From mikexcohen at gmail.com Mon May 1 11:13:57 2017 From: mikexcohen at gmail.com (Mike X Cohen) Date: Mon, 1 May 2017 11:13:57 +0200 Subject: [FieldTrip] Conference announcement: ICON XIII (Amsterdam, August 2017) Message-ID: We are happy to send a reminder for the ICON XIII conference, which will take place on 5-8 August 2017 in Amsterdam (the Netherlands). Amsterdam is an easily-accessible and progressive city. The venue is the Beurs van Berlage, located in downtown Amsterdam and one of the most beautiful conference venues in Europe! Visit the website: http://www.icon2017.org There is a very exciting line-up of keynote speakers and symposia, and there are new presentation formats including "ask-the-experts" panels and hackathons. Check out the "Program" tab at icon2017.org. Early-bird registration discount ends on May 15! The registration includes full conference attendance, lunch/snacks/coffee/tea every day, and the conference opening reception. Also note that although the official poster submission deadline is passed, we are still accepting some late poster submissions by special request. Contact us (icon2017 at icon2017.org) for details! FOLLOW US ON TWITTER For up-to-date announcements before and during the ICON meeting, follow @icon2017 (see also "Media" tab on the website). QUESTIONS ABOUT THE MEETING OR SPONSORSHIP? email icon2017 at icon2017.org http://www.icon2017.org We look forward to seeing you in beautiful Amsterdam! Mike X Cohen and Birte Forstmann -------------- next part -------------- An HTML attachment was scrubbed... URL: From christian.oreilly at epfl.ch Tue May 2 14:54:35 2017 From: christian.oreilly at epfl.ch (Christian O'Reilly) Date: Tue, 2 May 2017 14:54:35 +0200 Subject: [FieldTrip] Ordering of channels index in ft_read_data with egi_mff_v1 Message-ID: Hi, I've been trying for a while to find the source of an apparent swapping of channels in my data, and I suspect that the source of this issue comes from the ft_read_data function when it is used with egi_mff_v1. This code does not handle very well list of channel indexes that are not ordered. I am using: chanindx = [36, 224, 37, 18, 21, 109, 153, 101]; data = ft_read_data([path fileNames(iFile).name], 'headerformat', ... 'egi_mff_v1', 'dataformat', 'egi_mff_v1', ... 'header', header, ... ... #'begsample', begsample, 'endsample', endsample, ... 'chanindx', chanindx); ... and I have a strong suspicion that the 8 columns of the data matrix are ordered as if chanindx == [18, 21, 36, 37, 101, 109 153, 224] I think it has to do with ft_read_data code: for iSig = 1:length(hdr.orig.signal) % adjust chanindx to match with current signal [dum1, dum2, chanind_sig] = intersect(chanindx, find(chan2sig_ind==iSig)); if isempty(chanind_sig) % no channels requested from current signal else blockhdr = hdr.orig.signal(iSig).blockhdr; signalname = binfiles(iSig).name; %%%%%%%%%%%% ... skipping lines of codes ... %%%%%%%%%% dat{end} = dat{end}(:,begsel:endsel); end end % concat signals dat = cat(1,dat{:}); In any case, as long as this is not corrected, people using fieldtrip to read EGI MFF files should keep this in mind and order their channel indexes! Best, Christian -------------- next part -------------- An HTML attachment was scrubbed... URL: From C.vandenBoomen at uu.nl Tue May 2 16:26:00 2017 From: C.vandenBoomen at uu.nl (Boomen, C. van den (Carlijn)) Date: Tue, 2 May 2017 14:26:00 +0000 Subject: [FieldTrip] error ft_nargin Message-ID: Dear fieldtrip users, I'm using fieldtrip to analyse my ERP data. My script used to work (at least until November 2016) but now I get the following error message. I get the same error using singleplotER, which used to work before as well. Does anyone know a solution? Undefined function or variable 'ft_nargin'. Error in ft_preamble_init (line 34) if ft_nargin==0 Error in ft_preamble (line 56) evalin('caller', ['ft_preamble_' cmd]); Error in ft_timelockgrandaverage (line 71) ft_preamble init Error in ERP_script_nov2016 (line 532) granderp_ind{cond} = ft_timelockgrandaverage(cfg,EEGallsubj.incldata{cond,1:end}); I'm using a mac (10.9.5), with matlab 2014b and fieldtrip 20160105 (since some parts of the script didn't work with later versions, I hope to use this version for now) Thanks a lot! Best, Carlijn Dr. Carlijn van den Boomen | Departments of Developmental and Experimental Psychology | Utrecht University | Langeveld Building - room H066 | Heidelberglaan 1 | 3584 CS Utrecht | the Netherlands | phone: +31(30) 253 1266 | fax: +31(30) 253 4511 -------------- next part -------------- An HTML attachment was scrubbed... URL: From laetitia.lalla at inserm.fr Tue May 2 16:47:27 2017 From: laetitia.lalla at inserm.fr (laetitia.lalla at inserm.fr) Date: Tue, 02 May 2017 16:47:27 +0200 Subject: [FieldTrip] Granger-Causality in the Time Domain In-Reply-To: References: Message-ID: Dear FieldTrip community, I was looking for a way to perform Granger causality in the time domain with FieldTrip and I found this post from 2014 : "The Granger causality in ft_connectivityanalysis is always frequency-domain Granger (time-domain Granger is not implemented in FieldTrip)." We are in 2017 now, is it still the case ? If yes, could you give me some advice regarding other toolboxes than can compute time-domain Granger causality ? Thank you very much for your help. All the best, Laetitia Lalla -------------- next part -------------- An HTML attachment was scrubbed... URL: From lethuymy at live.com Tue May 2 18:24:17 2017 From: lethuymy at live.com (Thuy-My Le) Date: Tue, 2 May 2017 16:24:17 +0000 Subject: [FieldTrip] ft_spikedetection Message-ID: Hi, My name is Thuy-My. I am new to field trip. I am attempting to use ft_spikedetection on a CTF file. However, when I assign 'matlab' to my cfg.dataformat parameter, I receive an error that the format is not supported. Is this because my input file is CTF? Will it not work regardless if I change the specified dataformat parameter? I have tried all formats listed under ft_write_spike. Please let me know if there is a work around as well. Thanks, Thuy-My -------------------------------------------------------------------- Thuy-My Thi Le University of Pennsylvania School of Engineering and Applied Sciences Department of Bioengineering M.S.E. Class of 2016 -------------- next part -------------- An HTML attachment was scrubbed... URL: From schurgerlab at gmail.com Tue May 2 19:41:22 2017 From: schurgerlab at gmail.com (Schurger Lab) Date: Tue, 2 May 2017 19:41:22 +0200 Subject: [FieldTrip] Post-doctoral position in volition and self-initiated action (MEG / EEG) Message-ID: Interdisciplinary post-doctoral position in cognitive neuroscience (MEG / EEG) Brain-behavior forecasting: Neural antecedents of spontaneous self-initiated movement and the forecasting of behavior based on brain activity, studied with MEG / EEG Starting date: Fall 2017 or Spring 2018 Duration: 2 years (renewable for one additional year) The French Institute of Health and Medical Research (INSERM) invites applications for a post-doctoral position in the Cognitive Neuroimaging Group, at the NeuroSpin Research Center near Paris, France, as part of the research team of Dr. Aaron Schurger. The Schurger lab focuses on understanding how decisions are made and actions initiated spontaneously, without an external sensory cue, and how time series of neural activity can be used to forecast behavior. We pursue this research using a combination of behavioral experiments, neuroimaging, computational modeling, time-series analyses, and machine learning techniques. We are looking for applicants with experience in magnetoencephalography (MEG) experimentation and data analysis, including inverse source estimation. Experience with electroencephalography (EEG) is desirable. Applicants should have obtained a PhD in a relevant discipline prior to the starting date, have a solid working knowledge of cognitive neuroscience, and should have strong skills in the following areas: computer programming (MatLab, Python, C, C++), statistics, signal processing, FieldTrip or comparable data analysis tool Additionally, prior experience in any of the following areas is desirable: computational, mathematical, and/or neural network modeling, statistical learning / machine learning / mutivariate pattern classification, time series analysis, dynamical systems theory, scale-free dynamics, behavioral psychophysics Resources available at NeuroSpin include Siemens 3T and 7T MRI scanners; high-density EEG (EGI Inc.); Elekta NeuroMag 306-channel MEG (allowing for the simultaneous recording of EEG); eye tracking (available for MRI, MEG, and behavioral experiments); an in-house team of experts in signal processing and statistical learning; a dedicated staff handling subject recruitment, scheduling, and payment; various Nespresso devices; and proximity to Paris. Applicants should send a CV, letter of motivation (max 2 pages), and a list of three references via e-mail to schurgerlab at gmail.com. Review of applicants will begin on 15 May 2017, and will continue until the position is filled. The NeuroSpin Research Center is located on the campus of the CEA-Saclay, near Orsay, about 18 km southwest of Paris. For more information on the NeuroSpin Research Center and the Cognitive Neuroimaging Group: http://www-centre-saclay.cea.fr/fr/Visite-guidee-de-NeuroSpin http://meg-france.in2p3.fr/_lesCentres/Neurospin_en.php http://www-dsv.cea.fr/en/institutes/institute-of-biomedical-imaging-i2bm/departments/neurospin-neurospin http://www.unicog.org/pm/pmwiki.php ----------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From cornelia.quaedflieg at uni-hamburg.de Wed May 3 07:37:44 2017 From: cornelia.quaedflieg at uni-hamburg.de (cornelia.quaedflieg at uni-hamburg.de) Date: Wed, 3 May 2017 07:37:44 +0200 Subject: [FieldTrip] apply filter after ft-artefactreject Message-ID: <20170503053745.73475D206E@mailhost.uni-hamburg.de> Dear fieldtrip users, In the pre-processing, we applied a filter for the 50Hz noise (and harmonics) caused by the power supply in our MEG data. During ICA for EOG and ECG correction we noticed in some participants a 50Hz component. That is why we want to apply a bsfilter after ICA correction once more (different filter used the dft filter before). Our idea was to run ft_pre-processing on the cleaned ICA data. However, after running the ft-artefactreject you get an structure and ft_preprocessing doesn’t work with structures as input. An idea about how we could do this is appreciated. Best Dr. Conny Quaedflieg Hamburg University -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed May 3 09:31:51 2017 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 3 May 2017 09:31:51 +0200 Subject: [FieldTrip] apply filter after ft-artefactreject In-Reply-To: <20170503053745.73475D206E@mailhost.uni-hamburg.de> References: <20170503053745.73475D206E@mailhost.uni-hamburg.de> Message-ID: Dear Conny, you can call the preprocessing-options in (more or less) all subsequent functions by using cfg.preproc.XXX So, for example, in the ft_timelockanalysis, you can filter the data by using cfg.preproc.lpfilter = 'yes'; (as well as the other filter settings). However, please be careful with using multiple filters in one dataset. Good luck, Julian Am 03.05.2017 um 07:37 schrieb : > > Dear fieldtrip users, > > In the pre-processing, we applied a filter for the 50Hz noise (and harmonics) caused by the power supply in our MEG data. > During ICA for EOG and ECG correction we noticed in some participants a 50Hz component. > That is why we want to apply a bsfilter after ICA correction once more (different filter used the dft filter before). > Our idea was to run ft_pre-processing on the cleaned ICA data. However, after running the ft-artefactreject you get an structure and ft_preprocessing doesn’t work with structures as input. > > An idea about how we could do this is appreciated. > > Best > > Dr. Conny Quaedflieg > Hamburg 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 495 bytes Desc: Message signed with OpenPGP using GPGMail URL: From bruno.berberian at onera.fr Wed May 3 10:38:07 2017 From: bruno.berberian at onera.fr (Bruno Berberian) Date: Wed, 03 May 2017 10:38:07 +0200 Subject: [FieldTrip] Job opening at the french aerospace lab Message-ID: <590996EF.10200@onera.fr> COGNITIVE ENGINEERING RESEARCHER at ONERA ONERA is the French national aerospace research center. The present position is opened in the “Human-System Integration” team in Salon de Provence. The HSI team is a small (6 permanent peoples, 5 PhD students and 2 postdocs) but growing team. The HSI team is specialized in the design of innovative human-machine interface. It aims to make models of human cognition, perception, multisensory integration and action control and use these models to propose design principles and evaluation methodology. The team follows a multidisciplinary approach and the core competencies include: Cognitive Engineering, Computational Neurosciences, Cognitive Psychology, Human Factors, Electronics and Computer Science. Our collaborations include academic partners in several domains - aeronautic, cognitive science, neuro sciences and cognitive psychology, medicine but also Applied Research institute and industrial partners. You will complete and extend the team abilities. You will be a key contributor to the Human Systems Interaction research area within the HIS team. As a research scientist in Human-Machine Cognition, you’ll be tackling the scientific challenges to integrate new insights in cognitive engineering and computational neurosciences to the design of human machine interface. This involves both applied and basic science. Your primary task involves applying neurosciences knowledge, methodologies, and paradigm to the design of human-machine systems. You will be expected to conduct high-level innovative research, including the publication of research and research supervision. You will collaborate with academia to identify and answer novel research questions, performing research of factors both in isolation and as part of more ecologically valid system. You will also collaborate with industrial partner to perform more applied project. Crucially, you will contribute to initiate new funded research as well as to expand, complement, and collaborate with existing research programs. To be considered for this position, the successful candidate must possess a Ph.D. (by the start of the appointment) in Cognitive Engineering, Computational and Cognitive Neurosciences, Applied Psychology, or Human Factors. Candidates are particularly sought with research interests in one or more of the following areas: perception and multisensory integration, physiological markers of attention/vigilance, models of attention and consciousness, impact of stress and fatigue on human performance. Strong theoretical background in cognitive or computational neurosciences is mandatory. Expertise in handling and analyzing physiological data (EEG, fNIRS, ECG, ..) will be also critical. The position is anticipated to begin in mid-2017. It is a permanent position. To apply, follow this link: http://www.onera.fr/fr/rejoindre-onera/offres-emploi Regards, Berberian Bruno -- Dr Berberian Bruno ONERA The french Aerospace Lab DCSD – PSEV Base Aérienne 701 13661 Salon Air – France Tel. : +33 4 90 17 55 88 Fax : +33 4 90 17 01 09 From na.so.ir at gmail.com Wed May 3 13:20:26 2017 From: na.so.ir at gmail.com (Narjes Soltani) Date: Wed, 3 May 2017 15:50:26 +0430 Subject: [FieldTrip] Cross Frequency Coupling Message-ID: Dear fieldtrip users, Is there any implementation of different kinds of cross frequency coupling already available in fieldtrip? I would be very thankful if any one can share any example of the related coed snippets here. Thanks in advance. Best Narjes -------------- next part -------------- An HTML attachment was scrubbed... URL: From greg at think-now.com Wed May 3 20:53:25 2017 From: greg at think-now.com (GREG SIMPSON) Date: Wed, 3 May 2017 11:53:25 -0700 Subject: [FieldTrip] Post-Doctoral Positions Message-ID: Dear Colleagues - I would like to post the following announcement: *Post-Doctoral Fellow – EEG & Attention* Think Now Incorporated may be seeking 1-2 post-doctoral fellows in the fall of 2017 to work on NIMH funded projects analyzing novel EEG measures of slow fluctuations in sustained attention (10-20 seconds), including data from 400 subjects, and designing an entirely new type of EEG-based feedback system to improve sustained attention. The work will include performing sophisticated EEG data analyses and writing matlab code to create a closed loop feedback system. There is also the potential, as time permits, for exploratory research with machine learning methods to identify EEG activity patterns related to attentional states and their dynamics. We are seeking candidates with a solid background in signal processing, experience with EEG time series, and possibly modeling. We prefer self-directed individuals to take on this work. The successful candidate will work with EEG and signal processing/modeling faculty at UCB and UCLA as well as Dr. Simpson, and be able to regularly interact with other UC post-docs and graduate students. The position reports directly to Gregory V. Simpson, a cognitive neuroscientist and Chief Scientific Officer of Think Now. Think Now is located in San Francisco and is collaborating with faculty at UCB, UCLA and OHSU on these projects. Think Now is focused on creating solutions for the diagnosis and amelioration of neurological and psychiatric disorders with a focus on attention and its control. Please send your CV to jobs at think-now.com with a letter describing your prior experience with sophisticated signal (EEG) analyses and any BCI or modeling methods. Gregory V. Simpson, Ph.D. Think-Now.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From wanglinsisi at gmail.com Thu May 4 02:31:52 2017 From: wanglinsisi at gmail.com (Lin Wang) Date: Wed, 3 May 2017 20:31:52 -0400 Subject: [FieldTrip] how to show notches after plotting ERPs with ft_multiplotER Message-ID: Dear fieldtrip users, Is there a way to show the notches on the x-axis after plotting the ERPs of all channels with ft_multiplotER? I want to have an overview of the ERPs of all channels with the notches on the x-axis. I can only see the notches (i.e., the little bars on the x-axis) after I select a particular channel and view the ERP of that channel. Thanks a lot! Lin -------------- next part -------------- An HTML attachment was scrubbed... URL: From seymourr at aston.ac.uk Thu May 4 12:18:26 2017 From: seymourr at aston.ac.uk (Seymour, Robert (Research Student)) Date: Thu, 4 May 2017 10:18:26 +0000 Subject: [FieldTrip] Cross Frequency Coupling Message-ID: Hi Narjes, The current status of ft_crossfrequencyanalysis can be tracked here: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2523 . It’s not currently implemented in full yet. An alternative is the python library PACPY and associated MATLAB wrapper PACMAT https://github.com/voytekresearch/pacpy. An example of some CFC code (based on the Tort et al 2008 approach) can be found here: https://github.com/neurofractal/PAC_aliens/blob/master/calc_MI.m Good luck! Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From N.vanKlink-2 at umcutrecht.nl Thu May 4 17:05:18 2017 From: N.vanKlink-2 at umcutrecht.nl (Klink-3, N.E.C. van) Date: Thu, 4 May 2017 15:05:18 +0000 Subject: [FieldTrip] Incorrect BEM leadfields Message-ID: Dear all, I am trying SAM beamformer on EEG data, but the results I get are strange. I found out that my BEM model is probably the cause of this, because the leadfields obtained by the model look scattered, see figure. (Black dot is one dipole location, around the head are 60 EEG electrodes with leadfield value for that dipole.) This is the optimum leadfield at optimum orientation as calculated in beamformer_sam. The three original orientations look scattered as well. When I make a similar figure with concentric spheres, the leadfield looks like a dipolar field, as expected. When I make the figure for the simultaneously measured MEG, with the same BEM, the leadfield also looks good. (Probably because MEG doesn't care so much about the headmodel.) I have created my BEM with OpenMEEG (in Windows), BEMcp gives similar results. The meshes look fine to me, and changing the number of vertices to [3000 3000 3000] does not help. Does anyone have an idea what could be the problem here? Thanks in advance, Kind regards, Nicole Some code: %make headmodel cfg = []; cfg.output = {'brain' 'skull' 'scalp'}; seg = ft_volumesegment(cfg, MRI); %create mesh cfg = []; cfg.method = 'projectmesh'; cfg.numvertices = [1000 1500 3000]; cfg.tissue = {'scalp','skull','brain'}; mesh = ft_prepare_mesh(cfg,segi); % compute the subject's headmodel/volume conductor model cfg = []; cfg.method = 'openmeeg'; cfg.tissue = {'brain' 'skull' 'scalp'}; vol = ft_prepare_headmodel(cfg, mesh); vol = ft_convert_units(vol,'cm'); %create grid cfg = []; cfg.grid.pos = load([ptfile filesep pts]); % predetermined grid positions in mm cfg.grid.pos = cfg.grid.pos./10; %make unit = cm cfg.headmodel = vol; cfg.moveinward = 0.01; %check if all grid points are inside the brain grid = ft_prepare_sourcemodel(cfg); % Create leadfields hdr = ft_read_header('data.fif'); cfg = []; cfg.elec = hdr.elec; % electrode positions cfg.headmodel = vol; cfg.grid = grid; cfg.channel = {'EEG', '-EEG043', '-EEG036'}; cfg.normalize = 'column'; lf = ft_prepare_leadfield(cfg); % beamformer cfg=[]; cfg.method = 'sam'; cfg.senstype = 'EEG'; cfg.grid = lf; cfg.headmodel = vol; cfg.sam.lambda = '5%'; cfg.sam.meansphereorigin = 1; %unused but necessary to not crash the script cfg.sam.fixedori = 'robert'; source = ft_sourceanalysis(cfg, timelock); ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. 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Name: BEM_mesh.png Type: image/png Size: 164811 bytes Desc: BEM_mesh.png URL: From Alexander_Nakhnikian at hms.harvard.edu Thu May 4 20:39:24 2017 From: Alexander_Nakhnikian at hms.harvard.edu (Nakhnikian, Alexander) Date: Thu, 4 May 2017 18:39:24 +0000 Subject: [FieldTrip] Interpolation Error with Custom Lead Field Message-ID: Dear All, I'm trying to fine tune a forward model by first constraining the dipoles to the gray matter and then selecting only a subset of structures. It looks as though I need to write a custom script for this, which I have and the commented code is included below. Once I generate the lead field with this code I add it to the cfg structure for ft_sourceanalysis and proceed as usual. The error occurs when I attempt to interpolate the power to a structural MRI. ft_sourceinterpolate(cfg,sources,mri) - cfg.downsample=10; cfg.parameter='pow' - and 'mri' is FT's template structural scan. Calling ft_sourceinterpolate with sources generated using my custom forward model produces this error: Error using interpn (line 153) Wrong number of input arguments. Error in ft_sourceinterpolate>my_interpn (line 693) av(sel) = interpn(fv, ax(sel), ay(sel), az(sel), interpmethod); Error in ft_sourceinterpolate (line 535) interp.inside( sel) = my_interpn(double(functional.inside), ax(sel), ay(sel), az(sel), 'nearest', cfg.feedback); The only hint I've found is that for some reason the source structure returns for this analysis doesn't contain the field '.dim' but I added it manually. Once that's done, the setup looks identical to data returned using a automatically generated grid so I must be missing something. Thanks in advance if anyone can suggest where to look for the bug. Alexander Code: function [lf] = fT_constrainFM(cfg) %Creates a constrained forward model for source analysis in field trip. The %grid is constrained to a surface defined by two maps. One %restrains the dipoles to gray matter and the second is a list of labels corresponding to %ROIs within the GM. %Example: Constrain grey matter to cortical sites of interest. %cfg.roi = labelsNDL; %A cell array of strings with the name of each ROI %cfg.atlas = aal; %aal is a variable returned by ft_readatlas %cfg.inputcoord = 'mni'; %Choose coordinates %cfg.mri = mri; %A template MRI or subject sMRI %cfg.thres = 0.95; %Threshold for probabilistic masks %cfg.lf = C; %C is a structure with fields *.elec and *.headmodel. See %ft_prepareleadfield %[lf] = fT_contrainFM(cfg) mri = cfg.mri; cfgLF = cfg.lf; thres = cfg.thres; cfg = rmfield(cfg,{'mri','thres','lf'}); %Get the masks seg = ft_volumesegment([],mri); tissue = logical(seg.gray>=thres); roiMask = logical(ft_volumelookup(cfg,mri)); voxInds = tissue&roiMask; %dipole placement locations [rows,cols,pages] = ind2sub(size(roiMask),find(voxInds)); cfgLF.pos = zeros(length(rows),3); %adjustment vaues to move the origin rowAd = (size(roiMask,1)-1)/2; colAd = (size(roiMask,2)-1)/2; pageAd = (size(roiMask,3)-1)/2; %collect dipole positions into an Nx3 matrix for posInd = 1:length(rows) cfgLF.pos(posInd,:) = [rows(posInd)-rowAd,cols(posInd)-colAd,pages(posInd)-pageAd]'; end lf = ft_prepare_leadfield(cfgLF); Alexander Nakhnikian, Ph.D. Research Investigator VA Boston Healthcare System Instructor in Psychiatry, Harvard Medical School -------------- next part -------------- An HTML attachment was scrubbed... URL: From ido.davidesco at gmail.com Sat May 6 17:54:38 2017 From: ido.davidesco at gmail.com (Ido Davidesco) Date: Sat, 6 May 2017 11:54:38 -0400 Subject: [FieldTrip] Research Assistant Position - New York University Message-ID: The Poeppel lab at NYU’s Psychology Department is currently seeking a full-time Research Assistant for a National Science Foundation-funded project called “brain-to-brain synchrony in the classroom”. The expected start date for the position is Summer 2017. Application review will take place on a rolling basis until the position is filled. The successful candidate will work closely with the Principal Investigators (Prof. David Poeppel and Prof. Catherine Milne) to execute a complex research protocol, which involves collecting EEG data from multiple participants in a learning setting. As part of the project, we are also developing an EEG-based neuroscience curriculum for high schools. Primary responsibilities include: (1) Participant recruitment and testing; (2) experimental paradigm development; (3) management and analysis of behavioral and neural data; (4) documenting and presenting study results; (5) Project management and administration. A Bachelor's degree in Psychology, Neuroscience or other related fields, and excellent organizational, interpersonal, and communication skills are required. Other preferred qualifications include: - Prior research experience - Teaching and curriculum development experience - Computational, statistical, and technical skills (e.g. Matlab, Python, R) - Experience analyzing EEG and behavioral data Starting date: Summer 2017 Click here for more information about the project. To apply, please send your CV, a cover letter describing your interests and relevant experience, and the contact information of three references to: ido.davidesco at nyu.edu New York University is an Equal Opportunity Employer. New York University is committed to a policy of equal treatment and opportunity in every aspect of its hiring and promotion process without regard to race, color, creed, religion, sex, pregnancy or childbirth (or related medical condition), sexual orientation, partnership status, gender and/or gender identity or expression, marital, parental or familial status, caregiver status, national origin, ethnicity, alienage or citizenship status, veteran or military status, age, disability, predisposing genetic characteristics, domestic violence victim status, unemployment status, or any other legally protected basis. Women, racial and ethnic minorities, persons of minority sexual orientation or gender identity, individuals with disabilities, and veterans are encouraged to apply for vacant positions at all levels. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mehdy.dousty at gmail.com Tue May 9 03:51:24 2017 From: mehdy.dousty at gmail.com (mehdy dousty) Date: Tue, 09 May 2017 01:51:24 +0000 Subject: [FieldTrip] Parcelation source localization In-Reply-To: References: Message-ID: Hello all, I am working on source localization of HCP based on the eLoreta. I am trying to extract time series of Atlas AAL116. So firstly I interpolate the source model to AAL 116 by using: atlas = ft_read_atlas('/Desktop/EEG-1/fieldtrip-20160417/template/atlas/aal/ROI_MNI_V4.nii'); atlas = ft_convert_units(atlas,'mm'); cfg = []; cfg.interpmethod = 'nearest'; cfg.parameter = 'tissue'; individual_sourcemodel3d1 = ft_sourceinterpolate(cfg,atlas,individual_sourcemodel3d); and afterward interpolate the DATA to the parcellated source model by: cfg = []; cfg.parameter = 'pow'; cfg.keeptrials = 'yes'; source_eloreta_disc_int1 = ft_sourceinterpolate(cfg,source_eloreta,individual_sourcemodel3d1); and finally when I try to visualize the data by : cfg = []; cfg.method = 'ortho'; cfg.funparameter = 'pow'; cfg.maskparameter = 'mask'; cfg.funcolorlim = 'auto'; cfg.opacitylim = 'auto'; cfg.opacitymap = 'rampup'; cfg.atlas = atlas; ft_sourceplot(cfg,source_eloreta_disc_int1); I receive an error which says: "there is a mismatch between the coordinate system in the atlas and the coordinate system in the data, which cannot be resolved" I was wondering if anyone could possible help me to solve the issue, and also how accurate my approach is Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.papen at uni-koeln.de Tue May 9 10:44:34 2017 From: m.papen at uni-koeln.de (Michael von Papen) Date: Tue, 9 May 2017 10:44:34 +0200 Subject: [FieldTrip] 2nd CfP: Coupling & Causality in Complex Systems, Sep 25-27, Cologne, Germany Message-ID: ============================================================== 2nd CALL FOR PAPERS (Deadline: June 01, 2017) http://c3s.uni-koeln.de ============================================================== INTERNATIONAL CONFERENCE: *Coupling and Causality in Complex Systems* September 25-27, 2017, Cologne, Germany -------------------------------------------------------------- The interdisciplinary conference Coupling and Causality in Complex Systems (C3S) is hosted by the Competence Area 3: Quantitative Modeling of Complex Systems of the University of Cologne (UoC), Germany. It is organized by the Institute of Geophysics & Meteorology, UoC, the Institute of Clinical Neuroscience and Psychology, Heinrich-Heine University Düsseldorf and the Department of Cognitive Neuroscience at the Research Center Juelich. -------------------------------------------------- *Invited Speakers* Jörg Breitung - Macroeconomic Policy Institute, University of Cologne, Germany David Gross - Institute of Theoretical Physics, University of Cologne, Germany Philip Holmes - Mechanical and Aerospace Engineering / Princeton Neuroscience Institute, Princeton, USA Ankit Khambhati - Department of Bioengineering, University of Pennsylvania, USA Laura Marzetti - Department of Neuroscience, Università degli Studi "G. d'Annunzio" Chieti - Pescara Arkady Pikovsky - Institute of Physics and Astronomy, University Potsdam, Germany Michael Rosenblum - Institute of Physics and Astronomy, University Potsdam, Germany Jakob Runge - The Grantham Institute for Climate Change, Imperial College London -------------------------------------------------- *Preliminary Session Program* We will have different sessions with differing topics and each session will be opened by one of the invited speakers. Here is a preliminary version of our program: Session 1 Synchronization I Arkady Pikovsky Session 2 Synchronization II Silvia Daun Session 3 Coupled oscillators I Phil Holmes Session 4 Coupled oscillators II Michael Rosenblum Session 5 Phase coupling Laura Marzetti Session 6 Network structures Ankit Khambati Session 7 Bayesian networks David Gross Session 8 Granger causality I Jörg Breitung Session 9 Granger causality II Esther Florin Session 10 Causal network measures Jakob Runge Further topics of interest for the conference include, amongst others, research and methods development on: functional connectivity, (partial directed) coherence, network topology, graph-theoretic measures, directed graphs, nonlinear dynamics of complex systems, complex spatio-temporal systems, mutual information and transfer entropy. -------------------------------------------------------------- *Scientific Organizing Committee* Silvia Daun - Institute of Zoology, University of Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany Esther Florin - Institute of Clinical Neuroscience and Psychology, Düsseldorf, Germany Joachim Gross - Center for Cognitive Neuroimaging, Glasgow, UK Michael von Papen - Institute of Geophysics & Meteorology, Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany -------------------------------------------------------------- *Abstract* Complex systems such as the human brain, Earth’s climate and economy are characterized by a multitude of coupled processes on different spatial and temporal scales. In order to better understand the dynamics of the system at hand each scientific area has developed specific tools to identify, model and quantify these processes. The conference Coupling and Causality in Complex Systems (C3S) will present a collection of these approaches with the aim to provide scientists with new analysis strategies for their field. The conference focuses on how to characterize a complex system and on the methods for estimating and modeling of statistical coupling (e.g. network coherence, creation and modulation of small networks and local or long-range synchronization by cross frequency phase-phase and phase-amplitude coupling) and causality (e.g. Granger causality, transfer entropy). Therefore, data analysts from different study fields including neuroscience, mathematics, physics, biology, and economy will present their approaches with a particular focus on the methods they use. The aim of this conference is to foster discussions and the transdisciplinary exchange of advanced techniques, methods, and algorithms, thereby stimulating potential future collaborations. -------------------------------------------------------------- PAPER SUBMISSION AND REGISTRATION Authors are invited to submit conference abstracts with up to 400 words. Authors of exceptional abstracts will be given the opportunity to present their research in a talk. However, poster sessions will be provided with ample time for discussions. For your submission, please use the conference website c3s.uni-koeln.de. To register, please send an email with the subject "registration" to c3s-conference at uni-koeln.de. Please be sure to include your full name, your affiliation and whether you qualify as student (also PhD candidates) or not. The registration fee will cover snacks and refreshments during coffee breaks, lunch and a dinner with all participants. Early-bird registration is available until July 10 with a reduced fee of 100 EUR (50 EUR for students), after July 10 the registration fee will be 200 EUR (100 EUR for students). -------------------------------------------------------------- IMPORTANT DATES Paper Submission deadline: June 01, 2017 Author Notification: mid June, 2017 Early-bird registration: July 10, 2017 Conference: September 25-27, 2017 ============================================================== Please find the call for papers and more information at the conference website: http://c3s.uni-koeln.de. For questions regarding the conference feel free to contact us via c3s-conference at uni-koeln.de. -- ------------------------------------------ UNIVERSITY OF COLOGNE Institute of Geophysics & Meteorology Coordinator of Competence Area III: Quantitative Modeling of Complex Systems Dr. Michael von Papen Email: m.papen at uni-koeln.de http://www.uni-koeln.de/~vpapenm http://complexsystems.uni-koeln.de From andria.pelentritou at gmail.com Wed May 10 01:52:04 2017 From: andria.pelentritou at gmail.com (Andria Pelentritou) Date: Wed, 10 May 2017 09:52:04 +1000 Subject: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data Message-ID: Greetings from Melbourne! We've been using fieldtrip (v-20160801) for a while now and we are having issues when it comes to combining magnetometer and gradiometer MEG sensors types during (LCMV) beamforming for the Elekta Neuromag Triux 306-channel system. Beamforming the magnetometers or gradiometers separately on auditory evoked data works well, but we cannot successfully combine the two sensor types. We've played with the cfg.coilaccuracy variable as advised in one of the tutorials with no luck as there seem to be no obvious effects on the output. The documentation provides very little information on the topic. What strategies would you recommend when trying to combine the Neuromag 306-channel system magnetometer/gradiometer data? Many thanks in advance for your help and many more thanks for releasing such a valuable toolbox! Warm regards Andria -------------- next part -------------- An HTML attachment was scrubbed... URL: From N.vanKlink-2 at umcutrecht.nl Wed May 10 09:33:22 2017 From: N.vanKlink-2 at umcutrecht.nl (Klink-3, N.E.C. van) Date: Wed, 10 May 2017 07:33:22 +0000 Subject: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data Message-ID: Hi Andria, We have been struggling with the same problem, also using a 306-channel Neuromag system. We ended up correcting for the scale difference between magnetometer and gradiometer signals (i.e. noise 5e-15T vs 5e-13T/m). So we multiplied the signals of the magnetometers and the leadfield values of the magnetometers by a factor 100. This gave us the best result. Kind regards, Nicole Van: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] Namens Andria Pelentritou Verzonden: 10 mei 17 1:52 Aan: fieldtrip at science.ru.nl Onderwerp: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data Greetings from Melbourne! We've been using fieldtrip (v-20160801) for a while now and we are having issues when it comes to combining magnetometer and gradiometer MEG sensors types during (LCMV) beamforming for the Elekta Neuromag Triux 306-channel system. Beamforming the magnetometers or gradiometers separately on auditory evoked data works well, but we cannot successfully combine the two sensor types. We've played with the cfg.coilaccuracy variable as advised in one of the tutorials with no luck as there seem to be no obvious effects on the output. The documentation provides very little information on the topic. What strategies would you recommend when trying to combine the Neuromag 306-channel system magnetometer/gradiometer data? Many thanks in advance for your help and many more thanks for releasing such a valuable toolbox! Warm regards Andria ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.hartmann at th-ht.de Wed May 10 10:07:23 2017 From: thomas.hartmann at th-ht.de (Thomas Hartmann) Date: Wed, 10 May 2017 10:07:23 +0200 Subject: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data In-Reply-To: References: Message-ID: hi, i would suggest updating to a recent fieldtrip version. combining mags and grads has been implemented there and you basically do not need to do any extra steps. there are just these three pitfalls that you need to pay attention to because it might lead to wrong results: 1. make sure that you put in the original data. i.e. no prescaling etc. also make sure that you have not modified the .tra matrix of your grad structure. 2. always compute your own leadfield. i.e. always use ft_prepare_leadfield to compute the forward model and don't have it done by ft_sourceanalysis. i don't know if this is absolutely necessary but as the ft_prepare_leadfield step is the one in which the actual pitfalls are, i would strongly suggest you do it separately to have maximum control! 3. all the data going into ft_prepare_leadfield MUST BE in meters! i.e.: 1. the grid mus be either created directly in meters of converted to meters by using ft_convert_unit 2. the grad structure of your data must have been converted to meters. this is something you must do manually as according to my experience, fieldtrip does not take care of it. additionally, the default grad returned by ft_read_sens (and thus the one placed in your data structure) is in centimeters! so, it is a good idea to do something like this: data.grad = ft_convert_data(data.grad, 'm'); right after getting your data via ft_preprocessing! 3. if you provide your grad structure in the cfg structure, also make sure that it is in meters. the meters stuff is really extremely important!!! if your units are wrong, you are going to end up with wrong source projections and will not get an error message!!! if you see some fieldtrip output like: "converting XXX to cm", your results will be wrong! if you take care of all that, fieldtrip does the scaling automatically based on the distance between the two parts of each gradiometer. best, thomas Am 10.05.2017 um 09:33 schrieb Klink-3, N.E.C. van: > > Hi Andria, > > We have been struggling with the same problem, also using a > 306-channel Neuromag system. We ended up correcting for the scale > difference between magnetometer and gradiometer signals (i.e. noise > 5e-15T vs 5e-13T/m). So we multiplied the signals of the magnetometers > and the leadfield values of the magnetometers by a factor 100. This > gave us the best result. > > Kind regards, > > Nicole > > *Van:*fieldtrip-bounces at science.ru.nl > [mailto:fieldtrip-bounces at science.ru.nl] *Namens *Andria Pelentritou > *Verzonden:* 10 mei 17 1:52 > *Aan:* fieldtrip at science.ru.nl > *Onderwerp:* [FieldTrip] combining gradiometer/magnetometer sensors - > neuromag data > > Greetings from Melbourne! > > We've been using fieldtrip (v-20160801) for a while now and we are > having issues when it comes to combining magnetometer and gradiometer > MEG sensors types during (LCMV) beamforming for the Elekta Neuromag > Triux 306-channel system. Beamforming the magnetometers or > gradiometers separately on auditory evoked data works well, but we > cannot successfully combine the two sensor types. We've played with > the cfg.coilaccuracy variable as advised in one of the tutorials with > no luck as there seem to be no obvious effects on the output. The > documentation provides very little information on the topic. > > What strategies would you recommend when trying to combine the > Neuromag 306-channel system magnetometer/gradiometer data? > > Many thanks in advance for your help and many more thanks for > releasing such a valuable toolbox! > Warm regards > Andria > > ------------------------------------------------------------------------ > > /De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is > uitsluitend bestemd voor de geadresseerde. Indien u dit bericht > onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de > afzender direct te informeren door het bericht te retourneren. Het > Universitair Medisch Centrum Utrecht is een publiekrechtelijke > rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en > Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van > Koophandel voor Midden-Nederland onder nr. 30244197. / > > /Denk s.v.p aan het milieu voor u deze e-mail afdrukt. / > > ------------------------------------------------------------------------ > > /This message may contain confidential information and is intended > exclusively for the addressee. If you receive this message > unintentionally, please do not use the contents but notify the sender > immediately by return e-mail. University Medical Center Utrecht is a > legal person by public law and is registered at the Chamber of > Commerce for Midden-Nederland under no. 30244197. / > > /Please consider the environment before printing this e-mail. / > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Dr. Thomas Hartmann Centre for Cognitive Neuroscience FB Psychologie Universität Salzburg Hellbrunnerstraße 34/II 5020 Salzburg Tel: +43 662 8044 5109 Email: thomas.hartmann at th-ht.de "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarang at cfin.au.dk Wed May 10 10:59:39 2017 From: sarang at cfin.au.dk (Sarang S. Dalal) Date: Wed, 10 May 2017 08:59:39 +0000 Subject: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data In-Reply-To: References: Message-ID: <8076147A-E73C-419C-9F07-79B0419EA05E@cfin.au.dk> Dear Andria and Nicole, Combining sensor types (gradiometers and magnetometers, or MEG and EEG) is indeed something that is not documented, and there is not yet a unanimous agreement in the community about how to do this best. But, I can suggest one simple solution that was discussed at a recent beamformer workshop hosted by the Aston MEG Centre in February. (I believe John Mosher made the initial suggestion.) As you probably know, the covariance matrix is an essential ingredient to constructing beamformer solutions. Different sensor types will have different scales and different noise properties, which then complicates the covariance between channels of different types. So, one way around this is to zero out the ‘cross’ terms of the covariance matrix, i.e., set to 0 the elements of the covariance matrix that result from the product of a magnetometer channel and a gradiometer channel. This can be accomplished with something like the following code: timelock = ft_timelockanalysis(cfg, data); [~,megmagidx]=intersect(data.label,ft_channelselection('MEGMAG',data.label)); [~,meggradidx]=intersect(data.label,ft_channelselection('MEGGRAD',data.label)); timelock.cov(meggradidx,megmagidx)=0; timelock.cov(megmagidx,meggradidx)=0; In my experience, this allows source reconstruction using all channels, with results at least as good as analyzing the channels separately. This is not to say that is the best possible solution, but it is a simple one that should work well! Best wishes, Sarang On 10 May 2017, at 09:33, Klink-3, N.E.C. van > wrote: Hi Andria, We have been struggling with the same problem, also using a 306-channel Neuromag system. We ended up correcting for the scale difference between magnetometer and gradiometer signals (i.e. noise 5e-15T vs 5e-13T/m). So we multiplied the signals of the magnetometers and the leadfield values of the magnetometers by a factor 100. This gave us the best result. Kind regards, Nicole Van: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] Namens Andria Pelentritou Verzonden: 10 mei 17 1:52 Aan: fieldtrip at science.ru.nl Onderwerp: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data Greetings from Melbourne! We've been using fieldtrip (v-20160801) for a while now and we are having issues when it comes to combining magnetometer and gradiometer MEG sensors types during (LCMV) beamforming for the Elekta Neuromag Triux 306-channel system. Beamforming the magnetometers or gradiometers separately on auditory evoked data works well, but we cannot successfully combine the two sensor types. We've played with the cfg.coilaccuracy variable as advised in one of the tutorials with no luck as there seem to be no obvious effects on the output. The documentation provides very little information on the topic. What strategies would you recommend when trying to combine the Neuromag 306-channel system magnetometer/gradiometer data? Many thanks in advance for your help and many more thanks for releasing such a valuable toolbox! Warm regards Andria ________________________________ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ________________________________ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail. _______________________________________________ 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 maurice.goeldi at uzh.ch Wed May 10 11:24:30 2017 From: maurice.goeldi at uzh.ch (maurice.goeldi at uzh.ch) Date: Wed, 10 May 2017 11:24:30 +0200 Subject: [FieldTrip] Unwanted behavior of matlabs randomization functions? Message-ID: Dear Fieldtrippers I have just become aware of a 'feature' in matlabs randomization functions (rand, randi, randn and randperm). Every time matlab is restarted, the seed for the random number generator is reset. Therefore these functions always produce the same number sequence after a restart. This seems a very unintuitive use of these functions. I would think that people who need this reproducability should manually set a seed for their random number generator. Is this behaviour really wanted in FT? I did a quick check and ran ft_freqstatistics with montecarlo method. The stat.posdistribution is obviously different when i run it consecutive times.  However when I restart matlab I get exactly the same distributions again each time. I realize that in a standard analysis pipeline this is probably of absolutely no consequence.  But I still think it should not be that way and one should at least be aware of the fact. Even if it is not an issue for FT-analyses, this might very well be so for experimental procedures. E.g. some experimental stimuli are randomized for each subject. Then they are presented in randomized order. By the time the next subject comes in, chances are high that the computer or at least matlab has been restarted.  This subject will therefore recieve exactly the same 'randomized' list. Mostly these stimuli randomizations are checked by running the randomization script multiple times. So everything seems to work. Up to now at least I have never tested my scripts by restarting matlab after every run. And to catch this within the experiment is potentially impossible, depending on the procedure. Fortunately there is an easy fix for this. rng('shuffle');  before using the randomization function shuffles the seed for the random number generator (hopefully randomly). Even if this is not an issue for FT directly, I think many people do not know about this suboptimal (in my opinion) behaviour of the randomization functions and run into trouble. Appologies if this is an obvious and long known 'feature' to most of you. I hope it still helps some people getting strange results. Cheers Maurice --- University of Zürich Maurice Göldi, MSc Department of Psychology Biopsychology maurice.goeldi at uzh.ch -------------- next part -------------- An HTML attachment was scrubbed... URL: From dimitri.bayle at gmail.com Wed May 10 13:52:57 2017 From: dimitri.bayle at gmail.com (Dimitri Bayle) Date: Wed, 10 May 2017 13:52:57 +0200 Subject: [FieldTrip] Active versus Baseline statisitic on time-domain data Message-ID: <847a589e-b2ec-660b-90d8-7e01ae99fb0e@gmail.com> Hello, I want to do a test in time-domain data, to statistically compare each sample of an active time-windows with an average of the signal in a baseline time-windows. It work perfectly in frequency-domain data with the ft_statfun_actvsblT.m. However, when i try to apply the same test in my time-domain data (dimord = rpt_chan_time), it doesn't work and a realized that the function contain: switch cfg.dimord case 'chan_freq_time' nchan = cfg.dim(1); nfreq = cfg.dim(2); ntime = cfg.dim(3); [nsmpls,nrepl] = size(dat); nsmplsdivntime = floor(nsmpls/ntime); otherwise error('Inappropriate dimord for the statistics function STATFUN_ACTVSBLT.'); end; Is the ft_statfun_actvsblt.m only for time-frequency data? Does anyone has an other statfun function to compare active versus baseline windows in time-domain data. Thanks From v.piai.research at gmail.com Wed May 10 18:37:28 2017 From: v.piai.research at gmail.com (=?UTF-8?Q?Vit=c3=b3ria_Piai?=) Date: Wed, 10 May 2017 18:37:28 +0200 Subject: [FieldTrip] One or more output arguments not assigned during call to "read_16bit" Message-ID: <2c0a0f56-0466-3767-0e5c-f706f77e2677@gmail.com> Hi FT-ers, I'm trying to read a big .edf file (2.16GB), using a recent version, fieldtrip-20170401. I can read the header (attached, if it's of any use). However, when reading the data, I'm getting the following errors. _- If I specify begin and end sample:_ /X = ft_read_data(cfg.dataset,'begsample', 1, 'endsample', 30); /error opening file: /MaterSEEG04-17.edf One or more output arguments not assigned during call to "read_16bit". Error in read_edf>readLowLevel (line 449) buf = read_16bit(filename, offset, numwords); Error in read_edf (line 401) buf = readLowLevel(filename, offset, blocksize); % see below in subfunction Error in ft_read_data (line 683) dat = read_edf(filename, hdr, begsample, endsample, chanindx); _- If I specify channel index:_ /X = ft_read_data(cfg.dataset,'chanindx',chanindx); /Attempted to access EDF.chansel(34); index out of bounds because numel(EDF.chansel)=1. Error in read_edf (line 356) chanindx = EDF.chansel(chanindx); Error in ft_read_data (line 683) dat = read_edf(filename, hdr, begsample, endsample, chanindx);/ / I can then "fix" this error by commenting out line 356 in read_edf, which brings me back to the first error of "read_16bit". This happens on a PC and on a Mac. Something tells me the data isn't being read properly but I can't figure out why. Something with mex files maybe? I couldn't find anything similar in previous threads nor in Bugzilla, for as far as I could see. Any thoughts anyone? I have the data on Dropbox and can send the link if needed. Thanks loads, Vitoria -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hdr.mat Type: application/octet-stream Size: 67215 bytes Desc: not available URL: From a.stolk8 at gmail.com Wed May 10 18:50:34 2017 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Wed, 10 May 2017 09:50:34 -0700 Subject: [FieldTrip] One or more output arguments not assigned during call to "read_16bit" In-Reply-To: <2c0a0f56-0466-3767-0e5c-f706f77e2677@gmail.com> References: <2c0a0f56-0466-3767-0e5c-f706f77e2677@gmail.com> Message-ID: Hey Vitoria, Quick thoughts: what is cfg.dataset here? Is it '/MaterSEEG04-17.edf'? If so, please try without the '/', or specifying the full path location. Vaguely recalling here that read_16bit fails on statements such as '~', and perhaps also '/'. Hoping this was a good gamble. Best, Arjen 2017-05-10 9:37 GMT-07:00 Vitória Piai : > Hi FT-ers, > > I'm trying to read a big .edf file (2.16GB), using a recent version, > fieldtrip-20170401. > I can read the header (attached, if it's of any use). However, when > reading the data, I'm getting the following errors. > > *- If I specify begin and end sample:* > > > *X = ft_read_data(cfg.dataset,'begsample', 1, 'endsample', 30); *error > opening file: /MaterSEEG04-17.edf > One or more output arguments not assigned during call to "read_16bit". > > Error in read_edf>readLowLevel (line 449) > buf = read_16bit(filename, offset, numwords); > > Error in read_edf (line 401) > buf = readLowLevel(filename, offset, blocksize); % see below in > subfunction > > Error in ft_read_data (line 683) > dat = read_edf(filename, hdr, begsample, endsample, chanindx); > > *- If I specify channel index:* > > *X = ft_read_data(cfg.dataset,'chanindx',chanindx); *Attempted to access > EDF.chansel(34); index out of bounds because numel(EDF.chansel)=1. > > Error in read_edf (line 356) > chanindx = EDF.chansel(chanindx); > > Error in ft_read_data (line 683) > dat = read_edf(filename, hdr, begsample, endsample, chanindx); > > I can then "fix" this error by commenting out line 356 in read_edf, which > brings me back to the first error of "read_16bit". This happens on a PC and > on a Mac. Something tells me the data isn't being read properly but I can't > figure out why. Something with mex files maybe? I couldn't find anything > similar in previous threads nor in Bugzilla, for as far as I could see. > > Any thoughts anyone? I have the data on Dropbox and can send the link if > needed. > > Thanks loads, > Vitoria > > _______________________________________________ > 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 v.piai.research at gmail.com Thu May 11 08:08:46 2017 From: v.piai.research at gmail.com (=?UTF-8?Q?Vit=c3=b3ria_Piai?=) Date: Thu, 11 May 2017 08:08:46 +0200 Subject: [FieldTrip] One or more output arguments not assigned during call to "read_16bit" In-Reply-To: References: <2c0a0f56-0466-3767-0e5c-f706f77e2677@gmail.com> Message-ID: <056f91e6-4a9b-999a-3763-c1d9b372d340@gmail.com> Hey Arjen, Brilliant!! Thanks so much for the suggestion, it worked... I'm still having to comment out line 356 (chanindx = EDF.chansel;%(chanindx);), so something is going on but at least now I can work with the data! Thanks again, Vitória On 5/10/2017 6:50 PM, Arjen Stolk wrote: > Hey Vitoria, > > Quick thoughts: what is cfg.dataset here? Is it '/MaterSEEG04-17.edf'? > If so, please try without the '/', or specifying the full path > location. Vaguely recalling here that read_16bit fails on statements > such as '~', and perhaps also '/'. Hoping this was a good gamble. > > Best, > Arjen > > > > > > 2017-05-10 9:37 GMT-07:00 Vitória Piai >: > > Hi FT-ers, > > I'm trying to read a big .edf file (2.16GB), using a recent > version, fieldtrip-20170401. > I can read the header (attached, if it's of any use). However, > when reading the data, I'm getting the following errors. > > _- If I specify begin and end sample:_ > /X = ft_read_data(cfg.dataset,'begsample', 1, 'endsample', 30); > > /error opening file: /MaterSEEG04-17.edf > One or more output arguments not assigned during call to "read_16bit". > > Error in read_edf>readLowLevel (line 449) > buf = read_16bit(filename, offset, numwords); > > Error in read_edf (line 401) > buf = readLowLevel(filename, offset, blocksize); % see below > in subfunction > > Error in ft_read_data (line 683) > dat = read_edf(filename, hdr, begsample, endsample, chanindx); > > _- If I specify channel index:_ > /X = ft_read_data(cfg.dataset,'chanindx',chanindx); > /Attempted to access EDF.chansel(34); index out of bounds because > numel(EDF.chansel)=1. > > Error in read_edf (line 356) > chanindx = EDF.chansel(chanindx); > > Error in ft_read_data (line 683) > dat = read_edf(filename, hdr, begsample, endsample, chanindx);/ > / > I can then "fix" this error by commenting out line 356 in > read_edf, which brings me back to the first error of "read_16bit". > This happens on a PC and on a Mac. Something tells me the data > isn't being read properly but I can't figure out why. Something > with mex files maybe? I couldn't find anything similar in previous > threads nor in Bugzilla, for as far as I could see. > > Any thoughts anyone? I have the data on Dropbox and can send the > link if needed. > > Thanks loads, > Vitoria > > _______________________________________________ > 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 francois.tadel at mcgill.ca Thu May 11 12:26:31 2017 From: francois.tadel at mcgill.ca (=?UTF-8?Q?Fran=c3=a7ois_Tadel?=) Date: Thu, 11 May 2017 12:26:31 +0200 Subject: [FieldTrip] Correspondence channels-coils in HCP files Message-ID: <09bb7e15-f314-607c-e7e7-480f5a9d914e@mcgill.ca> Hello, I wrote a FieldTrip>Brainstorm import function based on Elekta files, and I was using the .tra matrix to get the correspondence between the channels and the coils: https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/io/in_data_fieldtrip.m#L107 I based this code on your description of the .tra field: "NxM matrix with the weight of each coil into each channel": http://www.fieldtriptoolbox.org/faq/how_are_electrodes_magnetometers_or_gradiometers_described This doesn't work with the processed 4D recordings from the HCP dataset because the .tra matrix is dense. Is this because the 4D compensation matrix is integrated in this .tra matrix? Or because there is some additional PCA/ICA projection done during the preprocessing? How do I recover the sparse .tra information that simply contains the weights channels-coils from the HCP processed files? Thanks, François -- François Tadel, MSc MEG / McConnell Brain Imaging Center / MNI / McGill University 3801 rue University, Montreal, QC H3A2B4, Canada From stefanwiens at gmail.com Thu May 11 16:17:13 2017 From: stefanwiens at gmail.com (Stefan Wiens) Date: Thu, 11 May 2017 16:17:13 +0200 Subject: [FieldTrip] reading offsets from Biosemi bdf file Message-ID: Hi! I am Stefan Wiens and am working with EEG in Stockholm, Sweden. ( people.su.se/~swiens/) I use a Cedrus Stimtracker to track visual events with a light diode and a TTL output to the Biosemi system. The onsets are save nicely in the bdf. I would also like to check duration by tracking not only onsets but also offsets. I tried the following but received a warning. event = ft_read_event(cfg.dataset, 'detectflank', 'both'); Warning: only up-going flanks are supported for Biosemi Do I understand correctly that there is not (reasonable) way to extract offsets? (I already have a work around by having a different picture at the offset of the first. This work but a direct approach with onset and offset might be better. Thanks for your input! Stefan -------------- next part -------------- An HTML attachment was scrubbed... URL: From u.pomper at ucl.ac.uk Thu May 11 19:21:42 2017 From: u.pomper at ucl.ac.uk (Pomper, Ulrich) Date: Thu, 11 May 2017 17:21:42 +0000 Subject: [FieldTrip] Rotating sensors using ft_transform_sens Message-ID: Dear Listmembers, Could someone please explain how to use ft_transform_sens in order to rotate sensors around a given axis? For example, how would the input variable 'transform' need to look like in order to perform a 90 degree rotation around the z-axis? Many thanks, Ulrich -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Fri May 12 09:44:01 2017 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 12 May 2017 09:44:01 +0200 Subject: [FieldTrip] Rotating sensors using ft_transform_sens In-Reply-To: References: Message-ID: Dear Ulrich, could you use ft_electroderealign with the interactive-option instead? Here you have an graphic interface that lets you rotate the electrodes in all directions to match your headshape. ft_transform_sens is used in this function, so the output should be the same. Moreover, if you check the code of ft_electroderealign, it can give you a hint to what the transform-matrix should look like: I think it should be a 3x3-matrix with scale, transform and rotate xyz-vectors. I hope this helps, Julian Am 11.05.2017 um 19:21 schrieb Pomper, Ulrich: > Dear Listmembers, > > Could someone please explain how to use ft_transform_sens in order to rotate sensors around a given axis? > For example, how would the input variable 'transform' need to look like in order to perform a 90 degree rotation around the z-axis? > > Many thanks, > Ulrich > > _______________________________________________ > 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: signature.asc Type: application/pgp-signature Size: 495 bytes Desc: Message signed with OpenPGP using GPGMail URL: From cornelia.quaedflieg at uni-hamburg.de Fri May 12 23:47:08 2017 From: cornelia.quaedflieg at uni-hamburg.de (cornelia.quaedflieg at uni-hamburg.de) Date: Fri, 12 May 2017 23:47:08 +0200 Subject: [FieldTrip] cluster based permutation tests - grandaverage - grad structure Message-ID: <20170512214709.BDD13F2D44@mailhost.uni-hamburg.de> Dear fieldtrip users,    we are having troubles running the cluster based permutation tests for MEG data analysis. We tried to run ft_freqstatistics for previously calculated grandaverages over subjects in two conditions. However, we are not sure how to specify cfg.neighbours. The grandaverage datasets in the fieldtrip tutorial contain a gradiometer structure, which is probably used to prepare neighbouring channels. When we run ft_freqgrandaverages on our data, this grad structure disappears because it cannot be averaged over subjects. Thus, we were wondering if there is a way to keep the gradiometer information in the averaged data or to append an example grad structure later on?   We appreciate any suggestions on that matter. Thank you in advance!   Best Dr Conny Quaedflieg & Hanna Stoffregen Hamburg University -------------- next part -------------- An HTML attachment was scrubbed... URL: From mailtome.2113 at gmail.com Sat May 13 16:18:27 2017 From: mailtome.2113 at gmail.com (Arti Abhishek) Date: Sun, 14 May 2017 00:18:27 +1000 Subject: [FieldTrip] Alternatives to cluster based permutation test Message-ID: Dear list, I was wondering whether it is appropriate to use cluster permutation tests on 32 channel ERP data. I am working on visual ERP response to text stimuli, and since there are only few electrodes I am expecting a focal effect (on P7 and P8). I was wondering whether it is appropriate to use cluster statistics here. If not, what test do you suggest? Thank you, Arti -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Sat May 13 18:10:08 2017 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Sat, 13 May 2017 17:10:08 +0100 Subject: [FieldTrip] randsample.m from fieldtrip toolbox does not work properly In-Reply-To: <3768651157128871.WA.violinist811googlemail.com@www.jiscmail.ac.uk> References: <3768651157128871.WA.violinist811googlemail.com@www.jiscmail.ac.uk> Message-ID: Dear Yuan-hao, I'm not sure whether what you found is a bug but the best way to report it is via http://bugzilla.fieldtriptoolbox.org . I also CC your e-mail to Fieldtrip mailing list. Best, Vladimir On Fri, May 12, 2017 at 9:18 PM, Yuan-hao Wu <00000a54691459fb-dmarc- request at jiscmail.ac.uk> wrote: > Dear all, > > I just want to inform you that the randsample.m function that is included > in the spm12/fieldtrip toolbox does not work properly. > It only draw samples WITH replacement. > > Best, > Yuan-hao > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanwiens at gmail.com Sun May 14 10:31:34 2017 From: stefanwiens at gmail.com (Stefan Wiens) Date: Sun, 14 May 2017 10:31:34 +0200 Subject: [FieldTrip] bug in ft_rejectvisual()? Message-ID: Hi! I downloaded a new version of ft last week (fieldtrip-20170511). I run these simple commands: cfg = []; cfg.layout = 'biosemi64.lay'; cfg.metric = 'range'; cfg.latency = [-.1 .6]; ft_rejectvisual(cfg, data); The plot seems to work, but when I want to plot a specific trial ("Plot trial", to the left of the quit button), ft does not plot the trial number I entered; instead, it plots the LAST trial. The matlab output actually states that whereas the figure title states the trial number that I entered. I remember that this worked well before, so maybe I am doing something wrong? Best Stefan Wiens people.su.se/~swiens/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From u.pomper at ucl.ac.uk Sun May 14 13:36:13 2017 From: u.pomper at ucl.ac.uk (Pomper, Ulrich) Date: Sun, 14 May 2017 11:36:13 +0000 Subject: [FieldTrip] Rotating sensors using ft_transform_sens In-Reply-To: References: , Message-ID: Dear Julian, Thanks a lot for your help! >From looking into the function as you suggested, it seems the transformation matrix is actually 4 dimensional, with one extra dimension for scaling. I managed to rotate the sensors but they are still quite far away from the headvolume. I tried using ft_sensorrealign (MEG equivalent of ft_electroderealign) but am getting an errormessage Undefined function or variable "pnt". Error in channelposition (line 327) pnt = pnt(sel2, :); which I haven't had time to follow up yet. I will post more once I have looked into it. Anyway, thanks again for the help so far. Cheers, Ulrich ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil Sent: 12 May 2017 08:44 To: FieldTrip discussion list Subject: Re: [FieldTrip] Rotating sensors using ft_transform_sens Dear Ulrich, could you use ft_electroderealign with the interactive-option instead? Here you have an graphic interface that lets you rotate the electrodes in all directions to match your headshape. ft_transform_sens is used in this function, so the output should be the same. Moreover, if you check the code of ft_electroderealign, it can give you a hint to what the transform-matrix should look like: I think it should be a 3x3-matrix with scale, transform and rotate xyz-vectors. I hope this helps, Julian Am 11.05.2017 um 19:21 schrieb Pomper, Ulrich: Dear Listmembers, Could someone please explain how to use ft_transform_sens in order to rotate sensors around a given axis? For example, how would the input variable 'transform' need to look like in order to perform a 90 degree rotation around the z-axis? Many thanks, Ulrich _______________________________________________ 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 laxmi.shaw22 at gmail.com Mon May 15 13:17:42 2017 From: laxmi.shaw22 at gmail.com (Laxmi Shaw) Date: Mon, 15 May 2017 16:47:42 +0530 Subject: [FieldTrip] fieldtrip Digest, Vol 78, Issue 13 In-Reply-To: References: Message-ID: Dear Fieldtrip Users, I am using fieldtrip plot function, and it was running fine. Last two days back the code is showing some error, and I am not able to figure it out. Could you please help me in this regard. I have attached the screen shot of that error window. Please find the screenshot. Thanks and Regards[image: Inline image 1] On Mon, May 15, 2017 at 3:30 PM, wrote: > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: Rotating sensors using ft_transform_sens (Pomper, Ulrich) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 14 May 2017 11:36:13 +0000 > From: "Pomper, Ulrich" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Rotating sensors using ft_transform_sens > Message-ID: > eurprd01.prod.exchangelabs.com> > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Julian, > > > Thanks a lot for your help! > > >From looking into the function as you suggested, it seems the > transformation matrix is actually 4 dimensional, with one extra dimension > for scaling. I managed to rotate the sensors but they are still quite far > away from the headvolume. > > I tried using ft_sensorrealign (MEG equivalent of ft_electroderealign) but > am getting an errormessage > > > Undefined function or variable "pnt". > > Error in channelposition (line 327) > pnt = pnt(sel2, :); > > > > which I haven't had time to follow up yet. I will post more once I have > looked into it. > > Anyway, thanks again for the help so far. > > > Cheers, > > Ulrich > > > > ________________________________ > From: fieldtrip-bounces at science.ru.nl > on behalf of Julian Keil > Sent: 12 May 2017 08:44 > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Rotating sensors using ft_transform_sens > > Dear Ulrich, > > could you use ft_electroderealign with the interactive-option instead? > Here you have an graphic interface that lets you rotate the electrodes in > all directions to match your headshape. > ft_transform_sens is used in this function, so the output should be the > same. > Moreover, if you check the code of ft_electroderealign, it can give you a > hint to what the transform-matrix should look like: I think it should be a > 3x3-matrix with scale, transform and rotate xyz-vectors. > > I hope this helps, > > Julian > > > Am 11.05.2017 um 19:21 schrieb Pomper, Ulrich: > > Dear Listmembers, > > Could someone please explain how to use ft_transform_sens in order to > rotate sensors around a given axis? > For example, how would the input variable 'transform' need to look like in > order to perform a 90 degree rotation around the z-axis? > > Many thanks, > Ulrich > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170514/c4c91a75/attachment-0001.html> > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 78, Issue 13 > ***************************************** > -- Laxmi Shaw Research Scholar(PhD) IIT Kharagpur West Bengal Ph no-08388837821 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Error_fig.png Type: image/png Size: 130728 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Error_fig.png Type: image/png Size: 130728 bytes Desc: not available URL: From david.m.groppe at gmail.com Mon May 15 16:24:20 2017 From: david.m.groppe at gmail.com (David Groppe) Date: Mon, 15 May 2017 10:24:20 -0400 Subject: [FieldTrip] Alternatives to cluster based permutation test In-Reply-To: References: Message-ID: Hi Arti, For very focal effects, the tmax permutation test and Benjamini & Hochberg false discovery rate (FDR) control algorithm are more powerful than cluster-based permutation tests: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4059014/ cheers, -David On Sat, May 13, 2017 at 10:18 AM, Arti Abhishek wrote: > Dear list, > > I was wondering whether it is appropriate to use cluster permutation tests > on 32 channel ERP data. I am working on visual ERP response to text > stimuli, and since there are only few electrodes I am expecting a focal > effect (on P7 and P8). I was wondering whether it is appropriate to use > cluster statistics here. If not, what test do you suggest? > > Thank you, > 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 HEROBINSON at augusta.edu Mon May 15 16:30:37 2017 From: HEROBINSON at augusta.edu (Robinson, Heath) Date: Mon, 15 May 2017 14:30:37 +0000 Subject: [FieldTrip] [EXTERNAL] Re: Alternatives to cluster based permutation test In-Reply-To: References: Message-ID: I tried to save my profile and it is sying that I am logged in as Anonymous. I logged out and logged back in and it did the same thing. From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of David Groppe Sent: Monday, May 15, 2017 10:24 AM To: FieldTrip discussion list Subject: [EXTERNAL] Re: [FieldTrip] Alternatives to cluster based permutation test This is an external email. Use caution responding, opening attachments and following links. Hi Arti, For very focal effects, the tmax permutation test and Benjamini & Hochberg false discovery rate (FDR) control algorithm are more powerful than cluster-based permutation tests: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4059014/ cheers, -David On Sat, May 13, 2017 at 10:18 AM, Arti Abhishek > wrote: Dear list, I was wondering whether it is appropriate to use cluster permutation tests on 32 channel ERP data. I am working on visual ERP response to text stimuli, and since there are only few electrodes I am expecting a focal effect (on P7 and P8). I was wondering whether it is appropriate to use cluster statistics here. If not, what test do you suggest? Thank you, 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 elam4hcp at gmail.com Mon May 15 19:37:09 2017 From: elam4hcp at gmail.com (Jennifer Elam) Date: Mon, 15 May 2017 12:37:09 -0500 Subject: [FieldTrip] Reminder to Register for HCP Course 2017 Message-ID: Only a few spaces remain for the *2017 HCP Course: "Exploring the Human Connectome"*. For more info and to register: https://store.humanconnectome. org/courses/2017/exploring-the-human-connectome.php Don't forget to also reserve your accommodation for the course by May 17, 2017 to be sure of securing a room on the UBC campus in the HCP Course room block. Before or after May 17, 2017, please use this link to make a reservation: https://reserve.ubcconferences.com/vancouver/availability.asp?hotelCode=%2A&startDate=06%2F18%2F2017&endDate=06%2F23%2F2017&adults=1&children=&rooms=1&requesttype=invBlockCode&code=G170618A HCP Course 2017 will be held June 19-23 (week before OHBM) at the Djavad Mowafagian Centre for Brain Health at University of British Columbia (UBC) in Vancouver, BC, Canada. The 5-day intensive course of lectures and hands-on practicals is a great opportunity to learn directly from HCP investigators about using HCP data, acquisition, processing methods, and software tools in your own studies. If you have any questions, please contact us at: hcpcourse at humanconnectome. org We look forward to seeing you in Vancouver! Best, 2017 HCP Course Staff -- 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 laxmi.shaw22 at gmail.com Tue May 16 05:48:00 2017 From: laxmi.shaw22 at gmail.com (Laxmi Shaw) Date: Tue, 16 May 2017 09:18:00 +0530 Subject: [FieldTrip] Some plotting error Message-ID: * Dear community, **I have a data such that every channel has 1 value that is result of some **calculation(I mean I have 14 channel thus a data vector of length14).I want **to plot map of head how? every channel has a color corresponding its? **value... **I tried using? ft_topoplotER to assess my data and I made the true layout ** but when I want to use ft_topoplotER receive the following error message:? **Subscript indices must either be real positive integers or logicals. ** Error in topoplot_common (line 79) ** data = varargin{indx}; **Error in ft_topoplotER (line 169) ** cfg = topoplot_common(cfg, varargin{:}); ** Error in top (line 19) **figure; ft_topoplotER(cfg,data); colorbar;? ** Could you please help to fix this problem How to remove this error.* *Thanks and Regards * Laxmi Shaw Research Scholar(PhD) IIT Kharagpur West Bengal Ph no-08388837821 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Patrick.Rollo at uth.tmc.edu Tue May 16 18:24:24 2017 From: Patrick.Rollo at uth.tmc.edu (Rollo, Patrick) Date: Tue, 16 May 2017 16:24:24 +0000 Subject: [FieldTrip] Job posting on FieldTrip message board Message-ID: FieldTrip, I have a job posting that I would like to make on this message board, our lab, Tandon Lab, has posted in the past. The advert is attached here. Please let me know if you have any questions, Thank you, Patrick Rollo -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Postdocs_U01_updated 5:17.pdf Type: application/pdf Size: 236167 bytes Desc: Postdocs_U01_updated 5:17.pdf URL: From stephen.whitmarsh at gmail.com Wed May 17 16:46:53 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Wed, 17 May 2017 16:46:53 +0200 Subject: [FieldTrip] source pos dimensions ft_sourcestatistics Message-ID: Hi there, After beamformer sourceanalysis I end up with datastructures looking like: struct with fields: freq: 10.5000 cfg: [1×1 struct] pos: [2982×3 double] pow: [2982×1 double] inside: [2982×1 logical] powdimord: 'pos' The .inside field is created by ft_selectdata used to average across frequencies, and contains all 1s. Running sourceanalysis with this data trows the following error: Error using spm_bwlabel spm_bwlabel: CONN must be 6, 18 or 26 Error in clusterstat (line 222) [negclusobs, negnum] = spm_bwlabel(tmp, 2*numdims); Error in ft_statistics_montecarlo (line 347) [stat, cfg] = clusterstat(cfg, statrand, statobs); Error in ft_sourcestatistics (line 205) [stat, cfg] = statmethod(cfg, dat, design); *222 * [negclusobs, negnum] = spm_bwlabel(tmp, 2*numdims); I think this results because of a wrong estimate of the dimensionality, resulting from the fact that the data is represented in an array rather than a 3-dimensional matrix, which it seems to expect. I think therefor that I might need to convert my data back into a 3-d representation, i..e not a sparse but full representation. I have tried using ft_source2full, but that is not straightforward as I only have inside voxels/positions. In other words, I would need to do exactly the same as ft_source_statistics seems to want to do with spm_bwlabel. So I guess I might just have put FieldTrip on the wrong leg, to use a Dutch expression. Any suggestions? Best, Stephen -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu May 18 21:35:38 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 18 May 2017 19:35:38 +0000 Subject: [FieldTrip] source pos dimensions ft_sourcestatistics In-Reply-To: References: Message-ID: <4EF37F95-710B-4EAC-8FE5-786964346094@donders.ru.nl> Hi Stephen, source2full and source2sparse are probably quite outdated, and do not seem to work well anymore with the latest type of source-level data structures. Most relevantly, the inside field these days is by default a boolean vector of size nposx1, whereas once upon a time the inside and outside fields together contained the indices of the dipole positions, indicating which positions are on the in-/outside. Do you need the source2sparse step to begin with? Best, JM On 17 May 2017, at 16:46, Stephen Whitmarsh > wrote: Hi there, After beamformer sourceanalysis I end up with datastructures looking like: struct with fields: freq: 10.5000 cfg: [1×1 struct] pos: [2982×3 double] pow: [2982×1 double] inside: [2982×1 logical] powdimord: 'pos' The .inside field is created by ft_selectdata used to average across frequencies, and contains all 1s. Running sourceanalysis with this data trows the following error: Error using spm_bwlabel spm_bwlabel: CONN must be 6, 18 or 26 Error in clusterstat (line 222) [negclusobs, negnum] = spm_bwlabel(tmp, 2*numdims); Error in ft_statistics_montecarlo (line 347) [stat, cfg] = clusterstat(cfg, statrand, statobs); Error in ft_sourcestatistics (line 205) [stat, cfg] = statmethod(cfg, dat, design); 222 [negclusobs, negnum] = spm_bwlabel(tmp, 2*numdims); I think this results because of a wrong estimate of the dimensionality, resulting from the fact that the data is represented in an array rather than a 3-dimensional matrix, which it seems to expect. I think therefor that I might need to convert my data back into a 3-d representation, i..e not a sparse but full representation. I have tried using ft_source2full, but that is not straightforward as I only have inside voxels/positions. In other words, I would need to do exactly the same as ft_source_statistics seems to want to do with spm_bwlabel. So I guess I might just have put FieldTrip on the wrong leg, to use a Dutch expression. Any suggestions? Best, Stephen _______________________________________________ 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 D.C.W.Klooster at tue.nl Thu May 18 22:10:20 2017 From: D.C.W.Klooster at tue.nl (Klooster, D.C.W.) Date: Thu, 18 May 2017 20:10:20 +0000 Subject: [FieldTrip] Error loreta2fieldtrip Message-ID: <94D6E99297013F46990EEBA320449F617D02D71A@xserver30b.campus.tue.nl> Dear fieldtrip users, Hopefully this is an easy to solve issue for some of you... If I run loreta2fieldtrip I get an accute error that ft_preamble_callinfo is not known. Indeed, I can not find this anywhere within my fieldtrip folder. Am I doing something wrong or do I really need these files (same holds for ft_postamble_callinfo). If so, can anybody provide me the files? Thank you! Best regards, Debby -------------- next part -------------- An HTML attachment was scrubbed... URL: From seymourr at aston.ac.uk Fri May 19 08:46:08 2017 From: seymourr at aston.ac.uk (Seymour, Robert (Research Student)) Date: Fri, 19 May 2017 06:46:08 +0000 Subject: [FieldTrip] Inter-trial Coherence Stats Message-ID: Dear Fieldtrippers, I am trying to statistically evaluate inter-trial coherence on a virtual electrode, comparing an active to baseline period. However I get the following error when using 'diff_ITC' and ft_freqstatistics: Subscripted assignment dimension mismatch. Error in ft_freqstatistics (line 141) dat(:,i) = tmp(:); I can't seem to figure out what's going wrong... (code below). Has anyone else come across this error? Many thanks, Robert %% Script to calculate inter-trial coherence for the alien clicktrain data subject = sort({'RS','DB','MP','GR','DS','EC','VS','LA','AE','SY','GW',... 'SW','DK','LH','KM','FL','AN'}); grandavgA = zeros(1,length(subject)); grandavgB = zeros(1,length(subject)); for i = 1:length(subject) load(['D:\Pilot\' subject{i} '\auditory\sourceloc\VE_A1_RH.mat']); cfg = []; cfg.foi = [30:1:80]; cfg.method = 'mtmconvol'; cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; cfg.tapsmofrq = ones(length(cfg.foi),1).*8; cfg.toi = 0:0.01:1.5; cfg.output = 'fourier'; freq_post = (ft_freqanalysis(cfg, VE_A1_RH)); freq_post.fourierspctrm = (freq_post.fourierspctrm); grandavgA{i} = freq_post; cfg.toi = -1.5:0.01:0; freq_pre = (ft_freqanalysis(cfg, VE_A1_RH)); freq_pre.fourierspctrm = (freq_pre.fourierspctrm); grandavgB{i} = freq_pre; end cfg = []; cfg.latency = [0 1.5]; cfg.parameter = 'fourierspctrm'; cfg.frequency = [30 80]; cfg.method = 'montecarlo'; cfg.statistic = 'diff_ITC' cfg.clusterstatistic = 'maxsum'; cfg.tail = 0; cfg.alpha = 0.05; cfg.numrandomization = 1000; % Create design matrix based on specific number of trials from each % participant nsubj=numel(grandavgA); cfg.design(1,:) = [1:nsubj 1:nsubj]; cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2]; cfg.uvar = 1; % row of design matrix that contains unit variable (in this case: subjects) cfg.ivar = 2; % row of design matrix that contains independent variable (the conditions) [stat] = ft_freqstatistics(cfg, grandavgA{:}, grandavgB{:}); -------------- next part -------------- An HTML attachment was scrubbed... URL: From CXK699 at student.bham.ac.uk Fri May 19 09:36:43 2017 From: CXK699 at student.bham.ac.uk (Casper Kerren) Date: Fri, 19 May 2017 07:36:43 +0000 Subject: [FieldTrip] Inter-trial Coherence Stats In-Reply-To: References: Message-ID: <817B246999EC6E49AFEEDFCEC604EED83C5111E7@EX11.adf.bham.ac.uk> Dear Robert, Not sure whether I will give an appropriate answer to your question, but it seems like Fieldtrip doesn't like .fourierspctrm, and you could change it to powerspctrm yourself. Like this: For each participant run the ft_freqanalysis with your specified parameters. Get the output 'freq' and then a = freq.fourierspctrm; tmpli = abs(mean(a./abs(a),1)); % "manually" compute PLI freq.powspctrm = squeeze(tmpli); freq.dimord = 'chan_freq_time'; freq = rmfield(freq, 'fourierspctrm'); % remove field "fourierspctrm" because it confuses Fieldtrip freq = rmfield(freq, 'trialinfo'); % trialinfo no longer valid Of course, when you later run statistics use cfg.parameter = 'powspctrm' If this wasn't what you were looking for, let me know. Kind regards, Casper From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Seymour, Robert (Research Student) Sent: 19 May 2017 07:46 To: fieldtrip at science.ru.nl Subject: [FieldTrip] Inter-trial Coherence Stats Dear Fieldtrippers, I am trying to statistically evaluate inter-trial coherence on a virtual electrode, comparing an active to baseline period. However I get the following error when using 'diff_ITC' and ft_freqstatistics: Subscripted assignment dimension mismatch. Error in ft_freqstatistics (line 141) dat(:,i) = tmp(:); I can't seem to figure out what's going wrong... (code below). Has anyone else come across this error? Many thanks, Robert %% Script to calculate inter-trial coherence for the alien clicktrain data subject = sort({'RS','DB','MP','GR','DS','EC','VS','LA','AE','SY','GW',... 'SW','DK','LH','KM','FL','AN'}); grandavgA = zeros(1,length(subject)); grandavgB = zeros(1,length(subject)); for i = 1:length(subject) load(['D:\Pilot\' subject{i} '\auditory\sourceloc\VE_A1_RH.mat']); cfg = []; cfg.foi = [30:1:80]; cfg.method = 'mtmconvol'; cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; cfg.tapsmofrq = ones(length(cfg.foi),1).*8; cfg.toi = 0:0.01:1.5; cfg.output = 'fourier'; freq_post = (ft_freqanalysis(cfg, VE_A1_RH)); freq_post.fourierspctrm = (freq_post.fourierspctrm); grandavgA{i} = freq_post; cfg.toi = -1.5:0.01:0; freq_pre = (ft_freqanalysis(cfg, VE_A1_RH)); freq_pre.fourierspctrm = (freq_pre.fourierspctrm); grandavgB{i} = freq_pre; end cfg = []; cfg.latency = [0 1.5]; cfg.parameter = 'fourierspctrm'; cfg.frequency = [30 80]; cfg.method = 'montecarlo'; cfg.statistic = 'diff_ITC' cfg.clusterstatistic = 'maxsum'; cfg.tail = 0; cfg.alpha = 0.05; cfg.numrandomization = 1000; % Create design matrix based on specific number of trials from each % participant nsubj=numel(grandavgA); cfg.design(1,:) = [1:nsubj 1:nsubj]; cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2]; cfg.uvar = 1; % row of design matrix that contains unit variable (in this case: subjects) cfg.ivar = 2; % row of design matrix that contains independent variable (the conditions) [stat] = ft_freqstatistics(cfg, grandavgA{:}, grandavgB{:}); -------------- next part -------------- An HTML attachment was scrubbed... URL: From Simon.VanEyndhoven at esat.kuleuven.be Fri May 19 13:51:10 2017 From: Simon.VanEyndhoven at esat.kuleuven.be (Simon Van Eyndhoven) Date: Fri, 19 May 2017 13:51:10 +0200 Subject: [FieldTrip] Interpretation of Granger spectrum and link with directed coherence Message-ID: <99d3059295300fb8c2d53e4f1ae6f145@esat.kuleuven.be> Dear FieldTrip community, As a novice in EEG connectivity analysis, I am trying to reproduce and understand the connectivity tutorial of the website (http://www.fieldtriptoolbox.org/tutorial/connectivity). I was hoping that someone could shed light on the computation of the Granger frequency spectrum: cfg = []; cfg.method = 'granger'; granger = ft_connectivityanalysis(cfg, mfreq); More specifically, I would like to know which computations are done to obtain the values in granger.grangerspctrm. (Unfortunately, inspecting the paper by Brovelli et al. PNAS (2004), as indicated in ft_connectivity_granger did not clear this up...) Moreover, I wonder what the relationship is between the Granger spectrum and other metrics such as (partial) directed coherence (DC / PDC) and directed transfer function (DTF), which also provide connectivity information in the form channels x channels x frequencies? In the appendix in Van Mierlo et al., "Functional brain connectivity from EEG in epilepsy: Seizure prediction and epileptogenic focus localization" and in Baccala and Sameshima, "Partial directed coherence: a new concept in neural structure determination", it is explained that both DC and DTF are computed using the transfer function matrix H(f), while PDC is computed using the A(f) matrix. Is this the reason why only PDC is termed 'partial', and the others not (even though they are also computed in a multivariate framework, i.e. taking all available variables into account)? Although I could not find an answer to my questions in the mailing archives, I apologize if this question has been asked before. Thank you in advance for your help! Best regards, Simon From jan.schoffelen at donders.ru.nl Fri May 19 14:12:48 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 19 May 2017 12:12:48 +0000 Subject: [FieldTrip] Interpretation of Granger spectrum and link with directed coherence In-Reply-To: <99d3059295300fb8c2d53e4f1ae6f145@esat.kuleuven.be> References: <99d3059295300fb8c2d53e4f1ae6f145@esat.kuleuven.be> Message-ID: <0E539AF5-0DC8-4D03-A4EB-4B0ED7255E6D@donders.ru.nl> Hi Simon, You may want to check the ‘connectivity’ section in the following link: http://www.fieldtriptoolbox.org/references_to_implemented_methods It contains links to papers that might be relevant for you. I’d start from the first one, sorry for the shameless self-promotion. Best, Jan-Mathijs > On 19 May 2017, at 13:51, Simon Van Eyndhoven wrote: > > Dear FieldTrip community, > > As a novice in EEG connectivity analysis, I am trying to reproduce and understand the connectivity tutorial of the website (http://www.fieldtriptoolbox.org/tutorial/connectivity). > > I was hoping that someone could shed light on the computation of the Granger frequency spectrum: > > cfg = []; > cfg.method = 'granger'; > granger = ft_connectivityanalysis(cfg, mfreq); > > More specifically, I would like to know which computations are done to obtain the values in granger.grangerspctrm. (Unfortunately, inspecting the paper by Brovelli et al. PNAS (2004), as indicated in ft_connectivity_granger did not clear this up...) > > Moreover, I wonder what the relationship is between the Granger spectrum and other metrics such as (partial) directed coherence (DC / PDC) and directed transfer function (DTF), which also provide connectivity information in the form channels x channels x frequencies? > > In the appendix in Van Mierlo et al., "Functional brain connectivity from EEG in epilepsy: Seizure prediction and epileptogenic focus localization" and in Baccala and Sameshima, "Partial directed coherence: a new concept in neural structure determination", it is explained that both DC and DTF are computed using the transfer function matrix H(f), while PDC is computed using the A(f) matrix. Is this the reason why only PDC is termed 'partial', and the others not (even though they are also computed in a multivariate framework, i.e. taking all available variables into account)? > > Although I could not find an answer to my questions in the mailing archives, I apologize if this question has been asked before. > > Thank you in advance for your help! > Best regards, > > Simon > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From laxmi.shaw22 at gmail.com Fri May 19 16:56:51 2017 From: laxmi.shaw22 at gmail.com (Laxmi Shaw) Date: Fri, 19 May 2017 20:26:51 +0530 Subject: [FieldTrip] Error_while using ft_freqanalysis for non parametric computation Message-ID: Dear Fieldtrip users, I am getting an error while using frequency analysis using ft_connectivity analysis. Could you please help me by looking at the screenshot of the error. The error in the dpss.m file. Any help will always be appreciated. Thanks and Regards -- Laxmi Shaw Research Scholar(Ph.D.) IIT Kharagpur West Bengal Ph no-08388837821 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2017-05-19.png Type: image/png Size: 355204 bytes Desc: not available URL: From ty.mckinney.412 at gmail.com Fri May 19 18:16:15 2017 From: ty.mckinney.412 at gmail.com (Ty McKinney) Date: Fri, 19 May 2017 10:16:15 -0600 Subject: [FieldTrip] ft_preprocessing error Message-ID: Hi, I am having some trouble getting the ft_preprocessing function to work. The ft_definetrial function works and gives the trl matrix in the cfg output. As best as I can tell the read data function is returning a matrix that is smaller than the dimensions of the event sample indexes (by several orders of magnitude) from the read event function. I confirmed with EEG lab's loading function that the data matrix is thee same size. What is odd is that this script was working several weeks ago... I get this error: Error using ft_read_data (line 221) cannot read data after the end of the file Error in ft_preprocessing (line 576) dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) Posted below is my code leading up to the execution of the function. Any and all helps you can give me would be greatly appreciated %% Set up fieldtrip path ft_dir = 'C:\Users\Public\Documents\Euler_electrophys (Not backed up)\EEG_scripts\fieldtrip-master'; addpath(ft_dir); ft_defaults; % run this line ft needs it clc %% Load data datainfo.origdir = input('Please copy and paste the filepath for the .CNT file ', 's'); %datainfo.savdir = input('Please copy and paste the filepath for save directory ', 's'); datainfo.SID = input('Enter the Subject Name, e.g., Hick99 use lowercase!!', 's'); datainfo.hp = input('Was the data highpass filtered at 0.1Hz? (y/n)', 's'); cd(datainfo.origdir); % cd into the S's directory wrkdir = pwd; %go get the scalp maps % use the line below on MJE's computer upstairs %chanlocdir = 'C:\Users\u0850304.ADCSBS\Documents\MATLAB\euler_ electrophys\All_purpose_fxs'; % use the line below on the downstairs lab computer chanlocdir = 'C:\Users\Public\Documents\Euler_electrophys (Not backed up)\EEG_scripts\All_purpose_fxs\Waveguard_scalp_coordinates'; cd(chanlocdir); load WG64_4topoplot.mat cd(wrkdir); %find the exact file we need myfname = dir(strcat(datainfo.SID, '*', 'hick', '*','.cnt')); %Note that the file needs to end in ft.cnt/ft.trg exactname = myfname.name; datainfo.sourcepth = strcat(datainfo.origdir, '\', exactname); %set file path for the data cfg.trialfun='trialfun_Hick_tm2'; cfg.datainfo=datainfo; cfg.padding=0; cfg.padtype='data'; cfg.continuous='yes'; cfg.datafile=datainfo.sourcepth; cfg.headerfile=datainfo.sourcepth; cfg.dataset=datainfo.sourcepth; cfg.fsample=512; cd(cfg.datainfo.origdir); fileattrib; savep=ans.Name; newfolder = strcat(datainfo.SID, '_FT'); mkdir(newfolder); % Create new folder in Current Subject folder for FT output cfg.datainfo.savepath = strcat(savep,'\', newfolder); %create save path to new folder cfg.hdr = ft_read_header(cfg.datafile); %things I think fieldtrip needs according to site cfg.event = ft_read_event(cfg.datafile); cfg.data = ft_read_data(cfg.datafile); %% Define Trial Stuff % How much time, in seconds, is retained on either side of trigger codes %cfg.trialdef.eventtype= 'backpanel trigger'; %cfg.trialdef.eventvalue= '55 '; cfg.trialdef.pre= 1; % in seconds cfg.trialdef.post= 1; % in seconds %% read the header (needed for the samping rate) and the events evtsamps = [cfg.event.sample]';% for the events of interest, find the sample numbers (these are integers) Evtypes = {cfg.event.value}';% for the events of interest, find the trigger values (these are strings in the case of BrainVision) evtsamps=evtsamps(2:end); %Trim off first event that crashes script Evtypes =Evtypes (2:end); evtypes=zeros(length(Evtypes),1); for kk=1:length(evtsamps); %Convert string to numbers evtypes(kk) = str2double(Evtypes{kk}); % end pretrig = -round(cfg.trialdef.pre * cfg.hdr.Fs); % pre-stimulus boundary in samples posttrig = round(cfg.trialdef.post * cfg.hdr.Fs); % post-STIMULUS boundary in samples %% Trial definition [cfg]=ft_definetrial(cfg); data=ft_preprocessing(cfg); Ty McKinney Graduate Student-University of Utah ty.mckinney.412 at gmail.com 385.321.4061 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nicolas.abichacra at gmail.com Fri May 19 20:20:19 2017 From: nicolas.abichacra at gmail.com (Nicolas Abichacra) Date: Fri, 19 May 2017 19:20:19 +0100 Subject: [FieldTrip] Problem Matlab Path Message-ID: Dear Filedtrip list, I am currently pre processing EEG data. I recently moved my data from a hard drive to another (cut and paste). After resetting the path to fieldtrip, I get this kind or response when I run any of my scripts : When I run startup.m it gives me a list of warning messages like this one : Warning: Function iscolumn has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. > In path (line 109) In addpath (line 88) In startup (line 1) Then if I run one of the prepro scripts, I get this kind of response : Error using nargin You can only call nargin/nargout from within a MATLAB function. Error in ft_preamble_init (line 34) if nargin==0 Error in ft_preamble (line 56) evalin('caller', ['ft_preamble_' cmd]); Error in ft_rejectvisual (line 125) ft_preamble init Error in FT_prepro_2_sus (line 68) data = ft_rejectvisual(cfg, data); Does anyone have any idea where it might come from ? Thank you very much for the help. Best, Nicolas -------------- next part -------------- An HTML attachment was scrubbed... URL: From frsantos at fpce.up.pt Fri May 19 20:39:05 2017 From: frsantos at fpce.up.pt (Fernando Ferreira-Santos) Date: Fri, 19 May 2017 18:39:05 +0000 Subject: [FieldTrip] 2017 Porto EEG/ERP Summer School Message-ID: <2BAB036A9BAEA44984A131DFCE446108020C0A4975@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 6th 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 event will take place from 4-8 of September 2017 in the lovely city of Porto. In last year's edition the course was fully booked and, as such, we recommend early registration (course places are attributed by order of registration). For additional details and instructions on how to register, please 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, PhD Lecturer Laboratory of Neuropsychophysiology Faculty of Psychology and Education Sciences University of Porto Rua Alfredo Allen, 4200-135 Porto (Portugal) Tel.: +351 226079700 (ext. 409) E-mail: frsantos at fpce.up.pt Lab: http://www.fpce.up.pt/labpsi/ Personal: https://sites.google.com/view/ferreira-santos -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikexcohen at gmail.com Mon May 22 17:58:33 2017 From: mikexcohen at gmail.com (Mike X Cohen) Date: Mon, 22 May 2017 17:58:33 +0200 Subject: [FieldTrip] New book on MATLAB programming techniques for neuroscience data analysis Message-ID: Dear colleagues, There is a new book on MATLAB programming that is designed for masters/PhD/postdoc level researchers. The book is called "MATLAB for Brain and Cognitive Scientists" and is published by MIT Press. The goal of this book is to teach programming skills from beginner to intermediate/advanced levels (many other learning resources provide only beginner-level training), with a specific focus on the myriad analysis approaches often applied in neuroscience and cognitive neuroscience. Chapters end with many exercises to test and develop programming skills, and there are >9000 lines of MATLAB code to learn from on the accompanying website. An important feature of the book is that it teaches not only how to write good code, but also how to recognize and avoid writing bad or error-prone code. More information about the book can be obtained from the following websites: mikexcohen.com/book/#mbcs mitpress.mit.edu/books/matlab-brain-and-cognitive-scientists amazon.com/MATLAB-Brain-Cognitive-Scientists-Press/dp/0262035820/ Mike -------------- next part -------------- An HTML attachment was scrubbed... URL: From malgorzata.wislowska at gmail.com Wed May 24 16:34:17 2017 From: malgorzata.wislowska at gmail.com (Malgorzata Wislowska) Date: Wed, 24 May 2017 16:34:17 +0200 Subject: [FieldTrip] source statistics - spm_bwlabel error Message-ID: Dear FT-community, when calculating cluster permutation statistics on the source level, I receive the following error: Error using spm_bwlabel spm_bwlabel: CONN must be 6, 18 or 26 Error in clusterstat (line 319) [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use spm_bwlabel for 2D/3D to avoid usage of image toolbox Error in ft_statistics_montecarlo (line 347) [stat, cfg] = clusterstat(cfg, statrand, statobs); Error in ft_sourcestatistics (line 218) [stat, cfg] = statmethod(cfg, dat, design); I used MNE method for the inverse problem. I have 8196 grid points 1555 time points. But the error occurs also when I average across the time. Here is my configuration structure for the source analysis: design = zeros(2, nb_of_sbj*2); design(1,:) = [1:nb_of_sbj 1:nb_of_sbj]; design(2,:) = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2]; cfg = []; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_depsamplesT'; cfg.parameter = 'pow'; cfg.correctm = 'cluster'; cfg.clusterstatistic = 'maxsum'; cfg.design = design; cfg.ivar = 2; cfg.uvar = 1; cfg.numrandomization = 5000; cfg.tail = 0; cfg.alpha = 0.025; [stat] = ft_sourcestatistics(cfg,avg_con_sel{:},avg_incon_sel{:}); As far as I can see somebody had asked the same question last year, but the post doesn't seem to have been addressed: https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html Thank you for your help in advance. Best regards, Malgorzata Wislowska, University of Salzburg -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed May 24 16:42:26 2017 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 24 May 2017 16:42:26 +0200 Subject: [FieldTrip] source statistics - spm_bwlabel error In-Reply-To: References: Message-ID: <849BF19E-E573-4781-9B9D-800EB2DDB083@gmail.com> Dear Malgorzata, from a quick glance, it appears that in the call to spm_bwlabel "numdims" should be 3 to give you 2*numdims = 6. So, could you check what numdims is in your case? I suspect that you have 4-dimensional data (time by 3 spatial dimensions), so it might help to check where the dimensions are coming from and what happens if you average over time. Good luck, Julian Am 24.05.2017 um 16:34 schrieb Malgorzata Wislowska: > Dear FT-community, > > > when calculating cluster permutation statistics on the source level, I receive the following error: > Error using spm_bwlabel > spm_bwlabel: CONN must be 6, 18 or 26 > > Error in clusterstat (line 319) > [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use spm_bwlabel for 2D/3D to avoid usage of image toolbox > > Error in ft_statistics_montecarlo (line 347) > [stat, cfg] = clusterstat(cfg, statrand, statobs); > > Error in ft_sourcestatistics (line 218) > [stat, cfg] = statmethod(cfg, dat, design); > > I used MNE method for the inverse problem. I have 8196 grid points 1555 time points. > But the error occurs also when I average across the time. > > Here is my configuration structure for the source analysis: > > design = zeros(2, nb_of_sbj*2); > design(1,:) = [1:nb_of_sbj 1:nb_of_sbj]; > design(2,:) = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2]; > > cfg = []; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_depsamplesT'; > cfg.parameter = 'pow'; > cfg.correctm = 'cluster'; > cfg.clusterstatistic = 'maxsum'; > cfg.design = design; > cfg.ivar = 2; > cfg.uvar = 1; > cfg.numrandomization = 5000; > cfg.tail = 0; > cfg.alpha = 0.025; > > [stat] = ft_sourcestatistics(cfg,avg_con_sel{:},avg_incon_sel{:}); > > As far as I can see somebody had asked the same question last year, but the post doesn't seem to have been addressed: > https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html > > > Thank you for your help in advance. > > Best regards, > Malgorzata Wislowska, > University of Salzburg > _______________________________________________ > 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: signature.asc Type: application/pgp-signature Size: 495 bytes Desc: Message signed with OpenPGP using GPGMail URL: From jiversen at ucsd.edu Thu May 25 23:03:08 2017 From: jiversen at ucsd.edu (John Iversen) Date: Thu, 25 May 2017 14:03:08 -0700 Subject: [FieldTrip] ft_sourceanalysis of component data In-Reply-To: <849BF19E-E573-4781-9B9D-800EB2DDB083@gmail.com> References: <849BF19E-E573-4781-9B9D-800EB2DDB083@gmail.com> Message-ID: <74026E48-8F22-4140-AB9D-304F91FD4F32@ucsd.edu> Dear Fieldtrip development team, I’m doing a long-delayed upgrade of my fieldtrip installation and came across this error. I’m not sure how long this has / will be the case, but I’d like to know your plans. I am available to help re-enable it if that would make a difference. It’s not a really critical feature for me, but it is something I’d relied on in my analysis. For now, I suppose I can revert to the old version, which I recall did have to massage things to work (it mapped components onto time if I remember correctly). elseif iscomp % FIXME, select the components here % FIXME, add the component numbers to the output error('the use of component data in ft_sourceanalysis is disabled for the time being: if you encounter this error message and you need this functionality please contact the FieldTrip development team'); end Thanks, John John R. Iversen, PhD University of California, San Diego Swartz Center for Computational Neuroscience Institute for Neural Computation 9500 Gilman Dr #0559 La Jolla, CA 92093 jiversen at ucsd.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From malgorzata.wislowska at gmail.com Fri May 26 11:52:20 2017 From: malgorzata.wislowska at gmail.com (Malgorzata Wislowska) Date: Fri, 26 May 2017 11:52:20 +0200 Subject: [FieldTrip] source statistics - spm_bwlabel error Message-ID: Dear Julian, thank you very much for your prompt response. Yes, my numdims == 2 because my cfg.dim == [8196 1] which comes from ft_sourcestatistics.m (code lines 131-132) datdim = find(~strcmp(dimtok, 'subj') & ~strcmp(dimtok, 'rpt') & ~strcmp(dimtok, 'rpttap')); datsiz = dimsiz(datdim); calculated on the following input data: varargin{1}: cfg: [1x1 struct] inside: [8196x1 logical] pos: [8196x3 double] time: 0.1750 pow: [8196x1 double] dimord: 'chan_time' The above source level structure comes from ft_sourceanalysis calculated with cfg.method = 'mne'. Averaging over time unfortunately doesn't help - the same error continues to occur: But data that is not averaged over time has numdims == 2 too, because length(cfg.dim) == 2, even though that cfg.dim itself is different (for not averaged data it's e.g cfg.dim == [8196 61], whereas for averaged data it's cfg.dim == [8196 1]), It helps (well, the function runs through without errors and produces some output) if the line: if numdims == 2 || numdims == 3 % if 2D or 3D data gets replaced with: if numdims == 3 In clusterstat.m, code line: 318 (and also 269, 215, 184) Do you (or anybody else) have maybe any better idea how to fix it? Thanks and best regards, Malgorzata, University Salzburg > Subject: Re: [FieldTrip] source statistics - spm_bwlabel error > Dear Malgorzata, > > from a quick glance, it appears that in the call to spm_bwlabel "numdims" > should be 3 to give you 2*numdims = 6. > So, could you check what numdims is in your case? > I suspect that you have 4-dimensional data (time by 3 spatial dimensions), > so it might help to check where the dimensions are coming from and what > happens if you average over time. > > Good luck, > > Julian > > Am 24.05.2017 um 16:34 schrieb Malgorzata Wislowska: > > Dear FT-community, > > > when calculating cluster permutation statistics on the source level, I > receive the following error: > > Error using spm_bwlabel > spm_bwlabel: CONN must be 6, 18 or 26 > > Error in clusterstat (line 319) > [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use > spm_bwlabel for 2D/3D to avoid usage of image toolbox > > Error in ft_statistics_montecarlo (line 347) > [stat, cfg] = clusterstat(cfg, statrand, statobs); > > Error in ft_sourcestatistics (line 218) > [stat, cfg] = statmethod(cfg, dat, design); > > > I used MNE method for the inverse problem. I have 8196 grid points 1555 > time points. > But the error occurs also when I average across the time. > > Here is my configuration structure for the source analysis: > > > design = zeros(2, nb_of_sbj*2); > design(1,:) = [1:nb_of_sbj 1:nb_of_sbj]; > design(2,:) = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2]; > > cfg = []; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_depsamplesT'; > cfg.parameter = 'pow'; > cfg.correctm = 'cluster'; > cfg.clusterstatistic = 'maxsum'; > cfg.design = design; > cfg.ivar = 2; > cfg.uvar = 1; > cfg.numrandomization = 5000; > cfg.tail = 0; > cfg.alpha = 0.025; > > [stat] = ft_sourcestatistics(cfg,avg_co > n_sel{:},avg_incon_sel{:}); > > > As far as I can see somebody had asked the same question last year, but > the post doesn't seem to have been addressed: > https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html > > > Thank you for your help in advance. > > Best regards, > Malgorzata Wislowska, > University of Salzburg > _______________________________________________ > 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 craiggrichter at gmail.com Sun May 28 10:34:48 2017 From: craiggrichter at gmail.com (Craig Richter) Date: Sun, 28 May 2017 11:34:48 +0300 Subject: [FieldTrip] Peercellfun on systems after R2013 Message-ID: <3E539B83-5BB0-49B8-A41C-12409B7F4B19@gmail.com> Dear Fieldtrip development team, I’m having trouble getting peercellfun to function on a Matlab system post R2013. The issue stems from new handling of Mx[De]Serialize.m after R2013. This issue is covered in bug 2452, http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2452 and emerged for the peer system in bug 2598. http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2598 For newer versions of Matlab, peercompile must run to update the mex files, but this fails when trying to compile peer.c. This file calls the mx[De]Serialize functions internally, which are now must be c++ files. I have successfully compiled the c++ versions of these files to mex, but it seems the calls in peer.c must be modified in some way since these must now be c++ files, whereas they were c before. I’m not sure how to make these modifications to peer.c, or if peer.c must be updated to a c++ file. If anyone has any expertise how to do this, and get the peer system operating on systems above R2013, I’d greatly appreciate it!! Thanks! Craig -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon May 29 09:51:30 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 29 May 2017 07:51:30 +0000 Subject: [FieldTrip] ft_sourceanalysis of component data References: Message-ID: Dear John, Sorry about this. I think that we disabled this feature at some point, because the original implementation was a bit hacky (and unpredictable in its behavior). In a bout of quality-of-code-perfectionism we probably cleaned up the code, disabled the feature, agreed that we should address it at some point, even remembered to put in an error message … and subsequently forgot about it. Anyway, after these lame excuses I suggest to try and get this fixed. Thanks for your willingness to contribute. These days our development workflow lives on github, which should make external contributions to the code much more straightforward (github.com/fieldtrip.git is where the main repo is located). Perhaps you could check out this chunk of documentation, to get on the road: http://www.fieldtriptoolbox.org/development/git). For this specific issue, I think it would be best to first discuss a bit the requested features before we start changing the code, so I suggest that you create a local fork of the repository, and within it a new branch, which I think you can subsequently 'pull-request’. This allows us to have a location where we can discuss stuff (for now the ‘issues’ feature for the fieldtrip repo is disabled, yet this would be a more natural way for discussing things). Does that sound like a plan? Best, JM On 25 May 2017, at 23:03, John Iversen > wrote: Dear Fieldtrip development team, I’m doing a long-delayed upgrade of my fieldtrip installation and came across this error. I’m not sure how long this has / will be the case, but I’d like to know your plans. I am available to help re-enable it if that would make a difference. It’s not a really critical feature for me, but it is something I’d relied on in my analysis. For now, I suppose I can revert to the old version, which I recall did have to massage things to work (it mapped components onto time if I remember correctly). elseif iscomp % FIXME, select the components here % FIXME, add the component numbers to the output error('the use of component data in ft_sourceanalysis is disabled for the time being: if you encounter this error message and you need this functionality please contact the FieldTrip development team'); end Thanks, John John R. Iversen, PhD University of California, San Diego Swartz Center for Computational Neuroscience Institute for Neural Computation 9500 Gilman Dr #0559 La Jolla, CA 92093 jiversen at ucsd.edu _______________________________________________ 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 Mon May 29 09:52:04 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 29 May 2017 07:52:04 +0000 Subject: [FieldTrip] source statistics - spm_bwlabel error References: Message-ID: Hi Malgorzata, Could you try to add the original ‘tri’ field to each of your varargins, and check whether the problem persists? Thanks, Jan-Mathijs On 26 May 2017, at 11:52, Malgorzata Wislowska > wrote: Dear Julian, thank you very much for your prompt response. Yes, my numdims == 2 because my cfg.dim == [8196 1] which comes from ft_sourcestatistics.m (code lines 131-132) datdim = find(~strcmp(dimtok, 'subj') & ~strcmp(dimtok, 'rpt') & ~strcmp(dimtok, 'rpttap')); datsiz = dimsiz(datdim); calculated on the following input data: varargin{1}: cfg: [1x1 struct] inside: [8196x1 logical] pos: [8196x3 double] time: 0.1750 pow: [8196x1 double] dimord: 'chan_time' The above source level structure comes from ft_sourceanalysis calculated with cfg.method = 'mne'. Averaging over time unfortunately doesn't help - the same error continues to occur: But data that is not averaged over time has numdims == 2 too, because length(cfg.dim) == 2, even though that cfg.dim itself is different (for not averaged data it's e.g cfg.dim == [8196 61], whereas for averaged data it's cfg.dim == [8196 1]), It helps (well, the function runs through without errors and produces some output) if the line: if numdims == 2 || numdims == 3 % if 2D or 3D data gets replaced with: if numdims == 3 In clusterstat.m, code line: 318 (and also 269, 215, 184) Do you (or anybody else) have maybe any better idea how to fix it? Thanks and best regards, Malgorzata, University Salzburg Subject: Re: [FieldTrip] source statistics - spm_bwlabel error Dear Malgorzata, from a quick glance, it appears that in the call to spm_bwlabel "numdims" should be 3 to give you 2*numdims = 6. So, could you check what numdims is in your case? I suspect that you have 4-dimensional data (time by 3 spatial dimensions), so it might help to check where the dimensions are coming from and what happens if you average over time. Good luck, Julian Am 24.05.2017 um 16:34 schrieb Malgorzata Wislowska: Dear FT-community, when calculating cluster permutation statistics on the source level, I receive the following error: Error using spm_bwlabel spm_bwlabel: CONN must be 6, 18 or 26 Error in clusterstat (line 319) [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use spm_bwlabel for 2D/3D to avoid usage of image toolbox Error in ft_statistics_montecarlo (line 347) [stat, cfg] = clusterstat(cfg, statrand, statobs); Error in ft_sourcestatistics (line 218) [stat, cfg] = statmethod(cfg, dat, design); I used MNE method for the inverse problem. I have 8196 grid points 1555 time points. But the error occurs also when I average across the time. Here is my configuration structure for the source analysis: design = zeros(2, nb_of_sbj*2); design(1,:) = [1:nb_of_sbj 1:nb_of_sbj]; design(2,:) = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2]; cfg = []; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_depsamplesT'; cfg.parameter = 'pow'; cfg.correctm = 'cluster'; cfg.clusterstatistic = 'maxsum'; cfg.design = design; cfg.ivar = 2; cfg.uvar = 1; cfg.numrandomization = 5000; cfg.tail = 0; cfg.alpha = 0.025; [stat] = ft_sourcestatistics(cfg,avg_con_sel{:},avg_incon_sel{:}); As far as I can see somebody had asked the same question last year, but the post doesn't seem to have been addressed: https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html Thank you for your help in advance. Best regards, Malgorzata Wislowska, University of Salzburg _______________________________________________ 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 angelika.lingnau at gmail.com Mon May 29 13:09:47 2017 From: angelika.lingnau at gmail.com (Angelika Lingnau) Date: Mon, 29 May 2017 12:09:47 +0100 Subject: [FieldTrip] 1-Year fMRI/ MEG Postdoc, Center for Mind/Brain Sciences, University of Trento, Italy Message-ID: At the Center for Mind/ Brain Sciences (CIMeC, http://www.cimec.unitn.it/en) at the University of Trento, Italy, there will soon be an opening for a one-year postdoctoral fellowship to work with Dr. Angelika Lingnau to examine the neural basis of visual imagery in normal sighted participants and hemianopic patients. Further descriptions of our ongoing research projects can be found under the following link: https://sites.google.com/site/angelikalingnau/. The postdoc will be responsible for the design of fMRI and/ or MEG studies, conducting data analysis and leading the write-up of scientific work. The ideal applicant is highly motivated and creative and is capable of working both independently as well as in a young, dynamic group. The applicant furthermore should have experience with functional magnetic resonance imaging and/ or magnetoencephalography and a solid background in Cognitive Neuroscience. Programming experience with MATLAB or C is very desirable. The Center offers an international and vibrant research setting with access to state-of-the-art neuroimaging methodologies, including a research-only 4T MRI scanner, MEG, EEG and TMS, as well as behavioral, eye tracking and motion tracking laboratories. The 2011-2014 ANVUR Report ranked CIMeC first among Italian universities in the field of psychological sciences. English is the official language of the CIMeC, where a large proportion of the faculty, postdocs and students come from a wide range of countries outside of Italy. Informal inquiries should be sent to Angelika Lingnau ( angelika.lingnau at rhul.ac.uk or angelika.lingnau at gmail.com). -------------- next part -------------- An HTML attachment was scrubbed... URL: From malgorzata.wislowska at gmail.com Mon May 29 18:30:40 2017 From: malgorzata.wislowska at gmail.com (Malgorzata Wislowska) Date: Mon, 29 May 2017 18:30:40 +0200 Subject: [FieldTrip] source statistics - spm_bwlabel error Message-ID: Dear Jan-Mathijs, thank you for your message. when I add the 'tri' field to the input data, FT recognizes that data is a mesh (*the input is mesh data with 8196 vertices and 16384 triangles*), but it keep throwing the same *spm_bwlabel* error message. This is the current input data (that's what you meant, right?): varargin{1}: cfg: [1x1 struct] inside: [8196x1 logical] pos: [8196x3 double] time: 0.1000 pow: [8196x1 double] tri: [16384x3 uint16] dimord: 'chan_time' If I don't average over time, and the size of varargin{1}.pow equals e.g., [8196 73], then datsiz == 8196. That's because dimsiz == [8196 73], but datdim == 1 (ft_sourcestatistics, lines 131-132). That leads to the following error: Error using ft_sourcestatistics (line 205) the length of the design matrix (2) does not match the number of observations in the data (3358) Best regards, Malgorzata > Subject: Re: [FieldTrip] source statistics - spm_bwlabel error > Hi Malgorzata, > > Could you try to add the original ‘tri’ field to each of your varargins, > and check whether the problem persists? > > Thanks, > Jan-Mathijs > > > > On 26 May 2017, at 11:52, Malgorzata Wislowska < > malgorzata.wislowska at gmail.com> wrote: > > Dear Julian, > > > thank you very much for your prompt response. > > Yes, my numdims == 2 because my cfg.dim == [8196 1] > which comes from ft_sourcestatistics.m (code lines 131-132) > > datdim = find(~strcmp(dimtok, 'subj') & ~strcmp(dimtok, 'rpt') & > ~strcmp(dimtok, 'rpttap')); > datsiz = dimsiz(datdim); > > calculated on the following input data: > > varargin{1}: > cfg: [1x1 struct] > inside: [8196x1 logical] > pos: [8196x3 double] > time: 0.1750 > pow: [8196x1 double] > dimord: 'chan_time' > > The above source level structure comes from ft_sourceanalysis calculated > with cfg.method = 'mne'. > > Averaging over time unfortunately doesn't help - the same error continues > to occur: > But data that is not averaged over time has numdims == 2 too, because > length(cfg.dim) == 2, even though that cfg.dim itself is different (for not > averaged data it's e.g cfg.dim == [8196 61], whereas for averaged data it's > cfg.dim == [8196 1]), > > It helps (well, the function runs through without errors and produces some > output) if the line: > > if numdims == 2 || numdims == 3 % if 2D or 3D data > > gets replaced with: > > if numdims == 3 > > In clusterstat.m, code line: 318 (and also 269, 215, 184) > > Do you (or anybody else) have maybe any better idea how to fix it? > > > Thanks and best regards, > Malgorzata, > University Salzburg > > > > >> Subject: Re: [FieldTrip] source statistics - spm_bwlabel error >> > > > Dear Malgorzata, >> >> from a quick glance, it appears that in the call to spm_bwlabel "numdims" >> should be 3 to give you 2*numdims = 6. >> So, could you check what numdims is in your case? >> I suspect that you have 4-dimensional data (time by 3 spatial >> dimensions), so it might help to check where the dimensions are coming from >> and what happens if you average over time. >> >> Good luck, >> >> Julian >> >> Am 24.05.2017 um 16:34 schrieb Malgorzata Wislowska: >> >> Dear FT-community, >> >> >> when calculating cluster permutation statistics on the source level, I >> receive the following error: >> >> Error using spm_bwlabel >> spm_bwlabel: CONN must be 6, 18 or 26 >> >> Error in clusterstat (line 319) >> [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use >> spm_bwlabel for 2D/3D to avoid usage of image toolbox >> >> Error in ft_statistics_montecarlo (line 347) >> [stat, cfg] = clusterstat(cfg, statrand, statobs); >> >> Error in ft_sourcestatistics (line 218) >> [stat, cfg] = statmethod(cfg, dat, design); >> >> >> I used MNE method for the inverse problem. I have 8196 grid points 1555 >> time points. >> But the error occurs also when I average across the time. >> >> Here is my configuration structure for the source analysis: >> >> >> design = zeros(2, nb_of_sbj*2); >> design(1,:) = [1:nb_of_sbj 1:nb_of_sbj]; >> design(2,:) = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2]; >> >> cfg = []; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'ft_statfun_depsamplesT'; >> cfg.parameter = 'pow'; >> cfg.correctm = 'cluster'; >> cfg.clusterstatistic = 'maxsum'; >> cfg.design = design; >> cfg.ivar = 2; >> cfg.uvar = 1; >> cfg.numrandomization = 5000; >> cfg.tail = 0; >> cfg.alpha = 0.025; >> >> [stat] = ft_sourcestatistics(cfg,avg_co >> n_sel{:},avg_incon_sel{:}); >> >> >> As far as I can see somebody had asked the same question last year, but >> the post doesn't seem to have been addressed: >> https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html >> >> >> Thank you for your help in advance. >> >> Best regards, >> Malgorzata Wislowska, >> University of Salzburg >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.papen at uni-koeln.de Tue May 30 09:35:37 2017 From: m.papen at uni-koeln.de (Michael von Papen) Date: Tue, 30 May 2017 09:35:37 +0200 Subject: [FieldTrip] Extended Deadline: Coupling & Causality in Complex Systems, Sep 25-27, Cologne, Germany Message-ID: ============================================================== CALL FOR PAPERS (*Extended Deadline June 15*, 2017) http://c3s.uni-koeln.de ============================================================== INTERNATIONAL CONFERENCE: *Coupling and Causality in Complex Systems* September 25-27, 2017, Cologne, Germany -------------------------------------------------------------- The interdisciplinary conference Coupling and Causality in Complex Systems (C3S) is hosted by the Competence Area 3: Quantitative Modeling of Complex Systems of the University of Cologne (UoC), Germany. It is organized by the Institute of Geophysics & Meteorology, UoC, the Institute of Clinical Neuroscience and Psychology, Heinrich-Heine University Düsseldorf and the Department of Cognitive Neuroscience at the Research Center Juelich. -------------------------------------------------- *Invited Speakers* Jörg Breitung - Macroeconomic Policy Institute, University of Cologne, Germany David Gross - Institute of Theoretical Physics, University of Cologne, Germany Philip Holmes - Mechanical and Aerospace Engineering / Princeton Neuroscience Institute, Princeton, USA Ankit Khambhati - Department of Bioengineering, University of Pennsylvania, USA Laura Marzetti - Department of Neuroscience, Università degli Studi "G. d'Annunzio" Chieti - Pescara Arkady Pikovsky - Institute of Physics and Astronomy, University Potsdam, Germany Michael Rosenblum - Institute of Physics and Astronomy, University Potsdam, Germany Jakob Runge - The Grantham Institute for Climate Change, Imperial College London -------------------------------------------------- *Preliminary Session Program* We will have different sessions with differing topics and each session will be opened by one of the invited speakers. Here is a preliminary version of our program: Session 1 Synchronization I Arkady Pikovsky Session 2 Synchronization II Silvia Daun Session 3 Coupled oscillators I Phil Holmes Session 4 Coupled oscillators II Michael Rosenblum Session 5 Phase coupling Laura Marzetti Session 6 Network structures Ankit Khambati Session 7 Bayesian networks David Gross Session 8 Granger causality I Jörg Breitung Session 9 Granger causality II Esther Florin Session 10 Causal network measures Jakob Runge Further topics of interest for the conference include, amongst others, research and methods development on: functional connectivity, (partial directed) coherence, network topology, graph-theoretic measures, directed graphs, nonlinear dynamics of complex systems, complex spatio-temporal systems, mutual information and transfer entropy. -------------------------------------------------------------- *Scientific Organizing Committee* Silvia Daun - Institute of Zoology, University of Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany Esther Florin - Institute of Clinical Neuroscience and Psychology, Düsseldorf, Germany Joachim Gross - Center for Cognitive Neuroimaging, Glasgow, UK Michael von Papen - Institute of Geophysics & Meteorology, Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany -------------------------------------------------------------- *Abstract* Complex systems such as the human brain, Earth’s climate and economy are characterized by a multitude of coupled processes on different spatial and temporal scales. In order to better understand the dynamics of the system at hand each scientific area has developed specific tools to identify, model and quantify these processes. The conference Coupling and Causality in Complex Systems (C3S) will present a collection of these approaches with the aim to provide scientists with new analysis strategies for their field. The conference focuses on how to characterize a complex system and on the methods for estimating and modeling of statistical coupling (e.g. network coherence, creation and modulation of small networks and local or long-range synchronization by cross frequency phase-phase and phase-amplitude coupling) and causality (e.g. Granger causality, transfer entropy). Therefore, data analysts from different study fields including neuroscience, mathematics, physics, biology, and economy will present their approaches with a particular focus on the methods they use. The aim of this conference is to foster discussions and the transdisciplinary exchange of advanced techniques, methods, and algorithms, thereby stimulating potential future collaborations. -------------------------------------------------------------- *PAPER SUBMISSION AND REGISTRATION* Authors are invited to submit conference abstracts with up to 400 words. Authors of exceptional abstracts will be given the opportunity to present their research in a talk. However, poster sessions will be provided with ample time for discussions. For your submission, please use the conference website c3s.uni-koeln.de. To register, please send an email with the subject "registration" to c3s-conference at uni-koeln.de. Please be sure to include your full name, your affiliation and whether you qualify as student (also PhD candidates) or not. The registration fee will cover snacks and refreshments during coffee breaks, lunch and a dinner with all participants. Early-bird registration is available until July 10 with a reduced fee of 100 EUR (50 EUR for students), after July 10 the registration fee will be 200 EUR (100 EUR for students). -------------------------------------------------------------- IMPORTANT DATES Paper Submission deadline: June 15, 2017 Author Notification: end June, 2017 Early-bird registration: July 10, 2017 Conference: September 25-27, 2017 ============================================================== Please find the call for papers and more information at the conference website: http://c3s.uni-koeln.de. For questions regarding the conference feel free to contact us via c3s-conference at uni-koeln.de. -- ------------------------------------------ UNIVERSITY OF COLOGNE Institute of Geophysics & Meteorology Coordinator of Competence Area III: Quantitative Modeling of Complex Systems Dr. Michael von Papen Email: m.papen at uni-koeln.de http://www.uni-koeln.de/~vpapenm http://complexsystems.uni-koeln.de From l.roeder at qut.edu.au Wed May 31 04:28:11 2017 From: l.roeder at qut.edu.au (Luisa Roeder) Date: Wed, 31 May 2017 02:28:11 +0000 Subject: [FieldTrip] input data structure ft_freqstatistics Message-ID: Dear Fieldtrip users, I am part of a research team at the Institute of Health and Biomedical Innovation at Queensland University of Technology in Brisbane, Australia. I am currently working on time-frequency analyses of EEG and EMG signals. I would like to use ft_freqstatistics for a cluster-based permutation test on my time-frequency data. In the function itself and in the online documentation I read that the input data into ft_freqstatistics should be the result/output from either FT_FREQANALYSIS, FT_FREQDESCRIPTIVES or from FT_FREQGRANDAVERAGE. I have not completed my time-frequency analysis via fieldtrip; hence, I am wondering if it is also possible to create my own input data structure to make it fit for ft_freqstatistics? (Basically, I would like to skip ft_freqanalysis and directly start with cluster-based permutation testing via ft_freqstatistics, and for that I need to adapt my data structure.) If it is possible, which fields have to be created in my variable to be fed into ft_freqstatistics, so it fulfils all requirements to make the function run? Are there any fields from the output of, for example, FT_FREQANALYSIS that are not needed for ft_freqstatistics? For example, [stat] = ft_freqstatistics(cfg, coh1, coh2, ...) What fields do coh1, coh2, ... have to have? E.g. >> display(coh1) labelcmb: {8×2 cell} dimord: 'chancmb_freq_time' cohspctrm: [8×80×2049 double] time: [1×2049 double] freq: [1×80 double] elec: [1×1 struct] cfg: [1×1 struct] Can I leave out some of these fields (particularly coh1.cfg), and it will still work for ft_freqstatistics? Would it be enough to only have coh1.cohspctrm, coh1.time and coh1.freq? I am still relatively new to Fieldtrip, and working my way through the tutorials etc., but I definitely having trouble to create an appropriate data structure as input into ft_freqstatistics (without using ft_freqanalysis or other functions alike beforehand). I would very much appreciate your help with this. Thank you, Kind regards Luisa Luisa Roeder, PhD | Research Associate | Movement Neuroscience Institute of Health and Biomedical Innovation | School of Exercise and Nutrition Science Queensland University of Technology | 60 Musk Ave, Kelvin Grove, Brisbane, QLD 4059, Australia. t: +61 7 3138 6428 | e: l.roeder at qut.edu.au | w: www.ihbi.qut.edu.au CRICOS No. 00213J -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed May 31 08:58:12 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 31 May 2017 06:58:12 +0000 Subject: [FieldTrip] input data structure ft_freqstatistics In-Reply-To: References: Message-ID: Hi Luisa, The minimum requirement for a data structure that fieldtrip can work with should contain at least the following fields: - a field with the data matrix, in your case it can be cohspctrm - a bunch of fields that indicate how to interpret the dimensions of the input data matrix: * dimord, a descriptor in the style of ‘chancmb_freq_time’ * freq * time * labelcmb (for univariate data, it should be label) The cfg should be optional. Anyway, this being said, probably you may want to try and fool fieldtrip into getting a univariate data-field, i.e. rename cohspctrm into powspctrm, and labelcmb into label. This should work under the assumption that you are cohering 8 different EEG electrodes with a single EMG (for the label you could just take the column of labelcmb that represents the EEG). Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 31 May 2017, at 04:28, Luisa Roeder > wrote: Dear Fieldtrip users, I am part of a research team at the Institute of Health and Biomedical Innovation at Queensland University of Technology in Brisbane, Australia. I am currently working on time-frequency analyses of EEG and EMG signals. I would like to use ft_freqstatistics for a cluster-based permutation test on my time-frequency data. In the function itself and in the online documentation I read that the input data into ft_freqstatistics should be the result/output from either FT_FREQANALYSIS, FT_FREQDESCRIPTIVES or from FT_FREQGRANDAVERAGE. I have not completed my time-frequency analysis via fieldtrip; hence, I am wondering if it is also possible to create my own input data structure to make it fit for ft_freqstatistics? (Basically, I would like to skip ft_freqanalysis and directly start with cluster-based permutation testing via ft_freqstatistics, and for that I need to adapt my data structure.) If it is possible, which fields have to be created in my variable to be fed into ft_freqstatistics, so it fulfils all requirements to make the function run? Are there any fields from the output of, for example, FT_FREQANALYSIS that are not needed for ft_freqstatistics? For example, [stat] = ft_freqstatistics(cfg, coh1, coh2, ...) What fields do coh1, coh2, … have to have? E.g. >> display(coh1) labelcmb: {8×2 cell} dimord: 'chancmb_freq_time' cohspctrm: [8×80×2049 double] time: [1×2049 double] freq: [1×80 double] elec: [1×1 struct] cfg: [1×1 struct] Can I leave out some of these fields (particularly coh1.cfg), and it will still work for ft_freqstatistics? Would it be enough to only have coh1.cohspctrm, coh1.time and coh1.freq? I am still relatively new to Fieldtrip, and working my way through the tutorials etc., but I definitely having trouble to create an appropriate data structure as input into ft_freqstatistics (without using ft_freqanalysis or other functions alike beforehand). I would very much appreciate your help with this. Thank you, Kind regards Luisa Luisa Roeder, PhD | Research Associate | Movement Neuroscience Institute of Health and Biomedical Innovation | School of Exercise and Nutrition Science Queensland University of Technology | 60 Musk Ave, Kelvin Grove, Brisbane, QLD 4059, Australia. t: +61 7 3138 6428 | e: l.roeder at qut.edu.au | w: www.ihbi.qut.edu.au CRICOS No. 00213J _______________________________________________ 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 kash.kgp at gmail.com Wed May 31 12:50:41 2017 From: kash.kgp at gmail.com (Kasturi Barik) Date: Wed, 31 May 2017 16:20:41 +0530 Subject: [FieldTrip] Fwd: Source Analysis from EEG data In-Reply-To: References: Message-ID: *Dear all, **I am trying to perform source localization in the frequency domain * *from EEG data using 'DICS' . As I have no mri data of the participants, * *I am using **'Subject01.mri' to read the anatomical data with ft_read_mri. * *The **head model created with 'bemcp'.* *Code:* *%% **Read the anatomical data* *mri = ft_read_mri('Subject01.mri');* *%% **Segment the anatomical information & triangulate the surfaces* *load segmentedmri % load from *ftp server (segmentedmri.mat). *load bnd* *%% **Create the headmodel* *cfg = [];cfg.method = 'bemcp'; vol = ft_prepare_headmodel(cfg, bnd);%% Position of the electrodesload('Face_sub.mat'); % data of participants' electrode positions electrodes = Face_sub.elec;%% Interactive alignmentcfg = [];cfg.method = 'interactive';cfg.elec = electrodes;cfg.headshape = vol.bnd(3); % scalpelec_aligned = ft_electroderealign(cfg);%% Compute leadfield:cfg = [];cfg.elec = elec_aligned;cfg.vol = vol;cfg.channel = {'EEG'};[grid] = ft_prepare_leadfield(cfg);%% Source Analysiscfg = []; cfg.method = 'dics';cfg.frequency = 10; cfg.grid = grid;cfg.vol = vol;cfg.dics.projectnoise = 'yes';cfg.dics.lambda = 0;sourceFace = ft_sourceanalysis(cfg, face_data); % face_data is obtained from the FT_FREQANALYSIS % [%% time frequency analysis || cfg = []; || cfg.channel = 'EEG'; || cfg.method = 'mtmfft'; || cfg.output = 'powandcsd'; || cfg.tapsmofrq = 4; || cfg.foi = 1:1:40; || face_data = ft_freqanalysis(cfg, Face_sub); ]* *When running DICS with these settings **I am getting the following error message:* *Error using svd Input to SVD must not contain NaN or Inf. Error in beamformer_dics>pinv (line 650) [U,S,V] = svd(A,0); Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 568) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Error in SourceAnalysis (line 133) sourceFace = ft_sourceanalysis(cfg, face_data);* * I am not able to detect, where is the problem. Another issue I have found that 'vol.mat' or 'grid.leadfield' are all NaN value. I cannot understand how to solve it. I would be very thankful if you can help me in this regard. * -- Thanks & Regards *Kasturi Barik* MS Research Scholar Audio and Bio-signal Processing Lab Department of Electronics and Electrical Engineering Indian Institute of Technology Kharagpur Mob: +91-8902400644 -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Wed May 31 13:49:35 2017 From: michelic72 at gmail.com (Cristiano Micheli) Date: Wed, 31 May 2017 13:49:35 +0200 Subject: [FieldTrip] Fwd: Source Analysis from EEG data In-Reply-To: References: Message-ID: Dear Kastouri, My hunch is that either ft_prepare_headmodel or ft_prepare_leadfield fail in generating a proper forward model for localization purposes. I would check that ft_prepare_headmodel's vol structure contains sensible data by plotting both the 'bnd' triangulated surface and the EEG electrodes together (you should be able to find instructions on the wiki) in the same image. Sometimes units (mm,cm) or coregistration (left/right swap) might influence a good outcome. Accordingly the grid.leadfield structure will not make sense because it uses the incorrect outcome of the vol structure. So if you manage to solve the 1st problem you'll kill two bird with a stone Good luck! Cris On Wed, May 31, 2017 at 12:50 PM, Kasturi Barik wrote: > *Dear all, > **I am trying to perform source localization in the frequency domain * > > *from EEG data using 'DICS' . As I have no mri data of the participants, * > > *I am using **'Subject01.mri' to read the anatomical data with ft_read_mri. * > > *The **head model created with 'bemcp'.* > > *Code:* > > *%% **Read the anatomical data* > > *mri = ft_read_mri('Subject01.mri');* > > *%% **Segment the anatomical information & triangulate the surfaces* > > *load segmentedmri % load from *ftp > server > > (segmentedmri.mat). > *load bnd* > > *%% **Create the headmodel* > > > > > > > > > > *cfg = [];cfg.method = 'bemcp'; vol = > ft_prepare_headmodel(cfg, bnd);%% Position of the > electrodesload('Face_sub.mat'); % data of > participants' electrode positions electrodes = Face_sub.elec;%% Interactive > alignmentcfg = [];cfg.method = 'interactive';cfg.elec = > electrodes;cfg.headshape = vol.bnd(3); % > scalpelec_aligned = ft_electroderealign(cfg);%% Compute leadfield:cfg > = [];cfg.elec = elec_aligned;cfg.vol = > vol;cfg.channel = {'EEG'};[grid] = ft_prepare_leadfield(cfg);%% > Source Analysiscfg = []; cfg.method = > 'dics';cfg.frequency = 10; cfg.grid = grid;cfg.vol = > vol;cfg.dics.projectnoise = 'yes';cfg.dics.lambda = 0;sourceFace = > ft_sourceanalysis(cfg, face_data); % face_data is obtained from the > FT_FREQANALYSIS % [%% time frequency analysis > || cfg = []; > || cfg.channel = 'EEG'; || > cfg.method = 'mtmfft'; || > cfg.output = 'powandcsd'; || > cfg.tapsmofrq = 4; || > cfg.foi = 1:1:40; || > face_data = ft_freqanalysis(cfg, Face_sub); ]* > > *When running DICS with these settings **I am getting the following error message:* > > > *Error using svd > Input to SVD must not contain NaN or Inf. > > Error in beamformer_dics>pinv (line 650) > [U,S,V] = svd(A,0); > > Error in beamformer_dics (line 339) > filt = pinv(lf' * invCf * lf) * lf' * invCf; > % Gross eqn. 3, use PINV/SVD to cover rank > deficient leadfield > > Error in ft_sourceanalysis (line 568) > dip(i) = beamformer_dics(grid, sens, vol, [], > squeeze(Cf(i,:,:)), optarg{:}); > > Error in SourceAnalysis (line 133) > sourceFace = ft_sourceanalysis(cfg, face_data);* > > > * I am not able to detect, where is the problem. Another issue I have found that 'vol.mat' or 'grid.leadfield' are all NaN value. I cannot understand how to solve it. I would be very thankful if you can help me in this regard. * > > > > > > -- > Thanks & Regards > > *Kasturi Barik* > > MS Research Scholar > Audio and Bio-signal Processing Lab > Department of Electronics and Electrical Engineering > Indian Institute of Technology Kharagpur > Mob: +91-8902400644 <+91%2089024%2000644> > > _______________________________________________ > 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 roycox.roycox at gmail.com Wed May 31 20:57:47 2017 From: roycox.roycox at gmail.com (Roy Cox) Date: Wed, 31 May 2017 14:57:47 -0400 Subject: [FieldTrip] cluster statistics on subset of channels Message-ID: hello, Does anyone know if it's possible to run ft_freqstatistics on only a subset of channels? Per my hypothesis, I'm only interested in the posterior half of the scalp. I know I could remove the channels entirely from the data, but for plotting purposes I'd like to retain the full set of data, and it would be cumbersome to stitch data and clusters back together. Alternatively, I could change the channel neighborhood structure for the frontal channels such that they don't enter the cluster formation procedure at all, but I'm not sure if this is valid. Maybe ft_freqstatistics already supports channel selection? Can't seem to find it in the documentation or tutorials, though. Thanks for any insights, Roy -------------- next part -------------- An HTML attachment was scrubbed... URL: From elmeri.syrjanen at gmail.com Wed May 31 21:24:07 2017 From: elmeri.syrjanen at gmail.com (=?UTF-8?Q?Elmeri_Syrj=C3=A4nen?=) Date: Wed, 31 May 2017 21:24:07 +0200 Subject: [FieldTrip] cluster statistics on subset of channels In-Reply-To: References: Message-ID: Hi Roy, I have pasted the relevant section from http://www.fieldtriptoolbox.org/reference/ft_freqstatistics the lines that would be applicable in your situation. The configuration can contain the following options for data selection *cfg.channel = Nx1 cell-array with selection of channels (default = 'all'), see FT_CHANNELSELECTION for details* *cfg.avgoverchan = 'yes'* or 'no' (default = 'no') /elmeri On Wed, May 31, 2017 at 8:57 PM, Roy Cox wrote: > hello, > > Does anyone know if it's possible to run ft_freqstatistics on only a > subset of channels? > > Per my hypothesis, I'm only interested in the posterior half of the scalp. > > I know I could remove the channels entirely from the data, but for > plotting purposes I'd like to retain the full set of data, and it would be > cumbersome to stitch data and clusters back together. Alternatively, I > could change the channel neighborhood structure for the frontal channels > such that they don't enter the cluster formation procedure at all, but I'm > not sure if this is valid. > > Maybe ft_freqstatistics already supports channel selection? Can't seem to > find it in the documentation or tutorials, though. > > Thanks for any insights, > > Roy > > _______________________________________________ > 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 mikexcohen at gmail.com Mon May 1 11:13:57 2017 From: mikexcohen at gmail.com (Mike X Cohen) Date: Mon, 1 May 2017 11:13:57 +0200 Subject: [FieldTrip] Conference announcement: ICON XIII (Amsterdam, August 2017) Message-ID: We are happy to send a reminder for the ICON XIII conference, which will take place on 5-8 August 2017 in Amsterdam (the Netherlands). Amsterdam is an easily-accessible and progressive city. The venue is the Beurs van Berlage, located in downtown Amsterdam and one of the most beautiful conference venues in Europe! Visit the website: http://www.icon2017.org There is a very exciting line-up of keynote speakers and symposia, and there are new presentation formats including "ask-the-experts" panels and hackathons. Check out the "Program" tab at icon2017.org. Early-bird registration discount ends on May 15! The registration includes full conference attendance, lunch/snacks/coffee/tea every day, and the conference opening reception. Also note that although the official poster submission deadline is passed, we are still accepting some late poster submissions by special request. Contact us (icon2017 at icon2017.org) for details! FOLLOW US ON TWITTER For up-to-date announcements before and during the ICON meeting, follow @icon2017 (see also "Media" tab on the website). QUESTIONS ABOUT THE MEETING OR SPONSORSHIP? email icon2017 at icon2017.org http://www.icon2017.org We look forward to seeing you in beautiful Amsterdam! Mike X Cohen and Birte Forstmann -------------- next part -------------- An HTML attachment was scrubbed... URL: From christian.oreilly at epfl.ch Tue May 2 14:54:35 2017 From: christian.oreilly at epfl.ch (Christian O'Reilly) Date: Tue, 2 May 2017 14:54:35 +0200 Subject: [FieldTrip] Ordering of channels index in ft_read_data with egi_mff_v1 Message-ID: Hi, I've been trying for a while to find the source of an apparent swapping of channels in my data, and I suspect that the source of this issue comes from the ft_read_data function when it is used with egi_mff_v1. This code does not handle very well list of channel indexes that are not ordered. I am using: chanindx = [36, 224, 37, 18, 21, 109, 153, 101]; data = ft_read_data([path fileNames(iFile).name], 'headerformat', ... 'egi_mff_v1', 'dataformat', 'egi_mff_v1', ... 'header', header, ... ... #'begsample', begsample, 'endsample', endsample, ... 'chanindx', chanindx); ... and I have a strong suspicion that the 8 columns of the data matrix are ordered as if chanindx == [18, 21, 36, 37, 101, 109 153, 224] I think it has to do with ft_read_data code: for iSig = 1:length(hdr.orig.signal) % adjust chanindx to match with current signal [dum1, dum2, chanind_sig] = intersect(chanindx, find(chan2sig_ind==iSig)); if isempty(chanind_sig) % no channels requested from current signal else blockhdr = hdr.orig.signal(iSig).blockhdr; signalname = binfiles(iSig).name; %%%%%%%%%%%% ... skipping lines of codes ... %%%%%%%%%% dat{end} = dat{end}(:,begsel:endsel); end end % concat signals dat = cat(1,dat{:}); In any case, as long as this is not corrected, people using fieldtrip to read EGI MFF files should keep this in mind and order their channel indexes! Best, Christian -------------- next part -------------- An HTML attachment was scrubbed... URL: From C.vandenBoomen at uu.nl Tue May 2 16:26:00 2017 From: C.vandenBoomen at uu.nl (Boomen, C. van den (Carlijn)) Date: Tue, 2 May 2017 14:26:00 +0000 Subject: [FieldTrip] error ft_nargin Message-ID: Dear fieldtrip users, I'm using fieldtrip to analyse my ERP data. My script used to work (at least until November 2016) but now I get the following error message. I get the same error using singleplotER, which used to work before as well. Does anyone know a solution? Undefined function or variable 'ft_nargin'. Error in ft_preamble_init (line 34) if ft_nargin==0 Error in ft_preamble (line 56) evalin('caller', ['ft_preamble_' cmd]); Error in ft_timelockgrandaverage (line 71) ft_preamble init Error in ERP_script_nov2016 (line 532) granderp_ind{cond} = ft_timelockgrandaverage(cfg,EEGallsubj.incldata{cond,1:end}); I'm using a mac (10.9.5), with matlab 2014b and fieldtrip 20160105 (since some parts of the script didn't work with later versions, I hope to use this version for now) Thanks a lot! Best, Carlijn Dr. Carlijn van den Boomen | Departments of Developmental and Experimental Psychology | Utrecht University | Langeveld Building - room H066 | Heidelberglaan 1 | 3584 CS Utrecht | the Netherlands | phone: +31(30) 253 1266 | fax: +31(30) 253 4511 -------------- next part -------------- An HTML attachment was scrubbed... URL: From laetitia.lalla at inserm.fr Tue May 2 16:47:27 2017 From: laetitia.lalla at inserm.fr (laetitia.lalla at inserm.fr) Date: Tue, 02 May 2017 16:47:27 +0200 Subject: [FieldTrip] Granger-Causality in the Time Domain In-Reply-To: References: Message-ID: Dear FieldTrip community, I was looking for a way to perform Granger causality in the time domain with FieldTrip and I found this post from 2014 : "The Granger causality in ft_connectivityanalysis is always frequency-domain Granger (time-domain Granger is not implemented in FieldTrip)." We are in 2017 now, is it still the case ? If yes, could you give me some advice regarding other toolboxes than can compute time-domain Granger causality ? Thank you very much for your help. All the best, Laetitia Lalla -------------- next part -------------- An HTML attachment was scrubbed... URL: From lethuymy at live.com Tue May 2 18:24:17 2017 From: lethuymy at live.com (Thuy-My Le) Date: Tue, 2 May 2017 16:24:17 +0000 Subject: [FieldTrip] ft_spikedetection Message-ID: Hi, My name is Thuy-My. I am new to field trip. I am attempting to use ft_spikedetection on a CTF file. However, when I assign 'matlab' to my cfg.dataformat parameter, I receive an error that the format is not supported. Is this because my input file is CTF? Will it not work regardless if I change the specified dataformat parameter? I have tried all formats listed under ft_write_spike. Please let me know if there is a work around as well. Thanks, Thuy-My -------------------------------------------------------------------- Thuy-My Thi Le University of Pennsylvania School of Engineering and Applied Sciences Department of Bioengineering M.S.E. Class of 2016 -------------- next part -------------- An HTML attachment was scrubbed... URL: From schurgerlab at gmail.com Tue May 2 19:41:22 2017 From: schurgerlab at gmail.com (Schurger Lab) Date: Tue, 2 May 2017 19:41:22 +0200 Subject: [FieldTrip] Post-doctoral position in volition and self-initiated action (MEG / EEG) Message-ID: Interdisciplinary post-doctoral position in cognitive neuroscience (MEG / EEG) Brain-behavior forecasting: Neural antecedents of spontaneous self-initiated movement and the forecasting of behavior based on brain activity, studied with MEG / EEG Starting date: Fall 2017 or Spring 2018 Duration: 2 years (renewable for one additional year) The French Institute of Health and Medical Research (INSERM) invites applications for a post-doctoral position in the Cognitive Neuroimaging Group, at the NeuroSpin Research Center near Paris, France, as part of the research team of Dr. Aaron Schurger. The Schurger lab focuses on understanding how decisions are made and actions initiated spontaneously, without an external sensory cue, and how time series of neural activity can be used to forecast behavior. We pursue this research using a combination of behavioral experiments, neuroimaging, computational modeling, time-series analyses, and machine learning techniques. We are looking for applicants with experience in magnetoencephalography (MEG) experimentation and data analysis, including inverse source estimation. Experience with electroencephalography (EEG) is desirable. Applicants should have obtained a PhD in a relevant discipline prior to the starting date, have a solid working knowledge of cognitive neuroscience, and should have strong skills in the following areas: computer programming (MatLab, Python, C, C++), statistics, signal processing, FieldTrip or comparable data analysis tool Additionally, prior experience in any of the following areas is desirable: computational, mathematical, and/or neural network modeling, statistical learning / machine learning / mutivariate pattern classification, time series analysis, dynamical systems theory, scale-free dynamics, behavioral psychophysics Resources available at NeuroSpin include Siemens 3T and 7T MRI scanners; high-density EEG (EGI Inc.); Elekta NeuroMag 306-channel MEG (allowing for the simultaneous recording of EEG); eye tracking (available for MRI, MEG, and behavioral experiments); an in-house team of experts in signal processing and statistical learning; a dedicated staff handling subject recruitment, scheduling, and payment; various Nespresso devices; and proximity to Paris. Applicants should send a CV, letter of motivation (max 2 pages), and a list of three references via e-mail to schurgerlab at gmail.com. Review of applicants will begin on 15 May 2017, and will continue until the position is filled. The NeuroSpin Research Center is located on the campus of the CEA-Saclay, near Orsay, about 18 km southwest of Paris. For more information on the NeuroSpin Research Center and the Cognitive Neuroimaging Group: http://www-centre-saclay.cea.fr/fr/Visite-guidee-de-NeuroSpin http://meg-france.in2p3.fr/_lesCentres/Neurospin_en.php http://www-dsv.cea.fr/en/institutes/institute-of-biomedical-imaging-i2bm/departments/neurospin-neurospin http://www.unicog.org/pm/pmwiki.php ----------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From cornelia.quaedflieg at uni-hamburg.de Wed May 3 07:37:44 2017 From: cornelia.quaedflieg at uni-hamburg.de (cornelia.quaedflieg at uni-hamburg.de) Date: Wed, 3 May 2017 07:37:44 +0200 Subject: [FieldTrip] apply filter after ft-artefactreject Message-ID: <20170503053745.73475D206E@mailhost.uni-hamburg.de> Dear fieldtrip users, In the pre-processing, we applied a filter for the 50Hz noise (and harmonics) caused by the power supply in our MEG data. During ICA for EOG and ECG correction we noticed in some participants a 50Hz component. That is why we want to apply a bsfilter after ICA correction once more (different filter used the dft filter before). Our idea was to run ft_pre-processing on the cleaned ICA data. However, after running the ft-artefactreject you get an structure and ft_preprocessing doesn’t work with structures as input. An idea about how we could do this is appreciated. Best Dr. Conny Quaedflieg Hamburg University -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed May 3 09:31:51 2017 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 3 May 2017 09:31:51 +0200 Subject: [FieldTrip] apply filter after ft-artefactreject In-Reply-To: <20170503053745.73475D206E@mailhost.uni-hamburg.de> References: <20170503053745.73475D206E@mailhost.uni-hamburg.de> Message-ID: Dear Conny, you can call the preprocessing-options in (more or less) all subsequent functions by using cfg.preproc.XXX So, for example, in the ft_timelockanalysis, you can filter the data by using cfg.preproc.lpfilter = 'yes'; (as well as the other filter settings). However, please be careful with using multiple filters in one dataset. Good luck, Julian Am 03.05.2017 um 07:37 schrieb : > > Dear fieldtrip users, > > In the pre-processing, we applied a filter for the 50Hz noise (and harmonics) caused by the power supply in our MEG data. > During ICA for EOG and ECG correction we noticed in some participants a 50Hz component. > That is why we want to apply a bsfilter after ICA correction once more (different filter used the dft filter before). > Our idea was to run ft_pre-processing on the cleaned ICA data. However, after running the ft-artefactreject you get an structure and ft_preprocessing doesn’t work with structures as input. > > An idea about how we could do this is appreciated. > > Best > > Dr. Conny Quaedflieg > Hamburg 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 495 bytes Desc: Message signed with OpenPGP using GPGMail URL: From bruno.berberian at onera.fr Wed May 3 10:38:07 2017 From: bruno.berberian at onera.fr (Bruno Berberian) Date: Wed, 03 May 2017 10:38:07 +0200 Subject: [FieldTrip] Job opening at the french aerospace lab Message-ID: <590996EF.10200@onera.fr> COGNITIVE ENGINEERING RESEARCHER at ONERA ONERA is the French national aerospace research center. The present position is opened in the “Human-System Integration” team in Salon de Provence. The HSI team is a small (6 permanent peoples, 5 PhD students and 2 postdocs) but growing team. The HSI team is specialized in the design of innovative human-machine interface. It aims to make models of human cognition, perception, multisensory integration and action control and use these models to propose design principles and evaluation methodology. The team follows a multidisciplinary approach and the core competencies include: Cognitive Engineering, Computational Neurosciences, Cognitive Psychology, Human Factors, Electronics and Computer Science. Our collaborations include academic partners in several domains - aeronautic, cognitive science, neuro sciences and cognitive psychology, medicine but also Applied Research institute and industrial partners. You will complete and extend the team abilities. You will be a key contributor to the Human Systems Interaction research area within the HIS team. As a research scientist in Human-Machine Cognition, you’ll be tackling the scientific challenges to integrate new insights in cognitive engineering and computational neurosciences to the design of human machine interface. This involves both applied and basic science. Your primary task involves applying neurosciences knowledge, methodologies, and paradigm to the design of human-machine systems. You will be expected to conduct high-level innovative research, including the publication of research and research supervision. You will collaborate with academia to identify and answer novel research questions, performing research of factors both in isolation and as part of more ecologically valid system. You will also collaborate with industrial partner to perform more applied project. Crucially, you will contribute to initiate new funded research as well as to expand, complement, and collaborate with existing research programs. To be considered for this position, the successful candidate must possess a Ph.D. (by the start of the appointment) in Cognitive Engineering, Computational and Cognitive Neurosciences, Applied Psychology, or Human Factors. Candidates are particularly sought with research interests in one or more of the following areas: perception and multisensory integration, physiological markers of attention/vigilance, models of attention and consciousness, impact of stress and fatigue on human performance. Strong theoretical background in cognitive or computational neurosciences is mandatory. Expertise in handling and analyzing physiological data (EEG, fNIRS, ECG, ..) will be also critical. The position is anticipated to begin in mid-2017. It is a permanent position. To apply, follow this link: http://www.onera.fr/fr/rejoindre-onera/offres-emploi Regards, Berberian Bruno -- Dr Berberian Bruno ONERA The french Aerospace Lab DCSD – PSEV Base Aérienne 701 13661 Salon Air – France Tel. : +33 4 90 17 55 88 Fax : +33 4 90 17 01 09 From na.so.ir at gmail.com Wed May 3 13:20:26 2017 From: na.so.ir at gmail.com (Narjes Soltani) Date: Wed, 3 May 2017 15:50:26 +0430 Subject: [FieldTrip] Cross Frequency Coupling Message-ID: Dear fieldtrip users, Is there any implementation of different kinds of cross frequency coupling already available in fieldtrip? I would be very thankful if any one can share any example of the related coed snippets here. Thanks in advance. Best Narjes -------------- next part -------------- An HTML attachment was scrubbed... URL: From greg at think-now.com Wed May 3 20:53:25 2017 From: greg at think-now.com (GREG SIMPSON) Date: Wed, 3 May 2017 11:53:25 -0700 Subject: [FieldTrip] Post-Doctoral Positions Message-ID: Dear Colleagues - I would like to post the following announcement: *Post-Doctoral Fellow – EEG & Attention* Think Now Incorporated may be seeking 1-2 post-doctoral fellows in the fall of 2017 to work on NIMH funded projects analyzing novel EEG measures of slow fluctuations in sustained attention (10-20 seconds), including data from 400 subjects, and designing an entirely new type of EEG-based feedback system to improve sustained attention. The work will include performing sophisticated EEG data analyses and writing matlab code to create a closed loop feedback system. There is also the potential, as time permits, for exploratory research with machine learning methods to identify EEG activity patterns related to attentional states and their dynamics. We are seeking candidates with a solid background in signal processing, experience with EEG time series, and possibly modeling. We prefer self-directed individuals to take on this work. The successful candidate will work with EEG and signal processing/modeling faculty at UCB and UCLA as well as Dr. Simpson, and be able to regularly interact with other UC post-docs and graduate students. The position reports directly to Gregory V. Simpson, a cognitive neuroscientist and Chief Scientific Officer of Think Now. Think Now is located in San Francisco and is collaborating with faculty at UCB, UCLA and OHSU on these projects. Think Now is focused on creating solutions for the diagnosis and amelioration of neurological and psychiatric disorders with a focus on attention and its control. Please send your CV to jobs at think-now.com with a letter describing your prior experience with sophisticated signal (EEG) analyses and any BCI or modeling methods. Gregory V. Simpson, Ph.D. Think-Now.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From wanglinsisi at gmail.com Thu May 4 02:31:52 2017 From: wanglinsisi at gmail.com (Lin Wang) Date: Wed, 3 May 2017 20:31:52 -0400 Subject: [FieldTrip] how to show notches after plotting ERPs with ft_multiplotER Message-ID: Dear fieldtrip users, Is there a way to show the notches on the x-axis after plotting the ERPs of all channels with ft_multiplotER? I want to have an overview of the ERPs of all channels with the notches on the x-axis. I can only see the notches (i.e., the little bars on the x-axis) after I select a particular channel and view the ERP of that channel. Thanks a lot! Lin -------------- next part -------------- An HTML attachment was scrubbed... URL: From seymourr at aston.ac.uk Thu May 4 12:18:26 2017 From: seymourr at aston.ac.uk (Seymour, Robert (Research Student)) Date: Thu, 4 May 2017 10:18:26 +0000 Subject: [FieldTrip] Cross Frequency Coupling Message-ID: Hi Narjes, The current status of ft_crossfrequencyanalysis can be tracked here: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2523 . It’s not currently implemented in full yet. An alternative is the python library PACPY and associated MATLAB wrapper PACMAT https://github.com/voytekresearch/pacpy. An example of some CFC code (based on the Tort et al 2008 approach) can be found here: https://github.com/neurofractal/PAC_aliens/blob/master/calc_MI.m Good luck! Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From N.vanKlink-2 at umcutrecht.nl Thu May 4 17:05:18 2017 From: N.vanKlink-2 at umcutrecht.nl (Klink-3, N.E.C. van) Date: Thu, 4 May 2017 15:05:18 +0000 Subject: [FieldTrip] Incorrect BEM leadfields Message-ID: Dear all, I am trying SAM beamformer on EEG data, but the results I get are strange. I found out that my BEM model is probably the cause of this, because the leadfields obtained by the model look scattered, see figure. (Black dot is one dipole location, around the head are 60 EEG electrodes with leadfield value for that dipole.) This is the optimum leadfield at optimum orientation as calculated in beamformer_sam. The three original orientations look scattered as well. When I make a similar figure with concentric spheres, the leadfield looks like a dipolar field, as expected. When I make the figure for the simultaneously measured MEG, with the same BEM, the leadfield also looks good. (Probably because MEG doesn't care so much about the headmodel.) I have created my BEM with OpenMEEG (in Windows), BEMcp gives similar results. The meshes look fine to me, and changing the number of vertices to [3000 3000 3000] does not help. Does anyone have an idea what could be the problem here? Thanks in advance, Kind regards, Nicole Some code: %make headmodel cfg = []; cfg.output = {'brain' 'skull' 'scalp'}; seg = ft_volumesegment(cfg, MRI); %create mesh cfg = []; cfg.method = 'projectmesh'; cfg.numvertices = [1000 1500 3000]; cfg.tissue = {'scalp','skull','brain'}; mesh = ft_prepare_mesh(cfg,segi); % compute the subject's headmodel/volume conductor model cfg = []; cfg.method = 'openmeeg'; cfg.tissue = {'brain' 'skull' 'scalp'}; vol = ft_prepare_headmodel(cfg, mesh); vol = ft_convert_units(vol,'cm'); %create grid cfg = []; cfg.grid.pos = load([ptfile filesep pts]); % predetermined grid positions in mm cfg.grid.pos = cfg.grid.pos./10; %make unit = cm cfg.headmodel = vol; cfg.moveinward = 0.01; %check if all grid points are inside the brain grid = ft_prepare_sourcemodel(cfg); % Create leadfields hdr = ft_read_header('data.fif'); cfg = []; cfg.elec = hdr.elec; % electrode positions cfg.headmodel = vol; cfg.grid = grid; cfg.channel = {'EEG', '-EEG043', '-EEG036'}; cfg.normalize = 'column'; lf = ft_prepare_leadfield(cfg); % beamformer cfg=[]; cfg.method = 'sam'; cfg.senstype = 'EEG'; cfg.grid = lf; cfg.headmodel = vol; cfg.sam.lambda = '5%'; cfg.sam.meansphereorigin = 1; %unused but necessary to not crash the script cfg.sam.fixedori = 'robert'; source = ft_sourceanalysis(cfg, timelock); ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: EEG_BEM_leadfields.png Type: image/png Size: 55751 bytes Desc: EEG_BEM_leadfields.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: EEG_concentricspheres_leadfields.png Type: image/png Size: 86901 bytes Desc: EEG_concentricspheres_leadfields.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MEG_BEM_leadfields.png Type: image/png Size: 46597 bytes Desc: MEG_BEM_leadfields.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: BEM_mesh.png Type: image/png Size: 164811 bytes Desc: BEM_mesh.png URL: From Alexander_Nakhnikian at hms.harvard.edu Thu May 4 20:39:24 2017 From: Alexander_Nakhnikian at hms.harvard.edu (Nakhnikian, Alexander) Date: Thu, 4 May 2017 18:39:24 +0000 Subject: [FieldTrip] Interpolation Error with Custom Lead Field Message-ID: Dear All, I'm trying to fine tune a forward model by first constraining the dipoles to the gray matter and then selecting only a subset of structures. It looks as though I need to write a custom script for this, which I have and the commented code is included below. Once I generate the lead field with this code I add it to the cfg structure for ft_sourceanalysis and proceed as usual. The error occurs when I attempt to interpolate the power to a structural MRI. ft_sourceinterpolate(cfg,sources,mri) - cfg.downsample=10; cfg.parameter='pow' - and 'mri' is FT's template structural scan. Calling ft_sourceinterpolate with sources generated using my custom forward model produces this error: Error using interpn (line 153) Wrong number of input arguments. Error in ft_sourceinterpolate>my_interpn (line 693) av(sel) = interpn(fv, ax(sel), ay(sel), az(sel), interpmethod); Error in ft_sourceinterpolate (line 535) interp.inside( sel) = my_interpn(double(functional.inside), ax(sel), ay(sel), az(sel), 'nearest', cfg.feedback); The only hint I've found is that for some reason the source structure returns for this analysis doesn't contain the field '.dim' but I added it manually. Once that's done, the setup looks identical to data returned using a automatically generated grid so I must be missing something. Thanks in advance if anyone can suggest where to look for the bug. Alexander Code: function [lf] = fT_constrainFM(cfg) %Creates a constrained forward model for source analysis in field trip. The %grid is constrained to a surface defined by two maps. One %restrains the dipoles to gray matter and the second is a list of labels corresponding to %ROIs within the GM. %Example: Constrain grey matter to cortical sites of interest. %cfg.roi = labelsNDL; %A cell array of strings with the name of each ROI %cfg.atlas = aal; %aal is a variable returned by ft_readatlas %cfg.inputcoord = 'mni'; %Choose coordinates %cfg.mri = mri; %A template MRI or subject sMRI %cfg.thres = 0.95; %Threshold for probabilistic masks %cfg.lf = C; %C is a structure with fields *.elec and *.headmodel. See %ft_prepareleadfield %[lf] = fT_contrainFM(cfg) mri = cfg.mri; cfgLF = cfg.lf; thres = cfg.thres; cfg = rmfield(cfg,{'mri','thres','lf'}); %Get the masks seg = ft_volumesegment([],mri); tissue = logical(seg.gray>=thres); roiMask = logical(ft_volumelookup(cfg,mri)); voxInds = tissue&roiMask; %dipole placement locations [rows,cols,pages] = ind2sub(size(roiMask),find(voxInds)); cfgLF.pos = zeros(length(rows),3); %adjustment vaues to move the origin rowAd = (size(roiMask,1)-1)/2; colAd = (size(roiMask,2)-1)/2; pageAd = (size(roiMask,3)-1)/2; %collect dipole positions into an Nx3 matrix for posInd = 1:length(rows) cfgLF.pos(posInd,:) = [rows(posInd)-rowAd,cols(posInd)-colAd,pages(posInd)-pageAd]'; end lf = ft_prepare_leadfield(cfgLF); Alexander Nakhnikian, Ph.D. Research Investigator VA Boston Healthcare System Instructor in Psychiatry, Harvard Medical School -------------- next part -------------- An HTML attachment was scrubbed... URL: From ido.davidesco at gmail.com Sat May 6 17:54:38 2017 From: ido.davidesco at gmail.com (Ido Davidesco) Date: Sat, 6 May 2017 11:54:38 -0400 Subject: [FieldTrip] Research Assistant Position - New York University Message-ID: The Poeppel lab at NYU’s Psychology Department is currently seeking a full-time Research Assistant for a National Science Foundation-funded project called “brain-to-brain synchrony in the classroom”. The expected start date for the position is Summer 2017. Application review will take place on a rolling basis until the position is filled. The successful candidate will work closely with the Principal Investigators (Prof. David Poeppel and Prof. Catherine Milne) to execute a complex research protocol, which involves collecting EEG data from multiple participants in a learning setting. As part of the project, we are also developing an EEG-based neuroscience curriculum for high schools. Primary responsibilities include: (1) Participant recruitment and testing; (2) experimental paradigm development; (3) management and analysis of behavioral and neural data; (4) documenting and presenting study results; (5) Project management and administration. A Bachelor's degree in Psychology, Neuroscience or other related fields, and excellent organizational, interpersonal, and communication skills are required. Other preferred qualifications include: - Prior research experience - Teaching and curriculum development experience - Computational, statistical, and technical skills (e.g. Matlab, Python, R) - Experience analyzing EEG and behavioral data Starting date: Summer 2017 Click here for more information about the project. To apply, please send your CV, a cover letter describing your interests and relevant experience, and the contact information of three references to: ido.davidesco at nyu.edu New York University is an Equal Opportunity Employer. New York University is committed to a policy of equal treatment and opportunity in every aspect of its hiring and promotion process without regard to race, color, creed, religion, sex, pregnancy or childbirth (or related medical condition), sexual orientation, partnership status, gender and/or gender identity or expression, marital, parental or familial status, caregiver status, national origin, ethnicity, alienage or citizenship status, veteran or military status, age, disability, predisposing genetic characteristics, domestic violence victim status, unemployment status, or any other legally protected basis. Women, racial and ethnic minorities, persons of minority sexual orientation or gender identity, individuals with disabilities, and veterans are encouraged to apply for vacant positions at all levels. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mehdy.dousty at gmail.com Tue May 9 03:51:24 2017 From: mehdy.dousty at gmail.com (mehdy dousty) Date: Tue, 09 May 2017 01:51:24 +0000 Subject: [FieldTrip] Parcelation source localization In-Reply-To: References: Message-ID: Hello all, I am working on source localization of HCP based on the eLoreta. I am trying to extract time series of Atlas AAL116. So firstly I interpolate the source model to AAL 116 by using: atlas = ft_read_atlas('/Desktop/EEG-1/fieldtrip-20160417/template/atlas/aal/ROI_MNI_V4.nii'); atlas = ft_convert_units(atlas,'mm'); cfg = []; cfg.interpmethod = 'nearest'; cfg.parameter = 'tissue'; individual_sourcemodel3d1 = ft_sourceinterpolate(cfg,atlas,individual_sourcemodel3d); and afterward interpolate the DATA to the parcellated source model by: cfg = []; cfg.parameter = 'pow'; cfg.keeptrials = 'yes'; source_eloreta_disc_int1 = ft_sourceinterpolate(cfg,source_eloreta,individual_sourcemodel3d1); and finally when I try to visualize the data by : cfg = []; cfg.method = 'ortho'; cfg.funparameter = 'pow'; cfg.maskparameter = 'mask'; cfg.funcolorlim = 'auto'; cfg.opacitylim = 'auto'; cfg.opacitymap = 'rampup'; cfg.atlas = atlas; ft_sourceplot(cfg,source_eloreta_disc_int1); I receive an error which says: "there is a mismatch between the coordinate system in the atlas and the coordinate system in the data, which cannot be resolved" I was wondering if anyone could possible help me to solve the issue, and also how accurate my approach is Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.papen at uni-koeln.de Tue May 9 10:44:34 2017 From: m.papen at uni-koeln.de (Michael von Papen) Date: Tue, 9 May 2017 10:44:34 +0200 Subject: [FieldTrip] 2nd CfP: Coupling & Causality in Complex Systems, Sep 25-27, Cologne, Germany Message-ID: ============================================================== 2nd CALL FOR PAPERS (Deadline: June 01, 2017) http://c3s.uni-koeln.de ============================================================== INTERNATIONAL CONFERENCE: *Coupling and Causality in Complex Systems* September 25-27, 2017, Cologne, Germany -------------------------------------------------------------- The interdisciplinary conference Coupling and Causality in Complex Systems (C3S) is hosted by the Competence Area 3: Quantitative Modeling of Complex Systems of the University of Cologne (UoC), Germany. It is organized by the Institute of Geophysics & Meteorology, UoC, the Institute of Clinical Neuroscience and Psychology, Heinrich-Heine University Düsseldorf and the Department of Cognitive Neuroscience at the Research Center Juelich. -------------------------------------------------- *Invited Speakers* Jörg Breitung - Macroeconomic Policy Institute, University of Cologne, Germany David Gross - Institute of Theoretical Physics, University of Cologne, Germany Philip Holmes - Mechanical and Aerospace Engineering / Princeton Neuroscience Institute, Princeton, USA Ankit Khambhati - Department of Bioengineering, University of Pennsylvania, USA Laura Marzetti - Department of Neuroscience, Università degli Studi "G. d'Annunzio" Chieti - Pescara Arkady Pikovsky - Institute of Physics and Astronomy, University Potsdam, Germany Michael Rosenblum - Institute of Physics and Astronomy, University Potsdam, Germany Jakob Runge - The Grantham Institute for Climate Change, Imperial College London -------------------------------------------------- *Preliminary Session Program* We will have different sessions with differing topics and each session will be opened by one of the invited speakers. Here is a preliminary version of our program: Session 1 Synchronization I Arkady Pikovsky Session 2 Synchronization II Silvia Daun Session 3 Coupled oscillators I Phil Holmes Session 4 Coupled oscillators II Michael Rosenblum Session 5 Phase coupling Laura Marzetti Session 6 Network structures Ankit Khambati Session 7 Bayesian networks David Gross Session 8 Granger causality I Jörg Breitung Session 9 Granger causality II Esther Florin Session 10 Causal network measures Jakob Runge Further topics of interest for the conference include, amongst others, research and methods development on: functional connectivity, (partial directed) coherence, network topology, graph-theoretic measures, directed graphs, nonlinear dynamics of complex systems, complex spatio-temporal systems, mutual information and transfer entropy. -------------------------------------------------------------- *Scientific Organizing Committee* Silvia Daun - Institute of Zoology, University of Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany Esther Florin - Institute of Clinical Neuroscience and Psychology, Düsseldorf, Germany Joachim Gross - Center for Cognitive Neuroimaging, Glasgow, UK Michael von Papen - Institute of Geophysics & Meteorology, Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany -------------------------------------------------------------- *Abstract* Complex systems such as the human brain, Earth’s climate and economy are characterized by a multitude of coupled processes on different spatial and temporal scales. In order to better understand the dynamics of the system at hand each scientific area has developed specific tools to identify, model and quantify these processes. The conference Coupling and Causality in Complex Systems (C3S) will present a collection of these approaches with the aim to provide scientists with new analysis strategies for their field. The conference focuses on how to characterize a complex system and on the methods for estimating and modeling of statistical coupling (e.g. network coherence, creation and modulation of small networks and local or long-range synchronization by cross frequency phase-phase and phase-amplitude coupling) and causality (e.g. Granger causality, transfer entropy). Therefore, data analysts from different study fields including neuroscience, mathematics, physics, biology, and economy will present their approaches with a particular focus on the methods they use. The aim of this conference is to foster discussions and the transdisciplinary exchange of advanced techniques, methods, and algorithms, thereby stimulating potential future collaborations. -------------------------------------------------------------- PAPER SUBMISSION AND REGISTRATION Authors are invited to submit conference abstracts with up to 400 words. Authors of exceptional abstracts will be given the opportunity to present their research in a talk. However, poster sessions will be provided with ample time for discussions. For your submission, please use the conference website c3s.uni-koeln.de. To register, please send an email with the subject "registration" to c3s-conference at uni-koeln.de. Please be sure to include your full name, your affiliation and whether you qualify as student (also PhD candidates) or not. The registration fee will cover snacks and refreshments during coffee breaks, lunch and a dinner with all participants. Early-bird registration is available until July 10 with a reduced fee of 100 EUR (50 EUR for students), after July 10 the registration fee will be 200 EUR (100 EUR for students). -------------------------------------------------------------- IMPORTANT DATES Paper Submission deadline: June 01, 2017 Author Notification: mid June, 2017 Early-bird registration: July 10, 2017 Conference: September 25-27, 2017 ============================================================== Please find the call for papers and more information at the conference website: http://c3s.uni-koeln.de. For questions regarding the conference feel free to contact us via c3s-conference at uni-koeln.de. -- ------------------------------------------ UNIVERSITY OF COLOGNE Institute of Geophysics & Meteorology Coordinator of Competence Area III: Quantitative Modeling of Complex Systems Dr. Michael von Papen Email: m.papen at uni-koeln.de http://www.uni-koeln.de/~vpapenm http://complexsystems.uni-koeln.de From andria.pelentritou at gmail.com Wed May 10 01:52:04 2017 From: andria.pelentritou at gmail.com (Andria Pelentritou) Date: Wed, 10 May 2017 09:52:04 +1000 Subject: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data Message-ID: Greetings from Melbourne! We've been using fieldtrip (v-20160801) for a while now and we are having issues when it comes to combining magnetometer and gradiometer MEG sensors types during (LCMV) beamforming for the Elekta Neuromag Triux 306-channel system. Beamforming the magnetometers or gradiometers separately on auditory evoked data works well, but we cannot successfully combine the two sensor types. We've played with the cfg.coilaccuracy variable as advised in one of the tutorials with no luck as there seem to be no obvious effects on the output. The documentation provides very little information on the topic. What strategies would you recommend when trying to combine the Neuromag 306-channel system magnetometer/gradiometer data? Many thanks in advance for your help and many more thanks for releasing such a valuable toolbox! Warm regards Andria -------------- next part -------------- An HTML attachment was scrubbed... URL: From N.vanKlink-2 at umcutrecht.nl Wed May 10 09:33:22 2017 From: N.vanKlink-2 at umcutrecht.nl (Klink-3, N.E.C. van) Date: Wed, 10 May 2017 07:33:22 +0000 Subject: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data Message-ID: Hi Andria, We have been struggling with the same problem, also using a 306-channel Neuromag system. We ended up correcting for the scale difference between magnetometer and gradiometer signals (i.e. noise 5e-15T vs 5e-13T/m). So we multiplied the signals of the magnetometers and the leadfield values of the magnetometers by a factor 100. This gave us the best result. Kind regards, Nicole Van: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] Namens Andria Pelentritou Verzonden: 10 mei 17 1:52 Aan: fieldtrip at science.ru.nl Onderwerp: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data Greetings from Melbourne! We've been using fieldtrip (v-20160801) for a while now and we are having issues when it comes to combining magnetometer and gradiometer MEG sensors types during (LCMV) beamforming for the Elekta Neuromag Triux 306-channel system. Beamforming the magnetometers or gradiometers separately on auditory evoked data works well, but we cannot successfully combine the two sensor types. We've played with the cfg.coilaccuracy variable as advised in one of the tutorials with no luck as there seem to be no obvious effects on the output. The documentation provides very little information on the topic. What strategies would you recommend when trying to combine the Neuromag 306-channel system magnetometer/gradiometer data? Many thanks in advance for your help and many more thanks for releasing such a valuable toolbox! Warm regards Andria ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.hartmann at th-ht.de Wed May 10 10:07:23 2017 From: thomas.hartmann at th-ht.de (Thomas Hartmann) Date: Wed, 10 May 2017 10:07:23 +0200 Subject: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data In-Reply-To: References: Message-ID: hi, i would suggest updating to a recent fieldtrip version. combining mags and grads has been implemented there and you basically do not need to do any extra steps. there are just these three pitfalls that you need to pay attention to because it might lead to wrong results: 1. make sure that you put in the original data. i.e. no prescaling etc. also make sure that you have not modified the .tra matrix of your grad structure. 2. always compute your own leadfield. i.e. always use ft_prepare_leadfield to compute the forward model and don't have it done by ft_sourceanalysis. i don't know if this is absolutely necessary but as the ft_prepare_leadfield step is the one in which the actual pitfalls are, i would strongly suggest you do it separately to have maximum control! 3. all the data going into ft_prepare_leadfield MUST BE in meters! i.e.: 1. the grid mus be either created directly in meters of converted to meters by using ft_convert_unit 2. the grad structure of your data must have been converted to meters. this is something you must do manually as according to my experience, fieldtrip does not take care of it. additionally, the default grad returned by ft_read_sens (and thus the one placed in your data structure) is in centimeters! so, it is a good idea to do something like this: data.grad = ft_convert_data(data.grad, 'm'); right after getting your data via ft_preprocessing! 3. if you provide your grad structure in the cfg structure, also make sure that it is in meters. the meters stuff is really extremely important!!! if your units are wrong, you are going to end up with wrong source projections and will not get an error message!!! if you see some fieldtrip output like: "converting XXX to cm", your results will be wrong! if you take care of all that, fieldtrip does the scaling automatically based on the distance between the two parts of each gradiometer. best, thomas Am 10.05.2017 um 09:33 schrieb Klink-3, N.E.C. van: > > Hi Andria, > > We have been struggling with the same problem, also using a > 306-channel Neuromag system. We ended up correcting for the scale > difference between magnetometer and gradiometer signals (i.e. noise > 5e-15T vs 5e-13T/m). So we multiplied the signals of the magnetometers > and the leadfield values of the magnetometers by a factor 100. This > gave us the best result. > > Kind regards, > > Nicole > > *Van:*fieldtrip-bounces at science.ru.nl > [mailto:fieldtrip-bounces at science.ru.nl] *Namens *Andria Pelentritou > *Verzonden:* 10 mei 17 1:52 > *Aan:* fieldtrip at science.ru.nl > *Onderwerp:* [FieldTrip] combining gradiometer/magnetometer sensors - > neuromag data > > Greetings from Melbourne! > > We've been using fieldtrip (v-20160801) for a while now and we are > having issues when it comes to combining magnetometer and gradiometer > MEG sensors types during (LCMV) beamforming for the Elekta Neuromag > Triux 306-channel system. Beamforming the magnetometers or > gradiometers separately on auditory evoked data works well, but we > cannot successfully combine the two sensor types. We've played with > the cfg.coilaccuracy variable as advised in one of the tutorials with > no luck as there seem to be no obvious effects on the output. The > documentation provides very little information on the topic. > > What strategies would you recommend when trying to combine the > Neuromag 306-channel system magnetometer/gradiometer data? > > Many thanks in advance for your help and many more thanks for > releasing such a valuable toolbox! > Warm regards > Andria > > ------------------------------------------------------------------------ > > /De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is > uitsluitend bestemd voor de geadresseerde. Indien u dit bericht > onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de > afzender direct te informeren door het bericht te retourneren. Het > Universitair Medisch Centrum Utrecht is een publiekrechtelijke > rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en > Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van > Koophandel voor Midden-Nederland onder nr. 30244197. / > > /Denk s.v.p aan het milieu voor u deze e-mail afdrukt. / > > ------------------------------------------------------------------------ > > /This message may contain confidential information and is intended > exclusively for the addressee. If you receive this message > unintentionally, please do not use the contents but notify the sender > immediately by return e-mail. University Medical Center Utrecht is a > legal person by public law and is registered at the Chamber of > Commerce for Midden-Nederland under no. 30244197. / > > /Please consider the environment before printing this e-mail. / > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Dr. Thomas Hartmann Centre for Cognitive Neuroscience FB Psychologie Universität Salzburg Hellbrunnerstraße 34/II 5020 Salzburg Tel: +43 662 8044 5109 Email: thomas.hartmann at th-ht.de "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarang at cfin.au.dk Wed May 10 10:59:39 2017 From: sarang at cfin.au.dk (Sarang S. Dalal) Date: Wed, 10 May 2017 08:59:39 +0000 Subject: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data In-Reply-To: References: Message-ID: <8076147A-E73C-419C-9F07-79B0419EA05E@cfin.au.dk> Dear Andria and Nicole, Combining sensor types (gradiometers and magnetometers, or MEG and EEG) is indeed something that is not documented, and there is not yet a unanimous agreement in the community about how to do this best. But, I can suggest one simple solution that was discussed at a recent beamformer workshop hosted by the Aston MEG Centre in February. (I believe John Mosher made the initial suggestion.) As you probably know, the covariance matrix is an essential ingredient to constructing beamformer solutions. Different sensor types will have different scales and different noise properties, which then complicates the covariance between channels of different types. So, one way around this is to zero out the ‘cross’ terms of the covariance matrix, i.e., set to 0 the elements of the covariance matrix that result from the product of a magnetometer channel and a gradiometer channel. This can be accomplished with something like the following code: timelock = ft_timelockanalysis(cfg, data); [~,megmagidx]=intersect(data.label,ft_channelselection('MEGMAG',data.label)); [~,meggradidx]=intersect(data.label,ft_channelselection('MEGGRAD',data.label)); timelock.cov(meggradidx,megmagidx)=0; timelock.cov(megmagidx,meggradidx)=0; In my experience, this allows source reconstruction using all channels, with results at least as good as analyzing the channels separately. This is not to say that is the best possible solution, but it is a simple one that should work well! Best wishes, Sarang On 10 May 2017, at 09:33, Klink-3, N.E.C. van > wrote: Hi Andria, We have been struggling with the same problem, also using a 306-channel Neuromag system. We ended up correcting for the scale difference between magnetometer and gradiometer signals (i.e. noise 5e-15T vs 5e-13T/m). So we multiplied the signals of the magnetometers and the leadfield values of the magnetometers by a factor 100. This gave us the best result. Kind regards, Nicole Van: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] Namens Andria Pelentritou Verzonden: 10 mei 17 1:52 Aan: fieldtrip at science.ru.nl Onderwerp: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data Greetings from Melbourne! We've been using fieldtrip (v-20160801) for a while now and we are having issues when it comes to combining magnetometer and gradiometer MEG sensors types during (LCMV) beamforming for the Elekta Neuromag Triux 306-channel system. Beamforming the magnetometers or gradiometers separately on auditory evoked data works well, but we cannot successfully combine the two sensor types. We've played with the cfg.coilaccuracy variable as advised in one of the tutorials with no luck as there seem to be no obvious effects on the output. The documentation provides very little information on the topic. What strategies would you recommend when trying to combine the Neuromag 306-channel system magnetometer/gradiometer data? Many thanks in advance for your help and many more thanks for releasing such a valuable toolbox! Warm regards Andria ________________________________ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ________________________________ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail. _______________________________________________ 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 maurice.goeldi at uzh.ch Wed May 10 11:24:30 2017 From: maurice.goeldi at uzh.ch (maurice.goeldi at uzh.ch) Date: Wed, 10 May 2017 11:24:30 +0200 Subject: [FieldTrip] Unwanted behavior of matlabs randomization functions? Message-ID: Dear Fieldtrippers I have just become aware of a 'feature' in matlabs randomization functions (rand, randi, randn and randperm). Every time matlab is restarted, the seed for the random number generator is reset. Therefore these functions always produce the same number sequence after a restart. This seems a very unintuitive use of these functions. I would think that people who need this reproducability should manually set a seed for their random number generator. Is this behaviour really wanted in FT? I did a quick check and ran ft_freqstatistics with montecarlo method. The stat.posdistribution is obviously different when i run it consecutive times.  However when I restart matlab I get exactly the same distributions again each time. I realize that in a standard analysis pipeline this is probably of absolutely no consequence.  But I still think it should not be that way and one should at least be aware of the fact. Even if it is not an issue for FT-analyses, this might very well be so for experimental procedures. E.g. some experimental stimuli are randomized for each subject. Then they are presented in randomized order. By the time the next subject comes in, chances are high that the computer or at least matlab has been restarted.  This subject will therefore recieve exactly the same 'randomized' list. Mostly these stimuli randomizations are checked by running the randomization script multiple times. So everything seems to work. Up to now at least I have never tested my scripts by restarting matlab after every run. And to catch this within the experiment is potentially impossible, depending on the procedure. Fortunately there is an easy fix for this. rng('shuffle');  before using the randomization function shuffles the seed for the random number generator (hopefully randomly). Even if this is not an issue for FT directly, I think many people do not know about this suboptimal (in my opinion) behaviour of the randomization functions and run into trouble. Appologies if this is an obvious and long known 'feature' to most of you. I hope it still helps some people getting strange results. Cheers Maurice --- University of Zürich Maurice Göldi, MSc Department of Psychology Biopsychology maurice.goeldi at uzh.ch -------------- next part -------------- An HTML attachment was scrubbed... URL: From dimitri.bayle at gmail.com Wed May 10 13:52:57 2017 From: dimitri.bayle at gmail.com (Dimitri Bayle) Date: Wed, 10 May 2017 13:52:57 +0200 Subject: [FieldTrip] Active versus Baseline statisitic on time-domain data Message-ID: <847a589e-b2ec-660b-90d8-7e01ae99fb0e@gmail.com> Hello, I want to do a test in time-domain data, to statistically compare each sample of an active time-windows with an average of the signal in a baseline time-windows. It work perfectly in frequency-domain data with the ft_statfun_actvsblT.m. However, when i try to apply the same test in my time-domain data (dimord = rpt_chan_time), it doesn't work and a realized that the function contain: switch cfg.dimord case 'chan_freq_time' nchan = cfg.dim(1); nfreq = cfg.dim(2); ntime = cfg.dim(3); [nsmpls,nrepl] = size(dat); nsmplsdivntime = floor(nsmpls/ntime); otherwise error('Inappropriate dimord for the statistics function STATFUN_ACTVSBLT.'); end; Is the ft_statfun_actvsblt.m only for time-frequency data? Does anyone has an other statfun function to compare active versus baseline windows in time-domain data. Thanks From v.piai.research at gmail.com Wed May 10 18:37:28 2017 From: v.piai.research at gmail.com (=?UTF-8?Q?Vit=c3=b3ria_Piai?=) Date: Wed, 10 May 2017 18:37:28 +0200 Subject: [FieldTrip] One or more output arguments not assigned during call to "read_16bit" Message-ID: <2c0a0f56-0466-3767-0e5c-f706f77e2677@gmail.com> Hi FT-ers, I'm trying to read a big .edf file (2.16GB), using a recent version, fieldtrip-20170401. I can read the header (attached, if it's of any use). However, when reading the data, I'm getting the following errors. _- If I specify begin and end sample:_ /X = ft_read_data(cfg.dataset,'begsample', 1, 'endsample', 30); /error opening file: /MaterSEEG04-17.edf One or more output arguments not assigned during call to "read_16bit". Error in read_edf>readLowLevel (line 449) buf = read_16bit(filename, offset, numwords); Error in read_edf (line 401) buf = readLowLevel(filename, offset, blocksize); % see below in subfunction Error in ft_read_data (line 683) dat = read_edf(filename, hdr, begsample, endsample, chanindx); _- If I specify channel index:_ /X = ft_read_data(cfg.dataset,'chanindx',chanindx); /Attempted to access EDF.chansel(34); index out of bounds because numel(EDF.chansel)=1. Error in read_edf (line 356) chanindx = EDF.chansel(chanindx); Error in ft_read_data (line 683) dat = read_edf(filename, hdr, begsample, endsample, chanindx);/ / I can then "fix" this error by commenting out line 356 in read_edf, which brings me back to the first error of "read_16bit". This happens on a PC and on a Mac. Something tells me the data isn't being read properly but I can't figure out why. Something with mex files maybe? I couldn't find anything similar in previous threads nor in Bugzilla, for as far as I could see. Any thoughts anyone? I have the data on Dropbox and can send the link if needed. Thanks loads, Vitoria -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hdr.mat Type: application/octet-stream Size: 67215 bytes Desc: not available URL: From a.stolk8 at gmail.com Wed May 10 18:50:34 2017 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Wed, 10 May 2017 09:50:34 -0700 Subject: [FieldTrip] One or more output arguments not assigned during call to "read_16bit" In-Reply-To: <2c0a0f56-0466-3767-0e5c-f706f77e2677@gmail.com> References: <2c0a0f56-0466-3767-0e5c-f706f77e2677@gmail.com> Message-ID: Hey Vitoria, Quick thoughts: what is cfg.dataset here? Is it '/MaterSEEG04-17.edf'? If so, please try without the '/', or specifying the full path location. Vaguely recalling here that read_16bit fails on statements such as '~', and perhaps also '/'. Hoping this was a good gamble. Best, Arjen 2017-05-10 9:37 GMT-07:00 Vitória Piai : > Hi FT-ers, > > I'm trying to read a big .edf file (2.16GB), using a recent version, > fieldtrip-20170401. > I can read the header (attached, if it's of any use). However, when > reading the data, I'm getting the following errors. > > *- If I specify begin and end sample:* > > > *X = ft_read_data(cfg.dataset,'begsample', 1, 'endsample', 30); *error > opening file: /MaterSEEG04-17.edf > One or more output arguments not assigned during call to "read_16bit". > > Error in read_edf>readLowLevel (line 449) > buf = read_16bit(filename, offset, numwords); > > Error in read_edf (line 401) > buf = readLowLevel(filename, offset, blocksize); % see below in > subfunction > > Error in ft_read_data (line 683) > dat = read_edf(filename, hdr, begsample, endsample, chanindx); > > *- If I specify channel index:* > > *X = ft_read_data(cfg.dataset,'chanindx',chanindx); *Attempted to access > EDF.chansel(34); index out of bounds because numel(EDF.chansel)=1. > > Error in read_edf (line 356) > chanindx = EDF.chansel(chanindx); > > Error in ft_read_data (line 683) > dat = read_edf(filename, hdr, begsample, endsample, chanindx); > > I can then "fix" this error by commenting out line 356 in read_edf, which > brings me back to the first error of "read_16bit". This happens on a PC and > on a Mac. Something tells me the data isn't being read properly but I can't > figure out why. Something with mex files maybe? I couldn't find anything > similar in previous threads nor in Bugzilla, for as far as I could see. > > Any thoughts anyone? I have the data on Dropbox and can send the link if > needed. > > Thanks loads, > Vitoria > > _______________________________________________ > 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 v.piai.research at gmail.com Thu May 11 08:08:46 2017 From: v.piai.research at gmail.com (=?UTF-8?Q?Vit=c3=b3ria_Piai?=) Date: Thu, 11 May 2017 08:08:46 +0200 Subject: [FieldTrip] One or more output arguments not assigned during call to "read_16bit" In-Reply-To: References: <2c0a0f56-0466-3767-0e5c-f706f77e2677@gmail.com> Message-ID: <056f91e6-4a9b-999a-3763-c1d9b372d340@gmail.com> Hey Arjen, Brilliant!! Thanks so much for the suggestion, it worked... I'm still having to comment out line 356 (chanindx = EDF.chansel;%(chanindx);), so something is going on but at least now I can work with the data! Thanks again, Vitória On 5/10/2017 6:50 PM, Arjen Stolk wrote: > Hey Vitoria, > > Quick thoughts: what is cfg.dataset here? Is it '/MaterSEEG04-17.edf'? > If so, please try without the '/', or specifying the full path > location. Vaguely recalling here that read_16bit fails on statements > such as '~', and perhaps also '/'. Hoping this was a good gamble. > > Best, > Arjen > > > > > > 2017-05-10 9:37 GMT-07:00 Vitória Piai >: > > Hi FT-ers, > > I'm trying to read a big .edf file (2.16GB), using a recent > version, fieldtrip-20170401. > I can read the header (attached, if it's of any use). However, > when reading the data, I'm getting the following errors. > > _- If I specify begin and end sample:_ > /X = ft_read_data(cfg.dataset,'begsample', 1, 'endsample', 30); > > /error opening file: /MaterSEEG04-17.edf > One or more output arguments not assigned during call to "read_16bit". > > Error in read_edf>readLowLevel (line 449) > buf = read_16bit(filename, offset, numwords); > > Error in read_edf (line 401) > buf = readLowLevel(filename, offset, blocksize); % see below > in subfunction > > Error in ft_read_data (line 683) > dat = read_edf(filename, hdr, begsample, endsample, chanindx); > > _- If I specify channel index:_ > /X = ft_read_data(cfg.dataset,'chanindx',chanindx); > /Attempted to access EDF.chansel(34); index out of bounds because > numel(EDF.chansel)=1. > > Error in read_edf (line 356) > chanindx = EDF.chansel(chanindx); > > Error in ft_read_data (line 683) > dat = read_edf(filename, hdr, begsample, endsample, chanindx);/ > / > I can then "fix" this error by commenting out line 356 in > read_edf, which brings me back to the first error of "read_16bit". > This happens on a PC and on a Mac. Something tells me the data > isn't being read properly but I can't figure out why. Something > with mex files maybe? I couldn't find anything similar in previous > threads nor in Bugzilla, for as far as I could see. > > Any thoughts anyone? I have the data on Dropbox and can send the > link if needed. > > Thanks loads, > Vitoria > > _______________________________________________ > 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 francois.tadel at mcgill.ca Thu May 11 12:26:31 2017 From: francois.tadel at mcgill.ca (=?UTF-8?Q?Fran=c3=a7ois_Tadel?=) Date: Thu, 11 May 2017 12:26:31 +0200 Subject: [FieldTrip] Correspondence channels-coils in HCP files Message-ID: <09bb7e15-f314-607c-e7e7-480f5a9d914e@mcgill.ca> Hello, I wrote a FieldTrip>Brainstorm import function based on Elekta files, and I was using the .tra matrix to get the correspondence between the channels and the coils: https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/io/in_data_fieldtrip.m#L107 I based this code on your description of the .tra field: "NxM matrix with the weight of each coil into each channel": http://www.fieldtriptoolbox.org/faq/how_are_electrodes_magnetometers_or_gradiometers_described This doesn't work with the processed 4D recordings from the HCP dataset because the .tra matrix is dense. Is this because the 4D compensation matrix is integrated in this .tra matrix? Or because there is some additional PCA/ICA projection done during the preprocessing? How do I recover the sparse .tra information that simply contains the weights channels-coils from the HCP processed files? Thanks, François -- François Tadel, MSc MEG / McConnell Brain Imaging Center / MNI / McGill University 3801 rue University, Montreal, QC H3A2B4, Canada From stefanwiens at gmail.com Thu May 11 16:17:13 2017 From: stefanwiens at gmail.com (Stefan Wiens) Date: Thu, 11 May 2017 16:17:13 +0200 Subject: [FieldTrip] reading offsets from Biosemi bdf file Message-ID: Hi! I am Stefan Wiens and am working with EEG in Stockholm, Sweden. ( people.su.se/~swiens/) I use a Cedrus Stimtracker to track visual events with a light diode and a TTL output to the Biosemi system. The onsets are save nicely in the bdf. I would also like to check duration by tracking not only onsets but also offsets. I tried the following but received a warning. event = ft_read_event(cfg.dataset, 'detectflank', 'both'); Warning: only up-going flanks are supported for Biosemi Do I understand correctly that there is not (reasonable) way to extract offsets? (I already have a work around by having a different picture at the offset of the first. This work but a direct approach with onset and offset might be better. Thanks for your input! Stefan -------------- next part -------------- An HTML attachment was scrubbed... URL: From u.pomper at ucl.ac.uk Thu May 11 19:21:42 2017 From: u.pomper at ucl.ac.uk (Pomper, Ulrich) Date: Thu, 11 May 2017 17:21:42 +0000 Subject: [FieldTrip] Rotating sensors using ft_transform_sens Message-ID: Dear Listmembers, Could someone please explain how to use ft_transform_sens in order to rotate sensors around a given axis? For example, how would the input variable 'transform' need to look like in order to perform a 90 degree rotation around the z-axis? Many thanks, Ulrich -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Fri May 12 09:44:01 2017 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 12 May 2017 09:44:01 +0200 Subject: [FieldTrip] Rotating sensors using ft_transform_sens In-Reply-To: References: Message-ID: Dear Ulrich, could you use ft_electroderealign with the interactive-option instead? Here you have an graphic interface that lets you rotate the electrodes in all directions to match your headshape. ft_transform_sens is used in this function, so the output should be the same. Moreover, if you check the code of ft_electroderealign, it can give you a hint to what the transform-matrix should look like: I think it should be a 3x3-matrix with scale, transform and rotate xyz-vectors. I hope this helps, Julian Am 11.05.2017 um 19:21 schrieb Pomper, Ulrich: > Dear Listmembers, > > Could someone please explain how to use ft_transform_sens in order to rotate sensors around a given axis? > For example, how would the input variable 'transform' need to look like in order to perform a 90 degree rotation around the z-axis? > > Many thanks, > Ulrich > > _______________________________________________ > 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: signature.asc Type: application/pgp-signature Size: 495 bytes Desc: Message signed with OpenPGP using GPGMail URL: From cornelia.quaedflieg at uni-hamburg.de Fri May 12 23:47:08 2017 From: cornelia.quaedflieg at uni-hamburg.de (cornelia.quaedflieg at uni-hamburg.de) Date: Fri, 12 May 2017 23:47:08 +0200 Subject: [FieldTrip] cluster based permutation tests - grandaverage - grad structure Message-ID: <20170512214709.BDD13F2D44@mailhost.uni-hamburg.de> Dear fieldtrip users,    we are having troubles running the cluster based permutation tests for MEG data analysis. We tried to run ft_freqstatistics for previously calculated grandaverages over subjects in two conditions. However, we are not sure how to specify cfg.neighbours. The grandaverage datasets in the fieldtrip tutorial contain a gradiometer structure, which is probably used to prepare neighbouring channels. When we run ft_freqgrandaverages on our data, this grad structure disappears because it cannot be averaged over subjects. Thus, we were wondering if there is a way to keep the gradiometer information in the averaged data or to append an example grad structure later on?   We appreciate any suggestions on that matter. Thank you in advance!   Best Dr Conny Quaedflieg & Hanna Stoffregen Hamburg University -------------- next part -------------- An HTML attachment was scrubbed... URL: From mailtome.2113 at gmail.com Sat May 13 16:18:27 2017 From: mailtome.2113 at gmail.com (Arti Abhishek) Date: Sun, 14 May 2017 00:18:27 +1000 Subject: [FieldTrip] Alternatives to cluster based permutation test Message-ID: Dear list, I was wondering whether it is appropriate to use cluster permutation tests on 32 channel ERP data. I am working on visual ERP response to text stimuli, and since there are only few electrodes I am expecting a focal effect (on P7 and P8). I was wondering whether it is appropriate to use cluster statistics here. If not, what test do you suggest? Thank you, Arti -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Sat May 13 18:10:08 2017 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Sat, 13 May 2017 17:10:08 +0100 Subject: [FieldTrip] randsample.m from fieldtrip toolbox does not work properly In-Reply-To: <3768651157128871.WA.violinist811googlemail.com@www.jiscmail.ac.uk> References: <3768651157128871.WA.violinist811googlemail.com@www.jiscmail.ac.uk> Message-ID: Dear Yuan-hao, I'm not sure whether what you found is a bug but the best way to report it is via http://bugzilla.fieldtriptoolbox.org . I also CC your e-mail to Fieldtrip mailing list. Best, Vladimir On Fri, May 12, 2017 at 9:18 PM, Yuan-hao Wu <00000a54691459fb-dmarc- request at jiscmail.ac.uk> wrote: > Dear all, > > I just want to inform you that the randsample.m function that is included > in the spm12/fieldtrip toolbox does not work properly. > It only draw samples WITH replacement. > > Best, > Yuan-hao > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanwiens at gmail.com Sun May 14 10:31:34 2017 From: stefanwiens at gmail.com (Stefan Wiens) Date: Sun, 14 May 2017 10:31:34 +0200 Subject: [FieldTrip] bug in ft_rejectvisual()? Message-ID: Hi! I downloaded a new version of ft last week (fieldtrip-20170511). I run these simple commands: cfg = []; cfg.layout = 'biosemi64.lay'; cfg.metric = 'range'; cfg.latency = [-.1 .6]; ft_rejectvisual(cfg, data); The plot seems to work, but when I want to plot a specific trial ("Plot trial", to the left of the quit button), ft does not plot the trial number I entered; instead, it plots the LAST trial. The matlab output actually states that whereas the figure title states the trial number that I entered. I remember that this worked well before, so maybe I am doing something wrong? Best Stefan Wiens people.su.se/~swiens/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From u.pomper at ucl.ac.uk Sun May 14 13:36:13 2017 From: u.pomper at ucl.ac.uk (Pomper, Ulrich) Date: Sun, 14 May 2017 11:36:13 +0000 Subject: [FieldTrip] Rotating sensors using ft_transform_sens In-Reply-To: References: , Message-ID: Dear Julian, Thanks a lot for your help! >From looking into the function as you suggested, it seems the transformation matrix is actually 4 dimensional, with one extra dimension for scaling. I managed to rotate the sensors but they are still quite far away from the headvolume. I tried using ft_sensorrealign (MEG equivalent of ft_electroderealign) but am getting an errormessage Undefined function or variable "pnt". Error in channelposition (line 327) pnt = pnt(sel2, :); which I haven't had time to follow up yet. I will post more once I have looked into it. Anyway, thanks again for the help so far. Cheers, Ulrich ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil Sent: 12 May 2017 08:44 To: FieldTrip discussion list Subject: Re: [FieldTrip] Rotating sensors using ft_transform_sens Dear Ulrich, could you use ft_electroderealign with the interactive-option instead? Here you have an graphic interface that lets you rotate the electrodes in all directions to match your headshape. ft_transform_sens is used in this function, so the output should be the same. Moreover, if you check the code of ft_electroderealign, it can give you a hint to what the transform-matrix should look like: I think it should be a 3x3-matrix with scale, transform and rotate xyz-vectors. I hope this helps, Julian Am 11.05.2017 um 19:21 schrieb Pomper, Ulrich: Dear Listmembers, Could someone please explain how to use ft_transform_sens in order to rotate sensors around a given axis? For example, how would the input variable 'transform' need to look like in order to perform a 90 degree rotation around the z-axis? Many thanks, Ulrich _______________________________________________ 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 laxmi.shaw22 at gmail.com Mon May 15 13:17:42 2017 From: laxmi.shaw22 at gmail.com (Laxmi Shaw) Date: Mon, 15 May 2017 16:47:42 +0530 Subject: [FieldTrip] fieldtrip Digest, Vol 78, Issue 13 In-Reply-To: References: Message-ID: Dear Fieldtrip Users, I am using fieldtrip plot function, and it was running fine. Last two days back the code is showing some error, and I am not able to figure it out. Could you please help me in this regard. I have attached the screen shot of that error window. Please find the screenshot. Thanks and Regards[image: Inline image 1] On Mon, May 15, 2017 at 3:30 PM, wrote: > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: Rotating sensors using ft_transform_sens (Pomper, Ulrich) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 14 May 2017 11:36:13 +0000 > From: "Pomper, Ulrich" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Rotating sensors using ft_transform_sens > Message-ID: > eurprd01.prod.exchangelabs.com> > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Julian, > > > Thanks a lot for your help! > > >From looking into the function as you suggested, it seems the > transformation matrix is actually 4 dimensional, with one extra dimension > for scaling. I managed to rotate the sensors but they are still quite far > away from the headvolume. > > I tried using ft_sensorrealign (MEG equivalent of ft_electroderealign) but > am getting an errormessage > > > Undefined function or variable "pnt". > > Error in channelposition (line 327) > pnt = pnt(sel2, :); > > > > which I haven't had time to follow up yet. I will post more once I have > looked into it. > > Anyway, thanks again for the help so far. > > > Cheers, > > Ulrich > > > > ________________________________ > From: fieldtrip-bounces at science.ru.nl > on behalf of Julian Keil > Sent: 12 May 2017 08:44 > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Rotating sensors using ft_transform_sens > > Dear Ulrich, > > could you use ft_electroderealign with the interactive-option instead? > Here you have an graphic interface that lets you rotate the electrodes in > all directions to match your headshape. > ft_transform_sens is used in this function, so the output should be the > same. > Moreover, if you check the code of ft_electroderealign, it can give you a > hint to what the transform-matrix should look like: I think it should be a > 3x3-matrix with scale, transform and rotate xyz-vectors. > > I hope this helps, > > Julian > > > Am 11.05.2017 um 19:21 schrieb Pomper, Ulrich: > > Dear Listmembers, > > Could someone please explain how to use ft_transform_sens in order to > rotate sensors around a given axis? > For example, how would the input variable 'transform' need to look like in > order to perform a 90 degree rotation around the z-axis? > > Many thanks, > Ulrich > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170514/c4c91a75/attachment-0001.html> > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 78, Issue 13 > ***************************************** > -- Laxmi Shaw Research Scholar(PhD) IIT Kharagpur West Bengal Ph no-08388837821 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Error_fig.png Type: image/png Size: 130728 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Error_fig.png Type: image/png Size: 130728 bytes Desc: not available URL: From david.m.groppe at gmail.com Mon May 15 16:24:20 2017 From: david.m.groppe at gmail.com (David Groppe) Date: Mon, 15 May 2017 10:24:20 -0400 Subject: [FieldTrip] Alternatives to cluster based permutation test In-Reply-To: References: Message-ID: Hi Arti, For very focal effects, the tmax permutation test and Benjamini & Hochberg false discovery rate (FDR) control algorithm are more powerful than cluster-based permutation tests: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4059014/ cheers, -David On Sat, May 13, 2017 at 10:18 AM, Arti Abhishek wrote: > Dear list, > > I was wondering whether it is appropriate to use cluster permutation tests > on 32 channel ERP data. I am working on visual ERP response to text > stimuli, and since there are only few electrodes I am expecting a focal > effect (on P7 and P8). I was wondering whether it is appropriate to use > cluster statistics here. If not, what test do you suggest? > > Thank you, > 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 HEROBINSON at augusta.edu Mon May 15 16:30:37 2017 From: HEROBINSON at augusta.edu (Robinson, Heath) Date: Mon, 15 May 2017 14:30:37 +0000 Subject: [FieldTrip] [EXTERNAL] Re: Alternatives to cluster based permutation test In-Reply-To: References: Message-ID: I tried to save my profile and it is sying that I am logged in as Anonymous. I logged out and logged back in and it did the same thing. From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of David Groppe Sent: Monday, May 15, 2017 10:24 AM To: FieldTrip discussion list Subject: [EXTERNAL] Re: [FieldTrip] Alternatives to cluster based permutation test This is an external email. Use caution responding, opening attachments and following links. Hi Arti, For very focal effects, the tmax permutation test and Benjamini & Hochberg false discovery rate (FDR) control algorithm are more powerful than cluster-based permutation tests: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4059014/ cheers, -David On Sat, May 13, 2017 at 10:18 AM, Arti Abhishek > wrote: Dear list, I was wondering whether it is appropriate to use cluster permutation tests on 32 channel ERP data. I am working on visual ERP response to text stimuli, and since there are only few electrodes I am expecting a focal effect (on P7 and P8). I was wondering whether it is appropriate to use cluster statistics here. If not, what test do you suggest? Thank you, 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 elam4hcp at gmail.com Mon May 15 19:37:09 2017 From: elam4hcp at gmail.com (Jennifer Elam) Date: Mon, 15 May 2017 12:37:09 -0500 Subject: [FieldTrip] Reminder to Register for HCP Course 2017 Message-ID: Only a few spaces remain for the *2017 HCP Course: "Exploring the Human Connectome"*. For more info and to register: https://store.humanconnectome. org/courses/2017/exploring-the-human-connectome.php Don't forget to also reserve your accommodation for the course by May 17, 2017 to be sure of securing a room on the UBC campus in the HCP Course room block. Before or after May 17, 2017, please use this link to make a reservation: https://reserve.ubcconferences.com/vancouver/availability.asp?hotelCode=%2A&startDate=06%2F18%2F2017&endDate=06%2F23%2F2017&adults=1&children=&rooms=1&requesttype=invBlockCode&code=G170618A HCP Course 2017 will be held June 19-23 (week before OHBM) at the Djavad Mowafagian Centre for Brain Health at University of British Columbia (UBC) in Vancouver, BC, Canada. The 5-day intensive course of lectures and hands-on practicals is a great opportunity to learn directly from HCP investigators about using HCP data, acquisition, processing methods, and software tools in your own studies. If you have any questions, please contact us at: hcpcourse at humanconnectome. org We look forward to seeing you in Vancouver! Best, 2017 HCP Course Staff -- 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 laxmi.shaw22 at gmail.com Tue May 16 05:48:00 2017 From: laxmi.shaw22 at gmail.com (Laxmi Shaw) Date: Tue, 16 May 2017 09:18:00 +0530 Subject: [FieldTrip] Some plotting error Message-ID: * Dear community, **I have a data such that every channel has 1 value that is result of some **calculation(I mean I have 14 channel thus a data vector of length14).I want **to plot map of head how? every channel has a color corresponding its? **value... **I tried using? ft_topoplotER to assess my data and I made the true layout ** but when I want to use ft_topoplotER receive the following error message:? **Subscript indices must either be real positive integers or logicals. ** Error in topoplot_common (line 79) ** data = varargin{indx}; **Error in ft_topoplotER (line 169) ** cfg = topoplot_common(cfg, varargin{:}); ** Error in top (line 19) **figure; ft_topoplotER(cfg,data); colorbar;? ** Could you please help to fix this problem How to remove this error.* *Thanks and Regards * Laxmi Shaw Research Scholar(PhD) IIT Kharagpur West Bengal Ph no-08388837821 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Patrick.Rollo at uth.tmc.edu Tue May 16 18:24:24 2017 From: Patrick.Rollo at uth.tmc.edu (Rollo, Patrick) Date: Tue, 16 May 2017 16:24:24 +0000 Subject: [FieldTrip] Job posting on FieldTrip message board Message-ID: FieldTrip, I have a job posting that I would like to make on this message board, our lab, Tandon Lab, has posted in the past. The advert is attached here. Please let me know if you have any questions, Thank you, Patrick Rollo -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Postdocs_U01_updated 5:17.pdf Type: application/pdf Size: 236167 bytes Desc: Postdocs_U01_updated 5:17.pdf URL: From stephen.whitmarsh at gmail.com Wed May 17 16:46:53 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Wed, 17 May 2017 16:46:53 +0200 Subject: [FieldTrip] source pos dimensions ft_sourcestatistics Message-ID: Hi there, After beamformer sourceanalysis I end up with datastructures looking like: struct with fields: freq: 10.5000 cfg: [1×1 struct] pos: [2982×3 double] pow: [2982×1 double] inside: [2982×1 logical] powdimord: 'pos' The .inside field is created by ft_selectdata used to average across frequencies, and contains all 1s. Running sourceanalysis with this data trows the following error: Error using spm_bwlabel spm_bwlabel: CONN must be 6, 18 or 26 Error in clusterstat (line 222) [negclusobs, negnum] = spm_bwlabel(tmp, 2*numdims); Error in ft_statistics_montecarlo (line 347) [stat, cfg] = clusterstat(cfg, statrand, statobs); Error in ft_sourcestatistics (line 205) [stat, cfg] = statmethod(cfg, dat, design); *222 * [negclusobs, negnum] = spm_bwlabel(tmp, 2*numdims); I think this results because of a wrong estimate of the dimensionality, resulting from the fact that the data is represented in an array rather than a 3-dimensional matrix, which it seems to expect. I think therefor that I might need to convert my data back into a 3-d representation, i..e not a sparse but full representation. I have tried using ft_source2full, but that is not straightforward as I only have inside voxels/positions. In other words, I would need to do exactly the same as ft_source_statistics seems to want to do with spm_bwlabel. So I guess I might just have put FieldTrip on the wrong leg, to use a Dutch expression. Any suggestions? Best, Stephen -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu May 18 21:35:38 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 18 May 2017 19:35:38 +0000 Subject: [FieldTrip] source pos dimensions ft_sourcestatistics In-Reply-To: References: Message-ID: <4EF37F95-710B-4EAC-8FE5-786964346094@donders.ru.nl> Hi Stephen, source2full and source2sparse are probably quite outdated, and do not seem to work well anymore with the latest type of source-level data structures. Most relevantly, the inside field these days is by default a boolean vector of size nposx1, whereas once upon a time the inside and outside fields together contained the indices of the dipole positions, indicating which positions are on the in-/outside. Do you need the source2sparse step to begin with? Best, JM On 17 May 2017, at 16:46, Stephen Whitmarsh > wrote: Hi there, After beamformer sourceanalysis I end up with datastructures looking like: struct with fields: freq: 10.5000 cfg: [1×1 struct] pos: [2982×3 double] pow: [2982×1 double] inside: [2982×1 logical] powdimord: 'pos' The .inside field is created by ft_selectdata used to average across frequencies, and contains all 1s. Running sourceanalysis with this data trows the following error: Error using spm_bwlabel spm_bwlabel: CONN must be 6, 18 or 26 Error in clusterstat (line 222) [negclusobs, negnum] = spm_bwlabel(tmp, 2*numdims); Error in ft_statistics_montecarlo (line 347) [stat, cfg] = clusterstat(cfg, statrand, statobs); Error in ft_sourcestatistics (line 205) [stat, cfg] = statmethod(cfg, dat, design); 222 [negclusobs, negnum] = spm_bwlabel(tmp, 2*numdims); I think this results because of a wrong estimate of the dimensionality, resulting from the fact that the data is represented in an array rather than a 3-dimensional matrix, which it seems to expect. I think therefor that I might need to convert my data back into a 3-d representation, i..e not a sparse but full representation. I have tried using ft_source2full, but that is not straightforward as I only have inside voxels/positions. In other words, I would need to do exactly the same as ft_source_statistics seems to want to do with spm_bwlabel. So I guess I might just have put FieldTrip on the wrong leg, to use a Dutch expression. Any suggestions? Best, Stephen _______________________________________________ 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 D.C.W.Klooster at tue.nl Thu May 18 22:10:20 2017 From: D.C.W.Klooster at tue.nl (Klooster, D.C.W.) Date: Thu, 18 May 2017 20:10:20 +0000 Subject: [FieldTrip] Error loreta2fieldtrip Message-ID: <94D6E99297013F46990EEBA320449F617D02D71A@xserver30b.campus.tue.nl> Dear fieldtrip users, Hopefully this is an easy to solve issue for some of you... If I run loreta2fieldtrip I get an accute error that ft_preamble_callinfo is not known. Indeed, I can not find this anywhere within my fieldtrip folder. Am I doing something wrong or do I really need these files (same holds for ft_postamble_callinfo). If so, can anybody provide me the files? Thank you! Best regards, Debby -------------- next part -------------- An HTML attachment was scrubbed... URL: From seymourr at aston.ac.uk Fri May 19 08:46:08 2017 From: seymourr at aston.ac.uk (Seymour, Robert (Research Student)) Date: Fri, 19 May 2017 06:46:08 +0000 Subject: [FieldTrip] Inter-trial Coherence Stats Message-ID: Dear Fieldtrippers, I am trying to statistically evaluate inter-trial coherence on a virtual electrode, comparing an active to baseline period. However I get the following error when using 'diff_ITC' and ft_freqstatistics: Subscripted assignment dimension mismatch. Error in ft_freqstatistics (line 141) dat(:,i) = tmp(:); I can't seem to figure out what's going wrong... (code below). Has anyone else come across this error? Many thanks, Robert %% Script to calculate inter-trial coherence for the alien clicktrain data subject = sort({'RS','DB','MP','GR','DS','EC','VS','LA','AE','SY','GW',... 'SW','DK','LH','KM','FL','AN'}); grandavgA = zeros(1,length(subject)); grandavgB = zeros(1,length(subject)); for i = 1:length(subject) load(['D:\Pilot\' subject{i} '\auditory\sourceloc\VE_A1_RH.mat']); cfg = []; cfg.foi = [30:1:80]; cfg.method = 'mtmconvol'; cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; cfg.tapsmofrq = ones(length(cfg.foi),1).*8; cfg.toi = 0:0.01:1.5; cfg.output = 'fourier'; freq_post = (ft_freqanalysis(cfg, VE_A1_RH)); freq_post.fourierspctrm = (freq_post.fourierspctrm); grandavgA{i} = freq_post; cfg.toi = -1.5:0.01:0; freq_pre = (ft_freqanalysis(cfg, VE_A1_RH)); freq_pre.fourierspctrm = (freq_pre.fourierspctrm); grandavgB{i} = freq_pre; end cfg = []; cfg.latency = [0 1.5]; cfg.parameter = 'fourierspctrm'; cfg.frequency = [30 80]; cfg.method = 'montecarlo'; cfg.statistic = 'diff_ITC' cfg.clusterstatistic = 'maxsum'; cfg.tail = 0; cfg.alpha = 0.05; cfg.numrandomization = 1000; % Create design matrix based on specific number of trials from each % participant nsubj=numel(grandavgA); cfg.design(1,:) = [1:nsubj 1:nsubj]; cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2]; cfg.uvar = 1; % row of design matrix that contains unit variable (in this case: subjects) cfg.ivar = 2; % row of design matrix that contains independent variable (the conditions) [stat] = ft_freqstatistics(cfg, grandavgA{:}, grandavgB{:}); -------------- next part -------------- An HTML attachment was scrubbed... URL: From CXK699 at student.bham.ac.uk Fri May 19 09:36:43 2017 From: CXK699 at student.bham.ac.uk (Casper Kerren) Date: Fri, 19 May 2017 07:36:43 +0000 Subject: [FieldTrip] Inter-trial Coherence Stats In-Reply-To: References: Message-ID: <817B246999EC6E49AFEEDFCEC604EED83C5111E7@EX11.adf.bham.ac.uk> Dear Robert, Not sure whether I will give an appropriate answer to your question, but it seems like Fieldtrip doesn't like .fourierspctrm, and you could change it to powerspctrm yourself. Like this: For each participant run the ft_freqanalysis with your specified parameters. Get the output 'freq' and then a = freq.fourierspctrm; tmpli = abs(mean(a./abs(a),1)); % "manually" compute PLI freq.powspctrm = squeeze(tmpli); freq.dimord = 'chan_freq_time'; freq = rmfield(freq, 'fourierspctrm'); % remove field "fourierspctrm" because it confuses Fieldtrip freq = rmfield(freq, 'trialinfo'); % trialinfo no longer valid Of course, when you later run statistics use cfg.parameter = 'powspctrm' If this wasn't what you were looking for, let me know. Kind regards, Casper From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Seymour, Robert (Research Student) Sent: 19 May 2017 07:46 To: fieldtrip at science.ru.nl Subject: [FieldTrip] Inter-trial Coherence Stats Dear Fieldtrippers, I am trying to statistically evaluate inter-trial coherence on a virtual electrode, comparing an active to baseline period. However I get the following error when using 'diff_ITC' and ft_freqstatistics: Subscripted assignment dimension mismatch. Error in ft_freqstatistics (line 141) dat(:,i) = tmp(:); I can't seem to figure out what's going wrong... (code below). Has anyone else come across this error? Many thanks, Robert %% Script to calculate inter-trial coherence for the alien clicktrain data subject = sort({'RS','DB','MP','GR','DS','EC','VS','LA','AE','SY','GW',... 'SW','DK','LH','KM','FL','AN'}); grandavgA = zeros(1,length(subject)); grandavgB = zeros(1,length(subject)); for i = 1:length(subject) load(['D:\Pilot\' subject{i} '\auditory\sourceloc\VE_A1_RH.mat']); cfg = []; cfg.foi = [30:1:80]; cfg.method = 'mtmconvol'; cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; cfg.tapsmofrq = ones(length(cfg.foi),1).*8; cfg.toi = 0:0.01:1.5; cfg.output = 'fourier'; freq_post = (ft_freqanalysis(cfg, VE_A1_RH)); freq_post.fourierspctrm = (freq_post.fourierspctrm); grandavgA{i} = freq_post; cfg.toi = -1.5:0.01:0; freq_pre = (ft_freqanalysis(cfg, VE_A1_RH)); freq_pre.fourierspctrm = (freq_pre.fourierspctrm); grandavgB{i} = freq_pre; end cfg = []; cfg.latency = [0 1.5]; cfg.parameter = 'fourierspctrm'; cfg.frequency = [30 80]; cfg.method = 'montecarlo'; cfg.statistic = 'diff_ITC' cfg.clusterstatistic = 'maxsum'; cfg.tail = 0; cfg.alpha = 0.05; cfg.numrandomization = 1000; % Create design matrix based on specific number of trials from each % participant nsubj=numel(grandavgA); cfg.design(1,:) = [1:nsubj 1:nsubj]; cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2]; cfg.uvar = 1; % row of design matrix that contains unit variable (in this case: subjects) cfg.ivar = 2; % row of design matrix that contains independent variable (the conditions) [stat] = ft_freqstatistics(cfg, grandavgA{:}, grandavgB{:}); -------------- next part -------------- An HTML attachment was scrubbed... URL: From Simon.VanEyndhoven at esat.kuleuven.be Fri May 19 13:51:10 2017 From: Simon.VanEyndhoven at esat.kuleuven.be (Simon Van Eyndhoven) Date: Fri, 19 May 2017 13:51:10 +0200 Subject: [FieldTrip] Interpretation of Granger spectrum and link with directed coherence Message-ID: <99d3059295300fb8c2d53e4f1ae6f145@esat.kuleuven.be> Dear FieldTrip community, As a novice in EEG connectivity analysis, I am trying to reproduce and understand the connectivity tutorial of the website (http://www.fieldtriptoolbox.org/tutorial/connectivity). I was hoping that someone could shed light on the computation of the Granger frequency spectrum: cfg = []; cfg.method = 'granger'; granger = ft_connectivityanalysis(cfg, mfreq); More specifically, I would like to know which computations are done to obtain the values in granger.grangerspctrm. (Unfortunately, inspecting the paper by Brovelli et al. PNAS (2004), as indicated in ft_connectivity_granger did not clear this up...) Moreover, I wonder what the relationship is between the Granger spectrum and other metrics such as (partial) directed coherence (DC / PDC) and directed transfer function (DTF), which also provide connectivity information in the form channels x channels x frequencies? In the appendix in Van Mierlo et al., "Functional brain connectivity from EEG in epilepsy: Seizure prediction and epileptogenic focus localization" and in Baccala and Sameshima, "Partial directed coherence: a new concept in neural structure determination", it is explained that both DC and DTF are computed using the transfer function matrix H(f), while PDC is computed using the A(f) matrix. Is this the reason why only PDC is termed 'partial', and the others not (even though they are also computed in a multivariate framework, i.e. taking all available variables into account)? Although I could not find an answer to my questions in the mailing archives, I apologize if this question has been asked before. Thank you in advance for your help! Best regards, Simon From jan.schoffelen at donders.ru.nl Fri May 19 14:12:48 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 19 May 2017 12:12:48 +0000 Subject: [FieldTrip] Interpretation of Granger spectrum and link with directed coherence In-Reply-To: <99d3059295300fb8c2d53e4f1ae6f145@esat.kuleuven.be> References: <99d3059295300fb8c2d53e4f1ae6f145@esat.kuleuven.be> Message-ID: <0E539AF5-0DC8-4D03-A4EB-4B0ED7255E6D@donders.ru.nl> Hi Simon, You may want to check the ‘connectivity’ section in the following link: http://www.fieldtriptoolbox.org/references_to_implemented_methods It contains links to papers that might be relevant for you. I’d start from the first one, sorry for the shameless self-promotion. Best, Jan-Mathijs > On 19 May 2017, at 13:51, Simon Van Eyndhoven wrote: > > Dear FieldTrip community, > > As a novice in EEG connectivity analysis, I am trying to reproduce and understand the connectivity tutorial of the website (http://www.fieldtriptoolbox.org/tutorial/connectivity). > > I was hoping that someone could shed light on the computation of the Granger frequency spectrum: > > cfg = []; > cfg.method = 'granger'; > granger = ft_connectivityanalysis(cfg, mfreq); > > More specifically, I would like to know which computations are done to obtain the values in granger.grangerspctrm. (Unfortunately, inspecting the paper by Brovelli et al. PNAS (2004), as indicated in ft_connectivity_granger did not clear this up...) > > Moreover, I wonder what the relationship is between the Granger spectrum and other metrics such as (partial) directed coherence (DC / PDC) and directed transfer function (DTF), which also provide connectivity information in the form channels x channels x frequencies? > > In the appendix in Van Mierlo et al., "Functional brain connectivity from EEG in epilepsy: Seizure prediction and epileptogenic focus localization" and in Baccala and Sameshima, "Partial directed coherence: a new concept in neural structure determination", it is explained that both DC and DTF are computed using the transfer function matrix H(f), while PDC is computed using the A(f) matrix. Is this the reason why only PDC is termed 'partial', and the others not (even though they are also computed in a multivariate framework, i.e. taking all available variables into account)? > > Although I could not find an answer to my questions in the mailing archives, I apologize if this question has been asked before. > > Thank you in advance for your help! > Best regards, > > Simon > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From laxmi.shaw22 at gmail.com Fri May 19 16:56:51 2017 From: laxmi.shaw22 at gmail.com (Laxmi Shaw) Date: Fri, 19 May 2017 20:26:51 +0530 Subject: [FieldTrip] Error_while using ft_freqanalysis for non parametric computation Message-ID: Dear Fieldtrip users, I am getting an error while using frequency analysis using ft_connectivity analysis. Could you please help me by looking at the screenshot of the error. The error in the dpss.m file. Any help will always be appreciated. Thanks and Regards -- Laxmi Shaw Research Scholar(Ph.D.) IIT Kharagpur West Bengal Ph no-08388837821 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2017-05-19.png Type: image/png Size: 355204 bytes Desc: not available URL: From ty.mckinney.412 at gmail.com Fri May 19 18:16:15 2017 From: ty.mckinney.412 at gmail.com (Ty McKinney) Date: Fri, 19 May 2017 10:16:15 -0600 Subject: [FieldTrip] ft_preprocessing error Message-ID: Hi, I am having some trouble getting the ft_preprocessing function to work. The ft_definetrial function works and gives the trl matrix in the cfg output. As best as I can tell the read data function is returning a matrix that is smaller than the dimensions of the event sample indexes (by several orders of magnitude) from the read event function. I confirmed with EEG lab's loading function that the data matrix is thee same size. What is odd is that this script was working several weeks ago... I get this error: Error using ft_read_data (line 221) cannot read data after the end of the file Error in ft_preprocessing (line 576) dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) Posted below is my code leading up to the execution of the function. Any and all helps you can give me would be greatly appreciated %% Set up fieldtrip path ft_dir = 'C:\Users\Public\Documents\Euler_electrophys (Not backed up)\EEG_scripts\fieldtrip-master'; addpath(ft_dir); ft_defaults; % run this line ft needs it clc %% Load data datainfo.origdir = input('Please copy and paste the filepath for the .CNT file ', 's'); %datainfo.savdir = input('Please copy and paste the filepath for save directory ', 's'); datainfo.SID = input('Enter the Subject Name, e.g., Hick99 use lowercase!!', 's'); datainfo.hp = input('Was the data highpass filtered at 0.1Hz? (y/n)', 's'); cd(datainfo.origdir); % cd into the S's directory wrkdir = pwd; %go get the scalp maps % use the line below on MJE's computer upstairs %chanlocdir = 'C:\Users\u0850304.ADCSBS\Documents\MATLAB\euler_ electrophys\All_purpose_fxs'; % use the line below on the downstairs lab computer chanlocdir = 'C:\Users\Public\Documents\Euler_electrophys (Not backed up)\EEG_scripts\All_purpose_fxs\Waveguard_scalp_coordinates'; cd(chanlocdir); load WG64_4topoplot.mat cd(wrkdir); %find the exact file we need myfname = dir(strcat(datainfo.SID, '*', 'hick', '*','.cnt')); %Note that the file needs to end in ft.cnt/ft.trg exactname = myfname.name; datainfo.sourcepth = strcat(datainfo.origdir, '\', exactname); %set file path for the data cfg.trialfun='trialfun_Hick_tm2'; cfg.datainfo=datainfo; cfg.padding=0; cfg.padtype='data'; cfg.continuous='yes'; cfg.datafile=datainfo.sourcepth; cfg.headerfile=datainfo.sourcepth; cfg.dataset=datainfo.sourcepth; cfg.fsample=512; cd(cfg.datainfo.origdir); fileattrib; savep=ans.Name; newfolder = strcat(datainfo.SID, '_FT'); mkdir(newfolder); % Create new folder in Current Subject folder for FT output cfg.datainfo.savepath = strcat(savep,'\', newfolder); %create save path to new folder cfg.hdr = ft_read_header(cfg.datafile); %things I think fieldtrip needs according to site cfg.event = ft_read_event(cfg.datafile); cfg.data = ft_read_data(cfg.datafile); %% Define Trial Stuff % How much time, in seconds, is retained on either side of trigger codes %cfg.trialdef.eventtype= 'backpanel trigger'; %cfg.trialdef.eventvalue= '55 '; cfg.trialdef.pre= 1; % in seconds cfg.trialdef.post= 1; % in seconds %% read the header (needed for the samping rate) and the events evtsamps = [cfg.event.sample]';% for the events of interest, find the sample numbers (these are integers) Evtypes = {cfg.event.value}';% for the events of interest, find the trigger values (these are strings in the case of BrainVision) evtsamps=evtsamps(2:end); %Trim off first event that crashes script Evtypes =Evtypes (2:end); evtypes=zeros(length(Evtypes),1); for kk=1:length(evtsamps); %Convert string to numbers evtypes(kk) = str2double(Evtypes{kk}); % end pretrig = -round(cfg.trialdef.pre * cfg.hdr.Fs); % pre-stimulus boundary in samples posttrig = round(cfg.trialdef.post * cfg.hdr.Fs); % post-STIMULUS boundary in samples %% Trial definition [cfg]=ft_definetrial(cfg); data=ft_preprocessing(cfg); Ty McKinney Graduate Student-University of Utah ty.mckinney.412 at gmail.com 385.321.4061 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nicolas.abichacra at gmail.com Fri May 19 20:20:19 2017 From: nicolas.abichacra at gmail.com (Nicolas Abichacra) Date: Fri, 19 May 2017 19:20:19 +0100 Subject: [FieldTrip] Problem Matlab Path Message-ID: Dear Filedtrip list, I am currently pre processing EEG data. I recently moved my data from a hard drive to another (cut and paste). After resetting the path to fieldtrip, I get this kind or response when I run any of my scripts : When I run startup.m it gives me a list of warning messages like this one : Warning: Function iscolumn has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. > In path (line 109) In addpath (line 88) In startup (line 1) Then if I run one of the prepro scripts, I get this kind of response : Error using nargin You can only call nargin/nargout from within a MATLAB function. Error in ft_preamble_init (line 34) if nargin==0 Error in ft_preamble (line 56) evalin('caller', ['ft_preamble_' cmd]); Error in ft_rejectvisual (line 125) ft_preamble init Error in FT_prepro_2_sus (line 68) data = ft_rejectvisual(cfg, data); Does anyone have any idea where it might come from ? Thank you very much for the help. Best, Nicolas -------------- next part -------------- An HTML attachment was scrubbed... URL: From frsantos at fpce.up.pt Fri May 19 20:39:05 2017 From: frsantos at fpce.up.pt (Fernando Ferreira-Santos) Date: Fri, 19 May 2017 18:39:05 +0000 Subject: [FieldTrip] 2017 Porto EEG/ERP Summer School Message-ID: <2BAB036A9BAEA44984A131DFCE446108020C0A4975@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 6th 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 event will take place from 4-8 of September 2017 in the lovely city of Porto. In last year's edition the course was fully booked and, as such, we recommend early registration (course places are attributed by order of registration). For additional details and instructions on how to register, please 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, PhD Lecturer Laboratory of Neuropsychophysiology Faculty of Psychology and Education Sciences University of Porto Rua Alfredo Allen, 4200-135 Porto (Portugal) Tel.: +351 226079700 (ext. 409) E-mail: frsantos at fpce.up.pt Lab: http://www.fpce.up.pt/labpsi/ Personal: https://sites.google.com/view/ferreira-santos -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikexcohen at gmail.com Mon May 22 17:58:33 2017 From: mikexcohen at gmail.com (Mike X Cohen) Date: Mon, 22 May 2017 17:58:33 +0200 Subject: [FieldTrip] New book on MATLAB programming techniques for neuroscience data analysis Message-ID: Dear colleagues, There is a new book on MATLAB programming that is designed for masters/PhD/postdoc level researchers. The book is called "MATLAB for Brain and Cognitive Scientists" and is published by MIT Press. The goal of this book is to teach programming skills from beginner to intermediate/advanced levels (many other learning resources provide only beginner-level training), with a specific focus on the myriad analysis approaches often applied in neuroscience and cognitive neuroscience. Chapters end with many exercises to test and develop programming skills, and there are >9000 lines of MATLAB code to learn from on the accompanying website. An important feature of the book is that it teaches not only how to write good code, but also how to recognize and avoid writing bad or error-prone code. More information about the book can be obtained from the following websites: mikexcohen.com/book/#mbcs mitpress.mit.edu/books/matlab-brain-and-cognitive-scientists amazon.com/MATLAB-Brain-Cognitive-Scientists-Press/dp/0262035820/ Mike -------------- next part -------------- An HTML attachment was scrubbed... URL: From malgorzata.wislowska at gmail.com Wed May 24 16:34:17 2017 From: malgorzata.wislowska at gmail.com (Malgorzata Wislowska) Date: Wed, 24 May 2017 16:34:17 +0200 Subject: [FieldTrip] source statistics - spm_bwlabel error Message-ID: Dear FT-community, when calculating cluster permutation statistics on the source level, I receive the following error: Error using spm_bwlabel spm_bwlabel: CONN must be 6, 18 or 26 Error in clusterstat (line 319) [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use spm_bwlabel for 2D/3D to avoid usage of image toolbox Error in ft_statistics_montecarlo (line 347) [stat, cfg] = clusterstat(cfg, statrand, statobs); Error in ft_sourcestatistics (line 218) [stat, cfg] = statmethod(cfg, dat, design); I used MNE method for the inverse problem. I have 8196 grid points 1555 time points. But the error occurs also when I average across the time. Here is my configuration structure for the source analysis: design = zeros(2, nb_of_sbj*2); design(1,:) = [1:nb_of_sbj 1:nb_of_sbj]; design(2,:) = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2]; cfg = []; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_depsamplesT'; cfg.parameter = 'pow'; cfg.correctm = 'cluster'; cfg.clusterstatistic = 'maxsum'; cfg.design = design; cfg.ivar = 2; cfg.uvar = 1; cfg.numrandomization = 5000; cfg.tail = 0; cfg.alpha = 0.025; [stat] = ft_sourcestatistics(cfg,avg_con_sel{:},avg_incon_sel{:}); As far as I can see somebody had asked the same question last year, but the post doesn't seem to have been addressed: https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html Thank you for your help in advance. Best regards, Malgorzata Wislowska, University of Salzburg -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed May 24 16:42:26 2017 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 24 May 2017 16:42:26 +0200 Subject: [FieldTrip] source statistics - spm_bwlabel error In-Reply-To: References: Message-ID: <849BF19E-E573-4781-9B9D-800EB2DDB083@gmail.com> Dear Malgorzata, from a quick glance, it appears that in the call to spm_bwlabel "numdims" should be 3 to give you 2*numdims = 6. So, could you check what numdims is in your case? I suspect that you have 4-dimensional data (time by 3 spatial dimensions), so it might help to check where the dimensions are coming from and what happens if you average over time. Good luck, Julian Am 24.05.2017 um 16:34 schrieb Malgorzata Wislowska: > Dear FT-community, > > > when calculating cluster permutation statistics on the source level, I receive the following error: > Error using spm_bwlabel > spm_bwlabel: CONN must be 6, 18 or 26 > > Error in clusterstat (line 319) > [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use spm_bwlabel for 2D/3D to avoid usage of image toolbox > > Error in ft_statistics_montecarlo (line 347) > [stat, cfg] = clusterstat(cfg, statrand, statobs); > > Error in ft_sourcestatistics (line 218) > [stat, cfg] = statmethod(cfg, dat, design); > > I used MNE method for the inverse problem. I have 8196 grid points 1555 time points. > But the error occurs also when I average across the time. > > Here is my configuration structure for the source analysis: > > design = zeros(2, nb_of_sbj*2); > design(1,:) = [1:nb_of_sbj 1:nb_of_sbj]; > design(2,:) = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2]; > > cfg = []; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_depsamplesT'; > cfg.parameter = 'pow'; > cfg.correctm = 'cluster'; > cfg.clusterstatistic = 'maxsum'; > cfg.design = design; > cfg.ivar = 2; > cfg.uvar = 1; > cfg.numrandomization = 5000; > cfg.tail = 0; > cfg.alpha = 0.025; > > [stat] = ft_sourcestatistics(cfg,avg_con_sel{:},avg_incon_sel{:}); > > As far as I can see somebody had asked the same question last year, but the post doesn't seem to have been addressed: > https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html > > > Thank you for your help in advance. > > Best regards, > Malgorzata Wislowska, > University of Salzburg > _______________________________________________ > 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: signature.asc Type: application/pgp-signature Size: 495 bytes Desc: Message signed with OpenPGP using GPGMail URL: From jiversen at ucsd.edu Thu May 25 23:03:08 2017 From: jiversen at ucsd.edu (John Iversen) Date: Thu, 25 May 2017 14:03:08 -0700 Subject: [FieldTrip] ft_sourceanalysis of component data In-Reply-To: <849BF19E-E573-4781-9B9D-800EB2DDB083@gmail.com> References: <849BF19E-E573-4781-9B9D-800EB2DDB083@gmail.com> Message-ID: <74026E48-8F22-4140-AB9D-304F91FD4F32@ucsd.edu> Dear Fieldtrip development team, I’m doing a long-delayed upgrade of my fieldtrip installation and came across this error. I’m not sure how long this has / will be the case, but I’d like to know your plans. I am available to help re-enable it if that would make a difference. It’s not a really critical feature for me, but it is something I’d relied on in my analysis. For now, I suppose I can revert to the old version, which I recall did have to massage things to work (it mapped components onto time if I remember correctly). elseif iscomp % FIXME, select the components here % FIXME, add the component numbers to the output error('the use of component data in ft_sourceanalysis is disabled for the time being: if you encounter this error message and you need this functionality please contact the FieldTrip development team'); end Thanks, John John R. Iversen, PhD University of California, San Diego Swartz Center for Computational Neuroscience Institute for Neural Computation 9500 Gilman Dr #0559 La Jolla, CA 92093 jiversen at ucsd.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From malgorzata.wislowska at gmail.com Fri May 26 11:52:20 2017 From: malgorzata.wislowska at gmail.com (Malgorzata Wislowska) Date: Fri, 26 May 2017 11:52:20 +0200 Subject: [FieldTrip] source statistics - spm_bwlabel error Message-ID: Dear Julian, thank you very much for your prompt response. Yes, my numdims == 2 because my cfg.dim == [8196 1] which comes from ft_sourcestatistics.m (code lines 131-132) datdim = find(~strcmp(dimtok, 'subj') & ~strcmp(dimtok, 'rpt') & ~strcmp(dimtok, 'rpttap')); datsiz = dimsiz(datdim); calculated on the following input data: varargin{1}: cfg: [1x1 struct] inside: [8196x1 logical] pos: [8196x3 double] time: 0.1750 pow: [8196x1 double] dimord: 'chan_time' The above source level structure comes from ft_sourceanalysis calculated with cfg.method = 'mne'. Averaging over time unfortunately doesn't help - the same error continues to occur: But data that is not averaged over time has numdims == 2 too, because length(cfg.dim) == 2, even though that cfg.dim itself is different (for not averaged data it's e.g cfg.dim == [8196 61], whereas for averaged data it's cfg.dim == [8196 1]), It helps (well, the function runs through without errors and produces some output) if the line: if numdims == 2 || numdims == 3 % if 2D or 3D data gets replaced with: if numdims == 3 In clusterstat.m, code line: 318 (and also 269, 215, 184) Do you (or anybody else) have maybe any better idea how to fix it? Thanks and best regards, Malgorzata, University Salzburg > Subject: Re: [FieldTrip] source statistics - spm_bwlabel error > Dear Malgorzata, > > from a quick glance, it appears that in the call to spm_bwlabel "numdims" > should be 3 to give you 2*numdims = 6. > So, could you check what numdims is in your case? > I suspect that you have 4-dimensional data (time by 3 spatial dimensions), > so it might help to check where the dimensions are coming from and what > happens if you average over time. > > Good luck, > > Julian > > Am 24.05.2017 um 16:34 schrieb Malgorzata Wislowska: > > Dear FT-community, > > > when calculating cluster permutation statistics on the source level, I > receive the following error: > > Error using spm_bwlabel > spm_bwlabel: CONN must be 6, 18 or 26 > > Error in clusterstat (line 319) > [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use > spm_bwlabel for 2D/3D to avoid usage of image toolbox > > Error in ft_statistics_montecarlo (line 347) > [stat, cfg] = clusterstat(cfg, statrand, statobs); > > Error in ft_sourcestatistics (line 218) > [stat, cfg] = statmethod(cfg, dat, design); > > > I used MNE method for the inverse problem. I have 8196 grid points 1555 > time points. > But the error occurs also when I average across the time. > > Here is my configuration structure for the source analysis: > > > design = zeros(2, nb_of_sbj*2); > design(1,:) = [1:nb_of_sbj 1:nb_of_sbj]; > design(2,:) = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2]; > > cfg = []; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_depsamplesT'; > cfg.parameter = 'pow'; > cfg.correctm = 'cluster'; > cfg.clusterstatistic = 'maxsum'; > cfg.design = design; > cfg.ivar = 2; > cfg.uvar = 1; > cfg.numrandomization = 5000; > cfg.tail = 0; > cfg.alpha = 0.025; > > [stat] = ft_sourcestatistics(cfg,avg_co > n_sel{:},avg_incon_sel{:}); > > > As far as I can see somebody had asked the same question last year, but > the post doesn't seem to have been addressed: > https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html > > > Thank you for your help in advance. > > Best regards, > Malgorzata Wislowska, > University of Salzburg > _______________________________________________ > 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 craiggrichter at gmail.com Sun May 28 10:34:48 2017 From: craiggrichter at gmail.com (Craig Richter) Date: Sun, 28 May 2017 11:34:48 +0300 Subject: [FieldTrip] Peercellfun on systems after R2013 Message-ID: <3E539B83-5BB0-49B8-A41C-12409B7F4B19@gmail.com> Dear Fieldtrip development team, I’m having trouble getting peercellfun to function on a Matlab system post R2013. The issue stems from new handling of Mx[De]Serialize.m after R2013. This issue is covered in bug 2452, http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2452 and emerged for the peer system in bug 2598. http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2598 For newer versions of Matlab, peercompile must run to update the mex files, but this fails when trying to compile peer.c. This file calls the mx[De]Serialize functions internally, which are now must be c++ files. I have successfully compiled the c++ versions of these files to mex, but it seems the calls in peer.c must be modified in some way since these must now be c++ files, whereas they were c before. I’m not sure how to make these modifications to peer.c, or if peer.c must be updated to a c++ file. If anyone has any expertise how to do this, and get the peer system operating on systems above R2013, I’d greatly appreciate it!! Thanks! Craig -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon May 29 09:51:30 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 29 May 2017 07:51:30 +0000 Subject: [FieldTrip] ft_sourceanalysis of component data References: Message-ID: Dear John, Sorry about this. I think that we disabled this feature at some point, because the original implementation was a bit hacky (and unpredictable in its behavior). In a bout of quality-of-code-perfectionism we probably cleaned up the code, disabled the feature, agreed that we should address it at some point, even remembered to put in an error message … and subsequently forgot about it. Anyway, after these lame excuses I suggest to try and get this fixed. Thanks for your willingness to contribute. These days our development workflow lives on github, which should make external contributions to the code much more straightforward (github.com/fieldtrip.git is where the main repo is located). Perhaps you could check out this chunk of documentation, to get on the road: http://www.fieldtriptoolbox.org/development/git). For this specific issue, I think it would be best to first discuss a bit the requested features before we start changing the code, so I suggest that you create a local fork of the repository, and within it a new branch, which I think you can subsequently 'pull-request’. This allows us to have a location where we can discuss stuff (for now the ‘issues’ feature for the fieldtrip repo is disabled, yet this would be a more natural way for discussing things). Does that sound like a plan? Best, JM On 25 May 2017, at 23:03, John Iversen > wrote: Dear Fieldtrip development team, I’m doing a long-delayed upgrade of my fieldtrip installation and came across this error. I’m not sure how long this has / will be the case, but I’d like to know your plans. I am available to help re-enable it if that would make a difference. It’s not a really critical feature for me, but it is something I’d relied on in my analysis. For now, I suppose I can revert to the old version, which I recall did have to massage things to work (it mapped components onto time if I remember correctly). elseif iscomp % FIXME, select the components here % FIXME, add the component numbers to the output error('the use of component data in ft_sourceanalysis is disabled for the time being: if you encounter this error message and you need this functionality please contact the FieldTrip development team'); end Thanks, John John R. Iversen, PhD University of California, San Diego Swartz Center for Computational Neuroscience Institute for Neural Computation 9500 Gilman Dr #0559 La Jolla, CA 92093 jiversen at ucsd.edu _______________________________________________ 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 Mon May 29 09:52:04 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 29 May 2017 07:52:04 +0000 Subject: [FieldTrip] source statistics - spm_bwlabel error References: Message-ID: Hi Malgorzata, Could you try to add the original ‘tri’ field to each of your varargins, and check whether the problem persists? Thanks, Jan-Mathijs On 26 May 2017, at 11:52, Malgorzata Wislowska > wrote: Dear Julian, thank you very much for your prompt response. Yes, my numdims == 2 because my cfg.dim == [8196 1] which comes from ft_sourcestatistics.m (code lines 131-132) datdim = find(~strcmp(dimtok, 'subj') & ~strcmp(dimtok, 'rpt') & ~strcmp(dimtok, 'rpttap')); datsiz = dimsiz(datdim); calculated on the following input data: varargin{1}: cfg: [1x1 struct] inside: [8196x1 logical] pos: [8196x3 double] time: 0.1750 pow: [8196x1 double] dimord: 'chan_time' The above source level structure comes from ft_sourceanalysis calculated with cfg.method = 'mne'. Averaging over time unfortunately doesn't help - the same error continues to occur: But data that is not averaged over time has numdims == 2 too, because length(cfg.dim) == 2, even though that cfg.dim itself is different (for not averaged data it's e.g cfg.dim == [8196 61], whereas for averaged data it's cfg.dim == [8196 1]), It helps (well, the function runs through without errors and produces some output) if the line: if numdims == 2 || numdims == 3 % if 2D or 3D data gets replaced with: if numdims == 3 In clusterstat.m, code line: 318 (and also 269, 215, 184) Do you (or anybody else) have maybe any better idea how to fix it? Thanks and best regards, Malgorzata, University Salzburg Subject: Re: [FieldTrip] source statistics - spm_bwlabel error Dear Malgorzata, from a quick glance, it appears that in the call to spm_bwlabel "numdims" should be 3 to give you 2*numdims = 6. So, could you check what numdims is in your case? I suspect that you have 4-dimensional data (time by 3 spatial dimensions), so it might help to check where the dimensions are coming from and what happens if you average over time. Good luck, Julian Am 24.05.2017 um 16:34 schrieb Malgorzata Wislowska: Dear FT-community, when calculating cluster permutation statistics on the source level, I receive the following error: Error using spm_bwlabel spm_bwlabel: CONN must be 6, 18 or 26 Error in clusterstat (line 319) [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use spm_bwlabel for 2D/3D to avoid usage of image toolbox Error in ft_statistics_montecarlo (line 347) [stat, cfg] = clusterstat(cfg, statrand, statobs); Error in ft_sourcestatistics (line 218) [stat, cfg] = statmethod(cfg, dat, design); I used MNE method for the inverse problem. I have 8196 grid points 1555 time points. But the error occurs also when I average across the time. Here is my configuration structure for the source analysis: design = zeros(2, nb_of_sbj*2); design(1,:) = [1:nb_of_sbj 1:nb_of_sbj]; design(2,:) = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2]; cfg = []; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_depsamplesT'; cfg.parameter = 'pow'; cfg.correctm = 'cluster'; cfg.clusterstatistic = 'maxsum'; cfg.design = design; cfg.ivar = 2; cfg.uvar = 1; cfg.numrandomization = 5000; cfg.tail = 0; cfg.alpha = 0.025; [stat] = ft_sourcestatistics(cfg,avg_con_sel{:},avg_incon_sel{:}); As far as I can see somebody had asked the same question last year, but the post doesn't seem to have been addressed: https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html Thank you for your help in advance. Best regards, Malgorzata Wislowska, University of Salzburg _______________________________________________ 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 angelika.lingnau at gmail.com Mon May 29 13:09:47 2017 From: angelika.lingnau at gmail.com (Angelika Lingnau) Date: Mon, 29 May 2017 12:09:47 +0100 Subject: [FieldTrip] 1-Year fMRI/ MEG Postdoc, Center for Mind/Brain Sciences, University of Trento, Italy Message-ID: At the Center for Mind/ Brain Sciences (CIMeC, http://www.cimec.unitn.it/en) at the University of Trento, Italy, there will soon be an opening for a one-year postdoctoral fellowship to work with Dr. Angelika Lingnau to examine the neural basis of visual imagery in normal sighted participants and hemianopic patients. Further descriptions of our ongoing research projects can be found under the following link: https://sites.google.com/site/angelikalingnau/. The postdoc will be responsible for the design of fMRI and/ or MEG studies, conducting data analysis and leading the write-up of scientific work. The ideal applicant is highly motivated and creative and is capable of working both independently as well as in a young, dynamic group. The applicant furthermore should have experience with functional magnetic resonance imaging and/ or magnetoencephalography and a solid background in Cognitive Neuroscience. Programming experience with MATLAB or C is very desirable. The Center offers an international and vibrant research setting with access to state-of-the-art neuroimaging methodologies, including a research-only 4T MRI scanner, MEG, EEG and TMS, as well as behavioral, eye tracking and motion tracking laboratories. The 2011-2014 ANVUR Report ranked CIMeC first among Italian universities in the field of psychological sciences. English is the official language of the CIMeC, where a large proportion of the faculty, postdocs and students come from a wide range of countries outside of Italy. Informal inquiries should be sent to Angelika Lingnau ( angelika.lingnau at rhul.ac.uk or angelika.lingnau at gmail.com). -------------- next part -------------- An HTML attachment was scrubbed... URL: From malgorzata.wislowska at gmail.com Mon May 29 18:30:40 2017 From: malgorzata.wislowska at gmail.com (Malgorzata Wislowska) Date: Mon, 29 May 2017 18:30:40 +0200 Subject: [FieldTrip] source statistics - spm_bwlabel error Message-ID: Dear Jan-Mathijs, thank you for your message. when I add the 'tri' field to the input data, FT recognizes that data is a mesh (*the input is mesh data with 8196 vertices and 16384 triangles*), but it keep throwing the same *spm_bwlabel* error message. This is the current input data (that's what you meant, right?): varargin{1}: cfg: [1x1 struct] inside: [8196x1 logical] pos: [8196x3 double] time: 0.1000 pow: [8196x1 double] tri: [16384x3 uint16] dimord: 'chan_time' If I don't average over time, and the size of varargin{1}.pow equals e.g., [8196 73], then datsiz == 8196. That's because dimsiz == [8196 73], but datdim == 1 (ft_sourcestatistics, lines 131-132). That leads to the following error: Error using ft_sourcestatistics (line 205) the length of the design matrix (2) does not match the number of observations in the data (3358) Best regards, Malgorzata > Subject: Re: [FieldTrip] source statistics - spm_bwlabel error > Hi Malgorzata, > > Could you try to add the original ‘tri’ field to each of your varargins, > and check whether the problem persists? > > Thanks, > Jan-Mathijs > > > > On 26 May 2017, at 11:52, Malgorzata Wislowska < > malgorzata.wislowska at gmail.com> wrote: > > Dear Julian, > > > thank you very much for your prompt response. > > Yes, my numdims == 2 because my cfg.dim == [8196 1] > which comes from ft_sourcestatistics.m (code lines 131-132) > > datdim = find(~strcmp(dimtok, 'subj') & ~strcmp(dimtok, 'rpt') & > ~strcmp(dimtok, 'rpttap')); > datsiz = dimsiz(datdim); > > calculated on the following input data: > > varargin{1}: > cfg: [1x1 struct] > inside: [8196x1 logical] > pos: [8196x3 double] > time: 0.1750 > pow: [8196x1 double] > dimord: 'chan_time' > > The above source level structure comes from ft_sourceanalysis calculated > with cfg.method = 'mne'. > > Averaging over time unfortunately doesn't help - the same error continues > to occur: > But data that is not averaged over time has numdims == 2 too, because > length(cfg.dim) == 2, even though that cfg.dim itself is different (for not > averaged data it's e.g cfg.dim == [8196 61], whereas for averaged data it's > cfg.dim == [8196 1]), > > It helps (well, the function runs through without errors and produces some > output) if the line: > > if numdims == 2 || numdims == 3 % if 2D or 3D data > > gets replaced with: > > if numdims == 3 > > In clusterstat.m, code line: 318 (and also 269, 215, 184) > > Do you (or anybody else) have maybe any better idea how to fix it? > > > Thanks and best regards, > Malgorzata, > University Salzburg > > > > >> Subject: Re: [FieldTrip] source statistics - spm_bwlabel error >> > > > Dear Malgorzata, >> >> from a quick glance, it appears that in the call to spm_bwlabel "numdims" >> should be 3 to give you 2*numdims = 6. >> So, could you check what numdims is in your case? >> I suspect that you have 4-dimensional data (time by 3 spatial >> dimensions), so it might help to check where the dimensions are coming from >> and what happens if you average over time. >> >> Good luck, >> >> Julian >> >> Am 24.05.2017 um 16:34 schrieb Malgorzata Wislowska: >> >> Dear FT-community, >> >> >> when calculating cluster permutation statistics on the source level, I >> receive the following error: >> >> Error using spm_bwlabel >> spm_bwlabel: CONN must be 6, 18 or 26 >> >> Error in clusterstat (line 319) >> [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use >> spm_bwlabel for 2D/3D to avoid usage of image toolbox >> >> Error in ft_statistics_montecarlo (line 347) >> [stat, cfg] = clusterstat(cfg, statrand, statobs); >> >> Error in ft_sourcestatistics (line 218) >> [stat, cfg] = statmethod(cfg, dat, design); >> >> >> I used MNE method for the inverse problem. I have 8196 grid points 1555 >> time points. >> But the error occurs also when I average across the time. >> >> Here is my configuration structure for the source analysis: >> >> >> design = zeros(2, nb_of_sbj*2); >> design(1,:) = [1:nb_of_sbj 1:nb_of_sbj]; >> design(2,:) = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2]; >> >> cfg = []; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'ft_statfun_depsamplesT'; >> cfg.parameter = 'pow'; >> cfg.correctm = 'cluster'; >> cfg.clusterstatistic = 'maxsum'; >> cfg.design = design; >> cfg.ivar = 2; >> cfg.uvar = 1; >> cfg.numrandomization = 5000; >> cfg.tail = 0; >> cfg.alpha = 0.025; >> >> [stat] = ft_sourcestatistics(cfg,avg_co >> n_sel{:},avg_incon_sel{:}); >> >> >> As far as I can see somebody had asked the same question last year, but >> the post doesn't seem to have been addressed: >> https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html >> >> >> Thank you for your help in advance. >> >> Best regards, >> Malgorzata Wislowska, >> University of Salzburg >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.papen at uni-koeln.de Tue May 30 09:35:37 2017 From: m.papen at uni-koeln.de (Michael von Papen) Date: Tue, 30 May 2017 09:35:37 +0200 Subject: [FieldTrip] Extended Deadline: Coupling & Causality in Complex Systems, Sep 25-27, Cologne, Germany Message-ID: ============================================================== CALL FOR PAPERS (*Extended Deadline June 15*, 2017) http://c3s.uni-koeln.de ============================================================== INTERNATIONAL CONFERENCE: *Coupling and Causality in Complex Systems* September 25-27, 2017, Cologne, Germany -------------------------------------------------------------- The interdisciplinary conference Coupling and Causality in Complex Systems (C3S) is hosted by the Competence Area 3: Quantitative Modeling of Complex Systems of the University of Cologne (UoC), Germany. It is organized by the Institute of Geophysics & Meteorology, UoC, the Institute of Clinical Neuroscience and Psychology, Heinrich-Heine University Düsseldorf and the Department of Cognitive Neuroscience at the Research Center Juelich. -------------------------------------------------- *Invited Speakers* Jörg Breitung - Macroeconomic Policy Institute, University of Cologne, Germany David Gross - Institute of Theoretical Physics, University of Cologne, Germany Philip Holmes - Mechanical and Aerospace Engineering / Princeton Neuroscience Institute, Princeton, USA Ankit Khambhati - Department of Bioengineering, University of Pennsylvania, USA Laura Marzetti - Department of Neuroscience, Università degli Studi "G. d'Annunzio" Chieti - Pescara Arkady Pikovsky - Institute of Physics and Astronomy, University Potsdam, Germany Michael Rosenblum - Institute of Physics and Astronomy, University Potsdam, Germany Jakob Runge - The Grantham Institute for Climate Change, Imperial College London -------------------------------------------------- *Preliminary Session Program* We will have different sessions with differing topics and each session will be opened by one of the invited speakers. Here is a preliminary version of our program: Session 1 Synchronization I Arkady Pikovsky Session 2 Synchronization II Silvia Daun Session 3 Coupled oscillators I Phil Holmes Session 4 Coupled oscillators II Michael Rosenblum Session 5 Phase coupling Laura Marzetti Session 6 Network structures Ankit Khambati Session 7 Bayesian networks David Gross Session 8 Granger causality I Jörg Breitung Session 9 Granger causality II Esther Florin Session 10 Causal network measures Jakob Runge Further topics of interest for the conference include, amongst others, research and methods development on: functional connectivity, (partial directed) coherence, network topology, graph-theoretic measures, directed graphs, nonlinear dynamics of complex systems, complex spatio-temporal systems, mutual information and transfer entropy. -------------------------------------------------------------- *Scientific Organizing Committee* Silvia Daun - Institute of Zoology, University of Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany Esther Florin - Institute of Clinical Neuroscience and Psychology, Düsseldorf, Germany Joachim Gross - Center for Cognitive Neuroimaging, Glasgow, UK Michael von Papen - Institute of Geophysics & Meteorology, Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany -------------------------------------------------------------- *Abstract* Complex systems such as the human brain, Earth’s climate and economy are characterized by a multitude of coupled processes on different spatial and temporal scales. In order to better understand the dynamics of the system at hand each scientific area has developed specific tools to identify, model and quantify these processes. The conference Coupling and Causality in Complex Systems (C3S) will present a collection of these approaches with the aim to provide scientists with new analysis strategies for their field. The conference focuses on how to characterize a complex system and on the methods for estimating and modeling of statistical coupling (e.g. network coherence, creation and modulation of small networks and local or long-range synchronization by cross frequency phase-phase and phase-amplitude coupling) and causality (e.g. Granger causality, transfer entropy). Therefore, data analysts from different study fields including neuroscience, mathematics, physics, biology, and economy will present their approaches with a particular focus on the methods they use. The aim of this conference is to foster discussions and the transdisciplinary exchange of advanced techniques, methods, and algorithms, thereby stimulating potential future collaborations. -------------------------------------------------------------- *PAPER SUBMISSION AND REGISTRATION* Authors are invited to submit conference abstracts with up to 400 words. Authors of exceptional abstracts will be given the opportunity to present their research in a talk. However, poster sessions will be provided with ample time for discussions. For your submission, please use the conference website c3s.uni-koeln.de. To register, please send an email with the subject "registration" to c3s-conference at uni-koeln.de. Please be sure to include your full name, your affiliation and whether you qualify as student (also PhD candidates) or not. The registration fee will cover snacks and refreshments during coffee breaks, lunch and a dinner with all participants. Early-bird registration is available until July 10 with a reduced fee of 100 EUR (50 EUR for students), after July 10 the registration fee will be 200 EUR (100 EUR for students). -------------------------------------------------------------- IMPORTANT DATES Paper Submission deadline: June 15, 2017 Author Notification: end June, 2017 Early-bird registration: July 10, 2017 Conference: September 25-27, 2017 ============================================================== Please find the call for papers and more information at the conference website: http://c3s.uni-koeln.de. For questions regarding the conference feel free to contact us via c3s-conference at uni-koeln.de. -- ------------------------------------------ UNIVERSITY OF COLOGNE Institute of Geophysics & Meteorology Coordinator of Competence Area III: Quantitative Modeling of Complex Systems Dr. Michael von Papen Email: m.papen at uni-koeln.de http://www.uni-koeln.de/~vpapenm http://complexsystems.uni-koeln.de From l.roeder at qut.edu.au Wed May 31 04:28:11 2017 From: l.roeder at qut.edu.au (Luisa Roeder) Date: Wed, 31 May 2017 02:28:11 +0000 Subject: [FieldTrip] input data structure ft_freqstatistics Message-ID: Dear Fieldtrip users, I am part of a research team at the Institute of Health and Biomedical Innovation at Queensland University of Technology in Brisbane, Australia. I am currently working on time-frequency analyses of EEG and EMG signals. I would like to use ft_freqstatistics for a cluster-based permutation test on my time-frequency data. In the function itself and in the online documentation I read that the input data into ft_freqstatistics should be the result/output from either FT_FREQANALYSIS, FT_FREQDESCRIPTIVES or from FT_FREQGRANDAVERAGE. I have not completed my time-frequency analysis via fieldtrip; hence, I am wondering if it is also possible to create my own input data structure to make it fit for ft_freqstatistics? (Basically, I would like to skip ft_freqanalysis and directly start with cluster-based permutation testing via ft_freqstatistics, and for that I need to adapt my data structure.) If it is possible, which fields have to be created in my variable to be fed into ft_freqstatistics, so it fulfils all requirements to make the function run? Are there any fields from the output of, for example, FT_FREQANALYSIS that are not needed for ft_freqstatistics? For example, [stat] = ft_freqstatistics(cfg, coh1, coh2, ...) What fields do coh1, coh2, ... have to have? E.g. >> display(coh1) labelcmb: {8×2 cell} dimord: 'chancmb_freq_time' cohspctrm: [8×80×2049 double] time: [1×2049 double] freq: [1×80 double] elec: [1×1 struct] cfg: [1×1 struct] Can I leave out some of these fields (particularly coh1.cfg), and it will still work for ft_freqstatistics? Would it be enough to only have coh1.cohspctrm, coh1.time and coh1.freq? I am still relatively new to Fieldtrip, and working my way through the tutorials etc., but I definitely having trouble to create an appropriate data structure as input into ft_freqstatistics (without using ft_freqanalysis or other functions alike beforehand). I would very much appreciate your help with this. Thank you, Kind regards Luisa Luisa Roeder, PhD | Research Associate | Movement Neuroscience Institute of Health and Biomedical Innovation | School of Exercise and Nutrition Science Queensland University of Technology | 60 Musk Ave, Kelvin Grove, Brisbane, QLD 4059, Australia. t: +61 7 3138 6428 | e: l.roeder at qut.edu.au | w: www.ihbi.qut.edu.au CRICOS No. 00213J -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed May 31 08:58:12 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 31 May 2017 06:58:12 +0000 Subject: [FieldTrip] input data structure ft_freqstatistics In-Reply-To: References: Message-ID: Hi Luisa, The minimum requirement for a data structure that fieldtrip can work with should contain at least the following fields: - a field with the data matrix, in your case it can be cohspctrm - a bunch of fields that indicate how to interpret the dimensions of the input data matrix: * dimord, a descriptor in the style of ‘chancmb_freq_time’ * freq * time * labelcmb (for univariate data, it should be label) The cfg should be optional. Anyway, this being said, probably you may want to try and fool fieldtrip into getting a univariate data-field, i.e. rename cohspctrm into powspctrm, and labelcmb into label. This should work under the assumption that you are cohering 8 different EEG electrodes with a single EMG (for the label you could just take the column of labelcmb that represents the EEG). Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 31 May 2017, at 04:28, Luisa Roeder > wrote: Dear Fieldtrip users, I am part of a research team at the Institute of Health and Biomedical Innovation at Queensland University of Technology in Brisbane, Australia. I am currently working on time-frequency analyses of EEG and EMG signals. I would like to use ft_freqstatistics for a cluster-based permutation test on my time-frequency data. In the function itself and in the online documentation I read that the input data into ft_freqstatistics should be the result/output from either FT_FREQANALYSIS, FT_FREQDESCRIPTIVES or from FT_FREQGRANDAVERAGE. I have not completed my time-frequency analysis via fieldtrip; hence, I am wondering if it is also possible to create my own input data structure to make it fit for ft_freqstatistics? (Basically, I would like to skip ft_freqanalysis and directly start with cluster-based permutation testing via ft_freqstatistics, and for that I need to adapt my data structure.) If it is possible, which fields have to be created in my variable to be fed into ft_freqstatistics, so it fulfils all requirements to make the function run? Are there any fields from the output of, for example, FT_FREQANALYSIS that are not needed for ft_freqstatistics? For example, [stat] = ft_freqstatistics(cfg, coh1, coh2, ...) What fields do coh1, coh2, … have to have? E.g. >> display(coh1) labelcmb: {8×2 cell} dimord: 'chancmb_freq_time' cohspctrm: [8×80×2049 double] time: [1×2049 double] freq: [1×80 double] elec: [1×1 struct] cfg: [1×1 struct] Can I leave out some of these fields (particularly coh1.cfg), and it will still work for ft_freqstatistics? Would it be enough to only have coh1.cohspctrm, coh1.time and coh1.freq? I am still relatively new to Fieldtrip, and working my way through the tutorials etc., but I definitely having trouble to create an appropriate data structure as input into ft_freqstatistics (without using ft_freqanalysis or other functions alike beforehand). I would very much appreciate your help with this. Thank you, Kind regards Luisa Luisa Roeder, PhD | Research Associate | Movement Neuroscience Institute of Health and Biomedical Innovation | School of Exercise and Nutrition Science Queensland University of Technology | 60 Musk Ave, Kelvin Grove, Brisbane, QLD 4059, Australia. t: +61 7 3138 6428 | e: l.roeder at qut.edu.au | w: www.ihbi.qut.edu.au CRICOS No. 00213J _______________________________________________ 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 kash.kgp at gmail.com Wed May 31 12:50:41 2017 From: kash.kgp at gmail.com (Kasturi Barik) Date: Wed, 31 May 2017 16:20:41 +0530 Subject: [FieldTrip] Fwd: Source Analysis from EEG data In-Reply-To: References: Message-ID: *Dear all, **I am trying to perform source localization in the frequency domain * *from EEG data using 'DICS' . As I have no mri data of the participants, * *I am using **'Subject01.mri' to read the anatomical data with ft_read_mri. * *The **head model created with 'bemcp'.* *Code:* *%% **Read the anatomical data* *mri = ft_read_mri('Subject01.mri');* *%% **Segment the anatomical information & triangulate the surfaces* *load segmentedmri % load from *ftp server (segmentedmri.mat). *load bnd* *%% **Create the headmodel* *cfg = [];cfg.method = 'bemcp'; vol = ft_prepare_headmodel(cfg, bnd);%% Position of the electrodesload('Face_sub.mat'); % data of participants' electrode positions electrodes = Face_sub.elec;%% Interactive alignmentcfg = [];cfg.method = 'interactive';cfg.elec = electrodes;cfg.headshape = vol.bnd(3); % scalpelec_aligned = ft_electroderealign(cfg);%% Compute leadfield:cfg = [];cfg.elec = elec_aligned;cfg.vol = vol;cfg.channel = {'EEG'};[grid] = ft_prepare_leadfield(cfg);%% Source Analysiscfg = []; cfg.method = 'dics';cfg.frequency = 10; cfg.grid = grid;cfg.vol = vol;cfg.dics.projectnoise = 'yes';cfg.dics.lambda = 0;sourceFace = ft_sourceanalysis(cfg, face_data); % face_data is obtained from the FT_FREQANALYSIS % [%% time frequency analysis || cfg = []; || cfg.channel = 'EEG'; || cfg.method = 'mtmfft'; || cfg.output = 'powandcsd'; || cfg.tapsmofrq = 4; || cfg.foi = 1:1:40; || face_data = ft_freqanalysis(cfg, Face_sub); ]* *When running DICS with these settings **I am getting the following error message:* *Error using svd Input to SVD must not contain NaN or Inf. Error in beamformer_dics>pinv (line 650) [U,S,V] = svd(A,0); Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 568) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Error in SourceAnalysis (line 133) sourceFace = ft_sourceanalysis(cfg, face_data);* * I am not able to detect, where is the problem. Another issue I have found that 'vol.mat' or 'grid.leadfield' are all NaN value. I cannot understand how to solve it. I would be very thankful if you can help me in this regard. * -- Thanks & Regards *Kasturi Barik* MS Research Scholar Audio and Bio-signal Processing Lab Department of Electronics and Electrical Engineering Indian Institute of Technology Kharagpur Mob: +91-8902400644 -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Wed May 31 13:49:35 2017 From: michelic72 at gmail.com (Cristiano Micheli) Date: Wed, 31 May 2017 13:49:35 +0200 Subject: [FieldTrip] Fwd: Source Analysis from EEG data In-Reply-To: References: Message-ID: Dear Kastouri, My hunch is that either ft_prepare_headmodel or ft_prepare_leadfield fail in generating a proper forward model for localization purposes. I would check that ft_prepare_headmodel's vol structure contains sensible data by plotting both the 'bnd' triangulated surface and the EEG electrodes together (you should be able to find instructions on the wiki) in the same image. Sometimes units (mm,cm) or coregistration (left/right swap) might influence a good outcome. Accordingly the grid.leadfield structure will not make sense because it uses the incorrect outcome of the vol structure. So if you manage to solve the 1st problem you'll kill two bird with a stone Good luck! Cris On Wed, May 31, 2017 at 12:50 PM, Kasturi Barik wrote: > *Dear all, > **I am trying to perform source localization in the frequency domain * > > *from EEG data using 'DICS' . As I have no mri data of the participants, * > > *I am using **'Subject01.mri' to read the anatomical data with ft_read_mri. * > > *The **head model created with 'bemcp'.* > > *Code:* > > *%% **Read the anatomical data* > > *mri = ft_read_mri('Subject01.mri');* > > *%% **Segment the anatomical information & triangulate the surfaces* > > *load segmentedmri % load from *ftp > server > > (segmentedmri.mat). > *load bnd* > > *%% **Create the headmodel* > > > > > > > > > > *cfg = [];cfg.method = 'bemcp'; vol = > ft_prepare_headmodel(cfg, bnd);%% Position of the > electrodesload('Face_sub.mat'); % data of > participants' electrode positions electrodes = Face_sub.elec;%% Interactive > alignmentcfg = [];cfg.method = 'interactive';cfg.elec = > electrodes;cfg.headshape = vol.bnd(3); % > scalpelec_aligned = ft_electroderealign(cfg);%% Compute leadfield:cfg > = [];cfg.elec = elec_aligned;cfg.vol = > vol;cfg.channel = {'EEG'};[grid] = ft_prepare_leadfield(cfg);%% > Source Analysiscfg = []; cfg.method = > 'dics';cfg.frequency = 10; cfg.grid = grid;cfg.vol = > vol;cfg.dics.projectnoise = 'yes';cfg.dics.lambda = 0;sourceFace = > ft_sourceanalysis(cfg, face_data); % face_data is obtained from the > FT_FREQANALYSIS % [%% time frequency analysis > || cfg = []; > || cfg.channel = 'EEG'; || > cfg.method = 'mtmfft'; || > cfg.output = 'powandcsd'; || > cfg.tapsmofrq = 4; || > cfg.foi = 1:1:40; || > face_data = ft_freqanalysis(cfg, Face_sub); ]* > > *When running DICS with these settings **I am getting the following error message:* > > > *Error using svd > Input to SVD must not contain NaN or Inf. > > Error in beamformer_dics>pinv (line 650) > [U,S,V] = svd(A,0); > > Error in beamformer_dics (line 339) > filt = pinv(lf' * invCf * lf) * lf' * invCf; > % Gross eqn. 3, use PINV/SVD to cover rank > deficient leadfield > > Error in ft_sourceanalysis (line 568) > dip(i) = beamformer_dics(grid, sens, vol, [], > squeeze(Cf(i,:,:)), optarg{:}); > > Error in SourceAnalysis (line 133) > sourceFace = ft_sourceanalysis(cfg, face_data);* > > > * I am not able to detect, where is the problem. Another issue I have found that 'vol.mat' or 'grid.leadfield' are all NaN value. I cannot understand how to solve it. I would be very thankful if you can help me in this regard. * > > > > > > -- > Thanks & Regards > > *Kasturi Barik* > > MS Research Scholar > Audio and Bio-signal Processing Lab > Department of Electronics and Electrical Engineering > Indian Institute of Technology Kharagpur > Mob: +91-8902400644 <+91%2089024%2000644> > > _______________________________________________ > 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 roycox.roycox at gmail.com Wed May 31 20:57:47 2017 From: roycox.roycox at gmail.com (Roy Cox) Date: Wed, 31 May 2017 14:57:47 -0400 Subject: [FieldTrip] cluster statistics on subset of channels Message-ID: hello, Does anyone know if it's possible to run ft_freqstatistics on only a subset of channels? Per my hypothesis, I'm only interested in the posterior half of the scalp. I know I could remove the channels entirely from the data, but for plotting purposes I'd like to retain the full set of data, and it would be cumbersome to stitch data and clusters back together. Alternatively, I could change the channel neighborhood structure for the frontal channels such that they don't enter the cluster formation procedure at all, but I'm not sure if this is valid. Maybe ft_freqstatistics already supports channel selection? Can't seem to find it in the documentation or tutorials, though. Thanks for any insights, Roy -------------- next part -------------- An HTML attachment was scrubbed... URL: From elmeri.syrjanen at gmail.com Wed May 31 21:24:07 2017 From: elmeri.syrjanen at gmail.com (=?UTF-8?Q?Elmeri_Syrj=C3=A4nen?=) Date: Wed, 31 May 2017 21:24:07 +0200 Subject: [FieldTrip] cluster statistics on subset of channels In-Reply-To: References: Message-ID: Hi Roy, I have pasted the relevant section from http://www.fieldtriptoolbox.org/reference/ft_freqstatistics the lines that would be applicable in your situation. The configuration can contain the following options for data selection *cfg.channel = Nx1 cell-array with selection of channels (default = 'all'), see FT_CHANNELSELECTION for details* *cfg.avgoverchan = 'yes'* or 'no' (default = 'no') /elmeri On Wed, May 31, 2017 at 8:57 PM, Roy Cox wrote: > hello, > > Does anyone know if it's possible to run ft_freqstatistics on only a > subset of channels? > > Per my hypothesis, I'm only interested in the posterior half of the scalp. > > I know I could remove the channels entirely from the data, but for > plotting purposes I'd like to retain the full set of data, and it would be > cumbersome to stitch data and clusters back together. Alternatively, I > could change the channel neighborhood structure for the frontal channels > such that they don't enter the cluster formation procedure at all, but I'm > not sure if this is valid. > > Maybe ft_freqstatistics already supports channel selection? Can't seem to > find it in the documentation or tutorials, though. > > Thanks for any insights, > > Roy > > _______________________________________________ > 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 mikexcohen at gmail.com Mon May 1 11:13:57 2017 From: mikexcohen at gmail.com (Mike X Cohen) Date: Mon, 1 May 2017 11:13:57 +0200 Subject: [FieldTrip] Conference announcement: ICON XIII (Amsterdam, August 2017) Message-ID: We are happy to send a reminder for the ICON XIII conference, which will take place on 5-8 August 2017 in Amsterdam (the Netherlands). Amsterdam is an easily-accessible and progressive city. The venue is the Beurs van Berlage, located in downtown Amsterdam and one of the most beautiful conference venues in Europe! Visit the website: http://www.icon2017.org There is a very exciting line-up of keynote speakers and symposia, and there are new presentation formats including "ask-the-experts" panels and hackathons. Check out the "Program" tab at icon2017.org. Early-bird registration discount ends on May 15! The registration includes full conference attendance, lunch/snacks/coffee/tea every day, and the conference opening reception. Also note that although the official poster submission deadline is passed, we are still accepting some late poster submissions by special request. Contact us (icon2017 at icon2017.org) for details! FOLLOW US ON TWITTER For up-to-date announcements before and during the ICON meeting, follow @icon2017 (see also "Media" tab on the website). QUESTIONS ABOUT THE MEETING OR SPONSORSHIP? email icon2017 at icon2017.org http://www.icon2017.org We look forward to seeing you in beautiful Amsterdam! Mike X Cohen and Birte Forstmann -------------- next part -------------- An HTML attachment was scrubbed... URL: From christian.oreilly at epfl.ch Tue May 2 14:54:35 2017 From: christian.oreilly at epfl.ch (Christian O'Reilly) Date: Tue, 2 May 2017 14:54:35 +0200 Subject: [FieldTrip] Ordering of channels index in ft_read_data with egi_mff_v1 Message-ID: Hi, I've been trying for a while to find the source of an apparent swapping of channels in my data, and I suspect that the source of this issue comes from the ft_read_data function when it is used with egi_mff_v1. This code does not handle very well list of channel indexes that are not ordered. I am using: chanindx = [36, 224, 37, 18, 21, 109, 153, 101]; data = ft_read_data([path fileNames(iFile).name], 'headerformat', ... 'egi_mff_v1', 'dataformat', 'egi_mff_v1', ... 'header', header, ... ... #'begsample', begsample, 'endsample', endsample, ... 'chanindx', chanindx); ... and I have a strong suspicion that the 8 columns of the data matrix are ordered as if chanindx == [18, 21, 36, 37, 101, 109 153, 224] I think it has to do with ft_read_data code: for iSig = 1:length(hdr.orig.signal) % adjust chanindx to match with current signal [dum1, dum2, chanind_sig] = intersect(chanindx, find(chan2sig_ind==iSig)); if isempty(chanind_sig) % no channels requested from current signal else blockhdr = hdr.orig.signal(iSig).blockhdr; signalname = binfiles(iSig).name; %%%%%%%%%%%% ... skipping lines of codes ... %%%%%%%%%% dat{end} = dat{end}(:,begsel:endsel); end end % concat signals dat = cat(1,dat{:}); In any case, as long as this is not corrected, people using fieldtrip to read EGI MFF files should keep this in mind and order their channel indexes! Best, Christian -------------- next part -------------- An HTML attachment was scrubbed... URL: From C.vandenBoomen at uu.nl Tue May 2 16:26:00 2017 From: C.vandenBoomen at uu.nl (Boomen, C. van den (Carlijn)) Date: Tue, 2 May 2017 14:26:00 +0000 Subject: [FieldTrip] error ft_nargin Message-ID: Dear fieldtrip users, I'm using fieldtrip to analyse my ERP data. My script used to work (at least until November 2016) but now I get the following error message. I get the same error using singleplotER, which used to work before as well. Does anyone know a solution? Undefined function or variable 'ft_nargin'. Error in ft_preamble_init (line 34) if ft_nargin==0 Error in ft_preamble (line 56) evalin('caller', ['ft_preamble_' cmd]); Error in ft_timelockgrandaverage (line 71) ft_preamble init Error in ERP_script_nov2016 (line 532) granderp_ind{cond} = ft_timelockgrandaverage(cfg,EEGallsubj.incldata{cond,1:end}); I'm using a mac (10.9.5), with matlab 2014b and fieldtrip 20160105 (since some parts of the script didn't work with later versions, I hope to use this version for now) Thanks a lot! Best, Carlijn Dr. Carlijn van den Boomen | Departments of Developmental and Experimental Psychology | Utrecht University | Langeveld Building - room H066 | Heidelberglaan 1 | 3584 CS Utrecht | the Netherlands | phone: +31(30) 253 1266 | fax: +31(30) 253 4511 -------------- next part -------------- An HTML attachment was scrubbed... URL: From laetitia.lalla at inserm.fr Tue May 2 16:47:27 2017 From: laetitia.lalla at inserm.fr (laetitia.lalla at inserm.fr) Date: Tue, 02 May 2017 16:47:27 +0200 Subject: [FieldTrip] Granger-Causality in the Time Domain In-Reply-To: References: Message-ID: Dear FieldTrip community, I was looking for a way to perform Granger causality in the time domain with FieldTrip and I found this post from 2014 : "The Granger causality in ft_connectivityanalysis is always frequency-domain Granger (time-domain Granger is not implemented in FieldTrip)." We are in 2017 now, is it still the case ? If yes, could you give me some advice regarding other toolboxes than can compute time-domain Granger causality ? Thank you very much for your help. All the best, Laetitia Lalla -------------- next part -------------- An HTML attachment was scrubbed... URL: From lethuymy at live.com Tue May 2 18:24:17 2017 From: lethuymy at live.com (Thuy-My Le) Date: Tue, 2 May 2017 16:24:17 +0000 Subject: [FieldTrip] ft_spikedetection Message-ID: Hi, My name is Thuy-My. I am new to field trip. I am attempting to use ft_spikedetection on a CTF file. However, when I assign 'matlab' to my cfg.dataformat parameter, I receive an error that the format is not supported. Is this because my input file is CTF? Will it not work regardless if I change the specified dataformat parameter? I have tried all formats listed under ft_write_spike. Please let me know if there is a work around as well. Thanks, Thuy-My -------------------------------------------------------------------- Thuy-My Thi Le University of Pennsylvania School of Engineering and Applied Sciences Department of Bioengineering M.S.E. Class of 2016 -------------- next part -------------- An HTML attachment was scrubbed... URL: From schurgerlab at gmail.com Tue May 2 19:41:22 2017 From: schurgerlab at gmail.com (Schurger Lab) Date: Tue, 2 May 2017 19:41:22 +0200 Subject: [FieldTrip] Post-doctoral position in volition and self-initiated action (MEG / EEG) Message-ID: Interdisciplinary post-doctoral position in cognitive neuroscience (MEG / EEG) Brain-behavior forecasting: Neural antecedents of spontaneous self-initiated movement and the forecasting of behavior based on brain activity, studied with MEG / EEG Starting date: Fall 2017 or Spring 2018 Duration: 2 years (renewable for one additional year) The French Institute of Health and Medical Research (INSERM) invites applications for a post-doctoral position in the Cognitive Neuroimaging Group, at the NeuroSpin Research Center near Paris, France, as part of the research team of Dr. Aaron Schurger. The Schurger lab focuses on understanding how decisions are made and actions initiated spontaneously, without an external sensory cue, and how time series of neural activity can be used to forecast behavior. We pursue this research using a combination of behavioral experiments, neuroimaging, computational modeling, time-series analyses, and machine learning techniques. We are looking for applicants with experience in magnetoencephalography (MEG) experimentation and data analysis, including inverse source estimation. Experience with electroencephalography (EEG) is desirable. Applicants should have obtained a PhD in a relevant discipline prior to the starting date, have a solid working knowledge of cognitive neuroscience, and should have strong skills in the following areas: computer programming (MatLab, Python, C, C++), statistics, signal processing, FieldTrip or comparable data analysis tool Additionally, prior experience in any of the following areas is desirable: computational, mathematical, and/or neural network modeling, statistical learning / machine learning / mutivariate pattern classification, time series analysis, dynamical systems theory, scale-free dynamics, behavioral psychophysics Resources available at NeuroSpin include Siemens 3T and 7T MRI scanners; high-density EEG (EGI Inc.); Elekta NeuroMag 306-channel MEG (allowing for the simultaneous recording of EEG); eye tracking (available for MRI, MEG, and behavioral experiments); an in-house team of experts in signal processing and statistical learning; a dedicated staff handling subject recruitment, scheduling, and payment; various Nespresso devices; and proximity to Paris. Applicants should send a CV, letter of motivation (max 2 pages), and a list of three references via e-mail to schurgerlab at gmail.com. Review of applicants will begin on 15 May 2017, and will continue until the position is filled. The NeuroSpin Research Center is located on the campus of the CEA-Saclay, near Orsay, about 18 km southwest of Paris. For more information on the NeuroSpin Research Center and the Cognitive Neuroimaging Group: http://www-centre-saclay.cea.fr/fr/Visite-guidee-de-NeuroSpin http://meg-france.in2p3.fr/_lesCentres/Neurospin_en.php http://www-dsv.cea.fr/en/institutes/institute-of-biomedical-imaging-i2bm/departments/neurospin-neurospin http://www.unicog.org/pm/pmwiki.php ----------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From cornelia.quaedflieg at uni-hamburg.de Wed May 3 07:37:44 2017 From: cornelia.quaedflieg at uni-hamburg.de (cornelia.quaedflieg at uni-hamburg.de) Date: Wed, 3 May 2017 07:37:44 +0200 Subject: [FieldTrip] apply filter after ft-artefactreject Message-ID: <20170503053745.73475D206E@mailhost.uni-hamburg.de> Dear fieldtrip users, In the pre-processing, we applied a filter for the 50Hz noise (and harmonics) caused by the power supply in our MEG data. During ICA for EOG and ECG correction we noticed in some participants a 50Hz component. That is why we want to apply a bsfilter after ICA correction once more (different filter used the dft filter before). Our idea was to run ft_pre-processing on the cleaned ICA data. However, after running the ft-artefactreject you get an structure and ft_preprocessing doesn’t work with structures as input. An idea about how we could do this is appreciated. Best Dr. Conny Quaedflieg Hamburg University -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed May 3 09:31:51 2017 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 3 May 2017 09:31:51 +0200 Subject: [FieldTrip] apply filter after ft-artefactreject In-Reply-To: <20170503053745.73475D206E@mailhost.uni-hamburg.de> References: <20170503053745.73475D206E@mailhost.uni-hamburg.de> Message-ID: Dear Conny, you can call the preprocessing-options in (more or less) all subsequent functions by using cfg.preproc.XXX So, for example, in the ft_timelockanalysis, you can filter the data by using cfg.preproc.lpfilter = 'yes'; (as well as the other filter settings). However, please be careful with using multiple filters in one dataset. Good luck, Julian Am 03.05.2017 um 07:37 schrieb : > > Dear fieldtrip users, > > In the pre-processing, we applied a filter for the 50Hz noise (and harmonics) caused by the power supply in our MEG data. > During ICA for EOG and ECG correction we noticed in some participants a 50Hz component. > That is why we want to apply a bsfilter after ICA correction once more (different filter used the dft filter before). > Our idea was to run ft_pre-processing on the cleaned ICA data. However, after running the ft-artefactreject you get an structure and ft_preprocessing doesn’t work with structures as input. > > An idea about how we could do this is appreciated. > > Best > > Dr. Conny Quaedflieg > Hamburg 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 495 bytes Desc: Message signed with OpenPGP using GPGMail URL: From bruno.berberian at onera.fr Wed May 3 10:38:07 2017 From: bruno.berberian at onera.fr (Bruno Berberian) Date: Wed, 03 May 2017 10:38:07 +0200 Subject: [FieldTrip] Job opening at the french aerospace lab Message-ID: <590996EF.10200@onera.fr> COGNITIVE ENGINEERING RESEARCHER at ONERA ONERA is the French national aerospace research center. The present position is opened in the “Human-System Integration” team in Salon de Provence. The HSI team is a small (6 permanent peoples, 5 PhD students and 2 postdocs) but growing team. The HSI team is specialized in the design of innovative human-machine interface. It aims to make models of human cognition, perception, multisensory integration and action control and use these models to propose design principles and evaluation methodology. The team follows a multidisciplinary approach and the core competencies include: Cognitive Engineering, Computational Neurosciences, Cognitive Psychology, Human Factors, Electronics and Computer Science. Our collaborations include academic partners in several domains - aeronautic, cognitive science, neuro sciences and cognitive psychology, medicine but also Applied Research institute and industrial partners. You will complete and extend the team abilities. You will be a key contributor to the Human Systems Interaction research area within the HIS team. As a research scientist in Human-Machine Cognition, you’ll be tackling the scientific challenges to integrate new insights in cognitive engineering and computational neurosciences to the design of human machine interface. This involves both applied and basic science. Your primary task involves applying neurosciences knowledge, methodologies, and paradigm to the design of human-machine systems. You will be expected to conduct high-level innovative research, including the publication of research and research supervision. You will collaborate with academia to identify and answer novel research questions, performing research of factors both in isolation and as part of more ecologically valid system. You will also collaborate with industrial partner to perform more applied project. Crucially, you will contribute to initiate new funded research as well as to expand, complement, and collaborate with existing research programs. To be considered for this position, the successful candidate must possess a Ph.D. (by the start of the appointment) in Cognitive Engineering, Computational and Cognitive Neurosciences, Applied Psychology, or Human Factors. Candidates are particularly sought with research interests in one or more of the following areas: perception and multisensory integration, physiological markers of attention/vigilance, models of attention and consciousness, impact of stress and fatigue on human performance. Strong theoretical background in cognitive or computational neurosciences is mandatory. Expertise in handling and analyzing physiological data (EEG, fNIRS, ECG, ..) will be also critical. The position is anticipated to begin in mid-2017. It is a permanent position. To apply, follow this link: http://www.onera.fr/fr/rejoindre-onera/offres-emploi Regards, Berberian Bruno -- Dr Berberian Bruno ONERA The french Aerospace Lab DCSD – PSEV Base Aérienne 701 13661 Salon Air – France Tel. : +33 4 90 17 55 88 Fax : +33 4 90 17 01 09 From na.so.ir at gmail.com Wed May 3 13:20:26 2017 From: na.so.ir at gmail.com (Narjes Soltani) Date: Wed, 3 May 2017 15:50:26 +0430 Subject: [FieldTrip] Cross Frequency Coupling Message-ID: Dear fieldtrip users, Is there any implementation of different kinds of cross frequency coupling already available in fieldtrip? I would be very thankful if any one can share any example of the related coed snippets here. Thanks in advance. Best Narjes -------------- next part -------------- An HTML attachment was scrubbed... URL: From greg at think-now.com Wed May 3 20:53:25 2017 From: greg at think-now.com (GREG SIMPSON) Date: Wed, 3 May 2017 11:53:25 -0700 Subject: [FieldTrip] Post-Doctoral Positions Message-ID: Dear Colleagues - I would like to post the following announcement: *Post-Doctoral Fellow – EEG & Attention* Think Now Incorporated may be seeking 1-2 post-doctoral fellows in the fall of 2017 to work on NIMH funded projects analyzing novel EEG measures of slow fluctuations in sustained attention (10-20 seconds), including data from 400 subjects, and designing an entirely new type of EEG-based feedback system to improve sustained attention. The work will include performing sophisticated EEG data analyses and writing matlab code to create a closed loop feedback system. There is also the potential, as time permits, for exploratory research with machine learning methods to identify EEG activity patterns related to attentional states and their dynamics. We are seeking candidates with a solid background in signal processing, experience with EEG time series, and possibly modeling. We prefer self-directed individuals to take on this work. The successful candidate will work with EEG and signal processing/modeling faculty at UCB and UCLA as well as Dr. Simpson, and be able to regularly interact with other UC post-docs and graduate students. The position reports directly to Gregory V. Simpson, a cognitive neuroscientist and Chief Scientific Officer of Think Now. Think Now is located in San Francisco and is collaborating with faculty at UCB, UCLA and OHSU on these projects. Think Now is focused on creating solutions for the diagnosis and amelioration of neurological and psychiatric disorders with a focus on attention and its control. Please send your CV to jobs at think-now.com with a letter describing your prior experience with sophisticated signal (EEG) analyses and any BCI or modeling methods. Gregory V. Simpson, Ph.D. Think-Now.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From wanglinsisi at gmail.com Thu May 4 02:31:52 2017 From: wanglinsisi at gmail.com (Lin Wang) Date: Wed, 3 May 2017 20:31:52 -0400 Subject: [FieldTrip] how to show notches after plotting ERPs with ft_multiplotER Message-ID: Dear fieldtrip users, Is there a way to show the notches on the x-axis after plotting the ERPs of all channels with ft_multiplotER? I want to have an overview of the ERPs of all channels with the notches on the x-axis. I can only see the notches (i.e., the little bars on the x-axis) after I select a particular channel and view the ERP of that channel. Thanks a lot! Lin -------------- next part -------------- An HTML attachment was scrubbed... URL: From seymourr at aston.ac.uk Thu May 4 12:18:26 2017 From: seymourr at aston.ac.uk (Seymour, Robert (Research Student)) Date: Thu, 4 May 2017 10:18:26 +0000 Subject: [FieldTrip] Cross Frequency Coupling Message-ID: Hi Narjes, The current status of ft_crossfrequencyanalysis can be tracked here: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2523 . It’s not currently implemented in full yet. An alternative is the python library PACPY and associated MATLAB wrapper PACMAT https://github.com/voytekresearch/pacpy. An example of some CFC code (based on the Tort et al 2008 approach) can be found here: https://github.com/neurofractal/PAC_aliens/blob/master/calc_MI.m Good luck! Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From N.vanKlink-2 at umcutrecht.nl Thu May 4 17:05:18 2017 From: N.vanKlink-2 at umcutrecht.nl (Klink-3, N.E.C. van) Date: Thu, 4 May 2017 15:05:18 +0000 Subject: [FieldTrip] Incorrect BEM leadfields Message-ID: Dear all, I am trying SAM beamformer on EEG data, but the results I get are strange. I found out that my BEM model is probably the cause of this, because the leadfields obtained by the model look scattered, see figure. (Black dot is one dipole location, around the head are 60 EEG electrodes with leadfield value for that dipole.) This is the optimum leadfield at optimum orientation as calculated in beamformer_sam. The three original orientations look scattered as well. When I make a similar figure with concentric spheres, the leadfield looks like a dipolar field, as expected. When I make the figure for the simultaneously measured MEG, with the same BEM, the leadfield also looks good. (Probably because MEG doesn't care so much about the headmodel.) I have created my BEM with OpenMEEG (in Windows), BEMcp gives similar results. The meshes look fine to me, and changing the number of vertices to [3000 3000 3000] does not help. Does anyone have an idea what could be the problem here? Thanks in advance, Kind regards, Nicole Some code: %make headmodel cfg = []; cfg.output = {'brain' 'skull' 'scalp'}; seg = ft_volumesegment(cfg, MRI); %create mesh cfg = []; cfg.method = 'projectmesh'; cfg.numvertices = [1000 1500 3000]; cfg.tissue = {'scalp','skull','brain'}; mesh = ft_prepare_mesh(cfg,segi); % compute the subject's headmodel/volume conductor model cfg = []; cfg.method = 'openmeeg'; cfg.tissue = {'brain' 'skull' 'scalp'}; vol = ft_prepare_headmodel(cfg, mesh); vol = ft_convert_units(vol,'cm'); %create grid cfg = []; cfg.grid.pos = load([ptfile filesep pts]); % predetermined grid positions in mm cfg.grid.pos = cfg.grid.pos./10; %make unit = cm cfg.headmodel = vol; cfg.moveinward = 0.01; %check if all grid points are inside the brain grid = ft_prepare_sourcemodel(cfg); % Create leadfields hdr = ft_read_header('data.fif'); cfg = []; cfg.elec = hdr.elec; % electrode positions cfg.headmodel = vol; cfg.grid = grid; cfg.channel = {'EEG', '-EEG043', '-EEG036'}; cfg.normalize = 'column'; lf = ft_prepare_leadfield(cfg); % beamformer cfg=[]; cfg.method = 'sam'; cfg.senstype = 'EEG'; cfg.grid = lf; cfg.headmodel = vol; cfg.sam.lambda = '5%'; cfg.sam.meansphereorigin = 1; %unused but necessary to not crash the script cfg.sam.fixedori = 'robert'; source = ft_sourceanalysis(cfg, timelock); ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. 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Name: BEM_mesh.png Type: image/png Size: 164811 bytes Desc: BEM_mesh.png URL: From Alexander_Nakhnikian at hms.harvard.edu Thu May 4 20:39:24 2017 From: Alexander_Nakhnikian at hms.harvard.edu (Nakhnikian, Alexander) Date: Thu, 4 May 2017 18:39:24 +0000 Subject: [FieldTrip] Interpolation Error with Custom Lead Field Message-ID: Dear All, I'm trying to fine tune a forward model by first constraining the dipoles to the gray matter and then selecting only a subset of structures. It looks as though I need to write a custom script for this, which I have and the commented code is included below. Once I generate the lead field with this code I add it to the cfg structure for ft_sourceanalysis and proceed as usual. The error occurs when I attempt to interpolate the power to a structural MRI. ft_sourceinterpolate(cfg,sources,mri) - cfg.downsample=10; cfg.parameter='pow' - and 'mri' is FT's template structural scan. Calling ft_sourceinterpolate with sources generated using my custom forward model produces this error: Error using interpn (line 153) Wrong number of input arguments. Error in ft_sourceinterpolate>my_interpn (line 693) av(sel) = interpn(fv, ax(sel), ay(sel), az(sel), interpmethod); Error in ft_sourceinterpolate (line 535) interp.inside( sel) = my_interpn(double(functional.inside), ax(sel), ay(sel), az(sel), 'nearest', cfg.feedback); The only hint I've found is that for some reason the source structure returns for this analysis doesn't contain the field '.dim' but I added it manually. Once that's done, the setup looks identical to data returned using a automatically generated grid so I must be missing something. Thanks in advance if anyone can suggest where to look for the bug. Alexander Code: function [lf] = fT_constrainFM(cfg) %Creates a constrained forward model for source analysis in field trip. The %grid is constrained to a surface defined by two maps. One %restrains the dipoles to gray matter and the second is a list of labels corresponding to %ROIs within the GM. %Example: Constrain grey matter to cortical sites of interest. %cfg.roi = labelsNDL; %A cell array of strings with the name of each ROI %cfg.atlas = aal; %aal is a variable returned by ft_readatlas %cfg.inputcoord = 'mni'; %Choose coordinates %cfg.mri = mri; %A template MRI or subject sMRI %cfg.thres = 0.95; %Threshold for probabilistic masks %cfg.lf = C; %C is a structure with fields *.elec and *.headmodel. See %ft_prepareleadfield %[lf] = fT_contrainFM(cfg) mri = cfg.mri; cfgLF = cfg.lf; thres = cfg.thres; cfg = rmfield(cfg,{'mri','thres','lf'}); %Get the masks seg = ft_volumesegment([],mri); tissue = logical(seg.gray>=thres); roiMask = logical(ft_volumelookup(cfg,mri)); voxInds = tissue&roiMask; %dipole placement locations [rows,cols,pages] = ind2sub(size(roiMask),find(voxInds)); cfgLF.pos = zeros(length(rows),3); %adjustment vaues to move the origin rowAd = (size(roiMask,1)-1)/2; colAd = (size(roiMask,2)-1)/2; pageAd = (size(roiMask,3)-1)/2; %collect dipole positions into an Nx3 matrix for posInd = 1:length(rows) cfgLF.pos(posInd,:) = [rows(posInd)-rowAd,cols(posInd)-colAd,pages(posInd)-pageAd]'; end lf = ft_prepare_leadfield(cfgLF); Alexander Nakhnikian, Ph.D. Research Investigator VA Boston Healthcare System Instructor in Psychiatry, Harvard Medical School -------------- next part -------------- An HTML attachment was scrubbed... URL: From ido.davidesco at gmail.com Sat May 6 17:54:38 2017 From: ido.davidesco at gmail.com (Ido Davidesco) Date: Sat, 6 May 2017 11:54:38 -0400 Subject: [FieldTrip] Research Assistant Position - New York University Message-ID: The Poeppel lab at NYU’s Psychology Department is currently seeking a full-time Research Assistant for a National Science Foundation-funded project called “brain-to-brain synchrony in the classroom”. The expected start date for the position is Summer 2017. Application review will take place on a rolling basis until the position is filled. The successful candidate will work closely with the Principal Investigators (Prof. David Poeppel and Prof. Catherine Milne) to execute a complex research protocol, which involves collecting EEG data from multiple participants in a learning setting. As part of the project, we are also developing an EEG-based neuroscience curriculum for high schools. Primary responsibilities include: (1) Participant recruitment and testing; (2) experimental paradigm development; (3) management and analysis of behavioral and neural data; (4) documenting and presenting study results; (5) Project management and administration. A Bachelor's degree in Psychology, Neuroscience or other related fields, and excellent organizational, interpersonal, and communication skills are required. Other preferred qualifications include: - Prior research experience - Teaching and curriculum development experience - Computational, statistical, and technical skills (e.g. Matlab, Python, R) - Experience analyzing EEG and behavioral data Starting date: Summer 2017 Click here for more information about the project. To apply, please send your CV, a cover letter describing your interests and relevant experience, and the contact information of three references to: ido.davidesco at nyu.edu New York University is an Equal Opportunity Employer. New York University is committed to a policy of equal treatment and opportunity in every aspect of its hiring and promotion process without regard to race, color, creed, religion, sex, pregnancy or childbirth (or related medical condition), sexual orientation, partnership status, gender and/or gender identity or expression, marital, parental or familial status, caregiver status, national origin, ethnicity, alienage or citizenship status, veteran or military status, age, disability, predisposing genetic characteristics, domestic violence victim status, unemployment status, or any other legally protected basis. Women, racial and ethnic minorities, persons of minority sexual orientation or gender identity, individuals with disabilities, and veterans are encouraged to apply for vacant positions at all levels. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mehdy.dousty at gmail.com Tue May 9 03:51:24 2017 From: mehdy.dousty at gmail.com (mehdy dousty) Date: Tue, 09 May 2017 01:51:24 +0000 Subject: [FieldTrip] Parcelation source localization In-Reply-To: References: Message-ID: Hello all, I am working on source localization of HCP based on the eLoreta. I am trying to extract time series of Atlas AAL116. So firstly I interpolate the source model to AAL 116 by using: atlas = ft_read_atlas('/Desktop/EEG-1/fieldtrip-20160417/template/atlas/aal/ROI_MNI_V4.nii'); atlas = ft_convert_units(atlas,'mm'); cfg = []; cfg.interpmethod = 'nearest'; cfg.parameter = 'tissue'; individual_sourcemodel3d1 = ft_sourceinterpolate(cfg,atlas,individual_sourcemodel3d); and afterward interpolate the DATA to the parcellated source model by: cfg = []; cfg.parameter = 'pow'; cfg.keeptrials = 'yes'; source_eloreta_disc_int1 = ft_sourceinterpolate(cfg,source_eloreta,individual_sourcemodel3d1); and finally when I try to visualize the data by : cfg = []; cfg.method = 'ortho'; cfg.funparameter = 'pow'; cfg.maskparameter = 'mask'; cfg.funcolorlim = 'auto'; cfg.opacitylim = 'auto'; cfg.opacitymap = 'rampup'; cfg.atlas = atlas; ft_sourceplot(cfg,source_eloreta_disc_int1); I receive an error which says: "there is a mismatch between the coordinate system in the atlas and the coordinate system in the data, which cannot be resolved" I was wondering if anyone could possible help me to solve the issue, and also how accurate my approach is Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.papen at uni-koeln.de Tue May 9 10:44:34 2017 From: m.papen at uni-koeln.de (Michael von Papen) Date: Tue, 9 May 2017 10:44:34 +0200 Subject: [FieldTrip] 2nd CfP: Coupling & Causality in Complex Systems, Sep 25-27, Cologne, Germany Message-ID: ============================================================== 2nd CALL FOR PAPERS (Deadline: June 01, 2017) http://c3s.uni-koeln.de ============================================================== INTERNATIONAL CONFERENCE: *Coupling and Causality in Complex Systems* September 25-27, 2017, Cologne, Germany -------------------------------------------------------------- The interdisciplinary conference Coupling and Causality in Complex Systems (C3S) is hosted by the Competence Area 3: Quantitative Modeling of Complex Systems of the University of Cologne (UoC), Germany. It is organized by the Institute of Geophysics & Meteorology, UoC, the Institute of Clinical Neuroscience and Psychology, Heinrich-Heine University Düsseldorf and the Department of Cognitive Neuroscience at the Research Center Juelich. -------------------------------------------------- *Invited Speakers* Jörg Breitung - Macroeconomic Policy Institute, University of Cologne, Germany David Gross - Institute of Theoretical Physics, University of Cologne, Germany Philip Holmes - Mechanical and Aerospace Engineering / Princeton Neuroscience Institute, Princeton, USA Ankit Khambhati - Department of Bioengineering, University of Pennsylvania, USA Laura Marzetti - Department of Neuroscience, Università degli Studi "G. d'Annunzio" Chieti - Pescara Arkady Pikovsky - Institute of Physics and Astronomy, University Potsdam, Germany Michael Rosenblum - Institute of Physics and Astronomy, University Potsdam, Germany Jakob Runge - The Grantham Institute for Climate Change, Imperial College London -------------------------------------------------- *Preliminary Session Program* We will have different sessions with differing topics and each session will be opened by one of the invited speakers. Here is a preliminary version of our program: Session 1 Synchronization I Arkady Pikovsky Session 2 Synchronization II Silvia Daun Session 3 Coupled oscillators I Phil Holmes Session 4 Coupled oscillators II Michael Rosenblum Session 5 Phase coupling Laura Marzetti Session 6 Network structures Ankit Khambati Session 7 Bayesian networks David Gross Session 8 Granger causality I Jörg Breitung Session 9 Granger causality II Esther Florin Session 10 Causal network measures Jakob Runge Further topics of interest for the conference include, amongst others, research and methods development on: functional connectivity, (partial directed) coherence, network topology, graph-theoretic measures, directed graphs, nonlinear dynamics of complex systems, complex spatio-temporal systems, mutual information and transfer entropy. -------------------------------------------------------------- *Scientific Organizing Committee* Silvia Daun - Institute of Zoology, University of Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany Esther Florin - Institute of Clinical Neuroscience and Psychology, Düsseldorf, Germany Joachim Gross - Center for Cognitive Neuroimaging, Glasgow, UK Michael von Papen - Institute of Geophysics & Meteorology, Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany -------------------------------------------------------------- *Abstract* Complex systems such as the human brain, Earth’s climate and economy are characterized by a multitude of coupled processes on different spatial and temporal scales. In order to better understand the dynamics of the system at hand each scientific area has developed specific tools to identify, model and quantify these processes. The conference Coupling and Causality in Complex Systems (C3S) will present a collection of these approaches with the aim to provide scientists with new analysis strategies for their field. The conference focuses on how to characterize a complex system and on the methods for estimating and modeling of statistical coupling (e.g. network coherence, creation and modulation of small networks and local or long-range synchronization by cross frequency phase-phase and phase-amplitude coupling) and causality (e.g. Granger causality, transfer entropy). Therefore, data analysts from different study fields including neuroscience, mathematics, physics, biology, and economy will present their approaches with a particular focus on the methods they use. The aim of this conference is to foster discussions and the transdisciplinary exchange of advanced techniques, methods, and algorithms, thereby stimulating potential future collaborations. -------------------------------------------------------------- PAPER SUBMISSION AND REGISTRATION Authors are invited to submit conference abstracts with up to 400 words. Authors of exceptional abstracts will be given the opportunity to present their research in a talk. However, poster sessions will be provided with ample time for discussions. For your submission, please use the conference website c3s.uni-koeln.de. To register, please send an email with the subject "registration" to c3s-conference at uni-koeln.de. Please be sure to include your full name, your affiliation and whether you qualify as student (also PhD candidates) or not. The registration fee will cover snacks and refreshments during coffee breaks, lunch and a dinner with all participants. Early-bird registration is available until July 10 with a reduced fee of 100 EUR (50 EUR for students), after July 10 the registration fee will be 200 EUR (100 EUR for students). -------------------------------------------------------------- IMPORTANT DATES Paper Submission deadline: June 01, 2017 Author Notification: mid June, 2017 Early-bird registration: July 10, 2017 Conference: September 25-27, 2017 ============================================================== Please find the call for papers and more information at the conference website: http://c3s.uni-koeln.de. For questions regarding the conference feel free to contact us via c3s-conference at uni-koeln.de. -- ------------------------------------------ UNIVERSITY OF COLOGNE Institute of Geophysics & Meteorology Coordinator of Competence Area III: Quantitative Modeling of Complex Systems Dr. Michael von Papen Email: m.papen at uni-koeln.de http://www.uni-koeln.de/~vpapenm http://complexsystems.uni-koeln.de From andria.pelentritou at gmail.com Wed May 10 01:52:04 2017 From: andria.pelentritou at gmail.com (Andria Pelentritou) Date: Wed, 10 May 2017 09:52:04 +1000 Subject: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data Message-ID: Greetings from Melbourne! We've been using fieldtrip (v-20160801) for a while now and we are having issues when it comes to combining magnetometer and gradiometer MEG sensors types during (LCMV) beamforming for the Elekta Neuromag Triux 306-channel system. Beamforming the magnetometers or gradiometers separately on auditory evoked data works well, but we cannot successfully combine the two sensor types. We've played with the cfg.coilaccuracy variable as advised in one of the tutorials with no luck as there seem to be no obvious effects on the output. The documentation provides very little information on the topic. What strategies would you recommend when trying to combine the Neuromag 306-channel system magnetometer/gradiometer data? Many thanks in advance for your help and many more thanks for releasing such a valuable toolbox! Warm regards Andria -------------- next part -------------- An HTML attachment was scrubbed... URL: From N.vanKlink-2 at umcutrecht.nl Wed May 10 09:33:22 2017 From: N.vanKlink-2 at umcutrecht.nl (Klink-3, N.E.C. van) Date: Wed, 10 May 2017 07:33:22 +0000 Subject: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data Message-ID: Hi Andria, We have been struggling with the same problem, also using a 306-channel Neuromag system. We ended up correcting for the scale difference between magnetometer and gradiometer signals (i.e. noise 5e-15T vs 5e-13T/m). So we multiplied the signals of the magnetometers and the leadfield values of the magnetometers by a factor 100. This gave us the best result. Kind regards, Nicole Van: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] Namens Andria Pelentritou Verzonden: 10 mei 17 1:52 Aan: fieldtrip at science.ru.nl Onderwerp: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data Greetings from Melbourne! We've been using fieldtrip (v-20160801) for a while now and we are having issues when it comes to combining magnetometer and gradiometer MEG sensors types during (LCMV) beamforming for the Elekta Neuromag Triux 306-channel system. Beamforming the magnetometers or gradiometers separately on auditory evoked data works well, but we cannot successfully combine the two sensor types. We've played with the cfg.coilaccuracy variable as advised in one of the tutorials with no luck as there seem to be no obvious effects on the output. The documentation provides very little information on the topic. What strategies would you recommend when trying to combine the Neuromag 306-channel system magnetometer/gradiometer data? Many thanks in advance for your help and many more thanks for releasing such a valuable toolbox! Warm regards Andria ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.hartmann at th-ht.de Wed May 10 10:07:23 2017 From: thomas.hartmann at th-ht.de (Thomas Hartmann) Date: Wed, 10 May 2017 10:07:23 +0200 Subject: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data In-Reply-To: References: Message-ID: hi, i would suggest updating to a recent fieldtrip version. combining mags and grads has been implemented there and you basically do not need to do any extra steps. there are just these three pitfalls that you need to pay attention to because it might lead to wrong results: 1. make sure that you put in the original data. i.e. no prescaling etc. also make sure that you have not modified the .tra matrix of your grad structure. 2. always compute your own leadfield. i.e. always use ft_prepare_leadfield to compute the forward model and don't have it done by ft_sourceanalysis. i don't know if this is absolutely necessary but as the ft_prepare_leadfield step is the one in which the actual pitfalls are, i would strongly suggest you do it separately to have maximum control! 3. all the data going into ft_prepare_leadfield MUST BE in meters! i.e.: 1. the grid mus be either created directly in meters of converted to meters by using ft_convert_unit 2. the grad structure of your data must have been converted to meters. this is something you must do manually as according to my experience, fieldtrip does not take care of it. additionally, the default grad returned by ft_read_sens (and thus the one placed in your data structure) is in centimeters! so, it is a good idea to do something like this: data.grad = ft_convert_data(data.grad, 'm'); right after getting your data via ft_preprocessing! 3. if you provide your grad structure in the cfg structure, also make sure that it is in meters. the meters stuff is really extremely important!!! if your units are wrong, you are going to end up with wrong source projections and will not get an error message!!! if you see some fieldtrip output like: "converting XXX to cm", your results will be wrong! if you take care of all that, fieldtrip does the scaling automatically based on the distance between the two parts of each gradiometer. best, thomas Am 10.05.2017 um 09:33 schrieb Klink-3, N.E.C. van: > > Hi Andria, > > We have been struggling with the same problem, also using a > 306-channel Neuromag system. We ended up correcting for the scale > difference between magnetometer and gradiometer signals (i.e. noise > 5e-15T vs 5e-13T/m). So we multiplied the signals of the magnetometers > and the leadfield values of the magnetometers by a factor 100. This > gave us the best result. > > Kind regards, > > Nicole > > *Van:*fieldtrip-bounces at science.ru.nl > [mailto:fieldtrip-bounces at science.ru.nl] *Namens *Andