: Mon, 21 May 2018 13:12:16 +0430 Subject: [FieldTrip] Normalized source model Message-ID: Dear Experts, Are the output source models of " ft_prepare_sourcemodel" function normalized on the surface by default? Thanks in advance! Regards, F.R -------------- next part -------------- An HTML attachment was scrubbed... URL: From deydhiman794 at gmail.com Mon May 21 11:35:36 2018 From: deydhiman794 at gmail.com (Dhiman Dey) Date: Mon, 21 May 2018 15:05:36 +0530 Subject: [FieldTrip] Brain Source Localization using EEG Signals In-Reply-To: References: Message-ID: Thank you for your reply but for brain source localization at first you need to solve forward problem then proceed with inverse problem. I already saw the workshop for inverse problem where the same MRI dataset is used. Kindly share the solution using EEG dataset. On 21 May 2018 at 13:20, Fereshte wrote: > Hi, > This tutorial explains how to create a FEM/BEM head model ( using MRI > dataset) for solving forward problem ( to obtain the leadfield) . I think > in your case ( using EEG signals) you need to solve the inverse problem > which is explained "http://www.fieldtriptoolbox.org/workshop/baci2017/ > inverseproblem". > Cheers > > On Mon, May 21, 2018 at 12:02 PM Dhiman Dey > wrote: > >> Hello everyone >> >> I am doing b.tech final year project on Brain Source Localization using >> EEG Signals. >> I am following the FieldTrip Toolbox for this project. >> >> The workshop http://www.fieldtriptoolbox.org/workshop/baci2017/ >> forwardproblem provides the solution of my project but they had used MRI >> dataset(i.e .mri file) instead of EEG dataset(i.e .eeg file) >> >> Please provide me the solution using EEG dataset. >> Thank you. >> >> mailid: deydhiman794 at gmail.com >> _______________________________________________ >> 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 paul.sowman at mq.edu.au Mon May 21 12:11:38 2018 From: paul.sowman at mq.edu.au (Paul Sowman) Date: Mon, 21 May 2018 10:11:38 +0000 Subject: [FieldTrip] MEG Professorship in Sydney Message-ID: <80BA9A1C-09D4-403C-83E2-82461BE2C9FD@contoso.com> Professor of Human Neuroscience/Neuroimaging Macquarie University is a vibrant multidisciplinary research environment with significant neuroimaging infrastructure and ample opportunities for training and collaboration. We are seeking a distinguished academic within a speciality of cognitive neuroscience to join a growing group of cognitive scientists, hearing scientists, experimental psychologists, linguists and education researchers making original, innovative and prominent contributions to teaching and research at Macquarie. As a senior member of the team, you will have access to resources including MEG, fMRI, fNIRS and TMS as well as the opportunity to build collaborative networks with specialists within Macquarie University Hospital, located on campus. We welcome applications from academics within any speciality of cognitive neuroscience, including hearing, language, motor control, emotion, memory, executive function, visual attention, perception, and decision-making. Methodological specialty within neuroimaging is open, but ideally the candidate would enhance our strong existing program in MEG imaging, and develop a translational, theory-based neuroimaging program focusing on utilising MEG in their area of interest. How to Apply https://www.seek.com.au/job/36254679 For a confidential discussion about the role and the University’s expectations, please contact Associate Professor Paul Sowman on +61 2 9850 6732 or email paul.sowman at mq.edu.au. Applications Close: Sunday, 24 June 2018 at 11.55pm -- Paul F Sowman Associate Professor Director HDR Deputy Head Department of Cognitive Science Level 3, Room 3.824 Australian Hearing Hub 16 University Drive Macquarie University, NSW 2109, Australia T: +61 2 9850 6732 W: Profile Page W: MQU Stuttering Research Facebook Page -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.daume at uke.de Mon May 21 20:36:20 2018 From: j.daume at uke.de (Jonathan Daume) Date: Mon, 21 May 2018 20:36:20 +0200 Subject: [FieldTrip] potential bug when using ft_icabrowser - help needed In-Reply-To: <1a107ce2-873f-8204-454e-a0bfe70deb2b@gmail.com> References: <1a107ce2-873f-8204-454e-a0bfe70deb2b@gmail.com> Message-ID: <9A9DC1CD-A8F7-43F5-B738-2810AA8EFAE9@uke.de> Hi Anne, There seems to be a problem with ft_prepare_layout as is doesn’t construct the correct sensors layout from your data. However, you can read the layout structure simply from the provided layout file without handing over your MEG data to the function. So just open the icabrowser ("edit ft_icabrowser.m") and change line 53 from lay = ft_prepare_layout(cfglay, comp); to lay = ft_prepare_layout(cfglay); The topotplot function should work again now. Nevertheless, you will still run into problems with the power spectrum (left panel in the figure) as it won’t show any data. I checked your data and saw that every ica component also contains NaNs. This means that the fft analysis will result in only NaNs as well. You may consider to just get rid of them before computing the power spectrum (which is done in lines 102-109). Moreover, the icabrowser was originally coded for trial-based data and only every 5th trial was considered for the power analysis. Otherwise, it just takes too long to plot every single component. However, I saw that your data only contains (continous?) data from a single trial. Computing the fft of the whole recording would take ages. So, in case your data is continuous data from resting state for example, you may also consider to divide your data into epochs and take only every 5th epoch or so for the power analysis. I have coded something in that direction for you but I am not sure what kind of data you have and if it suits your data. I just divided the data in epochs of 1s length and took every 5th epoch for the analysis. Please find the code below. You may just further adjust the code so that it better suits your data. Change line 34 from fft_data = cat(2,comp.trial{1:5:end}); to fft_data = comp.trial{1}; And lines 104 - 106 from Fs = comp.fsample; N = floor(size(fft_data,2)); xdft = fft(fft_data(i,:)); to comp_data = fft_data(i,~isnan(fft_data(i,:))); % kick out all NaNs first epochJump = 5; % how many trials to jump over? numEpochs = size(comp_data,2)/comp.fsample; fft_data_i = []; for i_epoch = 1:epochJump:numEpochs epochdata = comp_data((i_epoch-1)*comp.fsample+1:i_epoch*comp.fsample); fft_data_i = [fft_data_i,epochdata]; end N = floor(size(fft_data_i,2)); xdft = fft(fft_data_i); Or you just download the edited file from here . :) Hope this helps! Please get in touch with me if you have any further question. Cheers, Jonathan ----- Jonathan Daume, PhD Dept. of Neurophysiology and Pathophysiology University Medical Center Hamburg Eppendorf Martinistr. 52 20246 Hamburg Germany Phone: +49-40-7410-55856 Email: j.daume at uke.de www.uke.de > Am 17.05.2018 um 15:06 schrieb Annekathrin Weise : > > Dear all, > > I am interested in using the ft_icabrowser to inpsect ICA components. > > I run into a potential bug (see my code and the related error messages in the screenshot below). > > Note that I also used the ft_databrowser to inspect the independent components what worked nicely. So, there seems to be no issue with the data "ica_components' itself. > > In case you want to have a closer look to efficiently evaluate the problem, you can find the data here. > I appreciate any help to find a workaround. > > Cheers, > > Anne > > > > -- > Annekathrin Weise, Dr. > > Paris-Lodron Universität Salzburg > Division of Physiological Psychology > Hellbrunnerstraße 34 > 5020 Salzburg > Austria > > e-mail: annekathrin.weise at sbg.ac.at ; > annekathrinweise at gmail.com > > web: > http://www.oboblab.at/ > https://sites.google.com/site/weiseannekathrin/ > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Martina Saurin (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING -------------- next part -------------- An HTML attachment was scrubbed... URL: From radman.thomas at gmail.com Tue May 22 00:53:03 2018 From: radman.thomas at gmail.com (Thomas Radman) Date: Mon, 21 May 2018 18:53:03 -0400 Subject: [FieldTrip] Brain segmentation has strange spikes in it Message-ID: Hello, I am trying to segment an individual subject's MRI following this tutorial: http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting However, when plotting the mesh of the scalp segmentation I get these horrible disfigurations that are not in the original MRI. Here is a screenshot: These are the steps I'm taking mri=ft_read_mri( '/data/radmantc/projects/T1_mni.nii') mri.coordsys='mni' cfg = []; cfg.resolution = 1; mri_resliced = ft_volumereslice(cfg, mri); figure ft_sourceplot([], mri_resliced); %volume conduction model cfg = []; cfg.output = {'brain', 'skull', 'scalp'}; mri_segmented = ft_volumesegment(cfg, mri_resliced); % copy the anatomy into the segmented mri mri_segmented.anatomy = mri_resliced.anatomy; %reconstruct the three triangulated meshes. cfg = []; cfg.method = 'projectmesh'; cfg.tissue = 'brain'; cfg.numvertices = 3000; mesh_eeg(1) = ft_prepare_mesh(cfg, mri_segmented); cfg.tissue = 'skull'; cfg.numvertices = 2000; mesh_eeg(2) = ft_prepare_mesh(cfg, mri_segmented); cfg.tissue = 'scalp'; cfg.numvertices = 1000; mesh_eeg(3) = ft_prepare_mesh(cfg, mri_segmented); figure ft_plot_mesh(mesh_eeg(1), 'edgecolor', 'none', 'facecolor', 'r') ft_plot_mesh(mesh_eeg(2), 'edgecolor', 'none', 'facecolor', 'g') ft_plot_mesh(mesh_eeg(3), 'edgecolor', 'none', 'facecolor', 'b') %this is the only mesh that is distorted alpha 0.3 Also, can someone tell me how to respond to any replies I might get. In previous posts, I only see the replies in the listserv digest emails. Do I create a new email with the subject line of this case intact? I don't get an email directly from the person sending the reply to my email, I only see it in the digest. Thank you for the help, Thomas Radman -------------- next part -------------- An HTML attachment was scrubbed... URL: From w.kruijne at gmail.com Tue May 22 12:37:03 2018 From: w.kruijne at gmail.com (Wouter Kruijne) Date: Tue, 22 May 2018 12:37:03 +0200 Subject: [FieldTrip] artifact detection -- computing the accumulated z Message-ID: Hi everyone, When playing around with different ways of rejecting (muscle) artifacts, I came across something in the tutorial + code that I do not fully understand. The tutorial ( http://www.fieldtriptoolbox.org/tutorial/automatic_artifact_rejection#iii_z-transforming_the_filtered_data_and_averaging_it_over_channels ) states that: > 4. Per timepoint these z-values are averaged. Since an artifact might > occur on any and often on more than one electrode (think of eyeblinks and > muscle artifacts), averaging z-values over channels/electrodes allows > evidence for an artifact to accumulate. > ​This line of reasoning makes perfect sense to me. However, in the subsequent mathematical description, and in the implementation, averaging isn't applied at all: instead, a scaled summation is computed. zsum = SUM_{ch in C} = z(ch,t)/sqrt(C) ​ where C is the number of channels [forgive my math editing skills] . I fail to understand why the accumulated z-score uses a division by the _sqrt_ of the number of channels, rather than simple averaging. In fact, the potential downsides I see are: - The reported z-value, and the one used for thresholding does not correspond to the traditional interpretation of z. - The value of a 'good' z-threshold value is dependent on the number of channels, as this changes the scaling. - Should we wish to use the channel-level z-scores for identifying channels affected by the artefact, the accumulated threshold value now has a different scale than the channel-level z-values. Am I missing something? What are the upsides of the sqrt scaling? Thank you! Wouter -------------- next part -------------- An HTML attachment was scrubbed... URL: From antonio.tavella at virgilio.it Tue May 22 14:29:24 2018 From: antonio.tavella at virgilio.it (antonio.tavella at virgilio.it) Date: Tue, 22 May 2018 14:29:24 +0200 (CEST) Subject: [FieldTrip] Research assistantship with possible PhD scholarship Message-ID: <3844204.243454.1526992165001@mail.virgilio.it> Apologies for multiple posting The Group of Psychiatric Neuroscience at the University of Bari Aldo Moro will publish a call for a 1-year long Research Assistant position, renewable up to 4 years, in the field of Brain Imaging (MRI & MEG). Expressions of interest are welcome before June 30th. Candidates who are in the process of writing up their master thesis are encouraged to apply. The expected starting date is September 2018. Research Assistants interested in pursuing a PhD at our department will have the opportunity to enroll in the Doctoral School in November, following positive evaluation. The Group of Psychiatric Neuroscience is led by Prof. Alessandro Bertolino and Prof. Giuseppe Blasi and investigates the association of genetic variability with systems-level phenotypes, including structural and functional Magnetic Resonance Imaging, Diffusion Tensor Imaging, Arterial Spin Labeling, and Magnetoencephalography. The Group of Psychiatric Neuroscience has access to and routinely tests psychiatric patients, relatives of patients, and individuals at risk for psychosis. The department has an in-house Elekta Triux magnetoencephalography installed in October 2016 with a dedicated technician. The Research Assistant will work in the lab of Brain Imaging, Networks, and Data mining (BIND) directed by Dr. Giulio Pergola, with the aim to investigate the biological basis of major psychiatric disorders by integrating multimodal data (genetic variation, gene expression, structural and functional MRI, MEG, and neuropsychology). The Research Assistant will contribute to neuroimaging data acquisition and analysis for projects funded both at local and European level (for recent articles from the lab, see [1], [2], [3]). The ideal candidate is a young graduate interested in neuroimaging, with a Master’s Degree in Neuroscience, Psychology, Medicine, Biotechnology, Applied Physics, or related fields. Knowledge of statistics and skills regarding the integration of imaging and machine learning are a plus. We expect the successful candidate to be motivated and research-oriented. It is equally important to have a team-working attitude and a motivation to fit in the group. Knowledge of Italian is not required, as the lab already hosts two international PhD students and research meetings are held in English. Bari is a sunny city located by the sea in the east of southern Italy, and the third greatest city south of Rome. The cost of living is comparatively low relative to Italian standards. The net monthly salary of the Research Assistant will be > 1400 EUR. Please contact Dr. Giulio Pergola sending a CV and the contact details of at least two references if you would like to have more information on the position and on the ongoing projects (giulio.pergola at uniba.it mailto:giulio.pergola at uniba.it ). -------------- next part -------------- An HTML attachment was scrubbed... URL: From jose.herrero66 at gmail.com Tue May 22 15:42:28 2018 From: jose.herrero66 at gmail.com (Jose Herrero) Date: Tue, 22 May 2018 09:42:28 -0400 Subject: [FieldTrip] use_simulated_erps_to_explore_cluster_statistics ERROR Message-ID: Dear FT, after running the tutorial example/use_simulated_erps_to_explore_cluster_statistics.txt Error using ft_math (line 151) the requested parameter is not present in the data has anybody encounter this b4? thanks, JHerr -------------- next part -------------- An HTML attachment was scrubbed... URL: From mailtome.2113 at gmail.com Wed May 23 04:08:37 2018 From: mailtome.2113 at gmail.com (Arti Abhishek) Date: Wed, 23 May 2018 12:08:37 +1000 Subject: [FieldTrip] xdf format for EEG data Message-ID: Dear fieldtrip development team, I was wondering whether there is a plan to support xdf file format for the EEG data (eg: SMARTING system) in the future releases of fieldtrip? Thanks, Arti -------------- next part -------------- An HTML attachment was scrubbed... URL: From laetitia.grabot at gmail.com Wed May 23 13:42:56 2018 From: laetitia.grabot at gmail.com (Laetitia Grabot) Date: Wed, 23 May 2018 13:42:56 +0200 Subject: [FieldTrip] Error while reading in Fieldtrip an epochs file created with mne-python Message-ID: Dear all, I'm trying to read in Fieldtrip an Elekta Neuromag epochs file (.fif) created with mne-python (MEG and EEG data file). I used the following snippet of code, and got the following error: cfg = []; cfg.dataset = filename; data = ft_preprocessing(cfg); Error using fiff_read_epochs (line 47) Could not find epochs data Error in fiff_read_epochs (line 47) error(me,'Could not find epochs data'); Error in ft_read_header (line 1846) epochs = fiff_read_epochs(filename); Error in ft_read_header (line 125) hdr{i} = ft_read_header(filename{i}, varargin{:}); Error in ft_preprocessing (line 397) hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat,... I saw that a former thread reported the same error, but it seems that the code was changed meanwhile. I'm using Matlab R2017a ver 9.2 and the Fieldtrip version dated from 16-05-2018. Here you can download the epochs file I used. It would be very helpful is someone knows from where this problem could come. Thank you very much, Best, Laetitia -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.homolle at donders.ru.nl Wed May 23 14:01:04 2018 From: s.homolle at donders.ru.nl (Simon Homolle) Date: Wed, 23 May 2018 14:01:04 +0200 Subject: [FieldTrip] Brain segmentation has strange spikes in it In-Reply-To: References: Message-ID: Dear Thomas, unfortunately I cannot see the figure you send. But from the title of the email I think i have some suggestions for you. > %volume conduction model > cfg = []; > cfg.output = {'brain', 'skull', 'scalp'}; > mri_segmented = ft_volumesegment(cfg, mri_resliced); for this segment you can play around with to make the the tissues more smooth % cfg.brainsmooth = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5) % cfg.scalpsmooth = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5) % cfg.skullsmooth = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5) Or you can change the thresholds for the tissues % cfg.brainthreshold = 'no', or scalar, relative threshold value which is used to threshold the % tpm in order to create a volumetric brainmask (see below), (default = 0.5) % cfg.scalpthreshold = 'no', or scalar, relative threshold value which is used to threshold the % anatomical data in order to create a volumetric scalpmask (see below), % (default = 0.1) % cfg.skullthreshold = 'no', or scalar, relative threshold value which is used to threshold the % anatomical data in order to create a volumetric scalpmask (see below), % (default = 0.5). this parameter is only used when % the segmetnation contains 6 tissue types, % including 'bone’, > %reconstruct the three triangulated meshes. > cfg = []; > cfg.method = 'projectmesh'; > cfg.tissue = 'brain'; > cfg.numvertices = 3000; > mesh_eeg(1) = ft_prepare_mesh(cfg, mri_segmented); > > cfg.tissue = 'skull'; > cfg.numvertices = 2000; > mesh_eeg(2) = ft_prepare_mesh(cfg, mri_segmented); > > cfg.tissue = 'scalp'; > cfg.numvertices = 1000; > mesh_eeg(3) = ft_prepare_mesh(cfg, mri_segmented); If the previous steps to not solve your problems, you can also try to change something in the method % cfg.method = string, can be 'interactive', 'projectmesh', 'iso2mesh', 'isosurface', % 'headshape', 'hexahedral', 'tetrahedral', 'cortexhull' Cheers, Simon Homölle PhD Candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Phone: +31-(0)24-36-65059 > On 22 May 2018, at 00:53, Thomas Radman wrote: > > Hello, > > I am trying to segment an individual subject's MRI following this tutorial: > http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting > > However, when plotting the mesh of the scalp segmentation I get these horrible disfigurations that are not in the original MRI. Here is a screenshot: > > > > These are the steps I'm taking > mri=ft_read_mri( '/data/radmantc/projects/T1_mni.nii') > mri.coordsys='mni' > > cfg = []; > cfg.resolution = 1; > mri_resliced = ft_volumereslice(cfg, mri); > figure > ft_sourceplot([], mri_resliced); > > %volume conduction model > cfg = []; > cfg.output = {'brain', 'skull', 'scalp'}; > mri_segmented = ft_volumesegment(cfg, mri_resliced); > > % copy the anatomy into the segmented mri > mri_segmented.anatomy = mri_resliced.anatomy; > > %reconstruct the three triangulated meshes. > cfg = []; > cfg.method = 'projectmesh'; > cfg.tissue = 'brain'; > cfg.numvertices = 3000; > mesh_eeg(1) = ft_prepare_mesh(cfg, mri_segmented); > > cfg.tissue = 'skull'; > cfg.numvertices = 2000; > mesh_eeg(2) = ft_prepare_mesh(cfg, mri_segmented); > > cfg.tissue = 'scalp'; > cfg.numvertices = 1000; > mesh_eeg(3) = ft_prepare_mesh(cfg, mri_segmented); > > figure > ft_plot_mesh(mesh_eeg(1), 'edgecolor', 'none', 'facecolor', 'r') > ft_plot_mesh(mesh_eeg(2), 'edgecolor', 'none', 'facecolor', 'g') > ft_plot_mesh(mesh_eeg(3), 'edgecolor', 'none', 'facecolor', 'b') %this is the only mesh that is distorted > alpha 0.3 > > Also, can someone tell me how to respond to any replies I might get. In previous posts, I only see the replies in the listserv digest emails. Do I create a new email with the subject line of this case intact? I don't get an email directly from the person sending the reply to my email, I only see it in the digest. > > Thank you for the help, > Thomas Radman > > _______________________________________________ > 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 fereshte.ramezani at gmail.com Sat May 26 03:09:03 2018 From: fereshte.ramezani at gmail.com (Fereshte) Date: Sat, 26 May 2018 05:39:03 +0430 Subject: [FieldTrip] Project numerical values on a cortical mesh Message-ID: Dear Experts, I have assigned numerical values to 1000 vertices of a cortical mesh ( a matrix of 1000 rows and 4 columns; which the first 3 columns show the position of each vertex and the last column shows the numerical value) .How can I project and show these numerical values on the cortical mesh? Thanks in advance! Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From rhancock at email.arizona.edu Wed May 30 00:51:22 2018 From: rhancock at email.arizona.edu (Roeland Hancock) Date: Tue, 29 May 2018 18:51:22 -0400 Subject: [FieldTrip] Postdoctoral Scholar positions in neuroimaging Message-ID: NIDL and brainLENS-east labs (Neurobiology of Individual Differences in Language Lab http://nidl-lab.org, PI: Roeland Hancock PhD; and Laboratory for Learning Engineering and Neural Systems http://brainlens.org, PI: Fumiko Hoeft MD PhD) at University of Connecticut’s Brain Imaging Research Center (UCONN’s BIRC) are seeking: (1) two full-time neuroimaging postdoctoral fellows, and (2) two full-time Research Coordinators. BIRC is also seeking one full-time IT staff. *TWO NEUROIMAGING POSTDOC POSITIONS @ UCONN* We are seeking two postdoctoral scholars. The postdocs will manage and execute a large-scale neuroimaging project investigating the neurobiological mechanisms underlying: (1) language, literacy and cognition in generally healthy young adults using multimodal neuroimaging techniques such as MRI, MRS and TMS (“Perturbation Postdoc”); or (2) intergenerational transmission of language and literacy in parent-offspring dyads using MRI techniques (“Intergenerational Postdoc”). In addition, the successful candidates will have the opportunity to be involved in other federally and non-federally funded-research projects in the laboratories, gain experience in grant and manuscript writing and large-scale project management, outreach and community engagement projects, and access to a wealth of archival developmental and longitudinal neuroimaging data on language and literacy. *Required qualifications:* · PhD or equivalent in cognitive and systems neurosciences, computer science, engineering, psychology or a closely related field · Computational skills, including knowledge of at least one programming language and Unix commands · Strong written and verbal communication skills · Leadership and organizational skills *Preferred qualifications:* · Exceptional skills in collecting and analyzing MRI, MRS, and/or TMS data · Experience in M/EEG · Documented history of productivity and leadership · Advanced knowledge and expertise in statistics, e.g. multivariate statistics, behavioral genetics, Bayesian and Monte Carlo methods The position will be formally advertised at a later date. In the meantime, interested candidates should email *info at nidl-lab.org * with *"[Postdoc Job (YOUR FULL NAME)]" in the subject line*. In the email they should include (a) a current CV, (b) a one-page cover letter describing qualifications, interest, career goals and which postdoc position they are interested in (refer to as *“Perturbation Postdoc/Project” *or *“Intergenerational Postdoc/Project”)*, and (c) a list of 3 potential referees with their contact information. The position can begin immediately. *Postdoctoral scholars from the lab have gone onto a range of research faculty and imaging director positions at institutions such as Stanford, Caltech, Boston College, and University of Texas.* *The University of Connecticut is committed to building and supporting a multicultural and diverse community of students, faculty and staff. The diversity of students, faculty and staff continues to increase, as does the number of honor students, valedictorians and salutatorians who consistently make UConn their top choice. More than 100 research centers and instates serve the University’s teaching, research, diversity, and outreach missions, leading to UConn’s ranking as one of the nation’s top research universities. UConn’s faculty and staff are the critical link to fostering and expanding our vibrant, multicultural and diverse University community. As an Affirmative Action/Equal Employment Opportunity employer, UConn encourages applications from women, veterans, people with disabilities and members of traditionally underrepresented populations.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.homolle at donders.ru.nl Wed May 30 18:23:47 2018 From: s.homolle at donders.ru.nl (Simon Homolle) Date: Wed, 30 May 2018 18:23:47 +0200 Subject: [FieldTrip] EEG and MEG Source Reconstruction with FieldTrip @OHBM2018 Message-ID: <9A1E8D0A-EEA2-4211-AF4D-D6AC6EE257CB@donders.ru.nl> Dear all, on 17 June 2018 we will host a workshop at the OHBM2018 conference . The course is aimed at researchers who want to learn how to do MEG and/or EEG source reconstruction. We expect that you know the basics of MATLAB and that you already have experience with MEG/EEG preprocessing and analysis. In this intense one-day workshop we will explain state-of-the-art MEG and EEG source reconstruction methods. The workshop will consist of a number of lectures, followed by hands-on sessions in which you will be tutored through the complete analysis of a MEG, EEG and MRI data set using the FieldTrip toolbox. As the focus is on source reconstruction, topics that will NOT be covered in great detail are segmenting, artifact handling, averaging, frequency and time-frequency analysis, statistics. For the hands-on sessions you should bring a laptop with MATLAB installed. More information about the program can be found at the OHBM website or on the FieldTrip website. Best regards, Maria Carla Piastra1 , Sophie Schrader1 and Simon Homölle2 1 Institute for Biomagnetism and Biosignalanalysis, University of Münster, Münster, Germany. 2 Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands. -------------- next part -------------- An HTML attachment was scrubbed... URL: From elam4hcp at gmail.com Wed May 30 21:08:48 2018 From: elam4hcp at gmail.com (Jennifer Elam) Date: Wed, 30 May 2018 14:08:48 -0500 Subject: [FieldTrip] Spaces added, register today for HCP Course 2018! Message-ID: If you are considering joining us for the *2018 HCP Course: "Exploring the Human Connectome"* June 25 – 29 at the University of Oxford , a few additional lodging rooms at Worcester College have opened up for just $675 for 6 nights, first come first served. For more info and to register visit the HCP Course 2018 website . We will continue to take registrations for the course until our venue at the Blavatnik School of Government is full. HCP Course 2018 is a 5-day intensive course of lectures and hands-on practicals and your best opportunity to learn directly from HCP investigators and gain practical experience with the Human Connectome Project's data and approach to multimodal whole brain imaging, processing and analysis and to get up to speed on HCP tools including Connectome Workbench (v1.3.0 just released!) and sharing your own analyzed imaging datasets via the BALSA database. If you have any questions, please contact us at: hcpcourse at humanconnectome. org We look forward to seeing you in Oxford! Best, 2018 HCP Course Staff -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam at wustl.edu www.humanconnectome.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu May 31 10:00:54 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 31 May 2018 10:00:54 +0200 Subject: [FieldTrip] Project numerical values on a cortical mesh In-Reply-To: References: Message-ID: Dear Fereshte The mesh should be described with both vertices (points in 3-D space) and triangles (the specification how these points form a surface). If your values are an Nx1 vector and your mesh is mesh.pos = Nx3 % position of the vertices mesh.pos = Mx3 % indices into the vertices that together form M triangles then you can do ft_plot_mesh(mesh, ‘vertexcolor’, val) which uses one of the low level functions in the plotting module. If you organize your data as source structure (e.g. used for reconstructions of cortical activity) you could also use the high-level ft_sourceplot. See "help ft_datatype_source" for documentation on the source structure. best regards Robert > On 26 May 2018, at 03:09, Fereshte wrote: > > Dear Experts, > I have assigned numerical values to 1000 vertices of a cortical mesh ( a matrix of 1000 rows and 4 columns; which the first 3 columns show the position of each vertex and the last column shows the numerical value) .How can I project and show these numerical values on the cortical mesh? > Thanks in advance! > Regards > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Thu May 31 10:03:20 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 31 May 2018 10:03:20 +0200 Subject: [FieldTrip] Error while reading in Fieldtrip an epochs file created with mne-python In-Reply-To: References: Message-ID: Hi Laetitia The code you are referring to is fiff_read_epochs, which is in fieldtrip/external/mne. The external toolboxes are not maintained by the FieldTrip developpers themselves, only included for convenience. Please contact the maintaners at https://github.com/mne-tools/mne-matlab best regards, Robert > On 23 May 2018, at 13:42, Laetitia Grabot wrote: > > Dear all, > > I'm trying to read in Fieldtrip an Elekta Neuromag epochs file (.fif) created with mne-python (MEG and EEG data file). I used the following snippet of code, and got the following error: > > cfg = []; > cfg.dataset = filename; > data = ft_preprocessing(cfg); > > Error using fiff_read_epochs (line 47) > Could not find epochs data > Error in fiff_read_epochs (line 47) > error(me,'Could not find epochs data'); > Error in ft_read_header (line 1846) > epochs = fiff_read_epochs(filename); > Error in ft_read_header (line 125) > hdr{i} = ft_read_header(filename{i}, varargin{:}); > Error in ft_preprocessing (line 397) > hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat,... > > I saw that a former thread reported the same error, but it seems that the code was changed meanwhile. > I'm using Matlab R2017a ver 9.2 and the Fieldtrip version dated from 16-05-2018. Here you can download the epochs file I used. > It would be very helpful is someone knows from where this problem could come. > > Thank you very much, > Best, > Laetitia > _______________________________________________ > 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 Thu May 31 10:08:54 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 31 May 2018 10:08:54 +0200 Subject: [FieldTrip] xdf format for EEG data In-Reply-To: References: Message-ID: <69E5203E-986D-4455-B2BC-B5EF1393C31A@donders.ru.nl> Hi Arti, It would be nice to support the XDF format, and I think it would not be much work as some matlab code is already available here Since you probably have access to XDF data files, it would be great if you could implement this. Please see this FAQ on how to extend (start with ft_filetype and then add it to ft_read_header, data and event). On the git tutorial you can find how to submit the change to the code for inclusion in the release version. thanks Robert > On 23 May 2018, at 04:08, Arti Abhishek wrote: > > Dear fieldtrip development team, > > I was wondering whether there is a plan to support xdf file format for the EEG data (eg: SMARTING system) in the future releases of fieldtrip? > > Thanks, > Arti > > _______________________________________________ > 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 Tue May 1 10:49:44 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 1 May 2018 08:49:44 +0000 Subject: [FieldTrip] ft_freqanalysis fourier rpttap to rpt conversion? In-Reply-To: References: Message-ID: <92BEAED0-FD4D-44E5-80A3-81F63803596D@donders.ru.nl> Hi John, Yes, it is forced as a preventive measure. Averaging Fourier coefficients across tapers is not allowed. Best wishes, Jan-Mathijs On 27 Apr 2018, at 05:13, John Nguyen > wrote: Hi, I noticed that it's not an option to remove the tapers if the output is "fourier". Is this because the resulting output won't be a true Fourier if the tapers are removed, and is forced as a preventive measure? I was looking to reduce my fourier size by removing the tapers but not the trials, is there a danger to this? Thank you! John Nguyen _______________________________________________ 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 bioeng.yoosofzadeh at gmail.com Wed May 2 00:00:51 2018 From: bioeng.yoosofzadeh at gmail.com (bioeng.yoosofzadeh at gmail.com) Date: Tue, 1 May 2018 17:00:51 -0500 Subject: [FieldTrip] Issue in realigning MRI Message-ID: <038601d3e197$decb8ef0$9c62acd0$@gmail.com> Dear FT experts, I am not able to realign a T1 scan using the fiducial points and headshapes of a 4D/BTI system, can anyone help me on this? The "interactive" realignment helped a lot, but the end result was not perfect! Here's what I have tried,: individual_mri = ft_read_mri(mripath); % ..\MEG_4D\C-101_T1.nii ft_sourceplot([], individual_mri); cfg = []; cfg.method = 'flip'; mri.coordsys = '4d'; individual_mri = ft_volumereslice(cfg, individual_mri); ft_sourceplot([], individual_mri); individual_mri = ft_convert_units(individual_mri, 'm'); headshape = ft_read_headshape(headpath); % ..\MEG_4D\hs_file mri_fids = headshape.fid.pos; cfg = []; cfg.fiducial.nas = mri_fids(1,:); cfg.fiducial.lpa = mri_fids(2,:); cfg.fiducial.rpa = mri_fids(3,:); cfg.coordsys = '4d'; cfg.method = 'fiducial'; mri_realigned = ft_volumerealign(cfg, individual_mri); cfg = []; cfg.coordsys = '4d'; cfg.headshape = headshape; cfg.method = 'headshape'; mri_realigned = ft_volumerealign(cfg, individual_mri); % check that the MRI is consistent after realignment ft_determine_coordsys(mri_realigned, 'interactive', 'no'); hold on; drawnow; ft_plot_headshape(headshape); Data can be found at, https://www.dropbox.com/sh/e74pt2uc08q6z4q/AAB3fkp_9gvJxi-YtO0muRSca?dl=0 Best, Vahab -------------- next part -------------- An HTML attachment was scrubbed... URL: From acskwara at ucdavis.edu Wed May 2 04:05:21 2018 From: acskwara at ucdavis.edu (Alea Skwara) Date: Tue, 1 May 2018 19:05:21 -0700 Subject: [FieldTrip] Outputting band averages with ft_freqanalysis Message-ID: Hi All, I am attempting to output averages within frequency bands using ft_freqanalysis. I have implemented the two-step solution provided in this discussion https://mailman.science.ru.nl/pipermail/fieldtrip/2016-October/010984.html resulting in the following code: cfg =[]; cfg.method = 'mtmfft'; cfg.output = 'pow'; cfg.taper = 'hanning'; cfg.channel = 'all'; cfg.foilim = [fio1 foi2]; cfg.trials = 'all'; cfg.keeptrials = 'no'; freq_avg = ft_freqanalysis(cfg, data_segmented); cfg = []; cfg.avgoverfreq = 'yes'; freq_avg = ft_freqanalysis(cfg, freq_avg); However, when I run this, I get the following error: the input is freq data with 73 channels, 41 frequencybins and no timebins Error using ft_checkdata>freq2raw (line 1315) not supported for dimord chan_freq Error in ft_checkdata (line 432) data = freq2raw(data); Error in ft_freqanalysis (line 217) data = ft_checkdata(data, 'datatype', {'raw', 'raw+comp', 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); Is there a different way I need to format my data beyond providing the function with the output of the first iteration of ft_freqanalysis? Thank you! Alea -- Alea C. Skwara, M.A. PhD Candidate | Saron Lab http://saronlab.ucdavis.edu/ Center for Mind and Brain | University of California, Davis 267 Cousteau Place | Davis CA 95616 Cell: (828) 273-8595 -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Wed May 2 04:33:05 2018 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Tue, 1 May 2018 19:33:05 -0700 Subject: [FieldTrip] Outputting band averages with ft_freqanalysis In-Reply-To: References: Message-ID: Hi Alea, Have a look at ft_selectdata, which can do this operation for you. Arjen On Tue, May 1, 2018 at 7:05 PM, Alea Skwara wrote: > Hi All, > > I am attempting to output averages within frequency bands using > ft_freqanalysis. I have implemented the two-step solution provided in this > discussion https://mailman.science.ru.nl/pipermail/ > fieldtrip/2016-October/010984.html > resulting in the following code: > > cfg =[]; > cfg.method = 'mtmfft'; > cfg.output = 'pow'; > cfg.taper = 'hanning'; > cfg.channel = 'all'; > cfg.foilim = [fio1 foi2]; > cfg.trials = 'all'; > cfg.keeptrials = 'no'; > freq_avg = ft_freqanalysis(cfg, data_segmented); > > cfg = []; > cfg.avgoverfreq = 'yes'; > freq_avg = ft_freqanalysis(cfg, freq_avg); > > However, when I run this, I get the following error: > > the input is freq data with 73 channels, 41 frequencybins and no timebins > Error using ft_checkdata>freq2raw (line 1315) > not supported for dimord chan_freq > > Error in ft_checkdata (line 432) > data = freq2raw(data); > > Error in ft_freqanalysis (line 217) > data = ft_checkdata(data, 'datatype', {'raw', 'raw+comp', 'mvar'}, > 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); > > > Is there a different way I need to format my data beyond providing the > function with the output of the first iteration of ft_freqanalysis? > > Thank you! > Alea > > -- > Alea C. Skwara, M.A. > PhD Candidate | Saron Lab > http://saronlab.ucdavis.edu/ > > Center for Mind and Brain | University of California, Davis > 267 Cousteau Place | Davis CA 95616 > Cell: (828) 273-8595 > > > > _______________________________________________ > 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 acskwara at ucdavis.edu Wed May 2 19:35:47 2018 From: acskwara at ucdavis.edu (Alea Skwara) Date: Wed, 2 May 2018 10:35:47 -0700 Subject: [FieldTrip] Outputting band averages with ft_freqanalysis In-Reply-To: References: Message-ID: Hi Arjen, Thank you, following ft_freqanalysis with ft_selectdata (and using the .avgoverfreq = 'yes') works. Alea On Tue, May 1, 2018 at 7:33 PM, Arjen Stolk wrote: > Hi Alea, > > Have a look at ft_selectdata, which can do this operation for you. > > Arjen > > > On Tue, May 1, 2018 at 7:05 PM, Alea Skwara wrote: > >> Hi All, >> >> I am attempting to output averages within frequency bands using >> ft_freqanalysis. I have implemented the two-step solution provided in this >> discussion https://mailman.science.ru.nl/pipermail/fieldtrip >> /2016-October/010984.html >> resulting in the following code: >> >> cfg =[]; >> cfg.method = 'mtmfft'; >> cfg.output = 'pow'; >> cfg.taper = 'hanning'; >> cfg.channel = 'all'; >> cfg.foilim = [fio1 foi2]; >> cfg.trials = 'all'; >> cfg.keeptrials = 'no'; >> freq_avg = ft_freqanalysis(cfg, data_segmented); >> >> cfg = []; >> cfg.avgoverfreq = 'yes'; >> freq_avg = ft_freqanalysis(cfg, freq_avg); >> >> However, when I run this, I get the following error: >> >> the input is freq data with 73 channels, 41 frequencybins and no timebins >> Error using ft_checkdata>freq2raw (line 1315) >> not supported for dimord chan_freq >> >> Error in ft_checkdata (line 432) >> data = freq2raw(data); >> >> Error in ft_freqanalysis (line 217) >> data = ft_checkdata(data, 'datatype', {'raw', 'raw+comp', 'mvar'}, >> 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); >> >> >> Is there a different way I need to format my data beyond providing the >> function with the output of the first iteration of ft_freqanalysis? >> >> Thank you! >> Alea >> >> -- >> Alea C. Skwara, M.A. >> PhD Candidate | Saron Lab >> http://saronlab.ucdavis.edu/ >> >> Center for Mind and Brain | University of California, Davis >> 267 Cousteau Place | Davis CA 95616 >> Cell: (828) 273-8595 >> >> >> >> _______________________________________________ >> 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 > -- Alea C. Skwara, M.A. PhD Candidate | Saron Lab http://saronlab.ucdavis.edu/ Center for Mind and Brain | University of California, Davis 267 Cousteau Place | Davis CA 95616 Cell: (828) 273-8595 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcarlapiastra at gmail.com Thu May 3 15:29:22 2018 From: mcarlapiastra at gmail.com (Maria Carla Piastra) Date: Thu, 3 May 2018 15:29:22 +0200 Subject: [FieldTrip] openMEEG path Ubuntu16.04 Message-ID: <874cead0-9c9b-6c0f-7430-554f9af9863d@gmail.com> Dear all, I would like to use openMEEG for computing EEG and MEG forward model solutions on Ubuntu 16.04. I installed following https://github.com/openmeeg/openmeeg. As "/whereis om_assemble/" is giving me /usr/bin. I therefore did "/setenv('PATH', '/usr/bin')/". /W/hen I am launching: /cfg = [];// //cfg.method = 'openmeeg';// //cfg.conductivity = [0.33 0.01 0.33];// //headmodel_bem = ft_prepare_headmodel(cfg, mesh_bem)/ This is the output: /the input is mesh data with multiple surfaces// //reordering the boundaries to: 3 2 1 // ///bin/bash: chmod: command not found// ///bin/bash: ./tp2279842c_636c_485a_ac62_6c2e3c4e7b25.sh: Permission denied// //Warning: an error ocurred while running OpenMEEG // //Error using fread// //Invalid file identifier. Use fopen to generate a valid file identifier.// //Warning: File 'tp54b47429_45d4_47c4_ab6f_3a02b37de78f.bin' not found. // //Warning: File 'tp692ddbba_6d12_4b31_b1ee_f70fc7680936.bin' not found. // //the call to "ft_prepare_headmodel" took 0 seconds and required the additional allocation of an estimated 0 MB// // //headmodel_bem = // // //             bnd: [1x3 struct]// //            cond: [0.3300 0.0100 0.3300]// //    skin_surface: 1// //          source: 3// //            type: 'openmeeg'// //            unit: 'mm'// //             cfg: [1x1 struct]/ Any ideas? Best, Maria Carla -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Thu May 3 17:05:12 2018 From: michelic72 at gmail.com (Cristiano Micheli) Date: Thu, 3 May 2018 17:05:12 +0200 Subject: [FieldTrip] openMEEG path Ubuntu16.04 In-Reply-To: <874cead0-9c9b-6c0f-7430-554f9af9863d@gmail.com> References: <874cead0-9c9b-6c0f-7430-554f9af9863d@gmail.com> Message-ID: Dear Maria Carla it seems that you do not have permissions to write in your temporary files folder. As a consequence the shell file which is called to execute the OpenMEEG commands is not written and cannot be executed. I hope this helps Cris Micheli @MindAffect NovioTech Campus Nijmegen The Netherlands On Thu, May 3, 2018 at 3:29 PM, Maria Carla Piastra wrote: > Dear all, > > I would like to use openMEEG for computing EEG and MEG forward model > solutions on Ubuntu 16.04. > > I installed following https://github.com/openmeeg/openmeeg. > > As "*whereis om_assemble*" is giving me /usr/bin. I therefore did "*setenv('PATH', > '/usr/bin')*". > *W*hen I am launching: > *cfg = [];* > *cfg.method = 'openmeeg';* > *cfg.conductivity = [0.33 0.01 0.33];* > *headmodel_bem = ft_prepare_headmodel(cfg, mesh_bem)* > > This is the output: > > *the input is mesh data with multiple surfaces* > *reordering the boundaries to: 3 2 1 * > */bin/bash: chmod: command not found* > */bin/bash: ./tp2279842c_636c_485a_ac62_6c2e3c4e7b25.sh: Permission denied* > *Warning: an error ocurred while running OpenMEEG * > *Error using fread* > *Invalid file identifier. Use fopen to generate a valid file identifier.* > *Warning: File 'tp54b47429_45d4_47c4_ab6f_3a02b37de78f.bin' not found. * > *Warning: File 'tp692ddbba_6d12_4b31_b1ee_f70fc7680936.bin' not found. * > *the call to "ft_prepare_headmodel" took 0 seconds and required the > additional allocation of an estimated 0 MB* > > *headmodel_bem = * > > * bnd: [1x3 struct]* > * cond: [0.3300 0.0100 0.3300]* > * skin_surface: 1* > * source: 3* > * type: 'openmeeg'* > * unit: 'mm'* > * cfg: [1x1 struct]* > > > Any ideas? > > Best, > > Maria Carla > > _______________________________________________ > 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 christoph.kayser at uni-bielefeld.de Fri May 4 08:41:22 2018 From: christoph.kayser at uni-bielefeld.de (Christoph Kayser) Date: Fri, 04 May 2018 08:41:22 +0200 Subject: [FieldTrip] PostDoc & PhD Position, Cognitive Neuroscience, Bielefeld, Germany Message-ID: <00d601d3e372$ea9b9cc0$bfd2d640$@uni-bielefeld.de> The Department of Cognitive Neuroscience at Bielefeld University, Germany, is advertising a 3-year Postdoctoral position, and a 3-year PhD position in auditory and multisensory neuroimaging studies. We are looking to fill two positions to complement our research on auditory and multisensory perception based on a combination of psychophysics, neuroimaging (EEG) and statistical modelling. The Department for Cognitive Neuroscience is dedicated to understanding the integration of sensory information in the brain. Our studies use state of the art EEG imaging, combined with eyetracking, psychophysical paradigms, and substantive quantitative data analysis to better understand when and how the brain transforms sensory information into a conscious percept. Further details about our research can be found here http://www.uni-bielefeld.de/biologie/cns/ The positions involve all aspects of study design, implementation, data collection, data analysis and the write up of results. Contributions to the supervision of student projects or the preparation of practical courses are also expected. Applicants should have a background in neuroscience, cognitive science, psychology, mathematics, or a relevant discipline. Applicants for the post-doc position should have a doctoral degree or equivalent title. We are especially interested in devotion to advanced quantitative data analysis including the capabilities to program or modify analysis code. The ideal applicant will have a strong analytical background and direct experience using MATLAB. Applicants should have enthusiasm, and a clear, demonstrable capacity for acquiring expertise in these techniques. The positions are funded for 3 years starting ideally around September 2018, at Germany salary grades TV-L E13 (100% for post-doc, 65% for PhD student). Interested candidates please contact Christoph Kayser -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.rimmele at ae.mpg.de Wed May 2 10:48:03 2018 From: johanna.rimmele at ae.mpg.de (Rimmele, Johanna Maria) Date: Wed, 2 May 2018 08:48:03 +0000 Subject: [FieldTrip] PhD position on auditory timing in speech and music at MPIEA Frankfurt Message-ID: <63B92215-CA68-49D2-8E1D-C629CF949609@ae.mpg.de> Dear all, We are currently looking for an excellent candidate for a 3 year Ph.D. position in the Neuroscience Department at the MPI for Empirical Aesthetics in Frankfurt am Main. This is a chance to work in a relentlessly interdisciplinary and exciting place. The project focuses on auditory timing in speech and music using behavioral and neurophysiological measures. For details visit our homepage: https://www.aesthetics.mpg.de/en/the-institute/jobs/phd-position-neuroscience-department.html Please forward this info to interested and skilled candidates or people that might know suitable candidates! Many thanks! All the Best, Johanna _______ Dr. Johanna Rimmele Max-Planck-Institute for Empirical Aesthetics Department of Neuroscience Grüneburgweg 14 D-60322 Frankfurt am Main Phone: +49 69 8300479 323 j.rimmele at aesthetics.mpg.de www.aesthetics.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdhami06 at gmail.com Tue May 8 11:05:54 2018 From: pdhami06 at gmail.com (Paul Dhami) Date: Tue, 8 May 2018 05:05:54 -0400 Subject: [FieldTrip] requested data segment extends over a discontinuous trial boundary Message-ID: Hi FieldTrip, my name is Paul, and I'm a student studying response inhibition in psychiatric disorders, as well as working with corresponding TMS-EEG data. I was able to go through the analysis pipeline just fine with some ERP data (preprocessed before imported to FieldTrip), but when using essentially the same steps for some TMS-EEG data (also preprocessed before being imported into FieldTrip), I ran into the following error at the ft_preprocessing(cfg) command: Error using ft_read_data (line 270) > requested data segment extends over a discontinuous trial boundary > Error in ft_preprocessing (line 582) > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', > begsample, 'endsample', > endsample, 'chanindx', rawindx, 'checkboundary', > strcmp(cfg.continuous, 'no'), > 'dataformat', cfg.dataformat); My cfg that I entered with ft_preprocessing looked like this (altered the filename just for this email): dataset: 'subject1.set' > trialdef: [1×1 struct] > trackusage: 'B8F919AB' > trackconfig: 'off' > checkconfig: 'loose' > checksize: 100000 > showcallinfo: 'yes' > debug: 'no' > outputfilepresent: 'overwrite' > trackcallinfo: 'yes' > trackdatainfo: 'no' > toolbox: [1×1 struct] > notification: [1×1 struct] > progress: [1×1 struct] > callinfo: [1×1 struct] > version: [1×1 struct] > datafile: 'subject1.set' > headerfile: 'subject1.set' > dataformat: 'eeglab_set' > headerformat: 'eeglab_set' > trialfun: @ft_trialfun_general > event: [1×151 struct] > trl: [75×4 double] > Prior code to ft_preprocessing was: cfg = []; > > % adding dataset field to configuration file > cfg.dataset = [myfilepath '/' myfilename]; > %cfg.dataset = 'filename.set' > % adding trialdef information to configuration file > cfg.trialdef.eventtype = 'trigger'; > cfg.trialdef.eventvalue = 128; % TMS trigger > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 0.999; Is there something that I am doing wrong as to why the ERP files were able to be preprocessed just fine where as I am running into this error for the TMS-EEG data? Is this likely related to the TMS-EEG data having been collected in a "pseudo-continuous" manner, and in that case, is it as easy as including the cfg.continuous = 'yes' option (which I noted in a couple similar forum posts)? Any help would be greatly appreciated. Thank you. Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue May 8 15:28:25 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 8 May 2018 15:28:25 +0200 Subject: [FieldTrip] EEG/iEEG/MEG - short survey on data formats you use Message-ID: <44D7960D-DC95-4A7D-975C-3A6F68874F37@donders.ru.nl> Dear colleagues, Several members of the electrophysiology community (EEG, MEG, iEEG) are working on an open specification for storing cognitive electrophysiology data, called the Brain Imaging Data Structure . Its goal is to make our workflows more reproducible, more sharable, and more efficient. The BIDS format is not a new data format, but is a data specification. It should accommodate pre-existing workflows in cognitive neuroscience. As such, we are investigating what data formats researchers use already, and which they'd be willing to use for sharing their data. Please respond to this short (3 question, ~2 minute) survey at the link below, in order to share with us which data formats you currently use in your electrophysiological research. https://goo.gl/forms/Ytr6UmawWvwvIB9R2 If you know of any other interested parties in the cognitive electrophysiology community, please do forward along this link so that we can get a sample from as many people as possible. Thanks very much for your time! Robert, Chris, Cyril, Dora and others -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue May 8 16:53:21 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 8 May 2018 16:53:21 +0200 Subject: [FieldTrip] plot ft_sourceplot figures into a subplot In-Reply-To: References: Message-ID: Dear Hame ft_sourceplot is a high-level function that includes interaction with the data (i.e. clicking). Furthermore, depending on method (ortho/surface/montage/glassbrain/cloud) you will get one or mutliple sub-axes within one figure. So it is not suited for use in a loop with multiple axes or subplots. I know that people are using it to export images to pdf/ps or ai format and then use external software to glue them together. I also find it convenient to save the figures to a bitmap using “print -dpng” and use external software (such as Windows picture viewer) to browse through large numbers of files. I believe this is also mentioned somewhere on http://www.fieldtriptoolbox.org/tutorial/plotting If you want closer control over the figures and different axes within one figure, I recommend you use the lower-level plotting functions that you can find in fieldtrip/plotting. E.g. ft_plot_mesh , which you can give the mesh and the colors you want on each of the vertices or triangles. See also http://www.fieldtriptoolbox.org/reference#from_the_plotting_module best regards, Robert PS please use the fieldtrip mailing list next time, there are many people on it that can help, and providing answers on the list benefits others as well > On 27 Apr 2018, at 14:20, Hame Park wrote: > > Dear Robert > > Hello! > I was trying to make a big figure with many > sourceplots, created from ft_sourceplot with the 'surface' method, > but it seems it always creates a separate figure. > > I tried something like > > h = figure; > ha = nan(length(T), 1); > for t=1:length(T) > ha(t) = subplot(1, length(T), t); > end > > for t=1:length(T) > axes(ha(t)) > ft_sourceplot(cfg, data) > end > > but it still opens up a new figure for ft_sourceplot. > I tried to look into the code, and tried disabling the line > h=figure; but this gave me errors which I couldn't comprehend. > > Any help would be much appreciated! > > Thank you. > Best wishes, > Hame -------------- next part -------------- An HTML attachment was scrubbed... URL: From hame.hame.hame at gmail.com Tue May 8 17:40:16 2018 From: hame.hame.hame at gmail.com (Hame Park) Date: Tue, 8 May 2018 17:40:16 +0200 Subject: [FieldTrip] plot ft_sourceplot figures into a subplot In-Reply-To: References: Message-ID: Dear Robert Thank you! Best regards, Hame On Tue, May 8, 2018 at 4:53 PM, Robert Oostenveld < r.oostenveld at donders.ru.nl> wrote: > Dear Hame > > ft_sourceplot is a high-level function that includes interaction with the > data (i.e. clicking). Furthermore, depending on method > (ortho/surface/montage/glassbrain/cloud) you will get one or mutliple > sub-axes within one figure. So it is not suited for use in a loop with > multiple axes or subplots. > > I know that people are using it to export images to pdf/ps or ai format > and then use external software to glue them together. I also find it > convenient to save the figures to a bitmap using “print -dpng” and use > external software (such as Windows picture viewer) to browse through large > numbers of files. I believe this is also mentioned somewhere on > http://www.fieldtriptoolbox.org/tutorial/plotting > > If you want closer control over the figures and different axes within one > figure, I recommend you use the lower-level plotting functions that you can > find in fieldtrip/plotting. E.g. ft_plot_mesh > , which you can > give the mesh and the colors you want on each of the vertices or triangles. > See also http://www.fieldtriptoolbox.org/reference#from_the_plotting_ > module > > > best regards, > Robert > > PS please use the fieldtrip mailing list next time, there are many people > on it that can help, and providing answers on the list benefits others as > well > > > On 27 Apr 2018, at 14:20, Hame Park wrote: > > Dear Robert > > Hello! > I was trying to make a big figure with many > sourceplots, created from ft_sourceplot with the 'surface' method, > but it seems it always creates a separate figure. > > I tried something like > > h = figure; > ha = nan(length(T), 1); > for t=1:length(T) > ha(t) = subplot(1, length(T), t); > end > > for t=1:length(T) > axes(ha(t)) > ft_sourceplot(cfg, data) > end > > but it still opens up a new figure for ft_sourceplot. > I tried to look into the code, and tried disabling the line > h=figure; but this gave me errors which I couldn't comprehend. > > Any help would be much appreciated! > > Thank you. > Best wishes, > Hame > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.Hanslmayr at bham.ac.uk Wed May 9 14:50:12 2018 From: S.Hanslmayr at bham.ac.uk (Simon Hanslmayr) Date: Wed, 9 May 2018 12:50:12 +0000 Subject: [FieldTrip] PhD position in Birmingham Message-ID: <257F6C65A372A04CA41056EACC0DE7CED874ABCE@EX12.adf.bham.ac.uk> To anyone looking for a PhD position, Applications are sought for a fully-funded PhD position to work with Dr Simon Hanslmayr (University of Birmingham, School of Psychology, http://www.memorybham.com/people/#/simon-hanslmayr/). The project is focussed on generating computational models to simulate single-neuron responses and neural oscillations in the service of memory processes. The work will build on a theoretical framework, termed the Synch/deSync Model which assumes that memory processes are implemented via cortical desynchronization and hippocampal synchronization processes (see Parish et al., 2018). The PhD student will have the opportunity to work with single-unit and EEG data recorded from the human hippocampus in patients suffering from epilepsy. The candidate should have a strong background in computational neuroscience or related area. Apply for this post by sending an email with your CV and a short description (100 words) outlining your skills and motivation to Sophie Watson (Sophie Watson S.Watson.2 at bham.ac.uk). https://www.findaphd.com/search/ProjectDetails.aspx?PJID=97892 Dr. Simon Hanslmayr Reader in Cognitive Neuroscience Royal Society Wolfson Research Merit Award Holder School of Psychology Hills Building 2.37 University of Birmingham Edgbaston Birmingham B15 2TT UK Tel +44 121 4146203 http://www.memorybham.com/people/#/simon-hanslmayr/ [http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 8560 bytes Desc: image001.gif URL: From SSaleh at kesslerfoundation.org Wed May 9 16:29:19 2018 From: SSaleh at kesslerfoundation.org (Soha Saleh - Research Scientist) Date: Wed, 9 May 2018 14:29:19 +0000 Subject: [FieldTrip] Postdoctoral Fellowship in Neurorehabilitation and Neuroimaging Research - Kessler Foundation Message-ID: <92143A403B96384DB97C1AF41F645AD92397BBC9@EXCHANGE.kmrrec.org> Dear all, The Kessler Foundation (West Orange, New Jersey) is recruiting postdoctoral fellows to conduct Neurorehabilitation and Neuroimaging Research. Applications are being accepted for fellowships funded by an Advanced Rehabilitation Research Training (ARRT) grant from the National Institute on Disability and Rehabilitation Research (NIDILRR), and are expected to last for a two-year term. Qualifying candidates must have an earned doctorate in engineering (e.g., biomedical, rehabilitation mechanical), neuroscience, or a related field. Strong candidates will have prior experience in performing neuroimaging research studies in human subjects, as well as some history of publication and presentation of original research. The successful candidate will work on ongoing research that uses neuroimaging to better understand motor related impairment following neurological, neuromuscular and musculoskeletal diseases and injuries, for diverse patient populations including traumatic brain injury, multiple sclerosis, spinal cord injury, cancer, and stroke. To this end, our research uses a multimodality approach that includes neuroimaging (fMRI, MRI, fNIRS, EEG) combined with eye tracking, electrophysiology analysis, and motion analysis. The Kessler Foundation has research-dedicated 3 Tesla MRI scanner, state-of-the-art mobile imaging equipment (EEG, fNIRS), instrumented treadmill with virtual reality (C-Mill), Neurocom Balance Platform, biodex, and is a leader in powered exoskeleton assisted rehabilitation therapy. The successful applicant will also be expected to develop his/her own mentored research project. He/she will work on various aspects of research projects from inception (e.g., study formulation, grant-writing, etc.), through dissemination (conference presentation and manuscript publication). Requirements include: * Background and experience in functional and/or structural MRI image processing (DTI, fMRI), and ideally connectivity analysis (resting state functional connectivity, effective connectivity, graph theory-based analysis) * Experience in programming, preferentially Matlab * Knowledge of statistical data analysis * Excellent written communication skills Preferred experience/qualifications: * Research studies in human subjects, and history of publication and presentation of original research * EEG/EMG/fNIRS data collection and analysis * Biomedical Instrumentation * Neuromuscular rehabilitation; brain and muscle electrophysiology * Image-processing software such as FSL, AFNI, SPM, EEGLAB, Brainstorm Opportunities for collaborating with clinicians on existing or future clinical research are also available. All fellows participate in an extensive training curriculum and didactic offerings. Multidisciplinary mentored training opportunities are individually tailored to achieve specific goals considering each fellow's prior background and interests. Kessler Foundation is a public charity that advances its mission of improving the lives of people with disabilities through research and grant-making programs. The Kessler Foundation is a global leader in medical rehabilitation research and affiliated with the renowned Kessler Institute for Rehabilitation in West Orange, New Jersey and enjoys collaborations with partners at the New Jersey Institute of Technology and Rutgers New Jersey Medical School (RNJMS), Rutgers University in New Jersey. Applicants are encouraged to visit the Foundation's website (http://www.kesslerfoundation.org/research/) to learn about the missions, activities, and resources of the Foundation and its laboratories. Administration of the ARRT fellowships occurs within the academic Department of Physical Medicine and Rehabilitation at RNJMS. As such, fellows enjoy the benefits and academic resources available to all post-doctoral fellows at the Medical School. Fellows may also be recommended for an academic appointment at the rank of Instructor. Initial and informal inquiries about the fellowship may be directed by email to Guang Yue, Ph.D. ARRT Project Director, Kessler Foundation, and Professor at RNJMS GYue at kesslerfoundation.org Applicants for fellowships should refer to the "Neuro-Musculoskeletal Fellowship" and forward * Letter of application * Curriculum Vitae * One-page statement of research interests by email to: career at kesslerfoundation.org or by mail to: Kessler Foundation, Attn: Human Resources 120 Eagle Rock Ave, Suite 100 East Hanover, NJ 07936 Letters of recommendation: At the time of application, candidates should request letters of recommendation from three current or former professional associates to be mailed to the Project Director (address above). Alternatively, applicants may enclose sealed letters of recommendation with mailed applications. Due to limitations in resources, we regret that only candidates whose applications are brought forward by the fellowship committee will be contacted. In addition to citizens and permanent residents of the US, non-citizen nationals, and non-immigrants are eligible to apply provided they can be lawfully employed in the U.S. Thanks, Soha -------------------------------------------------------------------------- Soha Saleh, PhD Research Scientist Human Performance and Engineering Lab Kessler Foundation 1199 Pleasant Valley Way, West Orange, NJ, 07052 Tel: (973) 324 3520 Email: ssaleh at KesslerFoundation.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From mansoureh.aghabeig at yahoo.com Wed May 9 21:19:53 2018 From: mansoureh.aghabeig at yahoo.com (Mansoureh Aghabeig) Date: Wed, 9 May 2018 19:19:53 +0000 (UTC) Subject: [FieldTrip] How can I fix the "the 1/f power spectrum effect" in fieldtrip References: <280532632.1686057.1525893593539.ref@mail.yahoo.com> Message-ID: <280532632.1686057.1525893593539@mail.yahoo.com> Dear Sir/Madam, My name is Mansoureh Aghabeig and I am working in the ICNT lab in Torun, Poland as a Ph.D. student. Currently, I am working on time-frequency analysis with fieldtrip . But I obtained very strange TFR results. Please find the attachment. It is clear in the attached plot the lower frequencies dominate the higher one. In fact, there is the 1/f power spectrum effect. I think one solution for solving this problem is normalizing over power spectrum but I do not know how can I do it in fieldtrip . I would be appreciated if you kindly guide me. Thanks in advance Mansoureh Aghabeig        منصوره آقابیگ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: E124.jpg Type: image/jpeg Size: 32087 bytes Desc: not available URL: From r.oostenveld at donders.ru.nl Thu May 10 09:43:10 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 10 May 2018 09:43:10 +0200 Subject: [FieldTrip] Donders Brain Stimulation Toolkit in Sept 2018 Message-ID: <3F30C7E2-6931-4D41-99CF-3761569196DF@donders.ru.nl> — Please disseminate to PhD students, postdoctoral researchers, and other senior researchers interested in advanced brain stimulation (TMS, TDCS) On 10-13 September 2018 we will host the "Donders Brain Stimulation Toolkit" at the Donders Institute in Nijmegen, the Netherlands. This advanced course is designed for researchers who want to learn advanced transcranial magnetic stimulation (TMS) and/or transcranial current stimulation (tDCS/tACS) techniques. Lectures by expert researchers and hands-on training sessions will provide you with the latest on experimental design, stimulation application, data acquisition and data analysis. We place a special emphasis on state-of-the-art multi-modal techniques including: TMS-EEG; tD/ACS-MEG and tD/ACS-fMRI. Our main program (September 11-13) is therefore aimed at advanced brain stimulation topics. Need a basic refresher on TMS and TD/ACS? We will go over the basics in an extra day prior to the course (September 10). More information, including a preliminary program and registration, can be found at http://www.ru.nl/donders/agenda/donders-tool-kits/vm-tool-kits/donders-brain-stimulation-tool-kit-version-2/ Looking forward to welcoming you in Nijmegen, Ian Cameron _______________________________ Ian Cameron, PhD Senior Researcher Donders Centre for Cognitive Neuroimaging visiting address: Kapittelweg 29, 6525 EN mailing address: P.O. Box 9101, NL-6500 HB Nijmegen, The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From deydhiman794 at gmail.com Thu May 10 21:08:35 2018 From: deydhiman794 at gmail.com (Dhiman Dey) Date: Fri, 11 May 2018 00:38:35 +0530 Subject: [FieldTrip] EEG/MRI dataset Message-ID: I am a final year b.tech student. My project work is Source localization using EEG/MRI signals. I am in search of dataset.If anybody can provide me the dataset,it will be helpful for me. Mailid: deydhiman794 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.kochari at uva.nl Fri May 11 10:17:25 2018 From: a.kochari at uva.nl (Arnold Kochari) Date: Fri, 11 May 2018 10:17:25 +0200 Subject: [FieldTrip] EEG/MRI dataset In-Reply-To: References: Message-ID: Hi Dhiman Dey, Perhaps you can find something suitable here: https://openfmri.org/dataset/. Kind regards, Arnold On Thu, May 10, 2018 at 9:08 PM, Dhiman Dey wrote: > I am a final year b.tech student. > My project work is Source localization using EEG/MRI signals. > I am in search of dataset.If anybody can provide me the dataset,it will be > helpful for me. > > Mailid: deydhiman794 at gmail.com > > _______________________________________________ > 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 nathanweisz at me.com Fri May 11 10:46:45 2018 From: nathanweisz at me.com (Nathan Weisz) Date: Fri, 11 May 2018 10:46:45 +0200 Subject: [FieldTrip] PhD position in Salzburg Message-ID: <6867CF09-C780-4398-8375-31E8E31ADE52@me.com> We are currently seeking a motivated PhD student to join our team to study lipreading processes in normal hearing and deaf individuals using MEG+EEG. Please forward to any potentially interested person. Thanks, Nathan -------------- next part -------------- A non-text attachment was scrubbed... Name: Call_FWF_lipreading.pdf Type: application/pdf Size: 68024 bytes Desc: not available URL: From rssundar at gmail.com Fri May 11 14:13:23 2018 From: rssundar at gmail.com (Shyam Rajagopalan) Date: Fri, 11 May 2018 17:43:23 +0530 Subject: [FieldTrip] EEG/MRI dataset In-Reply-To: References: Message-ID: Hi Dhiman Dey, You may want to check https://paris-saclay-cds.github.io/autism_challenge/ as well. Regards Shyam On Fri, May 11, 2018 at 1:47 PM, Arnold Kochari wrote: > Hi Dhiman Dey, > > Perhaps you can find something suitable here: https://openfmri.org/ > dataset/. > > > Kind regards, > Arnold > > > On Thu, May 10, 2018 at 9:08 PM, Dhiman Dey > wrote: > >> I am a final year b.tech student. >> My project work is Source localization using EEG/MRI signals. >> I am in search of dataset.If anybody can provide me the dataset,it will >> be helpful for me. >> >> Mailid: deydhiman794 at gmail.com >> >> _______________________________________________ >> 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 deydhiman794 at gmail.com Fri May 11 18:28:31 2018 From: deydhiman794 at gmail.com (Dhiman Dey) Date: Fri, 11 May 2018 21:58:31 +0530 Subject: [FieldTrip] EEG/MRI dataset In-Reply-To: References: Message-ID: Thank you Arnold On Fri 11 May, 2018 2:05 pm Arnold Kochari, wrote: > Hi Dhiman Dey, > > Perhaps you can find something suitable here: > https://openfmri.org/dataset/. > > > Kind regards, > Arnold > > > On Thu, May 10, 2018 at 9:08 PM, Dhiman Dey > wrote: > >> I am a final year b.tech student. >> My project work is Source localization using EEG/MRI signals. >> I am in search of dataset.If anybody can provide me the dataset,it will >> be helpful for me. >> >> Mailid: deydhiman794 at gmail.com >> >> _______________________________________________ >> 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 deydhiman794 at gmail.com Fri May 11 18:28:50 2018 From: deydhiman794 at gmail.com (Dhiman Dey) Date: Fri, 11 May 2018 21:58:50 +0530 Subject: [FieldTrip] EEG/MRI dataset In-Reply-To: References: Message-ID: Thank you Shyam On Fri 11 May, 2018 6:05 pm Shyam Rajagopalan, wrote: > Hi Dhiman Dey, > > You may want to check https://paris-saclay-cds.github.io/autism_challenge/ > as well. > > Regards > Shyam > > On Fri, May 11, 2018 at 1:47 PM, Arnold Kochari wrote: > >> Hi Dhiman Dey, >> >> Perhaps you can find something suitable here: >> https://openfmri.org/dataset/. >> >> >> Kind regards, >> Arnold >> >> >> On Thu, May 10, 2018 at 9:08 PM, Dhiman Dey >> wrote: >> >>> I am a final year b.tech student. >>> My project work is Source localization using EEG/MRI signals. >>> I am in search of dataset.If anybody can provide me the dataset,it will >>> be helpful for me. >>> >>> Mailid: deydhiman794 at gmail.com >>> >>> _______________________________________________ >>> 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 Matthias.Franken at UGent.be Mon May 14 14:39:28 2018 From: Matthias.Franken at UGent.be (Matthias Franken) Date: Mon, 14 May 2018 12:39:28 +0000 Subject: [FieldTrip] partial artifact rejection for time-frequency analysis Message-ID: <549818693f0c4c31acabed976edb5fea@xmail303.UGent.be> Dear all, I have an EEG dataset that consists of quite long trials (>20s). Therefore, For artifact rejection I would like to only reject the part of the trial that contains the artifact, rather than throwing away the entire trial, and thus I will use the cfg.artfctdef.method = ‘partial’; option in ft_rejectartifact. However, this leads to some trials being cut in two shorter “trials” (i.e., the part before the artifact and the part after the artifact). I’m guessing this will lead to edge artifacts in my time-frequency analysis, not only at the edges of the original trials, but also at time points where artifacts were cut out. SO I’m not sure how to deal with this. I guess one option would be to perform the time-frequency analysis first, and afterwards cut out the artifacts, although (1) that might lead to the artifact smearing into data points that were not cut out, depending on the time window width during frequency analysis, and (2) the artifacts identified visually using ft_databrowser are define din ample numbers, and the result from ft_freqanalysis downsamples the data. Did anyone face similar issues or have ideas on how to get around this? ________________________________________ Matthias Franken postdoctoral researcher Experimental Psychology Department Ghent University -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon May 14 15:55:35 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 14 May 2018 13:55:35 +0000 Subject: [FieldTrip] partial artifact rejection for time-frequency analysis In-Reply-To: <549818693f0c4c31acabed976edb5fea@xmail303.UGent.be> References: <549818693f0c4c31acabed976edb5fea@xmail303.UGent.be> Message-ID: <9CBD4CAF-5EB2-432D-907B-15E728977F97@donders.ru.nl> Dear Matthias, Don’t worry. The partial rejection method indeed cuts original trials in smaller portions, but it preserves the local time axes, relative to the original trials. Since ft_freqanalysis returns per ‘segment’ TFRs with numeric data only for those portions of data for which the time windows are entirely filled with data (and nans otheriwse, with the average across segments is computed as a nanmean) there is no worry about ‘edge artifacts’ as such. The only thing to keep in the back of your head is that different time-frequency points may end up having slightly different degrees of freedom in the average. Best wishes, Jan-Mathijs On 14 May 2018, at 14:39, Matthias Franken > wrote: Dear all, I have an EEG dataset that consists of quite long trials (>20s). Therefore, For artifact rejection I would like to only reject the part of the trial that contains the artifact, rather than throwing away the entire trial, and thus I will use the cfg.artfctdef.method = ‘partial’; option in ft_rejectartifact. However, this leads to some trials being cut in two shorter “trials” (i.e., the part before the artifact and the part after the artifact). I’m guessing this will lead to edge artifacts in my time-frequency analysis, not only at the edges of the original trials, but also at time points where artifacts were cut out. SO I’m not sure how to deal with this. I guess one option would be to perform the time-frequency analysis first, and afterwards cut out the artifacts, although (1) that might lead to the artifact smearing into data points that were not cut out, depending on the time window width during frequency analysis, and (2) the artifacts identified visually using ft_databrowser are define din ample numbers, and the result from ft_freqanalysis downsamples the data. Did anyone face similar issues or have ideas on how to get around this? ________________________________________ Matthias Franken postdoctoral researcher Experimental Psychology Department Ghent University _______________________________________________ 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 m.manahova at gmail.com Mon May 14 16:04:03 2018 From: m.manahova at gmail.com (Mariya Manahova) Date: Mon, 14 May 2018 16:04:03 +0200 Subject: [FieldTrip] partial artifact rejection for time-frequency analysis In-Reply-To: <549818693f0c4c31acabed976edb5fea@xmail303.UGent.be> References: <549818693f0c4c31acabed976edb5fea@xmail303.UGent.be> Message-ID: Hi Matthias, Perhaps you could try taking the part of the trial you want to reject and replacing the values there with NaNs? Then you'd be able to remove the artifact-related part of the data while keeping your trials of the same length. I know that some FieldTrip functions can deal with NaNs, so this may be a solution. All the best, Marisha On Mon, May 14, 2018 at 3:35 PM Matthias Franken wrote: > Dear all, > > > > I have an EEG dataset that consists of quite long trials (>20s). > Therefore, For artifact rejection I would like to only reject the part of > the trial that contains the artifact, rather than throwing away the entire > trial, and thus I will use the cfg.artfctdef.method = ‘partial’; option in > ft_rejectartifact. > > However, this leads to some trials being cut in two shorter “trials” > (i.e., the part before the artifact and the part after the artifact). I’m > guessing this will lead to edge artifacts in my time-frequency analysis, > not only at the edges of the original trials, but also at time points where > artifacts were cut out. SO I’m not sure how to deal with this. > > > > I guess one option would be to perform the time-frequency analysis first, > and afterwards cut out the artifacts, although (1) that might lead to the > artifact smearing into data points that were not cut out, depending on the > time window width during frequency analysis, and (2) the artifacts > identified visually using ft_databrowser are define din ample numbers, and > the result from ft_freqanalysis downsamples the data. > > > > Did anyone face similar issues or have ideas on how to get around this? > > > > > > > ________________________________________ > Matthias Franken > postdoctoral researcher > Experimental Psychology Department > Ghent University > > > _______________________________________________ > 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 elam4hcp at gmail.com Mon May 14 23:22:26 2018 From: elam4hcp at gmail.com (Jennifer Elam) Date: Mon, 14 May 2018 16:22:26 -0500 Subject: [FieldTrip] Reminder to Register for HCP Course 2018 Message-ID: Only a few weeks remain to register for the *2018 HCP Course: "Exploring the Human Connectome"*. For more info visit the HCP Course 2018 website . A limited number of registrations with accommodation at Worcester College included are available until filled, or May 29 at the latest. HCP Course 2018 will be held June 25 – 29 at the Blavatnik School of Government , at the University of Oxford , in Oxford, UK. The 5-day intensive course of lectures and hands-on practicals is a great opportunity to learn directly from HCP investigators and gain practical experience with the Human Connectome Project's data and approach to multimodal whole brain imaging, processing and analysis. The course is also a great way to get up to speed on HCP tools including Connectome Workbench (v1.3.0 just released!) and sharing your own analyzed imaging datasets via the BALSA database. If you have any questions, please contact us at: hcpcourse at humanconnectome.org We look forward to seeing you in Oxford! Best, 2018 HCP Course Staff -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam at wustl.edu www.humanconnectome.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From fereshte.ramezani at gmail.com Wed May 16 05:59:29 2018 From: fereshte.ramezani at gmail.com (Fereshte) Date: Wed, 16 May 2018 08:29:29 +0430 Subject: [FieldTrip] EEG average In-Reply-To: References: Message-ID: Dear all, I've solved the forward problem for a FEM head model and as a result, obtained the lead field matrix. Now I'm going to do the Dipole Fit approch in order to solve the inverse problem. How can I obtain the ' EEG-avg ' data in the script below which is a part of " http://www.fieldtriptoolbox.org/workshop/baci2017/inverseproblem" due to the forward problem once I solved? Thank you! load elecload sourcemodelload headmodel_bemload leadfield_bemload mri_reslicedload EEG_avg Then we do the dipole fit % Dipole fit cfg = []; cfg.numdipoles = 1; %number of expected cfg.headmodel = headmodel_bem; %the head model cfg.grid = leadfield_bem; %the precomputed leadfield cfg.elec = elec; %the electrode model cfg.latency = 0.025; %the latency of interest dipfit_bem = ft_dipolefitting(cfg,EEG_avg); dipfit_bem.dip ans = pos: [13.958237048680118 34.388465910583285 97.809684095994314] %dipole position mom: [3x1 double ] %dipole moment pot: [74x1 double ] %potential at the electrodes rv: 0.034549469532012 %residual variance unit: 'mm' -------------- next part -------------- An HTML attachment was scrubbed... URL: From uwe.graichen at tu-ilmenau.de Wed May 16 15:42:24 2018 From: uwe.graichen at tu-ilmenau.de (Uwe Graichen) Date: Wed, 16 May 2018 15:42:24 +0200 Subject: [FieldTrip] =?utf-8?q?8th_International_Summer_School_=E2=80=9EMu?= =?utf-8?q?ltimodal_integration_of_brain_measurements_in_research_and_clin?= =?utf-8?q?ical_practice=E2=80=9C?= Message-ID: Dear colleagues, we are pleased to announce the 8th International Summer School in Biomedical Engineering „Multimodal integration of brain measurements in research and clinical practice“, 1st – 12th October 2018 in Chengdu, China. This event stands in the tradition of a series of successful summer schools on hot themes in biomedical engineering, dedicated to intense learning in the fruitful atmosphere of tight interaction between students and world-leading specialists. This year’s summer school is devoted to EEG/MEG source reconstruction technologies in the frame work of multimodal integration of brain measurements in research and clinical practice. In particular, the 8th International Summer School on Biomedical Engineering will focus on methodological approaches and challenges, measurement devices and characteristics, types of underlying theoretic modeling, specifics of data analysis, ability to derive conclusions about neuroscientific meaning. It will cover both theoretical foundations and practical applications. We aim at a thorough understanding of the underlying mechanisms. Thus, we will develop a critical view on current applications and possible future developments. The second important aim of the summer school consists in providing contact with both leading experts in the field and other students with similar interests, thereby facilitating the exchange of ideas on latest developments in the field. Target Group: - PhD students - Advanced Master students - Researchers entering the field of brain measurement and stimulation techniques Further Information about the 7th International Summer School in Biomedical Engineering: www.bme-school.org We would be happy to receive your application. Please pass this announcement to your colleagues who might be interested. Sincerely, Jens Haueisen and Thomas Knösche From jose.herrero66 at gmail.com Wed May 16 18:17:52 2018 From: jose.herrero66 at gmail.com (Jose Herrero) Date: Wed, 16 May 2018 12:17:52 -0400 Subject: [FieldTrip] ft_connectivity_laggedcoherence Message-ID: dear Fieldtrippers, I'm comparing different coherence methods including the fieldtrip method of lagged coherence. running the code with... cfg.method = 'laggedcoherence'; lcoh = ft_connectivityanalysis(cfg, freq) results on... Error using ft_connectivityanalysis (line 375) unknown method laggedcoherence running the code with... lcoh = ft_connectivity_laggedcoherence(cfg, freq) results on: In an assignment A(:) = B, the number of elements in A and B must be the same. Error in ft_connectivity_laggedcoherence (line 213) lagwidth(lagindx) = cfg.lag*cyclelength*lagindx; as 'cfg.lag' is assigned a length equal to the length of the trial (1x15000, single trial). if this method works, is it possible to use it to compute lagged coherence between an external signal (which oscillates at a freq <0.5Hz) and the iEEG brain signal? thanks, JHerr -------------- next part -------------- An HTML attachment was scrubbed... URL: From frsantos at fpce.up.pt Wed May 16 13:16:40 2018 From: frsantos at fpce.up.pt (Fernando Ferreira-Santos) Date: Wed, 16 May 2018 11:16:40 +0000 Subject: [FieldTrip] 2018 Porto EEG/ERP Summer School Message-ID: <2BAB036A9BAEA44984A131DFCE446108021F3E3905@SRVMBX01.fpceup.psi.up.pt> Dear colleagues, The Laboratory of Neuropsychopsysiology at the University of Porto (http://www.fpce.up.pt/labpsi/) is pleased to announce the 7th edition of the International Cognitive and Affective Neurophysiology Summer School: Acquisition, processing, and analysis of EEG signal (https://sites.google.com/view/can-summerschool-porto). This summer school is focused on the application of Electroencephalography (EEG) and Event Related Potential (ERP) techniques to the study of cognitive and affective processes. This 36h course will be fully taught in English and is aimed at an introductory level, so no previous experience with EEG or ERP is required. This year we are introducing a new module on reproducibility and open science practices in EEG/ERP research. This event will take place from 3-7 of September 2018 in the lovely city of Porto. The course is generally fully booked and, as such, we recommend early registration (course places are attributed by order of registration). For additional details and instructions on how to register, please visit the website (via http://www.fpce.up.pt/labpsi/summerschool/ or directly to the course website: https://sites.google.com/view/can-summerschool-porto). Please feel free to pass this information along to students or researchers that may be potentially interested. Thanks you and best wishes, Fernando Ferreira-Santos Professor Auxiliar | Assistant Professor Laboratório de Neuropsicofisiologia | Laboratory of Neuropsychophysiology Faculdade de Psicologia e de Ciências da Educação da Universidade do Porto Faculty of Psychology and Education Sciences - University of Porto Rua Alfredo Allen, 4200-135 Porto, Portugal http://www.fpce.up.pt | frsantos at fpce.up.pt | (+351) 22 607 97 00 (ext. 409) Lab: http://www.fpce.up.pt/labpsi Personal: http://ferreira-santos.eu -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu May 17 09:26:00 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 17 May 2018 07:26:00 +0000 Subject: [FieldTrip] ft_connectivity_laggedcoherence In-Reply-To: References: Message-ID: <01302D06-30B7-40BF-A655-4D280ACC0C13@donders.ru.nl> Dear Jose, As far as I know, this code is not functional. The first author of the paper started the implementation in fieldtrip-style, but never finished it. Also, note that the method itself is not strictly speaking a ‘connectivity’ measure, but it was intended to identify rhythmicity within signals. Best wishes, Jan Mathijs J.M.Schoffelen, MD PhD Associate PI, VIDI-fellow Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 16 May 2018, at 18:17, Jose Herrero > wrote: dear Fieldtrippers, I'm comparing different coherence methods including the fieldtrip method of lagged coherence. running the code with... cfg.method = 'laggedcoherence'; lcoh = ft_connectivityanalysis(cfg, freq) results on... Error using ft_connectivityanalysis (line 375) unknown method laggedcoherence running the code with... lcoh = ft_connectivity_laggedcoherence(cfg, freq) results on: In an assignment A(:) = B, the number of elements in A and B must be the same. Error in ft_connectivity_laggedcoherence (line 213) lagwidth(lagindx) = cfg.lag*cyclelength*lagindx; as 'cfg.lag' is assigned a length equal to the length of the trial (1x15000, single trial). if this method works, is it possible to use it to compute lagged coherence between an external signal (which oscillates at a freq <0.5Hz) and the iEEG brain signal? thanks, JHerr _______________________________________________ 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 jose.herrero66 at gmail.com Thu May 17 14:31:24 2018 From: jose.herrero66 at gmail.com (Jose Herrero) Date: Thu, 17 May 2018 08:31:24 -0400 Subject: [FieldTrip] ft_connectivity_laggedcoherence In-Reply-To: <01302D06-30B7-40BF-A655-4D280ACC0C13@donders.ru.nl> References: <01302D06-30B7-40BF-A655-4D280ACC0C13@donders.ru.nl> Message-ID: thanks Jan Mathijs for your reply, yes not to blame for not finishing up ... a lot of nice work already in his paper! after reading your tutorial ( http://www.fieldtriptoolbox.org/project/guidelines/paper/connectivity_analysis?s[]=coherence&s[]=lags) still would love your thoughts on this. ideally, I'd like to find out whether a specific phase of an ultraslow (<0.5Hz rhythmic external) signal is leading/lagging the phase of the iEEG signal at the same frequency (effective connectivity). Would it be adequate here to use 'granger' over 'pdc' since I'm not interested in the freq domain (as both signals have been filtered <0.5Hz). Note that dominant frequencies between signals differs a lot. Also, interesting to know if there are consistent phase lags in some iEEG electrodes but not others (functional connectivity). which ft measures would you advice particularly if you want to compute phase lags? The Nolte (2004) paper suggested cfg.method = 'coh' & cfg.complex = 'imag' as being a superior method. Is that right for this particular case? Would it be adequate here to use cfg.method='wpli' or 'wpli_debiased' ? I've explored other methods (Guo, 2007, PLoS) but not sure they're adequate for this specific case (where dominant frequencies between signals differs a lot). thanks On Thu, May 17, 2018 at 3:26 AM, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Dear Jose, > As far as I know, this code is not functional. The first author of the > paper started the implementation in fieldtrip-style, but never finished it. > Also, note that the method itself is not strictly speaking a > ‘connectivity’ measure, but it was intended to identify rhythmicity within > signals. > > Best wishes, > Jan Mathijs > > J.M.Schoffelen, MD PhD > Associate PI, VIDI-fellow > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > > On 16 May 2018, at 18:17, Jose Herrero wrote: > > dear Fieldtrippers, > > I'm comparing different coherence methods including the fieldtrip method > of lagged coherence. > > running the code with... > cfg.method = 'laggedcoherence'; > > lcoh = ft_connectivityanalysis(cfg, freq) > results on... > Error using ft_connectivityanalysis (line 375) > > unknown method laggedcoherence > > running the code with... > lcoh = ft_connectivity_laggedcoherence(cfg, freq) > results on: > In an assignment A(:) = B, the number of elements in A and B must be the > same. > Error in ft_connectivity_laggedcoherence (line 213) > lagwidth(lagindx) = cfg.lag*cyclelength*lagindx; > as 'cfg.lag' is assigned a length equal to the length of the trial > (1x15000, single trial). > > if this method works, is it possible to use it to compute lagged coherence > between an external signal (which oscillates at a freq <0.5Hz) and the iEEG > brain signal? > > thanks, > JHerr > > > _______________________________________________ > 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 > -- Jose L Herrero, PhD Department of Neurosurgery Northwell University Hospital Feinstein Institute for Medical Research New York -------------- next part -------------- An HTML attachment was scrubbed... URL: From annekathrinweise at gmail.com Thu May 17 15:06:34 2018 From: annekathrinweise at gmail.com (Annekathrin Weise) Date: Thu, 17 May 2018 15:06:34 +0200 Subject: [FieldTrip] potential bug when using ft_icabrowser - help needed Message-ID: <1a107ce2-873f-8204-454e-a0bfe70deb2b@gmail.com> Dear all, I am interested in using the ft_icabrowser to inpsect ICA components. I run into a potential bug (see my code and the related error messages in the screenshot below). Note that I also used the ft_databrowser to inspect the independent components what worked nicely. So, there seems to be no issue with the data "ica_components' itself. In case you want to have a closer look to efficiently evaluate the problem, you can find the data here. I appreciate any help to find a workaround. Cheers, Anne -- Annekathrin Weise, Dr. Paris-Lodron Universität Salzburg Division of Physiological Psychology Hellbrunnerstraße 34 5020 Salzburg Austria e-mail: annekathrin.weise at sbg.ac.at; annekathrinweise at gmail.com web: http://www.oboblab.at/ https://sites.google.com/site/weiseannekathrin/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hagbbfcodljipehl.png Type: image/png Size: 112378 bytes Desc: not available URL: From radman.thomas at gmail.com Sat May 19 16:04:09 2018 From: radman.thomas at gmail.com (Thomas Radman) Date: Sat, 19 May 2018 10:04:09 -0400 Subject: [FieldTrip] ft_determine_coordsys does not return coordinate system Message-ID: Hello, I would like to use individual MRIs to perform source analysis on EEG data. The problem I have is when importing dicoms into fieldtrip, and then using ft_determine_coordsys, the coordinate system is not returned. How can I determine the coordinate system and align this to my EEG sensors? Also, to use ft_volumerealign in interactive mode to select fiducials I need to know which side is right and which is left. Is it possible to do this if I did not have a vitamin E marker in my scans? Thank you, Tom Radman -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Sat May 19 17:57:41 2018 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Sat, 19 May 2018 08:57:41 -0700 Subject: [FieldTrip] ft_determine_coordsys does not return coordinate system In-Reply-To: References: Message-ID: Hi Thomas, First thing that comes to my mind is step 3 of this ECoG tutorial , which demonstrates how to determine the coordinate system of an anatomical image. You'll need Box 2 from the preprint , and Video 1 . Video 2 addresses your second point, on how to use the coordinate system to find left and right. Hope that helps, Arjen On Sat, May 19, 2018 at 7:04 AM, Thomas Radman wrote: > Hello, > > > > I would like to use individual MRIs to perform source analysis on EEG > data. > > > The problem I have is when importing dicoms into fieldtrip, and then using > ft_determine_coordsys, the coordinate system is not returned. How can I > determine the coordinate system and align this to my EEG sensors? > > > Also, to use ft_volumerealign in interactive mode to select fiducials I > need to know which side is right and which is left. Is it possible to do > this if I did not have a vitamin E marker in my scans? > > > Thank you, > > Tom Radman > > > _______________________________________________ > 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 diana-hime at yandex.ru Sun May 20 17:08:44 2018 From: diana-hime at yandex.ru (=?utf-8?B?LSDQlNC40LDQvdCw?=) Date: Sun, 20 May 2018 18:08:44 +0300 Subject: [FieldTrip] Wavelet spectrum is cut strangely on low frequencies Message-ID: <3893281526828924@web25o.yandex.ru> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: singleplot_TFRwaveA10.png Type: image/png Size: 17727 bytes Desc: not available URL: From julian.keil at gmail.com Sun May 20 17:17:22 2018 From: julian.keil at gmail.com (Julian Keil) Date: Sun, 20 May 2018 17:17:22 +0200 Subject: [FieldTrip] Wavelet spectrum is cut strangely on low frequencies In-Reply-To: <3893281526828924@web25o.yandex.ru> References: <3893281526828924@web25o.yandex.ru> Message-ID: Hi Diana, That is what you would expect given your wavelet settings. The "strange" cutting off of your low frequencies is due to the length of the wavelet combined with the length of your trial. Only frequencies for which your wavelet fits into your trial will be computed. For example, 7 cycles at 1 Hz will need 7s of data to compute, 7 cycles at 10 Hz will need 0.7s. Play around with the cfg.width setting to see the effect of different taper sizes. Good luck, Julian - Диана schrieb am So. 20. Mai 2018 um 17:11: > Hello! > > My name is Diana. Currently I'm triyng to do a wavelet analysis of my > data, which is 128 (129 with reference elctrode) EEG recording. > > The problem is thatthe result looks strangely - the low frequencies are > cut off. Can't understand the reason for this, and should it be this way or > it not. Would be happy with any help) > > The script I use: > > %preprocessing > cfg = []; > cfg.dataset = FileName; > cfg.continuous = 'yes'; %считываем файл как непрерывный > data_preproc = ft_preprocessing(cfg); > > > % deftrial > cfg = []; > cfg.dataset = FileName; > cfg.trialdef.eventtype = 'trigger'; > cfg.trialdef.eventvalue = 'tim0'; > cfg.trialdef.prestim = 0.2; > cfg.trialdef.poststim = 2.2; > > cfg_deftrial = ft_definetrial(cfg); > > data_deftrialed = ft_redefinetrial(cfg_deftrial, data_preproc); > > %wavelet > > cfg = []; > cfg.channel = 'all'; > cfg.method = 'wavelet'; > cfg.width = 7; > cfg.output = 'pow'; > cfg.foi = 1:1:45; > cfg.toi = 1:0.01:2; > TFRwave = ft_freqanalysis(cfg, data_deftrialed); > > > > The wavelet I get: > > > > > > Thanks in advance, Diana. > Undergraduate Student > Department of Biology of MSU > > P.S: Sorry for my english this time... > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: singleplot_TFRwaveA10.png Type: image/png Size: 17727 bytes Desc: not available URL: From a.stolk8 at gmail.com Sun May 20 17:26:30 2018 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Sun, 20 May 2018 08:26:30 -0700 Subject: [FieldTrip] Wavelet spectrum is cut strangely on low frequencies In-Reply-To: <3893281526828924@web25o.yandex.ru> References: <3893281526828924@web25o.yandex.ru> Message-ID: Hi Diana, This is because your time points of interest are close to the boundaries of the original time series, as described here: http://www.fieldtriptoolbox.org/faq/why_does_my_tfr_contain_nans You may want to include more data from your original time series (at call to ft_definetrial / ft_preprocessing) or use smaller spectral windows / fewer wavelet cycles (at ft_frequencyanalysis, spectral resolution permitting). Best regards, Arjen On Sun, May 20, 2018 at 8:08 AM, - Диана wrote: > Hello! > > My name is Diana. Currently I'm triyng to do a wavelet analysis of my > data, which is 128 (129 with reference elctrode) EEG recording. > > The problem is thatthe result looks strangely - the low frequencies are > cut off. Can't understand the reason for this, and should it be this way or > it not. Would be happy with any help) > > The script I use: > > %preprocessing > cfg = []; > cfg.dataset = FileName; > cfg.continuous = 'yes'; %считываем файл как непрерывный > data_preproc = ft_preprocessing(cfg); > > > % deftrial > cfg = []; > cfg.dataset = FileName; > cfg.trialdef.eventtype = 'trigger'; > cfg.trialdef.eventvalue = 'tim0'; > cfg.trialdef.prestim = 0.2; > cfg.trialdef.poststim = 2.2; > > cfg_deftrial = ft_definetrial(cfg); > > data_deftrialed = ft_redefinetrial(cfg_deftrial, data_preproc); > > %wavelet > > cfg = []; > cfg.channel = 'all'; > cfg.method = 'wavelet'; > cfg.width = 7; > cfg.output = 'pow'; > cfg.foi = 1:1:45; > cfg.toi = 1:0.01:2; > TFRwave = ft_freqanalysis(cfg, data_deftrialed); > > > > The wavelet I get: > > > > > > Thanks in advance, Diana. > Undergraduate Student > Department of Biology of MSU > > P.S: Sorry for my english this time... > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: singleplot_TFRwaveA10.png Type: image/png Size: 17727 bytes Desc: not available URL: From diana-hime at yandex.ru Mon May 21 00:02:56 2018 From: diana-hime at yandex.ru (=?utf-8?B?LSDQlNC40LDQvdCw?=) Date: Mon, 21 May 2018 01:02:56 +0300 Subject: [FieldTrip] Wavelet spectrum is cut strangely on low frequencies In-Reply-To: References: <3893281526828924@web25o.yandex.ru> Message-ID: <4339051526853776@web13o.yandex.ru> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: singleplot_TFRwaveA10.png Type: image/png Size: 17727 bytes Desc: not available URL: From deydhiman794 at gmail.com Mon May 21 09:30:01 2018 From: deydhiman794 at gmail.com (Dhiman Dey) Date: Mon, 21 May 2018 13:00:01 +0530 Subject: [FieldTrip] Brain Source Localization using EEG Signals Message-ID: Hello everyone I am doing b.tech final year project on Brain Source Localization using EEG Signals. I am following the FieldTrip Toolbox for this project. The workshop http://www.fieldtriptoolbox.org/workshop/baci2017/forwardproblem provides the solution of my project but they had used MRI dataset(i.e .mri file) instead of EEG dataset(i.e .eeg file) Please provide me the solution using EEG dataset. Thank you. mailid: deydhiman794 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From fereshte.ramezani at gmail.com Mon May 21 09:50:50 2018 From: fereshte.ramezani at gmail.com (Fereshte) Date: Mon, 21 May 2018 12:20:50 +0430 Subject: [FieldTrip] Brain Source Localization using EEG Signals In-Reply-To: References: Message-ID: Hi, This tutorial explains how to create a FEM/BEM head model ( using MRI dataset) for solving forward problem ( to obtain the leadfield) . I think in your case ( using EEG signals) you need to solve the inverse problem which is explained " http://www.fieldtriptoolbox.org/workshop/baci2017/inverseproblem". Cheers On Mon, May 21, 2018 at 12:02 PM Dhiman Dey wrote: > Hello everyone > > I am doing b.tech final year project on Brain Source Localization using > EEG Signals. > I am following the FieldTrip Toolbox for this project. > > The workshop > http://www.fieldtriptoolbox.org/workshop/baci2017/forwardproblem provides > the solution of my project but they had used MRI dataset(i.e .mri file) > instead of EEG dataset(i.e .eeg file) > > Please provide me the solution using EEG dataset. > Thank you. > > mailid: deydhiman794 at gmail.com > _______________________________________________ > 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 fereshte.ramezani at gmail.com Mon May 21 10:42:16 2018 From: fereshte.ramezani at gmail.com (Fereshte) Date: Mon, 21 May 2018 13:12:16 +0430 Subject: [FieldTrip] Normalized source model Message-ID: Dear Experts, Are the output source models of " ft_prepare_sourcemodel" function normalized on the surface by default? Thanks in advance! Regards, F.R -------------- next part -------------- An HTML attachment was scrubbed... URL: From deydhiman794 at gmail.com Mon May 21 11:35:36 2018 From: deydhiman794 at gmail.com (Dhiman Dey) Date: Mon, 21 May 2018 15:05:36 +0530 Subject: [FieldTrip] Brain Source Localization using EEG Signals In-Reply-To: References: Message-ID: Thank you for your reply but for brain source localization at first you need to solve forward problem then proceed with inverse problem. I already saw the workshop for inverse problem where the same MRI dataset is used. Kindly share the solution using EEG dataset. On 21 May 2018 at 13:20, Fereshte wrote: > Hi, > This tutorial explains how to create a FEM/BEM head model ( using MRI > dataset) for solving forward problem ( to obtain the leadfield) . I think > in your case ( using EEG signals) you need to solve the inverse problem > which is explained "http://www.fieldtriptoolbox.org/workshop/baci2017/ > inverseproblem". > Cheers > > On Mon, May 21, 2018 at 12:02 PM Dhiman Dey > wrote: > >> Hello everyone >> >> I am doing b.tech final year project on Brain Source Localization using >> EEG Signals. >> I am following the FieldTrip Toolbox for this project. >> >> The workshop http://www.fieldtriptoolbox.org/workshop/baci2017/ >> forwardproblem provides the solution of my project but they had used MRI >> dataset(i.e .mri file) instead of EEG dataset(i.e .eeg file) >> >> Please provide me the solution using EEG dataset. >> Thank you. >> >> mailid: deydhiman794 at gmail.com >> _______________________________________________ >> 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 paul.sowman at mq.edu.au Mon May 21 12:11:38 2018 From: paul.sowman at mq.edu.au (Paul Sowman) Date: Mon, 21 May 2018 10:11:38 +0000 Subject: [FieldTrip] MEG Professorship in Sydney Message-ID: <80BA9A1C-09D4-403C-83E2-82461BE2C9FD@contoso.com> Professor of Human Neuroscience/Neuroimaging Macquarie University is a vibrant multidisciplinary research environment with significant neuroimaging infrastructure and ample opportunities for training and collaboration. We are seeking a distinguished academic within a speciality of cognitive neuroscience to join a growing group of cognitive scientists, hearing scientists, experimental psychologists, linguists and education researchers making original, innovative and prominent contributions to teaching and research at Macquarie. As a senior member of the team, you will have access to resources including MEG, fMRI, fNIRS and TMS as well as the opportunity to build collaborative networks with specialists within Macquarie University Hospital, located on campus. We welcome applications from academics within any speciality of cognitive neuroscience, including hearing, language, motor control, emotion, memory, executive function, visual attention, perception, and decision-making. Methodological specialty within neuroimaging is open, but ideally the candidate would enhance our strong existing program in MEG imaging, and develop a translational, theory-based neuroimaging program focusing on utilising MEG in their area of interest. How to Apply https://www.seek.com.au/job/36254679 For a confidential discussion about the role and the University’s expectations, please contact Associate Professor Paul Sowman on +61 2 9850 6732 or email paul.sowman at mq.edu.au. Applications Close: Sunday, 24 June 2018 at 11.55pm -- Paul F Sowman Associate Professor Director HDR Deputy Head Department of Cognitive Science Level 3, Room 3.824 Australian Hearing Hub 16 University Drive Macquarie University, NSW 2109, Australia T: +61 2 9850 6732 W: Profile Page W: MQU Stuttering Research Facebook Page -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.daume at uke.de Mon May 21 20:36:20 2018 From: j.daume at uke.de (Jonathan Daume) Date: Mon, 21 May 2018 20:36:20 +0200 Subject: [FieldTrip] potential bug when using ft_icabrowser - help needed In-Reply-To: <1a107ce2-873f-8204-454e-a0bfe70deb2b@gmail.com> References: <1a107ce2-873f-8204-454e-a0bfe70deb2b@gmail.com> Message-ID: <9A9DC1CD-A8F7-43F5-B738-2810AA8EFAE9@uke.de> Hi Anne, There seems to be a problem with ft_prepare_layout as is doesn’t construct the correct sensors layout from your data. However, you can read the layout structure simply from the provided layout file without handing over your MEG data to the function. So just open the icabrowser ("edit ft_icabrowser.m") and change line 53 from lay = ft_prepare_layout(cfglay, comp); to lay = ft_prepare_layout(cfglay); The topotplot function should work again now. Nevertheless, you will still run into problems with the power spectrum (left panel in the figure) as it won’t show any data. I checked your data and saw that every ica component also contains NaNs. This means that the fft analysis will result in only NaNs as well. You may consider to just get rid of them before computing the power spectrum (which is done in lines 102-109). Moreover, the icabrowser was originally coded for trial-based data and only every 5th trial was considered for the power analysis. Otherwise, it just takes too long to plot every single component. However, I saw that your data only contains (continous?) data from a single trial. Computing the fft of the whole recording would take ages. So, in case your data is continuous data from resting state for example, you may also consider to divide your data into epochs and take only every 5th epoch or so for the power analysis. I have coded something in that direction for you but I am not sure what kind of data you have and if it suits your data. I just divided the data in epochs of 1s length and took every 5th epoch for the analysis. Please find the code below. You may just further adjust the code so that it better suits your data. Change line 34 from fft_data = cat(2,comp.trial{1:5:end}); to fft_data = comp.trial{1}; And lines 104 - 106 from Fs = comp.fsample; N = floor(size(fft_data,2)); xdft = fft(fft_data(i,:)); to comp_data = fft_data(i,~isnan(fft_data(i,:))); % kick out all NaNs first epochJump = 5; % how many trials to jump over? numEpochs = size(comp_data,2)/comp.fsample; fft_data_i = []; for i_epoch = 1:epochJump:numEpochs epochdata = comp_data((i_epoch-1)*comp.fsample+1:i_epoch*comp.fsample); fft_data_i = [fft_data_i,epochdata]; end N = floor(size(fft_data_i,2)); xdft = fft(fft_data_i); Or you just download the edited file from here . :) Hope this helps! Please get in touch with me if you have any further question. Cheers, Jonathan ----- Jonathan Daume, PhD Dept. of Neurophysiology and Pathophysiology University Medical Center Hamburg Eppendorf Martinistr. 52 20246 Hamburg Germany Phone: +49-40-7410-55856 Email: j.daume at uke.de www.uke.de > Am 17.05.2018 um 15:06 schrieb Annekathrin Weise : > > Dear all, > > I am interested in using the ft_icabrowser to inpsect ICA components. > > I run into a potential bug (see my code and the related error messages in the screenshot below). > > Note that I also used the ft_databrowser to inspect the independent components what worked nicely. So, there seems to be no issue with the data "ica_components' itself. > > In case you want to have a closer look to efficiently evaluate the problem, you can find the data here. > I appreciate any help to find a workaround. > > Cheers, > > Anne > > > > -- > Annekathrin Weise, Dr. > > Paris-Lodron Universität Salzburg > Division of Physiological Psychology > Hellbrunnerstraße 34 > 5020 Salzburg > Austria > > e-mail: annekathrin.weise at sbg.ac.at ; > annekathrinweise at gmail.com > > web: > http://www.oboblab.at/ > https://sites.google.com/site/weiseannekathrin/ > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Martina Saurin (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING -------------- next part -------------- An HTML attachment was scrubbed... URL: From radman.thomas at gmail.com Tue May 22 00:53:03 2018 From: radman.thomas at gmail.com (Thomas Radman) Date: Mon, 21 May 2018 18:53:03 -0400 Subject: [FieldTrip] Brain segmentation has strange spikes in it Message-ID: Hello, I am trying to segment an individual subject's MRI following this tutorial: http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting However, when plotting the mesh of the scalp segmentation I get these horrible disfigurations that are not in the original MRI. Here is a screenshot: These are the steps I'm taking mri=ft_read_mri( '/data/radmantc/projects/T1_mni.nii') mri.coordsys='mni' cfg = []; cfg.resolution = 1; mri_resliced = ft_volumereslice(cfg, mri); figure ft_sourceplot([], mri_resliced); %volume conduction model cfg = []; cfg.output = {'brain', 'skull', 'scalp'}; mri_segmented = ft_volumesegment(cfg, mri_resliced); % copy the anatomy into the segmented mri mri_segmented.anatomy = mri_resliced.anatomy; %reconstruct the three triangulated meshes. cfg = []; cfg.method = 'projectmesh'; cfg.tissue = 'brain'; cfg.numvertices = 3000; mesh_eeg(1) = ft_prepare_mesh(cfg, mri_segmented); cfg.tissue = 'skull'; cfg.numvertices = 2000; mesh_eeg(2) = ft_prepare_mesh(cfg, mri_segmented); cfg.tissue = 'scalp'; cfg.numvertices = 1000; mesh_eeg(3) = ft_prepare_mesh(cfg, mri_segmented); figure ft_plot_mesh(mesh_eeg(1), 'edgecolor', 'none', 'facecolor', 'r') ft_plot_mesh(mesh_eeg(2), 'edgecolor', 'none', 'facecolor', 'g') ft_plot_mesh(mesh_eeg(3), 'edgecolor', 'none', 'facecolor', 'b') %this is the only mesh that is distorted alpha 0.3 Also, can someone tell me how to respond to any replies I might get. In previous posts, I only see the replies in the listserv digest emails. Do I create a new email with the subject line of this case intact? I don't get an email directly from the person sending the reply to my email, I only see it in the digest. Thank you for the help, Thomas Radman -------------- next part -------------- An HTML attachment was scrubbed... URL: From w.kruijne at gmail.com Tue May 22 12:37:03 2018 From: w.kruijne at gmail.com (Wouter Kruijne) Date: Tue, 22 May 2018 12:37:03 +0200 Subject: [FieldTrip] artifact detection -- computing the accumulated z Message-ID: Hi everyone, When playing around with different ways of rejecting (muscle) artifacts, I came across something in the tutorial + code that I do not fully understand. The tutorial ( http://www.fieldtriptoolbox.org/tutorial/automatic_artifact_rejection#iii_z-transforming_the_filtered_data_and_averaging_it_over_channels ) states that: > 4. Per timepoint these z-values are averaged. Since an artifact might > occur on any and often on more than one electrode (think of eyeblinks and > muscle artifacts), averaging z-values over channels/electrodes allows > evidence for an artifact to accumulate. > ​This line of reasoning makes perfect sense to me. However, in the subsequent mathematical description, and in the implementation, averaging isn't applied at all: instead, a scaled summation is computed. zsum = SUM_{ch in C} = z(ch,t)/sqrt(C) ​ where C is the number of channels [forgive my math editing skills] . I fail to understand why the accumulated z-score uses a division by the _sqrt_ of the number of channels, rather than simple averaging. In fact, the potential downsides I see are: - The reported z-value, and the one used for thresholding does not correspond to the traditional interpretation of z. - The value of a 'good' z-threshold value is dependent on the number of channels, as this changes the scaling. - Should we wish to use the channel-level z-scores for identifying channels affected by the artefact, the accumulated threshold value now has a different scale than the channel-level z-values. Am I missing something? What are the upsides of the sqrt scaling? Thank you! Wouter -------------- next part -------------- An HTML attachment was scrubbed... URL: From antonio.tavella at virgilio.it Tue May 22 14:29:24 2018 From: antonio.tavella at virgilio.it (antonio.tavella at virgilio.it) Date: Tue, 22 May 2018 14:29:24 +0200 (CEST) Subject: [FieldTrip] Research assistantship with possible PhD scholarship Message-ID: <3844204.243454.1526992165001@mail.virgilio.it> Apologies for multiple posting The Group of Psychiatric Neuroscience at the University of Bari Aldo Moro will publish a call for a 1-year long Research Assistant position, renewable up to 4 years, in the field of Brain Imaging (MRI & MEG). Expressions of interest are welcome before June 30th. Candidates who are in the process of writing up their master thesis are encouraged to apply. The expected starting date is September 2018. Research Assistants interested in pursuing a PhD at our department will have the opportunity to enroll in the Doctoral School in November, following positive evaluation. The Group of Psychiatric Neuroscience is led by Prof. Alessandro Bertolino and Prof. Giuseppe Blasi and investigates the association of genetic variability with systems-level phenotypes, including structural and functional Magnetic Resonance Imaging, Diffusion Tensor Imaging, Arterial Spin Labeling, and Magnetoencephalography. The Group of Psychiatric Neuroscience has access to and routinely tests psychiatric patients, relatives of patients, and individuals at risk for psychosis. The department has an in-house Elekta Triux magnetoencephalography installed in October 2016 with a dedicated technician. The Research Assistant will work in the lab of Brain Imaging, Networks, and Data mining (BIND) directed by Dr. Giulio Pergola, with the aim to investigate the biological basis of major psychiatric disorders by integrating multimodal data (genetic variation, gene expression, structural and functional MRI, MEG, and neuropsychology). The Research Assistant will contribute to neuroimaging data acquisition and analysis for projects funded both at local and European level (for recent articles from the lab, see [1], [2], [3]). The ideal candidate is a young graduate interested in neuroimaging, with a Master’s Degree in Neuroscience, Psychology, Medicine, Biotechnology, Applied Physics, or related fields. Knowledge of statistics and skills regarding the integration of imaging and machine learning are a plus. We expect the successful candidate to be motivated and research-oriented. It is equally important to have a team-working attitude and a motivation to fit in the group. Knowledge of Italian is not required, as the lab already hosts two international PhD students and research meetings are held in English. Bari is a sunny city located by the sea in the east of southern Italy, and the third greatest city south of Rome. The cost of living is comparatively low relative to Italian standards. The net monthly salary of the Research Assistant will be > 1400 EUR. Please contact Dr. Giulio Pergola sending a CV and the contact details of at least two references if you would like to have more information on the position and on the ongoing projects (giulio.pergola at uniba.it mailto:giulio.pergola at uniba.it ). -------------- next part -------------- An HTML attachment was scrubbed... URL: From jose.herrero66 at gmail.com Tue May 22 15:42:28 2018 From: jose.herrero66 at gmail.com (Jose Herrero) Date: Tue, 22 May 2018 09:42:28 -0400 Subject: [FieldTrip] use_simulated_erps_to_explore_cluster_statistics ERROR Message-ID: Dear FT, after running the tutorial example/use_simulated_erps_to_explore_cluster_statistics.txt Error using ft_math (line 151) the requested parameter is not present in the data has anybody encounter this b4? thanks, JHerr -------------- next part -------------- An HTML attachment was scrubbed... URL: From mailtome.2113 at gmail.com Wed May 23 04:08:37 2018 From: mailtome.2113 at gmail.com (Arti Abhishek) Date: Wed, 23 May 2018 12:08:37 +1000 Subject: [FieldTrip] xdf format for EEG data Message-ID: Dear fieldtrip development team, I was wondering whether there is a plan to support xdf file format for the EEG data (eg: SMARTING system) in the future releases of fieldtrip? Thanks, Arti -------------- next part -------------- An HTML attachment was scrubbed... URL: From laetitia.grabot at gmail.com Wed May 23 13:42:56 2018 From: laetitia.grabot at gmail.com (Laetitia Grabot) Date: Wed, 23 May 2018 13:42:56 +0200 Subject: [FieldTrip] Error while reading in Fieldtrip an epochs file created with mne-python Message-ID: Dear all, I'm trying to read in Fieldtrip an Elekta Neuromag epochs file (.fif) created with mne-python (MEG and EEG data file). I used the following snippet of code, and got the following error: cfg = []; cfg.dataset = filename; data = ft_preprocessing(cfg); Error using fiff_read_epochs (line 47) Could not find epochs data Error in fiff_read_epochs (line 47) error(me,'Could not find epochs data'); Error in ft_read_header (line 1846) epochs = fiff_read_epochs(filename); Error in ft_read_header (line 125) hdr{i} = ft_read_header(filename{i}, varargin{:}); Error in ft_preprocessing (line 397) hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat,... I saw that a former thread reported the same error, but it seems that the code was changed meanwhile. I'm using Matlab R2017a ver 9.2 and the Fieldtrip version dated from 16-05-2018. Here you can download the epochs file I used. It would be very helpful is someone knows from where this problem could come. Thank you very much, Best, Laetitia -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.homolle at donders.ru.nl Wed May 23 14:01:04 2018 From: s.homolle at donders.ru.nl (Simon Homolle) Date: Wed, 23 May 2018 14:01:04 +0200 Subject: [FieldTrip] Brain segmentation has strange spikes in it In-Reply-To: References: Message-ID: Dear Thomas, unfortunately I cannot see the figure you send. But from the title of the email I think i have some suggestions for you. > %volume conduction model > cfg = []; > cfg.output = {'brain', 'skull', 'scalp'}; > mri_segmented = ft_volumesegment(cfg, mri_resliced); for this segment you can play around with to make the the tissues more smooth % cfg.brainsmooth = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5) % cfg.scalpsmooth = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5) % cfg.skullsmooth = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5) Or you can change the thresholds for the tissues % cfg.brainthreshold = 'no', or scalar, relative threshold value which is used to threshold the % tpm in order to create a volumetric brainmask (see below), (default = 0.5) % cfg.scalpthreshold = 'no', or scalar, relative threshold value which is used to threshold the % anatomical data in order to create a volumetric scalpmask (see below), % (default = 0.1) % cfg.skullthreshold = 'no', or scalar, relative threshold value which is used to threshold the % anatomical data in order to create a volumetric scalpmask (see below), % (default = 0.5). this parameter is only used when % the segmetnation contains 6 tissue types, % including 'bone’, > %reconstruct the three triangulated meshes. > cfg = []; > cfg.method = 'projectmesh'; > cfg.tissue = 'brain'; > cfg.numvertices = 3000; > mesh_eeg(1) = ft_prepare_mesh(cfg, mri_segmented); > > cfg.tissue = 'skull'; > cfg.numvertices = 2000; > mesh_eeg(2) = ft_prepare_mesh(cfg, mri_segmented); > > cfg.tissue = 'scalp'; > cfg.numvertices = 1000; > mesh_eeg(3) = ft_prepare_mesh(cfg, mri_segmented); If the previous steps to not solve your problems, you can also try to change something in the method % cfg.method = string, can be 'interactive', 'projectmesh', 'iso2mesh', 'isosurface', % 'headshape', 'hexahedral', 'tetrahedral', 'cortexhull' Cheers, Simon Homölle PhD Candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Phone: +31-(0)24-36-65059 > On 22 May 2018, at 00:53, Thomas Radman wrote: > > Hello, > > I am trying to segment an individual subject's MRI following this tutorial: > http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting > > However, when plotting the mesh of the scalp segmentation I get these horrible disfigurations that are not in the original MRI. Here is a screenshot: > > > > These are the steps I'm taking > mri=ft_read_mri( '/data/radmantc/projects/T1_mni.nii') > mri.coordsys='mni' > > cfg = []; > cfg.resolution = 1; > mri_resliced = ft_volumereslice(cfg, mri); > figure > ft_sourceplot([], mri_resliced); > > %volume conduction model > cfg = []; > cfg.output = {'brain', 'skull', 'scalp'}; > mri_segmented = ft_volumesegment(cfg, mri_resliced); > > % copy the anatomy into the segmented mri > mri_segmented.anatomy = mri_resliced.anatomy; > > %reconstruct the three triangulated meshes. > cfg = []; > cfg.method = 'projectmesh'; > cfg.tissue = 'brain'; > cfg.numvertices = 3000; > mesh_eeg(1) = ft_prepare_mesh(cfg, mri_segmented); > > cfg.tissue = 'skull'; > cfg.numvertices = 2000; > mesh_eeg(2) = ft_prepare_mesh(cfg, mri_segmented); > > cfg.tissue = 'scalp'; > cfg.numvertices = 1000; > mesh_eeg(3) = ft_prepare_mesh(cfg, mri_segmented); > > figure > ft_plot_mesh(mesh_eeg(1), 'edgecolor', 'none', 'facecolor', 'r') > ft_plot_mesh(mesh_eeg(2), 'edgecolor', 'none', 'facecolor', 'g') > ft_plot_mesh(mesh_eeg(3), 'edgecolor', 'none', 'facecolor', 'b') %this is the only mesh that is distorted > alpha 0.3 > > Also, can someone tell me how to respond to any replies I might get. In previous posts, I only see the replies in the listserv digest emails. Do I create a new email with the subject line of this case intact? I don't get an email directly from the person sending the reply to my email, I only see it in the digest. > > Thank you for the help, > Thomas Radman > > _______________________________________________ > 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 fereshte.ramezani at gmail.com Sat May 26 03:09:03 2018 From: fereshte.ramezani at gmail.com (Fereshte) Date: Sat, 26 May 2018 05:39:03 +0430 Subject: [FieldTrip] Project numerical values on a cortical mesh Message-ID: Dear Experts, I have assigned numerical values to 1000 vertices of a cortical mesh ( a matrix of 1000 rows and 4 columns; which the first 3 columns show the position of each vertex and the last column shows the numerical value) .How can I project and show these numerical values on the cortical mesh? Thanks in advance! Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From rhancock at email.arizona.edu Wed May 30 00:51:22 2018 From: rhancock at email.arizona.edu (Roeland Hancock) Date: Tue, 29 May 2018 18:51:22 -0400 Subject: [FieldTrip] Postdoctoral Scholar positions in neuroimaging Message-ID: NIDL and brainLENS-east labs (Neurobiology of Individual Differences in Language Lab http://nidl-lab.org, PI: Roeland Hancock PhD; and Laboratory for Learning Engineering and Neural Systems http://brainlens.org, PI: Fumiko Hoeft MD PhD) at University of Connecticut’s Brain Imaging Research Center (UCONN’s BIRC) are seeking: (1) two full-time neuroimaging postdoctoral fellows, and (2) two full-time Research Coordinators. BIRC is also seeking one full-time IT staff. *TWO NEUROIMAGING POSTDOC POSITIONS @ UCONN* We are seeking two postdoctoral scholars. The postdocs will manage and execute a large-scale neuroimaging project investigating the neurobiological mechanisms underlying: (1) language, literacy and cognition in generally healthy young adults using multimodal neuroimaging techniques such as MRI, MRS and TMS (“Perturbation Postdoc”); or (2) intergenerational transmission of language and literacy in parent-offspring dyads using MRI techniques (“Intergenerational Postdoc”). In addition, the successful candidates will have the opportunity to be involved in other federally and non-federally funded-research projects in the laboratories, gain experience in grant and manuscript writing and large-scale project management, outreach and community engagement projects, and access to a wealth of archival developmental and longitudinal neuroimaging data on language and literacy. *Required qualifications:* · PhD or equivalent in cognitive and systems neurosciences, computer science, engineering, psychology or a closely related field · Computational skills, including knowledge of at least one programming language and Unix commands · Strong written and verbal communication skills · Leadership and organizational skills *Preferred qualifications:* · Exceptional skills in collecting and analyzing MRI, MRS, and/or TMS data · Experience in M/EEG · Documented history of productivity and leadership · Advanced knowledge and expertise in statistics, e.g. multivariate statistics, behavioral genetics, Bayesian and Monte Carlo methods The position will be formally advertised at a later date. In the meantime, interested candidates should email *info at nidl-lab.org * with *"[Postdoc Job (YOUR FULL NAME)]" in the subject line*. In the email they should include (a) a current CV, (b) a one-page cover letter describing qualifications, interest, career goals and which postdoc position they are interested in (refer to as *“Perturbation Postdoc/Project” *or *“Intergenerational Postdoc/Project”)*, and (c) a list of 3 potential referees with their contact information. The position can begin immediately. *Postdoctoral scholars from the lab have gone onto a range of research faculty and imaging director positions at institutions such as Stanford, Caltech, Boston College, and University of Texas.* *The University of Connecticut is committed to building and supporting a multicultural and diverse community of students, faculty and staff. The diversity of students, faculty and staff continues to increase, as does the number of honor students, valedictorians and salutatorians who consistently make UConn their top choice. More than 100 research centers and instates serve the University’s teaching, research, diversity, and outreach missions, leading to UConn’s ranking as one of the nation’s top research universities. UConn’s faculty and staff are the critical link to fostering and expanding our vibrant, multicultural and diverse University community. As an Affirmative Action/Equal Employment Opportunity employer, UConn encourages applications from women, veterans, people with disabilities and members of traditionally underrepresented populations.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.homolle at donders.ru.nl Wed May 30 18:23:47 2018 From: s.homolle at donders.ru.nl (Simon Homolle) Date: Wed, 30 May 2018 18:23:47 +0200 Subject: [FieldTrip] EEG and MEG Source Reconstruction with FieldTrip @OHBM2018 Message-ID: <9A1E8D0A-EEA2-4211-AF4D-D6AC6EE257CB@donders.ru.nl> Dear all, on 17 June 2018 we will host a workshop at the OHBM2018 conference . The course is aimed at researchers who want to learn how to do MEG and/or EEG source reconstruction. We expect that you know the basics of MATLAB and that you already have experience with MEG/EEG preprocessing and analysis. In this intense one-day workshop we will explain state-of-the-art MEG and EEG source reconstruction methods. The workshop will consist of a number of lectures, followed by hands-on sessions in which you will be tutored through the complete analysis of a MEG, EEG and MRI data set using the FieldTrip toolbox. As the focus is on source reconstruction, topics that will NOT be covered in great detail are segmenting, artifact handling, averaging, frequency and time-frequency analysis, statistics. For the hands-on sessions you should bring a laptop with MATLAB installed. More information about the program can be found at the OHBM website or on the FieldTrip website. Best regards, Maria Carla Piastra1 , Sophie Schrader1 and Simon Homölle2 1 Institute for Biomagnetism and Biosignalanalysis, University of Münster, Münster, Germany. 2 Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands. -------------- next part -------------- An HTML attachment was scrubbed... URL: From elam4hcp at gmail.com Wed May 30 21:08:48 2018 From: elam4hcp at gmail.com (Jennifer Elam) Date: Wed, 30 May 2018 14:08:48 -0500 Subject: [FieldTrip] Spaces added, register today for HCP Course 2018! Message-ID: If you are considering joining us for the *2018 HCP Course: "Exploring the Human Connectome"* June 25 – 29 at the University of Oxford , a few additional lodging rooms at Worcester College have opened up for just $675 for 6 nights, first come first served. For more info and to register visit the HCP Course 2018 website . We will continue to take registrations for the course until our venue at the Blavatnik School of Government is full. HCP Course 2018 is a 5-day intensive course of lectures and hands-on practicals and your best opportunity to learn directly from HCP investigators and gain practical experience with the Human Connectome Project's data and approach to multimodal whole brain imaging, processing and analysis and to get up to speed on HCP tools including Connectome Workbench (v1.3.0 just released!) and sharing your own analyzed imaging datasets via the BALSA database. If you have any questions, please contact us at: hcpcourse at humanconnectome. org We look forward to seeing you in Oxford! Best, 2018 HCP Course Staff -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam at wustl.edu www.humanconnectome.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu May 31 10:00:54 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 31 May 2018 10:00:54 +0200 Subject: [FieldTrip] Project numerical values on a cortical mesh In-Reply-To: References: Message-ID: Dear Fereshte The mesh should be described with both vertices (points in 3-D space) and triangles (the specification how these points form a surface). If your values are an Nx1 vector and your mesh is mesh.pos = Nx3 % position of the vertices mesh.pos = Mx3 % indices into the vertices that together form M triangles then you can do ft_plot_mesh(mesh, ‘vertexcolor’, val) which uses one of the low level functions in the plotting module. If you organize your data as source structure (e.g. used for reconstructions of cortical activity) you could also use the high-level ft_sourceplot. See "help ft_datatype_source" for documentation on the source structure. best regards Robert > On 26 May 2018, at 03:09, Fereshte wrote: > > Dear Experts, > I have assigned numerical values to 1000 vertices of a cortical mesh ( a matrix of 1000 rows and 4 columns; which the first 3 columns show the position of each vertex and the last column shows the numerical value) .How can I project and show these numerical values on the cortical mesh? > Thanks in advance! > Regards > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Thu May 31 10:03:20 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 31 May 2018 10:03:20 +0200 Subject: [FieldTrip] Error while reading in Fieldtrip an epochs file created with mne-python In-Reply-To: References: Message-ID: Hi Laetitia The code you are referring to is fiff_read_epochs, which is in fieldtrip/external/mne. The external toolboxes are not maintained by the FieldTrip developpers themselves, only included for convenience. Please contact the maintaners at https://github.com/mne-tools/mne-matlab best regards, Robert > On 23 May 2018, at 13:42, Laetitia Grabot wrote: > > Dear all, > > I'm trying to read in Fieldtrip an Elekta Neuromag epochs file (.fif) created with mne-python (MEG and EEG data file). I used the following snippet of code, and got the following error: > > cfg = []; > cfg.dataset = filename; > data = ft_preprocessing(cfg); > > Error using fiff_read_epochs (line 47) > Could not find epochs data > Error in fiff_read_epochs (line 47) > error(me,'Could not find epochs data'); > Error in ft_read_header (line 1846) > epochs = fiff_read_epochs(filename); > Error in ft_read_header (line 125) > hdr{i} = ft_read_header(filename{i}, varargin{:}); > Error in ft_preprocessing (line 397) > hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat,... > > I saw that a former thread reported the same error, but it seems that the code was changed meanwhile. > I'm using Matlab R2017a ver 9.2 and the Fieldtrip version dated from 16-05-2018. Here you can download the epochs file I used. > It would be very helpful is someone knows from where this problem could come. > > Thank you very much, > Best, > Laetitia > _______________________________________________ > 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 Thu May 31 10:08:54 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 31 May 2018 10:08:54 +0200 Subject: [FieldTrip] xdf format for EEG data In-Reply-To: References: Message-ID: <69E5203E-986D-4455-B2BC-B5EF1393C31A@donders.ru.nl> Hi Arti, It would be nice to support the XDF format, and I think it would not be much work as some matlab code is already available here Since you probably have access to XDF data files, it would be great if you could implement this. Please see this FAQ on how to extend (start with ft_filetype and then add it to ft_read_header, data and event). On the git tutorial you can find how to submit the change to the code for inclusion in the release version. thanks Robert > On 23 May 2018, at 04:08, Arti Abhishek wrote: > > Dear fieldtrip development team, > > I was wondering whether there is a plan to support xdf file format for the EEG data (eg: SMARTING system) in the future releases of fieldtrip? > > Thanks, > Arti > > _______________________________________________ > 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 Tue May 1 10:49:44 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 1 May 2018 08:49:44 +0000 Subject: [FieldTrip] ft_freqanalysis fourier rpttap to rpt conversion? In-Reply-To: References: Message-ID: <92BEAED0-FD4D-44E5-80A3-81F63803596D@donders.ru.nl> Hi John, Yes, it is forced as a preventive measure. Averaging Fourier coefficients across tapers is not allowed. Best wishes, Jan-Mathijs On 27 Apr 2018, at 05:13, John Nguyen > wrote: Hi, I noticed that it's not an option to remove the tapers if the output is "fourier". Is this because the resulting output won't be a true Fourier if the tapers are removed, and is forced as a preventive measure? I was looking to reduce my fourier size by removing the tapers but not the trials, is there a danger to this? Thank you! John Nguyen _______________________________________________ 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 bioeng.yoosofzadeh at gmail.com Wed May 2 00:00:51 2018 From: bioeng.yoosofzadeh at gmail.com (bioeng.yoosofzadeh at gmail.com) Date: Tue, 1 May 2018 17:00:51 -0500 Subject: [FieldTrip] Issue in realigning MRI Message-ID: <038601d3e197$decb8ef0$9c62acd0$@gmail.com> Dear FT experts, I am not able to realign a T1 scan using the fiducial points and headshapes of a 4D/BTI system, can anyone help me on this? The "interactive" realignment helped a lot, but the end result was not perfect! Here's what I have tried,: individual_mri = ft_read_mri(mripath); % ..\MEG_4D\C-101_T1.nii ft_sourceplot([], individual_mri); cfg = []; cfg.method = 'flip'; mri.coordsys = '4d'; individual_mri = ft_volumereslice(cfg, individual_mri); ft_sourceplot([], individual_mri); individual_mri = ft_convert_units(individual_mri, 'm'); headshape = ft_read_headshape(headpath); % ..\MEG_4D\hs_file mri_fids = headshape.fid.pos; cfg = []; cfg.fiducial.nas = mri_fids(1,:); cfg.fiducial.lpa = mri_fids(2,:); cfg.fiducial.rpa = mri_fids(3,:); cfg.coordsys = '4d'; cfg.method = 'fiducial'; mri_realigned = ft_volumerealign(cfg, individual_mri); cfg = []; cfg.coordsys = '4d'; cfg.headshape = headshape; cfg.method = 'headshape'; mri_realigned = ft_volumerealign(cfg, individual_mri); % check that the MRI is consistent after realignment ft_determine_coordsys(mri_realigned, 'interactive', 'no'); hold on; drawnow; ft_plot_headshape(headshape); Data can be found at, https://www.dropbox.com/sh/e74pt2uc08q6z4q/AAB3fkp_9gvJxi-YtO0muRSca?dl=0 Best, Vahab -------------- next part -------------- An HTML attachment was scrubbed... URL: From acskwara at ucdavis.edu Wed May 2 04:05:21 2018 From: acskwara at ucdavis.edu (Alea Skwara) Date: Tue, 1 May 2018 19:05:21 -0700 Subject: [FieldTrip] Outputting band averages with ft_freqanalysis Message-ID: Hi All, I am attempting to output averages within frequency bands using ft_freqanalysis. I have implemented the two-step solution provided in this discussion https://mailman.science.ru.nl/pipermail/fieldtrip/2016-October/010984.html resulting in the following code: cfg =[]; cfg.method = 'mtmfft'; cfg.output = 'pow'; cfg.taper = 'hanning'; cfg.channel = 'all'; cfg.foilim = [fio1 foi2]; cfg.trials = 'all'; cfg.keeptrials = 'no'; freq_avg = ft_freqanalysis(cfg, data_segmented); cfg = []; cfg.avgoverfreq = 'yes'; freq_avg = ft_freqanalysis(cfg, freq_avg); However, when I run this, I get the following error: the input is freq data with 73 channels, 41 frequencybins and no timebins Error using ft_checkdata>freq2raw (line 1315) not supported for dimord chan_freq Error in ft_checkdata (line 432) data = freq2raw(data); Error in ft_freqanalysis (line 217) data = ft_checkdata(data, 'datatype', {'raw', 'raw+comp', 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); Is there a different way I need to format my data beyond providing the function with the output of the first iteration of ft_freqanalysis? Thank you! Alea -- Alea C. Skwara, M.A. PhD Candidate | Saron Lab http://saronlab.ucdavis.edu/ Center for Mind and Brain | University of California, Davis 267 Cousteau Place | Davis CA 95616 Cell: (828) 273-8595 -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Wed May 2 04:33:05 2018 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Tue, 1 May 2018 19:33:05 -0700 Subject: [FieldTrip] Outputting band averages with ft_freqanalysis In-Reply-To: References: Message-ID: Hi Alea, Have a look at ft_selectdata, which can do this operation for you. Arjen On Tue, May 1, 2018 at 7:05 PM, Alea Skwara wrote: > Hi All, > > I am attempting to output averages within frequency bands using > ft_freqanalysis. I have implemented the two-step solution provided in this > discussion https://mailman.science.ru.nl/pipermail/ > fieldtrip/2016-October/010984.html > resulting in the following code: > > cfg =[]; > cfg.method = 'mtmfft'; > cfg.output = 'pow'; > cfg.taper = 'hanning'; > cfg.channel = 'all'; > cfg.foilim = [fio1 foi2]; > cfg.trials = 'all'; > cfg.keeptrials = 'no'; > freq_avg = ft_freqanalysis(cfg, data_segmented); > > cfg = []; > cfg.avgoverfreq = 'yes'; > freq_avg = ft_freqanalysis(cfg, freq_avg); > > However, when I run this, I get the following error: > > the input is freq data with 73 channels, 41 frequencybins and no timebins > Error using ft_checkdata>freq2raw (line 1315) > not supported for dimord chan_freq > > Error in ft_checkdata (line 432) > data = freq2raw(data); > > Error in ft_freqanalysis (line 217) > data = ft_checkdata(data, 'datatype', {'raw', 'raw+comp', 'mvar'}, > 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); > > > Is there a different way I need to format my data beyond providing the > function with the output of the first iteration of ft_freqanalysis? > > Thank you! > Alea > > -- > Alea C. Skwara, M.A. > PhD Candidate | Saron Lab > http://saronlab.ucdavis.edu/ > > Center for Mind and Brain | University of California, Davis > 267 Cousteau Place | Davis CA 95616 > Cell: (828) 273-8595 > > > > _______________________________________________ > 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 acskwara at ucdavis.edu Wed May 2 19:35:47 2018 From: acskwara at ucdavis.edu (Alea Skwara) Date: Wed, 2 May 2018 10:35:47 -0700 Subject: [FieldTrip] Outputting band averages with ft_freqanalysis In-Reply-To: References: Message-ID: Hi Arjen, Thank you, following ft_freqanalysis with ft_selectdata (and using the .avgoverfreq = 'yes') works. Alea On Tue, May 1, 2018 at 7:33 PM, Arjen Stolk wrote: > Hi Alea, > > Have a look at ft_selectdata, which can do this operation for you. > > Arjen > > > On Tue, May 1, 2018 at 7:05 PM, Alea Skwara wrote: > >> Hi All, >> >> I am attempting to output averages within frequency bands using >> ft_freqanalysis. I have implemented the two-step solution provided in this >> discussion https://mailman.science.ru.nl/pipermail/fieldtrip >> /2016-October/010984.html >> resulting in the following code: >> >> cfg =[]; >> cfg.method = 'mtmfft'; >> cfg.output = 'pow'; >> cfg.taper = 'hanning'; >> cfg.channel = 'all'; >> cfg.foilim = [fio1 foi2]; >> cfg.trials = 'all'; >> cfg.keeptrials = 'no'; >> freq_avg = ft_freqanalysis(cfg, data_segmented); >> >> cfg = []; >> cfg.avgoverfreq = 'yes'; >> freq_avg = ft_freqanalysis(cfg, freq_avg); >> >> However, when I run this, I get the following error: >> >> the input is freq data with 73 channels, 41 frequencybins and no timebins >> Error using ft_checkdata>freq2raw (line 1315) >> not supported for dimord chan_freq >> >> Error in ft_checkdata (line 432) >> data = freq2raw(data); >> >> Error in ft_freqanalysis (line 217) >> data = ft_checkdata(data, 'datatype', {'raw', 'raw+comp', 'mvar'}, >> 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); >> >> >> Is there a different way I need to format my data beyond providing the >> function with the output of the first iteration of ft_freqanalysis? >> >> Thank you! >> Alea >> >> -- >> Alea C. Skwara, M.A. >> PhD Candidate | Saron Lab >> http://saronlab.ucdavis.edu/ >> >> Center for Mind and Brain | University of California, Davis >> 267 Cousteau Place | Davis CA 95616 >> Cell: (828) 273-8595 >> >> >> >> _______________________________________________ >> 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 > -- Alea C. Skwara, M.A. PhD Candidate | Saron Lab http://saronlab.ucdavis.edu/ Center for Mind and Brain | University of California, Davis 267 Cousteau Place | Davis CA 95616 Cell: (828) 273-8595 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcarlapiastra at gmail.com Thu May 3 15:29:22 2018 From: mcarlapiastra at gmail.com (Maria Carla Piastra) Date: Thu, 3 May 2018 15:29:22 +0200 Subject: [FieldTrip] openMEEG path Ubuntu16.04 Message-ID: <874cead0-9c9b-6c0f-7430-554f9af9863d@gmail.com> Dear all, I would like to use openMEEG for computing EEG and MEG forward model solutions on Ubuntu 16.04. I installed following https://github.com/openmeeg/openmeeg. As "/whereis om_assemble/" is giving me /usr/bin. I therefore did "/setenv('PATH', '/usr/bin')/". /W/hen I am launching: /cfg = [];// //cfg.method = 'openmeeg';// //cfg.conductivity = [0.33 0.01 0.33];// //headmodel_bem = ft_prepare_headmodel(cfg, mesh_bem)/ This is the output: /the input is mesh data with multiple surfaces// //reordering the boundaries to: 3 2 1 // ///bin/bash: chmod: command not found// ///bin/bash: ./tp2279842c_636c_485a_ac62_6c2e3c4e7b25.sh: Permission denied// //Warning: an error ocurred while running OpenMEEG // //Error using fread// //Invalid file identifier. Use fopen to generate a valid file identifier.// //Warning: File 'tp54b47429_45d4_47c4_ab6f_3a02b37de78f.bin' not found. // //Warning: File 'tp692ddbba_6d12_4b31_b1ee_f70fc7680936.bin' not found. // //the call to "ft_prepare_headmodel" took 0 seconds and required the additional allocation of an estimated 0 MB// // //headmodel_bem = // // //             bnd: [1x3 struct]// //            cond: [0.3300 0.0100 0.3300]// //    skin_surface: 1// //          source: 3// //            type: 'openmeeg'// //            unit: 'mm'// //             cfg: [1x1 struct]/ Any ideas? Best, Maria Carla -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Thu May 3 17:05:12 2018 From: michelic72 at gmail.com (Cristiano Micheli) Date: Thu, 3 May 2018 17:05:12 +0200 Subject: [FieldTrip] openMEEG path Ubuntu16.04 In-Reply-To: <874cead0-9c9b-6c0f-7430-554f9af9863d@gmail.com> References: <874cead0-9c9b-6c0f-7430-554f9af9863d@gmail.com> Message-ID: Dear Maria Carla it seems that you do not have permissions to write in your temporary files folder. As a consequence the shell file which is called to execute the OpenMEEG commands is not written and cannot be executed. I hope this helps Cris Micheli @MindAffect NovioTech Campus Nijmegen The Netherlands On Thu, May 3, 2018 at 3:29 PM, Maria Carla Piastra wrote: > Dear all, > > I would like to use openMEEG for computing EEG and MEG forward model > solutions on Ubuntu 16.04. > > I installed following https://github.com/openmeeg/openmeeg. > > As "*whereis om_assemble*" is giving me /usr/bin. I therefore did "*setenv('PATH', > '/usr/bin')*". > *W*hen I am launching: > *cfg = [];* > *cfg.method = 'openmeeg';* > *cfg.conductivity = [0.33 0.01 0.33];* > *headmodel_bem = ft_prepare_headmodel(cfg, mesh_bem)* > > This is the output: > > *the input is mesh data with multiple surfaces* > *reordering the boundaries to: 3 2 1 * > */bin/bash: chmod: command not found* > */bin/bash: ./tp2279842c_636c_485a_ac62_6c2e3c4e7b25.sh: Permission denied* > *Warning: an error ocurred while running OpenMEEG * > *Error using fread* > *Invalid file identifier. Use fopen to generate a valid file identifier.* > *Warning: File 'tp54b47429_45d4_47c4_ab6f_3a02b37de78f.bin' not found. * > *Warning: File 'tp692ddbba_6d12_4b31_b1ee_f70fc7680936.bin' not found. * > *the call to "ft_prepare_headmodel" took 0 seconds and required the > additional allocation of an estimated 0 MB* > > *headmodel_bem = * > > * bnd: [1x3 struct]* > * cond: [0.3300 0.0100 0.3300]* > * skin_surface: 1* > * source: 3* > * type: 'openmeeg'* > * unit: 'mm'* > * cfg: [1x1 struct]* > > > Any ideas? > > Best, > > Maria Carla > > _______________________________________________ > 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 christoph.kayser at uni-bielefeld.de Fri May 4 08:41:22 2018 From: christoph.kayser at uni-bielefeld.de (Christoph Kayser) Date: Fri, 04 May 2018 08:41:22 +0200 Subject: [FieldTrip] PostDoc & PhD Position, Cognitive Neuroscience, Bielefeld, Germany Message-ID: <00d601d3e372$ea9b9cc0$bfd2d640$@uni-bielefeld.de> The Department of Cognitive Neuroscience at Bielefeld University, Germany, is advertising a 3-year Postdoctoral position, and a 3-year PhD position in auditory and multisensory neuroimaging studies. We are looking to fill two positions to complement our research on auditory and multisensory perception based on a combination of psychophysics, neuroimaging (EEG) and statistical modelling. The Department for Cognitive Neuroscience is dedicated to understanding the integration of sensory information in the brain. Our studies use state of the art EEG imaging, combined with eyetracking, psychophysical paradigms, and substantive quantitative data analysis to better understand when and how the brain transforms sensory information into a conscious percept. Further details about our research can be found here http://www.uni-bielefeld.de/biologie/cns/ The positions involve all aspects of study design, implementation, data collection, data analysis and the write up of results. Contributions to the supervision of student projects or the preparation of practical courses are also expected. Applicants should have a background in neuroscience, cognitive science, psychology, mathematics, or a relevant discipline. Applicants for the post-doc position should have a doctoral degree or equivalent title. We are especially interested in devotion to advanced quantitative data analysis including the capabilities to program or modify analysis code. The ideal applicant will have a strong analytical background and direct experience using MATLAB. Applicants should have enthusiasm, and a clear, demonstrable capacity for acquiring expertise in these techniques. The positions are funded for 3 years starting ideally around September 2018, at Germany salary grades TV-L E13 (100% for post-doc, 65% for PhD student). Interested candidates please contact Christoph Kayser -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.rimmele at ae.mpg.de Wed May 2 10:48:03 2018 From: johanna.rimmele at ae.mpg.de (Rimmele, Johanna Maria) Date: Wed, 2 May 2018 08:48:03 +0000 Subject: [FieldTrip] PhD position on auditory timing in speech and music at MPIEA Frankfurt Message-ID: <63B92215-CA68-49D2-8E1D-C629CF949609@ae.mpg.de> Dear all, We are currently looking for an excellent candidate for a 3 year Ph.D. position in the Neuroscience Department at the MPI for Empirical Aesthetics in Frankfurt am Main. This is a chance to work in a relentlessly interdisciplinary and exciting place. The project focuses on auditory timing in speech and music using behavioral and neurophysiological measures. For details visit our homepage: https://www.aesthetics.mpg.de/en/the-institute/jobs/phd-position-neuroscience-department.html Please forward this info to interested and skilled candidates or people that might know suitable candidates! Many thanks! All the Best, Johanna _______ Dr. Johanna Rimmele Max-Planck-Institute for Empirical Aesthetics Department of Neuroscience Grüneburgweg 14 D-60322 Frankfurt am Main Phone: +49 69 8300479 323 j.rimmele at aesthetics.mpg.de www.aesthetics.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdhami06 at gmail.com Tue May 8 11:05:54 2018 From: pdhami06 at gmail.com (Paul Dhami) Date: Tue, 8 May 2018 05:05:54 -0400 Subject: [FieldTrip] requested data segment extends over a discontinuous trial boundary Message-ID: Hi FieldTrip, my name is Paul, and I'm a student studying response inhibition in psychiatric disorders, as well as working with corresponding TMS-EEG data. I was able to go through the analysis pipeline just fine with some ERP data (preprocessed before imported to FieldTrip), but when using essentially the same steps for some TMS-EEG data (also preprocessed before being imported into FieldTrip), I ran into the following error at the ft_preprocessing(cfg) command: Error using ft_read_data (line 270) > requested data segment extends over a discontinuous trial boundary > Error in ft_preprocessing (line 582) > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', > begsample, 'endsample', > endsample, 'chanindx', rawindx, 'checkboundary', > strcmp(cfg.continuous, 'no'), > 'dataformat', cfg.dataformat); My cfg that I entered with ft_preprocessing looked like this (altered the filename just for this email): dataset: 'subject1.set' > trialdef: [1×1 struct] > trackusage: 'B8F919AB' > trackconfig: 'off' > checkconfig: 'loose' > checksize: 100000 > showcallinfo: 'yes' > debug: 'no' > outputfilepresent: 'overwrite' > trackcallinfo: 'yes' > trackdatainfo: 'no' > toolbox: [1×1 struct] > notification: [1×1 struct] > progress: [1×1 struct] > callinfo: [1×1 struct] > version: [1×1 struct] > datafile: 'subject1.set' > headerfile: 'subject1.set' > dataformat: 'eeglab_set' > headerformat: 'eeglab_set' > trialfun: @ft_trialfun_general > event: [1×151 struct] > trl: [75×4 double] > Prior code to ft_preprocessing was: cfg = []; > > % adding dataset field to configuration file > cfg.dataset = [myfilepath '/' myfilename]; > %cfg.dataset = 'filename.set' > % adding trialdef information to configuration file > cfg.trialdef.eventtype = 'trigger'; > cfg.trialdef.eventvalue = 128; % TMS trigger > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 0.999; Is there something that I am doing wrong as to why the ERP files were able to be preprocessed just fine where as I am running into this error for the TMS-EEG data? Is this likely related to the TMS-EEG data having been collected in a "pseudo-continuous" manner, and in that case, is it as easy as including the cfg.continuous = 'yes' option (which I noted in a couple similar forum posts)? Any help would be greatly appreciated. Thank you. Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue May 8 15:28:25 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 8 May 2018 15:28:25 +0200 Subject: [FieldTrip] EEG/iEEG/MEG - short survey on data formats you use Message-ID: <44D7960D-DC95-4A7D-975C-3A6F68874F37@donders.ru.nl> Dear colleagues, Several members of the electrophysiology community (EEG, MEG, iEEG) are working on an open specification for storing cognitive electrophysiology data, called the Brain Imaging Data Structure . Its goal is to make our workflows more reproducible, more sharable, and more efficient. The BIDS format is not a new data format, but is a data specification. It should accommodate pre-existing workflows in cognitive neuroscience. As such, we are investigating what data formats researchers use already, and which they'd be willing to use for sharing their data. Please respond to this short (3 question, ~2 minute) survey at the link below, in order to share with us which data formats you currently use in your electrophysiological research. https://goo.gl/forms/Ytr6UmawWvwvIB9R2 If you know of any other interested parties in the cognitive electrophysiology community, please do forward along this link so that we can get a sample from as many people as possible. Thanks very much for your time! Robert, Chris, Cyril, Dora and others -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue May 8 16:53:21 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 8 May 2018 16:53:21 +0200 Subject: [FieldTrip] plot ft_sourceplot figures into a subplot In-Reply-To: References: Message-ID: Dear Hame ft_sourceplot is a high-level function that includes interaction with the data (i.e. clicking). Furthermore, depending on method (ortho/surface/montage/glassbrain/cloud) you will get one or mutliple sub-axes within one figure. So it is not suited for use in a loop with multiple axes or subplots. I know that people are using it to export images to pdf/ps or ai format and then use external software to glue them together. I also find it convenient to save the figures to a bitmap using “print -dpng” and use external software (such as Windows picture viewer) to browse through large numbers of files. I believe this is also mentioned somewhere on http://www.fieldtriptoolbox.org/tutorial/plotting If you want closer control over the figures and different axes within one figure, I recommend you use the lower-level plotting functions that you can find in fieldtrip/plotting. E.g. ft_plot_mesh , which you can give the mesh and the colors you want on each of the vertices or triangles. See also http://www.fieldtriptoolbox.org/reference#from_the_plotting_module best regards, Robert PS please use the fieldtrip mailing list next time, there are many people on it that can help, and providing answers on the list benefits others as well > On 27 Apr 2018, at 14:20, Hame Park wrote: > > Dear Robert > > Hello! > I was trying to make a big figure with many > sourceplots, created from ft_sourceplot with the 'surface' method, > but it seems it always creates a separate figure. > > I tried something like > > h = figure; > ha = nan(length(T), 1); > for t=1:length(T) > ha(t) = subplot(1, length(T), t); > end > > for t=1:length(T) > axes(ha(t)) > ft_sourceplot(cfg, data) > end > > but it still opens up a new figure for ft_sourceplot. > I tried to look into the code, and tried disabling the line > h=figure; but this gave me errors which I couldn't comprehend. > > Any help would be much appreciated! > > Thank you. > Best wishes, > Hame -------------- next part -------------- An HTML attachment was scrubbed... URL: From hame.hame.hame at gmail.com Tue May 8 17:40:16 2018 From: hame.hame.hame at gmail.com (Hame Park) Date: Tue, 8 May 2018 17:40:16 +0200 Subject: [FieldTrip] plot ft_sourceplot figures into a subplot In-Reply-To: References: Message-ID: Dear Robert Thank you! Best regards, Hame On Tue, May 8, 2018 at 4:53 PM, Robert Oostenveld < r.oostenveld at donders.ru.nl> wrote: > Dear Hame > > ft_sourceplot is a high-level function that includes interaction with the > data (i.e. clicking). Furthermore, depending on method > (ortho/surface/montage/glassbrain/cloud) you will get one or mutliple > sub-axes within one figure. So it is not suited for use in a loop with > multiple axes or subplots. > > I know that people are using it to export images to pdf/ps or ai format > and then use external software to glue them together. I also find it > convenient to save the figures to a bitmap using “print -dpng” and use > external software (such as Windows picture viewer) to browse through large > numbers of files. I believe this is also mentioned somewhere on > http://www.fieldtriptoolbox.org/tutorial/plotting > > If you want closer control over the figures and different axes within one > figure, I recommend you use the lower-level plotting functions that you can > find in fieldtrip/plotting. E.g. ft_plot_mesh > , which you can > give the mesh and the colors you want on each of the vertices or triangles. > See also http://www.fieldtriptoolbox.org/reference#from_the_plotting_ > module > > > best regards, > Robert > > PS please use the fieldtrip mailing list next time, there are many people > on it that can help, and providing answers on the list benefits others as > well > > > On 27 Apr 2018, at 14:20, Hame Park wrote: > > Dear Robert > > Hello! > I was trying to make a big figure with many > sourceplots, created from ft_sourceplot with the 'surface' method, > but it seems it always creates a separate figure. > > I tried something like > > h = figure; > ha = nan(length(T), 1); > for t=1:length(T) > ha(t) = subplot(1, length(T), t); > end > > for t=1:length(T) > axes(ha(t)) > ft_sourceplot(cfg, data) > end > > but it still opens up a new figure for ft_sourceplot. > I tried to look into the code, and tried disabling the line > h=figure; but this gave me errors which I couldn't comprehend. > > Any help would be much appreciated! > > Thank you. > Best wishes, > Hame > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.Hanslmayr at bham.ac.uk Wed May 9 14:50:12 2018 From: S.Hanslmayr at bham.ac.uk (Simon Hanslmayr) Date: Wed, 9 May 2018 12:50:12 +0000 Subject: [FieldTrip] PhD position in Birmingham Message-ID: <257F6C65A372A04CA41056EACC0DE7CED874ABCE@EX12.adf.bham.ac.uk> To anyone looking for a PhD position, Applications are sought for a fully-funded PhD position to work with Dr Simon Hanslmayr (University of Birmingham, School of Psychology, http://www.memorybham.com/people/#/simon-hanslmayr/). The project is focussed on generating computational models to simulate single-neuron responses and neural oscillations in the service of memory processes. The work will build on a theoretical framework, termed the Synch/deSync Model which assumes that memory processes are implemented via cortical desynchronization and hippocampal synchronization processes (see Parish et al., 2018). The PhD student will have the opportunity to work with single-unit and EEG data recorded from the human hippocampus in patients suffering from epilepsy. The candidate should have a strong background in computational neuroscience or related area. Apply for this post by sending an email with your CV and a short description (100 words) outlining your skills and motivation to Sophie Watson (Sophie Watson S.Watson.2 at bham.ac.uk). https://www.findaphd.com/search/ProjectDetails.aspx?PJID=97892 Dr. Simon Hanslmayr Reader in Cognitive Neuroscience Royal Society Wolfson Research Merit Award Holder School of Psychology Hills Building 2.37 University of Birmingham Edgbaston Birmingham B15 2TT UK Tel +44 121 4146203 http://www.memorybham.com/people/#/simon-hanslmayr/ [http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 8560 bytes Desc: image001.gif URL: From SSaleh at kesslerfoundation.org Wed May 9 16:29:19 2018 From: SSaleh at kesslerfoundation.org (Soha Saleh - Research Scientist) Date: Wed, 9 May 2018 14:29:19 +0000 Subject: [FieldTrip] Postdoctoral Fellowship in Neurorehabilitation and Neuroimaging Research - Kessler Foundation Message-ID: <92143A403B96384DB97C1AF41F645AD92397BBC9@EXCHANGE.kmrrec.org> Dear all, The Kessler Foundation (West Orange, New Jersey) is recruiting postdoctoral fellows to conduct Neurorehabilitation and Neuroimaging Research. Applications are being accepted for fellowships funded by an Advanced Rehabilitation Research Training (ARRT) grant from the National Institute on Disability and Rehabilitation Research (NIDILRR), and are expected to last for a two-year term. Qualifying candidates must have an earned doctorate in engineering (e.g., biomedical, rehabilitation mechanical), neuroscience, or a related field. Strong candidates will have prior experience in performing neuroimaging research studies in human subjects, as well as some history of publication and presentation of original research. The successful candidate will work on ongoing research that uses neuroimaging to better understand motor related impairment following neurological, neuromuscular and musculoskeletal diseases and injuries, for diverse patient populations including traumatic brain injury, multiple sclerosis, spinal cord injury, cancer, and stroke. To this end, our research uses a multimodality approach that includes neuroimaging (fMRI, MRI, fNIRS, EEG) combined with eye tracking, electrophysiology analysis, and motion analysis. The Kessler Foundation has research-dedicated 3 Tesla MRI scanner, state-of-the-art mobile imaging equipment (EEG, fNIRS), instrumented treadmill with virtual reality (C-Mill), Neurocom Balance Platform, biodex, and is a leader in powered exoskeleton assisted rehabilitation therapy. The successful applicant will also be expected to develop his/her own mentored research project. He/she will work on various aspects of research projects from inception (e.g., study formulation, grant-writing, etc.), through dissemination (conference presentation and manuscript publication). Requirements include: * Background and experience in functional and/or structural MRI image processing (DTI, fMRI), and ideally connectivity analysis (resting state functional connectivity, effective connectivity, graph theory-based analysis) * Experience in programming, preferentially Matlab * Knowledge of statistical data analysis * Excellent written communication skills Preferred experience/qualifications: * Research studies in human subjects, and history of publication and presentation of original research * EEG/EMG/fNIRS data collection and analysis * Biomedical Instrumentation * Neuromuscular rehabilitation; brain and muscle electrophysiology * Image-processing software such as FSL, AFNI, SPM, EEGLAB, Brainstorm Opportunities for collaborating with clinicians on existing or future clinical research are also available. All fellows participate in an extensive training curriculum and didactic offerings. Multidisciplinary mentored training opportunities are individually tailored to achieve specific goals considering each fellow's prior background and interests. Kessler Foundation is a public charity that advances its mission of improving the lives of people with disabilities through research and grant-making programs. The Kessler Foundation is a global leader in medical rehabilitation research and affiliated with the renowned Kessler Institute for Rehabilitation in West Orange, New Jersey and enjoys collaborations with partners at the New Jersey Institute of Technology and Rutgers New Jersey Medical School (RNJMS), Rutgers University in New Jersey. Applicants are encouraged to visit the Foundation's website (http://www.kesslerfoundation.org/research/) to learn about the missions, activities, and resources of the Foundation and its laboratories. Administration of the ARRT fellowships occurs within the academic Department of Physical Medicine and Rehabilitation at RNJMS. As such, fellows enjoy the benefits and academic resources available to all post-doctoral fellows at the Medical School. Fellows may also be recommended for an academic appointment at the rank of Instructor. Initial and informal inquiries about the fellowship may be directed by email to Guang Yue, Ph.D. ARRT Project Director, Kessler Foundation, and Professor at RNJMS GYue at kesslerfoundation.org Applicants for fellowships should refer to the "Neuro-Musculoskeletal Fellowship" and forward * Letter of application * Curriculum Vitae * One-page statement of research interests by email to: career at kesslerfoundation.org or by mail to: Kessler Foundation, Attn: Human Resources 120 Eagle Rock Ave, Suite 100 East Hanover, NJ 07936 Letters of recommendation: At the time of application, candidates should request letters of recommendation from three current or former professional associates to be mailed to the Project Director (address above). Alternatively, applicants may enclose sealed letters of recommendation with mailed applications. Due to limitations in resources, we regret that only candidates whose applications are brought forward by the fellowship committee will be contacted. In addition to citizens and permanent residents of the US, non-citizen nationals, and non-immigrants are eligible to apply provided they can be lawfully employed in the U.S. Thanks, Soha -------------------------------------------------------------------------- Soha Saleh, PhD Research Scientist Human Performance and Engineering Lab Kessler Foundation 1199 Pleasant Valley Way, West Orange, NJ, 07052 Tel: (973) 324 3520 Email: ssaleh at KesslerFoundation.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From mansoureh.aghabeig at yahoo.com Wed May 9 21:19:53 2018 From: mansoureh.aghabeig at yahoo.com (Mansoureh Aghabeig) Date: Wed, 9 May 2018 19:19:53 +0000 (UTC) Subject: [FieldTrip] How can I fix the "the 1/f power spectrum effect" in fieldtrip References: <280532632.1686057.1525893593539.ref@mail.yahoo.com> Message-ID: <280532632.1686057.1525893593539@mail.yahoo.com> Dear Sir/Madam, My name is Mansoureh Aghabeig and I am working in the ICNT lab in Torun, Poland as a Ph.D. student. Currently, I am working on time-frequency analysis with fieldtrip . But I obtained very strange TFR results. Please find the attachment. It is clear in the attached plot the lower frequencies dominate the higher one. In fact, there is the 1/f power spectrum effect. I think one solution for solving this problem is normalizing over power spectrum but I do not know how can I do it in fieldtrip . I would be appreciated if you kindly guide me. Thanks in advance Mansoureh Aghabeig        منصوره آقابیگ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: E124.jpg Type: image/jpeg Size: 32087 bytes Desc: not available URL: From r.oostenveld at donders.ru.nl Thu May 10 09:43:10 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 10 May 2018 09:43:10 +0200 Subject: [FieldTrip] Donders Brain Stimulation Toolkit in Sept 2018 Message-ID: <3F30C7E2-6931-4D41-99CF-3761569196DF@donders.ru.nl> — Please disseminate to PhD students, postdoctoral researchers, and other senior researchers interested in advanced brain stimulation (TMS, TDCS) On 10-13 September 2018 we will host the "Donders Brain Stimulation Toolkit" at the Donders Institute in Nijmegen, the Netherlands. This advanced course is designed for researchers who want to learn advanced transcranial magnetic stimulation (TMS) and/or transcranial current stimulation (tDCS/tACS) techniques. Lectures by expert researchers and hands-on training sessions will provide you with the latest on experimental design, stimulation application, data acquisition and data analysis. We place a special emphasis on state-of-the-art multi-modal techniques including: TMS-EEG; tD/ACS-MEG and tD/ACS-fMRI. Our main program (September 11-13) is therefore aimed at advanced brain stimulation topics. Need a basic refresher on TMS and TD/ACS? We will go over the basics in an extra day prior to the course (September 10). More information, including a preliminary program and registration, can be found at http://www.ru.nl/donders/agenda/donders-tool-kits/vm-tool-kits/donders-brain-stimulation-tool-kit-version-2/ Looking forward to welcoming you in Nijmegen, Ian Cameron _______________________________ Ian Cameron, PhD Senior Researcher Donders Centre for Cognitive Neuroimaging visiting address: Kapittelweg 29, 6525 EN mailing address: P.O. Box 9101, NL-6500 HB Nijmegen, The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From deydhiman794 at gmail.com Thu May 10 21:08:35 2018 From: deydhiman794 at gmail.com (Dhiman Dey) Date: Fri, 11 May 2018 00:38:35 +0530 Subject: [FieldTrip] EEG/MRI dataset Message-ID: I am a final year b.tech student. My project work is Source localization using EEG/MRI signals. I am in search of dataset.If anybody can provide me the dataset,it will be helpful for me. Mailid: deydhiman794 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.kochari at uva.nl Fri May 11 10:17:25 2018 From: a.kochari at uva.nl (Arnold Kochari) Date: Fri, 11 May 2018 10:17:25 +0200 Subject: [FieldTrip] EEG/MRI dataset In-Reply-To: References: Message-ID: Hi Dhiman Dey, Perhaps you can find something suitable here: https://openfmri.org/dataset/. Kind regards, Arnold On Thu, May 10, 2018 at 9:08 PM, Dhiman Dey wrote: > I am a final year b.tech student. > My project work is Source localization using EEG/MRI signals. > I am in search of dataset.If anybody can provide me the dataset,it will be > helpful for me. > > Mailid: deydhiman794 at gmail.com > > _______________________________________________ > 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 nathanweisz at me.com Fri May 11 10:46:45 2018 From: nathanweisz at me.com (Nathan Weisz) Date: Fri, 11 May 2018 10:46:45 +0200 Subject: [FieldTrip] PhD position in Salzburg Message-ID: <6867CF09-C780-4398-8375-31E8E31ADE52@me.com> We are currently seeking a motivated PhD student to join our team to study lipreading processes in normal hearing and deaf individuals using MEG+EEG. Please forward to any potentially interested person. Thanks, Nathan -------------- next part -------------- A non-text attachment was scrubbed... Name: Call_FWF_lipreading.pdf Type: application/pdf Size: 68024 bytes Desc: not available URL: From rssundar at gmail.com Fri May 11 14:13:23 2018 From: rssundar at gmail.com (Shyam Rajagopalan) Date: Fri, 11 May 2018 17:43:23 +0530 Subject: [FieldTrip] EEG/MRI dataset In-Reply-To: References: Message-ID: Hi Dhiman Dey, You may want to check https://paris-saclay-cds.github.io/autism_challenge/ as well. Regards Shyam On Fri, May 11, 2018 at 1:47 PM, Arnold Kochari wrote: > Hi Dhiman Dey, > > Perhaps you can find something suitable here: https://openfmri.org/ > dataset/. > > > Kind regards, > Arnold > > > On Thu, May 10, 2018 at 9:08 PM, Dhiman Dey > wrote: > >> I am a final year b.tech student. >> My project work is Source localization using EEG/MRI signals. >> I am in search of dataset.If anybody can provide me the dataset,it will >> be helpful for me. >> >> Mailid: deydhiman794 at gmail.com >> >> _______________________________________________ >> 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 deydhiman794 at gmail.com Fri May 11 18:28:31 2018 From: deydhiman794 at gmail.com (Dhiman Dey) Date: Fri, 11 May 2018 21:58:31 +0530 Subject: [FieldTrip] EEG/MRI dataset In-Reply-To: References: Message-ID: Thank you Arnold On Fri 11 May, 2018 2:05 pm Arnold Kochari, wrote: > Hi Dhiman Dey, > > Perhaps you can find something suitable here: > https://openfmri.org/dataset/. > > > Kind regards, > Arnold > > > On Thu, May 10, 2018 at 9:08 PM, Dhiman Dey > wrote: > >> I am a final year b.tech student. >> My project work is Source localization using EEG/MRI signals. >> I am in search of dataset.If anybody can provide me the dataset,it will >> be helpful for me. >> >> Mailid: deydhiman794 at gmail.com >> >> _______________________________________________ >> 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 deydhiman794 at gmail.com Fri May 11 18:28:50 2018 From: deydhiman794 at gmail.com (Dhiman Dey) Date: Fri, 11 May 2018 21:58:50 +0530 Subject: [FieldTrip] EEG/MRI dataset In-Reply-To: References: Message-ID: Thank you Shyam On Fri 11 May, 2018 6:05 pm Shyam Rajagopalan, wrote: > Hi Dhiman Dey, > > You may want to check https://paris-saclay-cds.github.io/autism_challenge/ > as well. > > Regards > Shyam > > On Fri, May 11, 2018 at 1:47 PM, Arnold Kochari wrote: > >> Hi Dhiman Dey, >> >> Perhaps you can find something suitable here: >> https://openfmri.org/dataset/. >> >> >> Kind regards, >> Arnold >> >> >> On Thu, May 10, 2018 at 9:08 PM, Dhiman Dey >> wrote: >> >>> I am a final year b.tech student. >>> My project work is Source localization using EEG/MRI signals. >>> I am in search of dataset.If anybody can provide me the dataset,it will >>> be helpful for me. >>> >>> Mailid: deydhiman794 at gmail.com >>> >>> _______________________________________________ >>> 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 Matthias.Franken at UGent.be Mon May 14 14:39:28 2018 From: Matthias.Franken at UGent.be (Matthias Franken) Date: Mon, 14 May 2018 12:39:28 +0000 Subject: [FieldTrip] partial artifact rejection for time-frequency analysis Message-ID: <549818693f0c4c31acabed976edb5fea@xmail303.UGent.be> Dear all, I have an EEG dataset that consists of quite long trials (>20s). Therefore, For artifact rejection I would like to only reject the part of the trial that contains the artifact, rather than throwing away the entire trial, and thus I will use the cfg.artfctdef.method = ‘partial’; option in ft_rejectartifact. However, this leads to some trials being cut in two shorter “trials” (i.e., the part before the artifact and the part after the artifact). I’m guessing this will lead to edge artifacts in my time-frequency analysis, not only at the edges of the original trials, but also at time points where artifacts were cut out. SO I’m not sure how to deal with this. I guess one option would be to perform the time-frequency analysis first, and afterwards cut out the artifacts, although (1) that might lead to the artifact smearing into data points that were not cut out, depending on the time window width during frequency analysis, and (2) the artifacts identified visually using ft_databrowser are define din ample numbers, and the result from ft_freqanalysis downsamples the data. Did anyone face similar issues or have ideas on how to get around this? ________________________________________ Matthias Franken postdoctoral researcher Experimental Psychology Department Ghent University -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon May 14 15:55:35 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 14 May 2018 13:55:35 +0000 Subject: [FieldTrip] partial artifact rejection for time-frequency analysis In-Reply-To: <549818693f0c4c31acabed976edb5fea@xmail303.UGent.be> References: <549818693f0c4c31acabed976edb5fea@xmail303.UGent.be> Message-ID: <9CBD4CAF-5EB2-432D-907B-15E728977F97@donders.ru.nl> Dear Matthias, Don’t worry. The partial rejection method indeed cuts original trials in smaller portions, but it preserves the local time axes, relative to the original trials. Since ft_freqanalysis returns per ‘segment’ TFRs with numeric data only for those portions of data for which the time windows are entirely filled with data (and nans otheriwse, with the average across segments is computed as a nanmean) there is no worry about ‘edge artifacts’ as such. The only thing to keep in the back of your head is that different time-frequency points may end up having slightly different degrees of freedom in the average. Best wishes, Jan-Mathijs On 14 May 2018, at 14:39, Matthias Franken > wrote: Dear all, I have an EEG dataset that consists of quite long trials (>20s). Therefore, For artifact rejection I would like to only reject the part of the trial that contains the artifact, rather than throwing away the entire trial, and thus I will use the cfg.artfctdef.method = ‘partial’; option in ft_rejectartifact. However, this leads to some trials being cut in two shorter “trials” (i.e., the part before the artifact and the part after the artifact). I’m guessing this will lead to edge artifacts in my time-frequency analysis, not only at the edges of the original trials, but also at time points where artifacts were cut out. SO I’m not sure how to deal with this. I guess one option would be to perform the time-frequency analysis first, and afterwards cut out the artifacts, although (1) that might lead to the artifact smearing into data points that were not cut out, depending on the time window width during frequency analysis, and (2) the artifacts identified visually using ft_databrowser are define din ample numbers, and the result from ft_freqanalysis downsamples the data. Did anyone face similar issues or have ideas on how to get around this? ________________________________________ Matthias Franken postdoctoral researcher Experimental Psychology Department Ghent University _______________________________________________ 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 m.manahova at gmail.com Mon May 14 16:04:03 2018 From: m.manahova at gmail.com (Mariya Manahova) Date: Mon, 14 May 2018 16:04:03 +0200 Subject: [FieldTrip] partial artifact rejection for time-frequency analysis In-Reply-To: <549818693f0c4c31acabed976edb5fea@xmail303.UGent.be> References: <549818693f0c4c31acabed976edb5fea@xmail303.UGent.be> Message-ID: Hi Matthias, Perhaps you could try taking the part of the trial you want to reject and replacing the values there with NaNs? Then you'd be able to remove the artifact-related part of the data while keeping your trials of the same length. I know that some FieldTrip functions can deal with NaNs, so this may be a solution. All the best, Marisha On Mon, May 14, 2018 at 3:35 PM Matthias Franken wrote: > Dear all, > > > > I have an EEG dataset that consists of quite long trials (>20s). > Therefore, For artifact rejection I would like to only reject the part of > the trial that contains the artifact, rather than throwing away the entire > trial, and thus I will use the cfg.artfctdef.method = ‘partial’; option in > ft_rejectartifact. > > However, this leads to some trials being cut in two shorter “trials” > (i.e., the part before the artifact and the part after the artifact). I’m > guessing this will lead to edge artifacts in my time-frequency analysis, > not only at the edges of the original trials, but also at time points where > artifacts were cut out. SO I’m not sure how to deal with this. > > > > I guess one option would be to perform the time-frequency analysis first, > and afterwards cut out the artifacts, although (1) that might lead to the > artifact smearing into data points that were not cut out, depending on the > time window width during frequency analysis, and (2) the artifacts > identified visually using ft_databrowser are define din ample numbers, and > the result from ft_freqanalysis downsamples the data. > > > > Did anyone face similar issues or have ideas on how to get around this? > > > > > > > ________________________________________ > Matthias Franken > postdoctoral researcher > Experimental Psychology Department > Ghent University > > > _______________________________________________ > 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 elam4hcp at gmail.com Mon May 14 23:22:26 2018 From: elam4hcp at gmail.com (Jennifer Elam) Date: Mon, 14 May 2018 16:22:26 -0500 Subject: [FieldTrip] Reminder to Register for HCP Course 2018 Message-ID: Only a few weeks remain to register for the *2018 HCP Course: "Exploring the Human Connectome"*. For more info visit the HCP Course 2018 website . A limited number of registrations with accommodation at Worcester College included are available until filled, or May 29 at the latest. HCP Course 2018 will be held June 25 – 29 at the Blavatnik School of Government , at the University of Oxford , in Oxford, UK. The 5-day intensive course of lectures and hands-on practicals is a great opportunity to learn directly from HCP investigators and gain practical experience with the Human Connectome Project's data and approach to multimodal whole brain imaging, processing and analysis. The course is also a great way to get up to speed on HCP tools including Connectome Workbench (v1.3.0 just released!) and sharing your own analyzed imaging datasets via the BALSA database. If you have any questions, please contact us at: hcpcourse at humanconnectome.org We look forward to seeing you in Oxford! Best, 2018 HCP Course Staff -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam at wustl.edu www.humanconnectome.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From fereshte.ramezani at gmail.com Wed May 16 05:59:29 2018 From: fereshte.ramezani at gmail.com (Fereshte) Date: Wed, 16 May 2018 08:29:29 +0430 Subject: [FieldTrip] EEG average In-Reply-To: References: Message-ID: Dear all, I've solved the forward problem for a FEM head model and as a result, obtained the lead field matrix. Now I'm going to do the Dipole Fit approch in order to solve the inverse problem. How can I obtain the ' EEG-avg ' data in the script below which is a part of " http://www.fieldtriptoolbox.org/workshop/baci2017/inverseproblem" due to the forward problem once I solved? Thank you! load elecload sourcemodelload headmodel_bemload leadfield_bemload mri_reslicedload EEG_avg Then we do the dipole fit % Dipole fit cfg = []; cfg.numdipoles = 1; %number of expected cfg.headmodel = headmodel_bem; %the head model cfg.grid = leadfield_bem; %the precomputed leadfield cfg.elec = elec; %the electrode model cfg.latency = 0.025; %the latency of interest dipfit_bem = ft_dipolefitting(cfg,EEG_avg); dipfit_bem.dip ans = pos: [13.958237048680118 34.388465910583285 97.809684095994314] %dipole position mom: [3x1 double ] %dipole moment pot: [74x1 double ] %potential at the electrodes rv: 0.034549469532012 %residual variance unit: 'mm' -------------- next part -------------- An HTML attachment was scrubbed... URL: From uwe.graichen at tu-ilmenau.de Wed May 16 15:42:24 2018 From: uwe.graichen at tu-ilmenau.de (Uwe Graichen) Date: Wed, 16 May 2018 15:42:24 +0200 Subject: [FieldTrip] =?utf-8?q?8th_International_Summer_School_=E2=80=9EMu?= =?utf-8?q?ltimodal_integration_of_brain_measurements_in_research_and_clin?= =?utf-8?q?ical_practice=E2=80=9C?= Message-ID: Dear colleagues, we are pleased to announce the 8th International Summer School in Biomedical Engineering „Multimodal integration of brain measurements in research and clinical practice“, 1st – 12th October 2018 in Chengdu, China. This event stands in the tradition of a series of successful summer schools on hot themes in biomedical engineering, dedicated to intense learning in the fruitful atmosphere of tight interaction between students and world-leading specialists. This year’s summer school is devoted to EEG/MEG source reconstruction technologies in the frame work of multimodal integration of brain measurements in research and clinical practice. In particular, the 8th International Summer School on Biomedical Engineering will focus on methodological approaches and challenges, measurement devices and characteristics, types of underlying theoretic modeling, specifics of data analysis, ability to derive conclusions about neuroscientific meaning. It will cover both theoretical foundations and practical applications. We aim at a thorough understanding of the underlying mechanisms. Thus, we will develop a critical view on current applications and possible future developments. The second important aim of the summer school consists in providing contact with both leading experts in the field and other students with similar interests, thereby facilitating the exchange of ideas on latest developments in the field. Target Group: - PhD students - Advanced Master students - Researchers entering the field of brain measurement and stimulation techniques Further Information about the 7th International Summer School in Biomedical Engineering: www.bme-school.org We would be happy to receive your application. Please pass this announcement to your colleagues who might be interested. Sincerely, Jens Haueisen and Thomas Knösche From jose.herrero66 at gmail.com Wed May 16 18:17:52 2018 From: jose.herrero66 at gmail.com (Jose Herrero) Date: Wed, 16 May 2018 12:17:52 -0400 Subject: [FieldTrip] ft_connectivity_laggedcoherence Message-ID: dear Fieldtrippers, I'm comparing different coherence methods including the fieldtrip method of lagged coherence. running the code with... cfg.method = 'laggedcoherence'; lcoh = ft_connectivityanalysis(cfg, freq) results on... Error using ft_connectivityanalysis (line 375) unknown method laggedcoherence running the code with... lcoh = ft_connectivity_laggedcoherence(cfg, freq) results on: In an assignment A(:) = B, the number of elements in A and B must be the same. Error in ft_connectivity_laggedcoherence (line 213) lagwidth(lagindx) = cfg.lag*cyclelength*lagindx; as 'cfg.lag' is assigned a length equal to the length of the trial (1x15000, single trial). if this method works, is it possible to use it to compute lagged coherence between an external signal (which oscillates at a freq <0.5Hz) and the iEEG brain signal? thanks, JHerr -------------- next part -------------- An HTML attachment was scrubbed... URL: From frsantos at fpce.up.pt Wed May 16 13:16:40 2018 From: frsantos at fpce.up.pt (Fernando Ferreira-Santos) Date: Wed, 16 May 2018 11:16:40 +0000 Subject: [FieldTrip] 2018 Porto EEG/ERP Summer School Message-ID: <2BAB036A9BAEA44984A131DFCE446108021F3E3905@SRVMBX01.fpceup.psi.up.pt> Dear colleagues, The Laboratory of Neuropsychopsysiology at the University of Porto (http://www.fpce.up.pt/labpsi/) is pleased to announce the 7th edition of the International Cognitive and Affective Neurophysiology Summer School: Acquisition, processing, and analysis of EEG signal (https://sites.google.com/view/can-summerschool-porto). This summer school is focused on the application of Electroencephalography (EEG) and Event Related Potential (ERP) techniques to the study of cognitive and affective processes. This 36h course will be fully taught in English and is aimed at an introductory level, so no previous experience with EEG or ERP is required. This year we are introducing a new module on reproducibility and open science practices in EEG/ERP research. This event will take place from 3-7 of September 2018 in the lovely city of Porto. The course is generally fully booked and, as such, we recommend early registration (course places are attributed by order of registration). For additional details and instructions on how to register, please visit the website (via http://www.fpce.up.pt/labpsi/summerschool/ or directly to the course website: https://sites.google.com/view/can-summerschool-porto). Please feel free to pass this information along to students or researchers that may be potentially interested. Thanks you and best wishes, Fernando Ferreira-Santos Professor Auxiliar | Assistant Professor Laboratório de Neuropsicofisiologia | Laboratory of Neuropsychophysiology Faculdade de Psicologia e de Ciências da Educação da Universidade do Porto Faculty of Psychology and Education Sciences - University of Porto Rua Alfredo Allen, 4200-135 Porto, Portugal http://www.fpce.up.pt | frsantos at fpce.up.pt | (+351) 22 607 97 00 (ext. 409) Lab: http://www.fpce.up.pt/labpsi Personal: http://ferreira-santos.eu -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu May 17 09:26:00 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 17 May 2018 07:26:00 +0000 Subject: [FieldTrip] ft_connectivity_laggedcoherence In-Reply-To: References: Message-ID: <01302D06-30B7-40BF-A655-4D280ACC0C13@donders.ru.nl> Dear Jose, As far as I know, this code is not functional. The first author of the paper started the implementation in fieldtrip-style, but never finished it. Also, note that the method itself is not strictly speaking a ‘connectivity’ measure, but it was intended to identify rhythmicity within signals. Best wishes, Jan Mathijs J.M.Schoffelen, MD PhD Associate PI, VIDI-fellow Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 16 May 2018, at 18:17, Jose Herrero > wrote: dear Fieldtrippers, I'm comparing different coherence methods including the fieldtrip method of lagged coherence. running the code with... cfg.method = 'laggedcoherence'; lcoh = ft_connectivityanalysis(cfg, freq) results on... Error using ft_connectivityanalysis (line 375) unknown method laggedcoherence running the code with... lcoh = ft_connectivity_laggedcoherence(cfg, freq) results on: In an assignment A(:) = B, the number of elements in A and B must be the same. Error in ft_connectivity_laggedcoherence (line 213) lagwidth(lagindx) = cfg.lag*cyclelength*lagindx; as 'cfg.lag' is assigned a length equal to the length of the trial (1x15000, single trial). if this method works, is it possible to use it to compute lagged coherence between an external signal (which oscillates at a freq <0.5Hz) and the iEEG brain signal? thanks, JHerr _______________________________________________ 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 jose.herrero66 at gmail.com Thu May 17 14:31:24 2018 From: jose.herrero66 at gmail.com (Jose Herrero) Date: Thu, 17 May 2018 08:31:24 -0400 Subject: [FieldTrip] ft_connectivity_laggedcoherence In-Reply-To: <01302D06-30B7-40BF-A655-4D280ACC0C13@donders.ru.nl> References: <01302D06-30B7-40BF-A655-4D280ACC0C13@donders.ru.nl> Message-ID: thanks Jan Mathijs for your reply, yes not to blame for not finishing up ... a lot of nice work already in his paper! after reading your tutorial ( http://www.fieldtriptoolbox.org/project/guidelines/paper/connectivity_analysis?s[]=coherence&s[]=lags) still would love your thoughts on this. ideally, I'd like to find out whether a specific phase of an ultraslow (<0.5Hz rhythmic external) signal is leading/lagging the phase of the iEEG signal at the same frequency (effective connectivity). Would it be adequate here to use 'granger' over 'pdc' since I'm not interested in the freq domain (as both signals have been filtered <0.5Hz). Note that dominant frequencies between signals differs a lot. Also, interesting to know if there are consistent phase lags in some iEEG electrodes but not others (functional connectivity). which ft measures would you advice particularly if you want to compute phase lags? The Nolte (2004) paper suggested cfg.method = 'coh' & cfg.complex = 'imag' as being a superior method. Is that right for this particular case? Would it be adequate here to use cfg.method='wpli' or 'wpli_debiased' ? I've explored other methods (Guo, 2007, PLoS) but not sure they're adequate for this specific case (where dominant frequencies between signals differs a lot). thanks On Thu, May 17, 2018 at 3:26 AM, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Dear Jose, > As far as I know, this code is not functional. The first author of the > paper started the implementation in fieldtrip-style, but never finished it. > Also, note that the method itself is not strictly speaking a > ‘connectivity’ measure, but it was intended to identify rhythmicity within > signals. > > Best wishes, > Jan Mathijs > > J.M.Schoffelen, MD PhD > Associate PI, VIDI-fellow > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > > On 16 May 2018, at 18:17, Jose Herrero wrote: > > dear Fieldtrippers, > > I'm comparing different coherence methods including the fieldtrip method > of lagged coherence. > > running the code with... > cfg.method = 'laggedcoherence'; > > lcoh = ft_connectivityanalysis(cfg, freq) > results on... > Error using ft_connectivityanalysis (line 375) > > unknown method laggedcoherence > > running the code with... > lcoh = ft_connectivity_laggedcoherence(cfg, freq) > results on: > In an assignment A(:) = B, the number of elements in A and B must be the > same. > Error in ft_connectivity_laggedcoherence (line 213) > lagwidth(lagindx) = cfg.lag*cyclelength*lagindx; > as 'cfg.lag' is assigned a length equal to the length of the trial > (1x15000, single trial). > > if this method works, is it possible to use it to compute lagged coherence > between an external signal (which oscillates at a freq <0.5Hz) and the iEEG > brain signal? > > thanks, > JHerr > > > _______________________________________________ > 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 > -- Jose L Herrero, PhD Department of Neurosurgery Northwell University Hospital Feinstein Institute for Medical Research New York -------------- next part -------------- An HTML attachment was scrubbed... URL: From annekathrinweise at gmail.com Thu May 17 15:06:34 2018 From: annekathrinweise at gmail.com (Annekathrin Weise) Date: Thu, 17 May 2018 15:06:34 +0200 Subject: [FieldTrip] potential bug when using ft_icabrowser - help needed Message-ID: <1a107ce2-873f-8204-454e-a0bfe70deb2b@gmail.com> Dear all, I am interested in using the ft_icabrowser to inpsect ICA components. I run into a potential bug (see my code and the related error messages in the screenshot below). Note that I also used the ft_databrowser to inspect the independent components what worked nicely. So, there seems to be no issue with the data "ica_components' itself. In case you want to have a closer look to efficiently evaluate the problem, you can find the data here. I appreciate any help to find a workaround. Cheers, Anne -- Annekathrin Weise, Dr. Paris-Lodron Universität Salzburg Division of Physiological Psychology Hellbrunnerstraße 34 5020 Salzburg Austria e-mail: annekathrin.weise at sbg.ac.at; annekathrinweise at gmail.com web: http://www.oboblab.at/ https://sites.google.com/site/weiseannekathrin/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hagbbfcodljipehl.png Type: image/png Size: 112378 bytes Desc: not available URL: From radman.thomas at gmail.com Sat May 19 16:04:09 2018 From: radman.thomas at gmail.com (Thomas Radman) Date: Sat, 19 May 2018 10:04:09 -0400 Subject: [FieldTrip] ft_determine_coordsys does not return coordinate system Message-ID: Hello, I would like to use individual MRIs to perform source analysis on EEG data. The problem I have is when importing dicoms into fieldtrip, and then using ft_determine_coordsys, the coordinate system is not returned. How can I determine the coordinate system and align this to my EEG sensors? Also, to use ft_volumerealign in interactive mode to select fiducials I need to know which side is right and which is left. Is it possible to do this if I did not have a vitamin E marker in my scans? Thank you, Tom Radman -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Sat May 19 17:57:41 2018 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Sat, 19 May 2018 08:57:41 -0700 Subject: [FieldTrip] ft_determine_coordsys does not return coordinate system In-Reply-To: References: Message-ID: Hi Thomas, First thing that comes to my mind is step 3 of this ECoG tutorial , which demonstrates how to determine the coordinate system of an anatomical image. You'll need Box 2 from the preprint , and Video 1 . Video 2 addresses your second point, on how to use the coordinate system to find left and right. Hope that helps, Arjen On Sat, May 19, 2018 at 7:04 AM, Thomas Radman wrote: > Hello, > > > > I would like to use individual MRIs to perform source analysis on EEG > data. > > > The problem I have is when importing dicoms into fieldtrip, and then using > ft_determine_coordsys, the coordinate system is not returned. How can I > determine the coordinate system and align this to my EEG sensors? > > > Also, to use ft_volumerealign in interactive mode to select fiducials I > need to know which side is right and which is left. Is it possible to do > this if I did not have a vitamin E marker in my scans? > > > Thank you, > > Tom Radman > > > _______________________________________________ > 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 diana-hime at yandex.ru Sun May 20 17:08:44 2018 From: diana-hime at yandex.ru (=?utf-8?B?LSDQlNC40LDQvdCw?=) Date: Sun, 20 May 2018 18:08:44 +0300 Subject: [FieldTrip] Wavelet spectrum is cut strangely on low frequencies Message-ID: <3893281526828924@web25o.yandex.ru> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: singleplot_TFRwaveA10.png Type: image/png Size: 17727 bytes Desc: not available URL: From julian.keil at gmail.com Sun May 20 17:17:22 2018 From: julian.keil at gmail.com (Julian Keil) Date: Sun, 20 May 2018 17:17:22 +0200 Subject: [FieldTrip] Wavelet spectrum is cut strangely on low frequencies In-Reply-To: <3893281526828924@web25o.yandex.ru> References: <3893281526828924@web25o.yandex.ru> Message-ID: Hi Diana, That is what you would expect given your wavelet settings. The "strange" cutting off of your low frequencies is due to the length of the wavelet combined with the length of your trial. Only frequencies for which your wavelet fits into your trial will be computed. For example, 7 cycles at 1 Hz will need 7s of data to compute, 7 cycles at 10 Hz will need 0.7s. Play around with the cfg.width setting to see the effect of different taper sizes. Good luck, Julian - Диана schrieb am So. 20. Mai 2018 um 17:11: > Hello! > > My name is Diana. Currently I'm triyng to do a wavelet analysis of my > data, which is 128 (129 with reference elctrode) EEG recording. > > The problem is thatthe result looks strangely - the low frequencies are > cut off. Can't understand the reason for this, and should it be this way or > it not. Would be happy with any help) > > The script I use: > > %preprocessing > cfg = []; > cfg.dataset = FileName; > cfg.continuous = 'yes'; %считываем файл как непрерывный > data_preproc = ft_preprocessing(cfg); > > > % deftrial > cfg = []; > cfg.dataset = FileName; > cfg.trialdef.eventtype = 'trigger'; > cfg.trialdef.eventvalue = 'tim0'; > cfg.trialdef.prestim = 0.2; > cfg.trialdef.poststim = 2.2; > > cfg_deftrial = ft_definetrial(cfg); > > data_deftrialed = ft_redefinetrial(cfg_deftrial, data_preproc); > > %wavelet > > cfg = []; > cfg.channel = 'all'; > cfg.method = 'wavelet'; > cfg.width = 7; > cfg.output = 'pow'; > cfg.foi = 1:1:45; > cfg.toi = 1:0.01:2; > TFRwave = ft_freqanalysis(cfg, data_deftrialed); > > > > The wavelet I get: > > > > > > Thanks in advance, Diana. > Undergraduate Student > Department of Biology of MSU > > P.S: Sorry for my english this time... > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: singleplot_TFRwaveA10.png Type: image/png Size: 17727 bytes Desc: not available URL: From a.stolk8 at gmail.com Sun May 20 17:26:30 2018 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Sun, 20 May 2018 08:26:30 -0700 Subject: [FieldTrip] Wavelet spectrum is cut strangely on low frequencies In-Reply-To: <3893281526828924@web25o.yandex.ru> References: <3893281526828924@web25o.yandex.ru> Message-ID: Hi Diana, This is because your time points of interest are close to the boundaries of the original time series, as described here: http://www.fieldtriptoolbox.org/faq/why_does_my_tfr_contain_nans You may want to include more data from your original time series (at call to ft_definetrial / ft_preprocessing) or use smaller spectral windows / fewer wavelet cycles (at ft_frequencyanalysis, spectral resolution permitting). Best regards, Arjen On Sun, May 20, 2018 at 8:08 AM, - Диана wrote: > Hello! > > My name is Diana. Currently I'm triyng to do a wavelet analysis of my > data, which is 128 (129 with reference elctrode) EEG recording. > > The problem is thatthe result looks strangely - the low frequencies are > cut off. Can't understand the reason for this, and should it be this way or > it not. Would be happy with any help) > > The script I use: > > %preprocessing > cfg = []; > cfg.dataset = FileName; > cfg.continuous = 'yes'; %считываем файл как непрерывный > data_preproc = ft_preprocessing(cfg); > > > % deftrial > cfg = []; > cfg.dataset = FileName; > cfg.trialdef.eventtype = 'trigger'; > cfg.trialdef.eventvalue = 'tim0'; > cfg.trialdef.prestim = 0.2; > cfg.trialdef.poststim = 2.2; > > cfg_deftrial = ft_definetrial(cfg); > > data_deftrialed = ft_redefinetrial(cfg_deftrial, data_preproc); > > %wavelet > > cfg = []; > cfg.channel = 'all'; > cfg.method = 'wavelet'; > cfg.width = 7; > cfg.output = 'pow'; > cfg.foi = 1:1:45; > cfg.toi = 1:0.01:2; > TFRwave = ft_freqanalysis(cfg, data_deftrialed); > > > > The wavelet I get: > > > > > > Thanks in advance, Diana. > Undergraduate Student > Department of Biology of MSU > > P.S: Sorry for my english this time... > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: singleplot_TFRwaveA10.png Type: image/png Size: 17727 bytes Desc: not available URL: From diana-hime at yandex.ru Mon May 21 00:02:56 2018 From: diana-hime at yandex.ru (=?utf-8?B?LSDQlNC40LDQvdCw?=) Date: Mon, 21 May 2018 01:02:56 +0300 Subject: [FieldTrip] Wavelet spectrum is cut strangely on low frequencies In-Reply-To: References: <3893281526828924@web25o.yandex.ru> Message-ID: <4339051526853776@web13o.yandex.ru> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: singleplot_TFRwaveA10.png Type: image/png Size: 17727 bytes Desc: not available URL: From deydhiman794 at gmail.com Mon May 21 09:30:01 2018 From: deydhiman794 at gmail.com (Dhiman Dey) Date: Mon, 21 May 2018 13:00:01 +0530 Subject: [FieldTrip] Brain Source Localization using EEG Signals Message-ID: Hello everyone I am doing b.tech final year project on Brain Source Localization using EEG Signals. I am following the FieldTrip Toolbox for this project. The workshop http://www.fieldtriptoolbox.org/workshop/baci2017/forwardproblem provides the solution of my project but they had used MRI dataset(i.e .mri file) instead of EEG dataset(i.e .eeg file) Please provide me the solution using EEG dataset. Thank you. mailid: deydhiman794 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From fereshte.ramezani at gmail.com Mon May 21 09:50:50 2018 From: fereshte.ramezani at gmail.com (Fereshte) Date: Mon, 21 May 2018 12:20:50 +0430 Subject: [FieldTrip] Brain Source Localization using EEG Signals In-Reply-To: References: Message-ID: Hi, This tutorial explains how to create a FEM/BEM head model ( using MRI dataset) for solving forward problem ( to obtain the leadfield) . I think in your case ( using EEG signals) you need to solve the inverse problem which is explained " http://www.fieldtriptoolbox.org/workshop/baci2017/inverseproblem". Cheers On Mon, May 21, 2018 at 12:02 PM Dhiman Dey wrote: > Hello everyone > > I am doing b.tech final year project on Brain Source Localization using > EEG Signals. > I am following the FieldTrip Toolbox for this project. > > The workshop > http://www.fieldtriptoolbox.org/workshop/baci2017/forwardproblem provides > the solution of my project but they had used MRI dataset(i.e .mri file) > instead of EEG dataset(i.e .eeg file) > > Please provide me the solution using EEG dataset. > Thank you. > > mailid: deydhiman794 at gmail.com > _______________________________________________ > 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 fereshte.ramezani at gmail.com Mon May 21 10:42:16 2018 From: fereshte.ramezani at gmail.com (Fereshte) Date: Mon, 21 May 2018 13:12:16 +0430 Subject: [FieldTrip] Normalized source model Message-ID: Dear Experts, Are the output source models of " ft_prepare_sourcemodel" function normalized on the surface by default? Thanks in advance! Regards, F.R -------------- next part -------------- An HTML attachment was scrubbed... URL: From deydhiman794 at gmail.com Mon May 21 11:35:36 2018 From: deydhiman794 at gmail.com (Dhiman Dey) Date: Mon, 21 May 2018 15:05:36 +0530 Subject: [FieldTrip] Brain Source Localization using EEG Signals In-Reply-To: References: Message-ID: Thank you for your reply but for brain source localization at first you need to solve forward problem then proceed with inverse problem. I already saw the workshop for inverse problem where the same MRI dataset is used. Kindly share the solution using EEG dataset. On 21 May 2018 at 13:20, Fereshte wrote: > Hi, > This tutorial explains how to create a FEM/BEM head model ( using MRI > dataset) for solving forward problem ( to obtain the leadfield) . I think > in your case ( using EEG signals) you need to solve the inverse problem > which is explained "http://www.fieldtriptoolbox.org/workshop/baci2017/ > inverseproblem". > Cheers > > On Mon, May 21, 2018 at 12:02 PM Dhiman Dey > wrote: > >> Hello everyone >> >> I am doing b.tech final year project on Brain Source Localization using >> EEG Signals. >> I am following the FieldTrip Toolbox for this project. >> >> The workshop http://www.fieldtriptoolbox.org/workshop/baci2017/ >> forwardproblem provides the solution of my project but they had used MRI >> dataset(i.e .mri file) instead of EEG dataset(i.e .eeg file) >> >> Please provide me the solution using EEG dataset. >> Thank you. >> >> mailid: deydhiman794 at gmail.com >> _______________________________________________ >> 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 paul.sowman at mq.edu.au Mon May 21 12:11:38 2018 From: paul.sowman at mq.edu.au (Paul Sowman) Date: Mon, 21 May 2018 10:11:38 +0000 Subject: [FieldTrip] MEG Professorship in Sydney Message-ID: <80BA9A1C-09D4-403C-83E2-82461BE2C9FD@contoso.com> Professor of Human Neuroscience/Neuroimaging Macquarie University is a vibrant multidisciplinary research environment with significant neuroimaging infrastructure and ample opportunities for training and collaboration. We are seeking a distinguished academic within a speciality of cognitive neuroscience to join a growing group of cognitive scientists, hearing scientists, experimental psychologists, linguists and education researchers making original, innovative and prominent contributions to teaching and research at Macquarie. As a senior member of the team, you will have access to resources including MEG, fMRI, fNIRS and TMS as well as the opportunity to build collaborative networks with specialists within Macquarie University Hospital, located on campus. We welcome applications from academics within any speciality of cognitive neuroscience, including hearing, language, motor control, emotion, memory, executive function, visual attention, perception, and decision-making. Methodological specialty within neuroimaging is open, but ideally the candidate would enhance our strong existing program in MEG imaging, and develop a translational, theory-based neuroimaging program focusing on utilising MEG in their area of interest. How to Apply https://www.seek.com.au/job/36254679 For a confidential discussion about the role and the University’s expectations, please contact Associate Professor Paul Sowman on +61 2 9850 6732 or email paul.sowman at mq.edu.au. Applications Close: Sunday, 24 June 2018 at 11.55pm -- Paul F Sowman Associate Professor Director HDR Deputy Head Department of Cognitive Science Level 3, Room 3.824 Australian Hearing Hub 16 University Drive Macquarie University, NSW 2109, Australia T: +61 2 9850 6732 W: Profile Page W: MQU Stuttering Research Facebook Page -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.daume at uke.de Mon May 21 20:36:20 2018 From: j.daume at uke.de (Jonathan Daume) Date: Mon, 21 May 2018 20:36:20 +0200 Subject: [FieldTrip] potential bug when using ft_icabrowser - help needed In-Reply-To: <1a107ce2-873f-8204-454e-a0bfe70deb2b@gmail.com> References: <1a107ce2-873f-8204-454e-a0bfe70deb2b@gmail.com> Message-ID: <9A9DC1CD-A8F7-43F5-B738-2810AA8EFAE9@uke.de> Hi Anne, There seems to be a problem with ft_prepare_layout as is doesn’t construct the correct sensors layout from your data. However, you can read the layout structure simply from the provided layout file without handing over your MEG data to the function. So just open the icabrowser ("edit ft_icabrowser.m") and change line 53 from lay = ft_prepare_layout(cfglay, comp); to lay = ft_prepare_layout(cfglay); The topotplot function should work again now. Nevertheless, you will still run into problems with the power spectrum (left panel in the figure) as it won’t show any data. I checked your data and saw that every ica component also contains NaNs. This means that the fft analysis will result in only NaNs as well. You may consider to just get rid of them before computing the power spectrum (which is done in lines 102-109). Moreover, the icabrowser was originally coded for trial-based data and only every 5th trial was considered for the power analysis. Otherwise, it just takes too long to plot every single component. However, I saw that your data only contains (continous?) data from a single trial. Computing the fft of the whole recording would take ages. So, in case your data is continuous data from resting state for example, you may also consider to divide your data into epochs and take only every 5th epoch or so for the power analysis. I have coded something in that direction for you but I am not sure what kind of data you have and if it suits your data. I just divided the data in epochs of 1s length and took every 5th epoch for the analysis. Please find the code below. You may just further adjust the code so that it better suits your data. Change line 34 from fft_data = cat(2,comp.trial{1:5:end}); to fft_data = comp.trial{1}; And lines 104 - 106 from Fs = comp.fsample; N = floor(size(fft_data,2)); xdft = fft(fft_data(i,:)); to comp_data = fft_data(i,~isnan(fft_data(i,:))); % kick out all NaNs first epochJump = 5; % how many trials to jump over? numEpochs = size(comp_data,2)/comp.fsample; fft_data_i = []; for i_epoch = 1:epochJump:numEpochs epochdata = comp_data((i_epoch-1)*comp.fsample+1:i_epoch*comp.fsample); fft_data_i = [fft_data_i,epochdata]; end N = floor(size(fft_data_i,2)); xdft = fft(fft_data_i); Or you just download the edited file from here . :) Hope this helps! Please get in touch with me if you have any further question. Cheers, Jonathan ----- Jonathan Daume, PhD Dept. of Neurophysiology and Pathophysiology University Medical Center Hamburg Eppendorf Martinistr. 52 20246 Hamburg Germany Phone: +49-40-7410-55856 Email: j.daume at uke.de www.uke.de > Am 17.05.2018 um 15:06 schrieb Annekathrin Weise : > > Dear all, > > I am interested in using the ft_icabrowser to inpsect ICA components. > > I run into a potential bug (see my code and the related error messages in the screenshot below). > > Note that I also used the ft_databrowser to inspect the independent components what worked nicely. So, there seems to be no issue with the data "ica_components' itself. > > In case you want to have a closer look to efficiently evaluate the problem, you can find the data here. > I appreciate any help to find a workaround. > > Cheers, > > Anne > > > > -- > Annekathrin Weise, Dr. > > Paris-Lodron Universität Salzburg > Division of Physiological Psychology > Hellbrunnerstraße 34 > 5020 Salzburg > Austria > > e-mail: annekathrin.weise at sbg.ac.at ; > annekathrinweise at gmail.com > > web: > http://www.oboblab.at/ > https://sites.google.com/site/weiseannekathrin/ > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Martina Saurin (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING -------------- next part -------------- An HTML attachment was scrubbed... URL: From radman.thomas at gmail.com Tue May 22 00:53:03 2018 From: radman.thomas at gmail.com (Thomas Radman) Date: Mon, 21 May 2018 18:53:03 -0400 Subject: [FieldTrip] Brain segmentation has strange spikes in it Message-ID: Hello, I am trying to segment an individual subject's MRI following this tutorial: http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting However, when plotting the mesh of the scalp segmentation I get these horrible disfigurations that are not in the original MRI. Here is a screenshot: These are the steps I'm taking mri=ft_read_mri( '/data/radmantc/projects/T1_mni.nii') mri.coordsys='mni' cfg = []; cfg.resolution = 1; mri_resliced = ft_volumereslice(cfg, mri); figure ft_sourceplot([], mri_resliced); %volume conduction model cfg = []; cfg.output = {'brain', 'skull', 'scalp'}; mri_segmented = ft_volumesegment(cfg, mri_resliced); % copy the anatomy into the segmented mri mri_segmented.anatomy = mri_resliced.anatomy; %reconstruct the three triangulated meshes. cfg = []; cfg.method = 'projectmesh'; cfg.tissue = 'brain'; cfg.numvertices = 3000; mesh_eeg(1) = ft_prepare_mesh(cfg, mri_segmented); cfg.tissue = 'skull'; cfg.numvertices = 2000; mesh_eeg(2) = ft_prepare_mesh(cfg, mri_segmented); cfg.tissue = 'scalp'; cfg.numvertices = 1000; mesh_eeg(3) = ft_prepare_mesh(cfg, mri_segmented); figure ft_plot_mesh(mesh_eeg(1), 'edgecolor', 'none', 'facecolor', 'r') ft_plot_mesh(mesh_eeg(2), 'edgecolor', 'none', 'facecolor', 'g') ft_plot_mesh(mesh_eeg(3), 'edgecolor', 'none', 'facecolor', 'b') %this is the only mesh that is distorted alpha 0.3 Also, can someone tell me how to respond to any replies I might get. In previous posts, I only see the replies in the listserv digest emails. Do I create a new email with the subject line of this case intact? I don't get an email directly from the person sending the reply to my email, I only see it in the digest. Thank you for the help, Thomas Radman -------------- next part -------------- An HTML attachment was scrubbed... URL: From w.kruijne at gmail.com Tue May 22 12:37:03 2018 From: w.kruijne at gmail.com (Wouter Kruijne) Date: Tue, 22 May 2018 12:37:03 +0200 Subject: [FieldTrip] artifact detection -- computing the accumulated z Message-ID: Hi everyone, When playing around with different ways of rejecting (muscle) artifacts, I came across something in the tutorial + code that I do not fully understand. The tutorial ( http://www.fieldtriptoolbox.org/tutorial/automatic_artifact_rejection#iii_z-transforming_the_filtered_data_and_averaging_it_over_channels ) states that: > 4. Per timepoint these z-values are averaged. Since an artifact might > occur on any and often on more than one electrode (think of eyeblinks and > muscle artifacts), averaging z-values over channels/electrodes allows > evidence for an artifact to accumulate. > ​This line of reasoning makes perfect sense to me. However, in the subsequent mathematical description, and in the implementation, averaging isn't applied at all: instead, a scaled summation is computed. zsum = SUM_{ch in C} = z(ch,t)/sqrt(C) ​ where C is the number of channels [forgive my math editing skills] . I fail to understand why the accumulated z-score uses a division by the _sqrt_ of the number of channels, rather than simple averaging. In fact, the potential downsides I see are: - The reported z-value, and the one used for thresholding does not correspond to the traditional interpretation of z. - The value of a 'good' z-threshold value is dependent on the number of channels, as this changes the scaling. - Should we wish to use the channel-level z-scores for identifying channels affected by the artefact, the accumulated threshold value now has a different scale than the channel-level z-values. Am I missing something? What are the upsides of the sqrt scaling? Thank you! Wouter -------------- next part -------------- An HTML attachment was scrubbed... URL: From antonio.tavella at virgilio.it Tue May 22 14:29:24 2018 From: antonio.tavella at virgilio.it (antonio.tavella at virgilio.it) Date: Tue, 22 May 2018 14:29:24 +0200 (CEST) Subject: [FieldTrip] Research assistantship with possible PhD scholarship Message-ID: <3844204.243454.1526992165001@mail.virgilio.it> Apologies for multiple posting The Group of Psychiatric Neuroscience at the University of Bari Aldo Moro will publish a call for a 1-year long Research Assistant position, renewable up to 4 years, in the field of Brain Imaging (MRI & MEG). Expressions of interest are welcome before June 30th. Candidates who are in the process of writing up their master thesis are encouraged to apply. The expected starting date is September 2018. Research Assistants interested in pursuing a PhD at our department will have the opportunity to enroll in the Doctoral School in November, following positive evaluation. The Group of Psychiatric Neuroscience is led by Prof. Alessandro Bertolino and Prof. Giuseppe Blasi and investigates the association of genetic variability with systems-level phenotypes, including structural and functional Magnetic Resonance Imaging, Diffusion Tensor Imaging, Arterial Spin Labeling, and Magnetoencephalography. The Group of Psychiatric Neuroscience has access to and routinely tests psychiatric patients, relatives of patients, and individuals at risk for psychosis. The department has an in-house Elekta Triux magnetoencephalography installed in October 2016 with a dedicated technician. The Research Assistant will work in the lab of Brain Imaging, Networks, and Data mining (BIND) directed by Dr. Giulio Pergola, with the aim to investigate the biological basis of major psychiatric disorders by integrating multimodal data (genetic variation, gene expression, structural and functional MRI, MEG, and neuropsychology). The Research Assistant will contribute to neuroimaging data acquisition and analysis for projects funded both at local and European level (for recent articles from the lab, see [1], [2], [3]). The ideal candidate is a young graduate interested in neuroimaging, with a Master’s Degree in Neuroscience, Psychology, Medicine, Biotechnology, Applied Physics, or related fields. Knowledge of statistics and skills regarding the integration of imaging and machine learning are a plus. We expect the successful candidate to be motivated and research-oriented. It is equally important to have a team-working attitude and a motivation to fit in the group. Knowledge of Italian is not required, as the lab already hosts two international PhD students and research meetings are held in English. Bari is a sunny city located by the sea in the east of southern Italy, and the third greatest city south of Rome. The cost of living is comparatively low relative to Italian standards. The net monthly salary of the Research Assistant will be > 1400 EUR. Please contact Dr. Giulio Pergola sending a CV and the contact details of at least two references if you would like to have more information on the position and on the ongoing projects (giulio.pergola at uniba.it mailto:giulio.pergola at uniba.it ). -------------- next part -------------- An HTML attachment was scrubbed... URL: From jose.herrero66 at gmail.com Tue May 22 15:42:28 2018 From: jose.herrero66 at gmail.com (Jose Herrero) Date: Tue, 22 May 2018 09:42:28 -0400 Subject: [FieldTrip] use_simulated_erps_to_explore_cluster_statistics ERROR Message-ID: Dear FT, after running the tutorial example/use_simulated_erps_to_explore_cluster_statistics.txt Error using ft_math (line 151) the requested parameter is not present in the data has anybody encounter this b4? thanks, JHerr -------------- next part -------------- An HTML attachment was scrubbed... URL: From mailtome.2113 at gmail.com Wed May 23 04:08:37 2018 From: mailtome.2113 at gmail.com (Arti Abhishek) Date: Wed, 23 May 2018 12:08:37 +1000 Subject: [FieldTrip] xdf format for EEG data Message-ID: Dear fieldtrip development team, I was wondering whether there is a plan to support xdf file format for the EEG data (eg: SMARTING system) in the future releases of fieldtrip? Thanks, Arti -------------- next part -------------- An HTML attachment was scrubbed... URL: From laetitia.grabot at gmail.com Wed May 23 13:42:56 2018 From: laetitia.grabot at gmail.com (Laetitia Grabot) Date: Wed, 23 May 2018 13:42:56 +0200 Subject: [FieldTrip] Error while reading in Fieldtrip an epochs file created with mne-python Message-ID: Dear all, I'm trying to read in Fieldtrip an Elekta Neuromag epochs file (.fif) created with mne-python (MEG and EEG data file). I used the following snippet of code, and got the following error: cfg = []; cfg.dataset = filename; data = ft_preprocessing(cfg); Error using fiff_read_epochs (line 47) Could not find epochs data Error in fiff_read_epochs (line 47) error(me,'Could not find epochs data'); Error in ft_read_header (line 1846) epochs = fiff_read_epochs(filename); Error in ft_read_header (line 125) hdr{i} = ft_read_header(filename{i}, varargin{:}); Error in ft_preprocessing (line 397) hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat,... I saw that a former thread reported the same error, but it seems that the code was changed meanwhile. I'm using Matlab R2017a ver 9.2 and the Fieldtrip version dated from 16-05-2018. Here you can download the epochs file I used. It would be very helpful is someone knows from where this problem could come. Thank you very much, Best, Laetitia -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.homolle at donders.ru.nl Wed May 23 14:01:04 2018 From: s.homolle at donders.ru.nl (Simon Homolle) Date: Wed, 23 May 2018 14:01:04 +0200 Subject: [FieldTrip] Brain segmentation has strange spikes in it In-Reply-To: References: Message-ID: Dear Thomas, unfortunately I cannot see the figure you send. But from the title of the email I think i have some suggestions for you. > %volume conduction model > cfg = []; > cfg.output = {'brain', 'skull', 'scalp'}; > mri_segmented = ft_volumesegment(cfg, mri_resliced); for this segment you can play around with to make the the tissues more smooth % cfg.brainsmooth = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5) % cfg.scalpsmooth = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5) % cfg.skullsmooth = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5) Or you can change the thresholds for the tissues % cfg.brainthreshold = 'no', or scalar, relative threshold value which is used to threshold the % tpm in order to create a volumetric brainmask (see below), (default = 0.5) % cfg.scalpthreshold = 'no', or scalar, relative threshold value which is used to threshold the % anatomical data in order to create a volumetric scalpmask (see below), % (default = 0.1) % cfg.skullthreshold = 'no', or scalar, relative threshold value which is used to threshold the % anatomical data in order to create a volumetric scalpmask (see below), % (default = 0.5). this parameter is only used when % the segmetnation contains 6 tissue types, % including 'bone’, > %reconstruct the three triangulated meshes. > cfg = []; > cfg.method = 'projectmesh'; > cfg.tissue = 'brain'; > cfg.numvertices = 3000; > mesh_eeg(1) = ft_prepare_mesh(cfg, mri_segmented); > > cfg.tissue = 'skull'; > cfg.numvertices = 2000; > mesh_eeg(2) = ft_prepare_mesh(cfg, mri_segmented); > > cfg.tissue = 'scalp'; > cfg.numvertices = 1000; > mesh_eeg(3) = ft_prepare_mesh(cfg, mri_segmented); If the previous steps to not solve your problems, you can also try to change something in the method % cfg.method = string, can be 'interactive', 'projectmesh', 'iso2mesh', 'isosurface', % 'headshape', 'hexahedral', 'tetrahedral', 'cortexhull' Cheers, Simon Homölle PhD Candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Phone: +31-(0)24-36-65059 > On 22 May 2018, at 00:53, Thomas Radman wrote: > > Hello, > > I am trying to segment an individual subject's MRI following this tutorial: > http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting > > However, when plotting the mesh of the scalp segmentation I get these horrible disfigurations that are not in the original MRI. Here is a screenshot: > > > > These are the steps I'm taking > mri=ft_read_mri( '/data/radmantc/projects/T1_mni.nii') > mri.coordsys='mni' > > cfg = []; > cfg.resolution = 1; > mri_resliced = ft_volumereslice(cfg, mri); > figure > ft_sourceplot([], mri_resliced); > > %volume conduction model > cfg = []; > cfg.output = {'brain', 'skull', 'scalp'}; > mri_segmented = ft_volumesegment(cfg, mri_resliced); > > % copy the anatomy into the segmented mri > mri_segmented.anatomy = mri_resliced.anatomy; > > %reconstruct the three triangulated meshes. > cfg = []; > cfg.method = 'projectmesh'; > cfg.tissue = 'brain'; > cfg.numvertices = 3000; > mesh_eeg(1) = ft_prepare_mesh(cfg, mri_segmented); > > cfg.tissue = 'skull'; > cfg.numvertices = 2000; > mesh_eeg(2) = ft_prepare_mesh(cfg, mri_segmented); > > cfg.tissue = 'scalp'; > cfg.numvertices = 1000; > mesh_eeg(3) = ft_prepare_mesh(cfg, mri_segmented); > > figure > ft_plot_mesh(mesh_eeg(1), 'edgecolor', 'none', 'facecolor', 'r') > ft_plot_mesh(mesh_eeg(2), 'edgecolor', 'none', 'facecolor', 'g') > ft_plot_mesh(mesh_eeg(3), 'edgecolor', 'none', 'facecolor', 'b') %this is the only mesh that is distorted > alpha 0.3 > > Also, can someone tell me how to respond to any replies I might get. In previous posts, I only see the replies in the listserv digest emails. Do I create a new email with the subject line of this case intact? I don't get an email directly from the person sending the reply to my email, I only see it in the digest. > > Thank you for the help, > Thomas Radman > > _______________________________________________ > 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 fereshte.ramezani at gmail.com Sat May 26 03:09:03 2018 From: fereshte.ramezani at gmail.com (Fereshte) Date: Sat, 26 May 2018 05:39:03 +0430 Subject: [FieldTrip] Project numerical values on a cortical mesh Message-ID: Dear Experts, I have assigned numerical values to 1000 vertices of a cortical mesh ( a matrix of 1000 rows and 4 columns; which the first 3 columns show the position of each vertex and the last column shows the numerical value) .How can I project and show these numerical values on the cortical mesh? Thanks in advance! Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From rhancock at email.arizona.edu Wed May 30 00:51:22 2018 From: rhancock at email.arizona.edu (Roeland Hancock) Date: Tue, 29 May 2018 18:51:22 -0400 Subject: [FieldTrip] Postdoctoral Scholar positions in neuroimaging Message-ID: NIDL and brainLENS-east labs (Neurobiology of Individual Differences in Language Lab http://nidl-lab.org, PI: Roeland Hancock PhD; and Laboratory for Learning Engineering and Neural Systems http://brainlens.org, PI: Fumiko Hoeft MD PhD) at University of Connecticut’s Brain Imaging Research Center (UCONN’s BIRC) are seeking: (1) two full-time neuroimaging postdoctoral fellows, and (2) two full-time Research Coordinators. BIRC is also seeking one full-time IT staff. *TWO NEUROIMAGING POSTDOC POSITIONS @ UCONN* We are seeking two postdoctoral scholars. The postdocs will manage and execute a large-scale neuroimaging project investigating the neurobiological mechanisms underlying: (1) language, literacy and cognition in generally healthy young adults using multimodal neuroimaging techniques such as MRI, MRS and TMS (“Perturbation Postdoc”); or (2) intergenerational transmission of language and literacy in parent-offspring dyads using MRI techniques (“Intergenerational Postdoc”). In addition, the successful candidates will have the opportunity to be involved in other federally and non-federally funded-research projects in the laboratories, gain experience in grant and manuscript writing and large-scale project management, outreach and community engagement projects, and access to a wealth of archival developmental and longitudinal neuroimaging data on language and literacy. *Required qualifications:* · PhD or equivalent in cognitive and systems neurosciences, computer science, engineering, psychology or a closely related field · Computational skills, including knowledge of at least one programming language and Unix commands · Strong written and verbal communication skills · Leadership and organizational skills *Preferred qualifications:* · Exceptional skills in collecting and analyzing MRI, MRS, and/or TMS data · Experience in M/EEG · Documented history of productivity and leadership · Advanced knowledge and expertise in statistics, e.g. multivariate statistics, behavioral genetics, Bayesian and Monte Carlo methods The position will be formally advertised at a later date. In the meantime, interested candidates should email *info at nidl-lab.org * with *"[Postdoc Job (YOUR FULL NAME)]" in the subject line*. In the email they should include (a) a current CV, (b) a one-page cover letter describing qualifications, interest, career goals and which postdoc position they are interested in (refer to as *“Perturbation Postdoc/Project” *or *“Intergenerational Postdoc/Project”)*, and (c) a list of 3 potential referees with their contact information. The position can begin immediately. *Postdoctoral scholars from the lab have gone onto a range of research faculty and imaging director positions at institutions such as Stanford, Caltech, Boston College, and University of Texas.* *The University of Connecticut is committed to building and supporting a multicultural and diverse community of students, faculty and staff. The diversity of students, faculty and staff continues to increase, as does the number of honor students, valedictorians and salutatorians who consistently make UConn their top choice. More than 100 research centers and instates serve the University’s teaching, research, diversity, and outreach missions, leading to UConn’s ranking as one of the nation’s top research universities. UConn’s faculty and staff are the critical link to fostering and expanding our vibrant, multicultural and diverse University community. As an Affirmative Action/Equal Employment Opportunity employer, UConn encourages applications from women, veterans, people with disabilities and members of traditionally underrepresented populations.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.homolle at donders.ru.nl Wed May 30 18:23:47 2018 From: s.homolle at donders.ru.nl (Simon Homolle) Date: Wed, 30 May 2018 18:23:47 +0200 Subject: [FieldTrip] EEG and MEG Source Reconstruction with FieldTrip @OHBM2018 Message-ID: <9A1E8D0A-EEA2-4211-AF4D-D6AC6EE257CB@donders.ru.nl> Dear all, on 17 June 2018 we will host a workshop at the OHBM2018 conference . The course is aimed at researchers who want to learn how to do MEG and/or EEG source reconstruction. We expect that you know the basics of MATLAB and that you already have experience with MEG/EEG preprocessing and analysis. In this intense one-day workshop we will explain state-of-the-art MEG and EEG source reconstruction methods. The workshop will consist of a number of lectures, followed by hands-on sessions in which you will be tutored through the complete analysis of a MEG, EEG and MRI data set using the FieldTrip toolbox. As the focus is on source reconstruction, topics that will NOT be covered in great detail are segmenting, artifact handling, averaging, frequency and time-frequency analysis, statistics. For the hands-on sessions you should bring a laptop with MATLAB installed. More information about the program can be found at the OHBM website or on the FieldTrip website. Best regards, Maria Carla Piastra1 , Sophie Schrader1 and Simon Homölle2 1 Institute for Biomagnetism and Biosignalanalysis, University of Münster, Münster, Germany. 2 Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands. -------------- next part -------------- An HTML attachment was scrubbed... URL: From elam4hcp at gmail.com Wed May 30 21:08:48 2018 From: elam4hcp at gmail.com (Jennifer Elam) Date: Wed, 30 May 2018 14:08:48 -0500 Subject: [FieldTrip] Spaces added, register today for HCP Course 2018! Message-ID: If you are considering joining us for the *2018 HCP Course: "Exploring the Human Connectome"* June 25 – 29 at the University of Oxford , a few additional lodging rooms at Worcester College have opened up for just $675 for 6 nights, first come first served. For more info and to register visit the HCP Course 2018 website . We will continue to take registrations for the course until our venue at the Blavatnik School of Government is full. HCP Course 2018 is a 5-day intensive course of lectures and hands-on practicals and your best opportunity to learn directly from HCP investigators and gain practical experience with the Human Connectome Project's data and approach to multimodal whole brain imaging, processing and analysis and to get up to speed on HCP tools including Connectome Workbench (v1.3.0 just released!) and sharing your own analyzed imaging datasets via the BALSA database. If you have any questions, please contact us at: hcpcourse at humanconnectome. org We look forward to seeing you in Oxford! Best, 2018 HCP Course Staff -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam at wustl.edu www.humanconnectome.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu May 31 10:00:54 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 31 May 2018 10:00:54 +0200 Subject: [FieldTrip] Project numerical values on a cortical mesh In-Reply-To: References: Message-ID: Dear Fereshte The mesh should be described with both vertices (points in 3-D space) and triangles (the specification how these points form a surface). If your values are an Nx1 vector and your mesh is mesh.pos = Nx3 % position of the vertices mesh.pos = Mx3 % indices into the vertices that together form M triangles then you can do ft_plot_mesh(mesh, ‘vertexcolor’, val) which uses one of the low level functions in the plotting module. If you organize your data as source structure (e.g. used for reconstructions of cortical activity) you could also use the high-level ft_sourceplot. See "help ft_datatype_source" for documentation on the source structure. best regards Robert > On 26 May 2018, at 03:09, Fereshte wrote: > > Dear Experts, > I have assigned numerical values to 1000 vertices of a cortical mesh ( a matrix of 1000 rows and 4 columns; which the first 3 columns show the position of each vertex and the last column shows the numerical value) .How can I project and show these numerical values on the cortical mesh? > Thanks in advance! > Regards > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Thu May 31 10:03:20 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 31 May 2018 10:03:20 +0200 Subject: [FieldTrip] Error while reading in Fieldtrip an epochs file created with mne-python In-Reply-To: References: Message-ID: Hi Laetitia The code you are referring to is fiff_read_epochs, which is in fieldtrip/external/mne. The external toolboxes are not maintained by the FieldTrip developpers themselves, only included for convenience. Please contact the maintaners at https://github.com/mne-tools/mne-matlab best regards, Robert > On 23 May 2018, at 13:42, Laetitia Grabot wrote: > > Dear all, > > I'm trying to read in Fieldtrip an Elekta Neuromag epochs file (.fif) created with mne-python (MEG and EEG data file). I used the following snippet of code, and got the following error: > > cfg = []; > cfg.dataset = filename; > data = ft_preprocessing(cfg); > > Error using fiff_read_epochs (line 47) > Could not find epochs data > Error in fiff_read_epochs (line 47) > error(me,'Could not find epochs data'); > Error in ft_read_header (line 1846) > epochs = fiff_read_epochs(filename); > Error in ft_read_header (line 125) > hdr{i} = ft_read_header(filename{i}, varargin{:}); > Error in ft_preprocessing (line 397) > hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat,... > > I saw that a former thread reported the same error, but it seems that the code was changed meanwhile. > I'm using Matlab R2017a ver 9.2 and the Fieldtrip version dated from 16-05-2018. Here you can download the epochs file I used. > It would be very helpful is someone knows from where this problem could come. > > Thank you very much, > Best, > Laetitia > _______________________________________________ > 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 Thu May 31 10:08:54 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 31 May 2018 10:08:54 +0200 Subject: [FieldTrip] xdf format for EEG data In-Reply-To: References: Message-ID: <69E5203E-986D-4455-B2BC-B5EF1393C31A@donders.ru.nl> Hi Arti, It would be nice to support the XDF format, and I think it would not be much work as some matlab code is already available here Since you probably have access to XDF data files, it would be great if you could implement this. Please see this FAQ on how to extend (start with ft_filetype and then add it to ft_read_header, data and event). On the git tutorial you can find how to submit the change to the code for inclusion in the release version. thanks Robert > On 23 May 2018, at 04:08, Arti Abhishek wrote: > > Dear fieldtrip development team, > > I was wondering whether there is a plan to support xdf file format for the EEG data (eg: SMARTING system) in the future releases of fieldtrip? > > Thanks, > Arti > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: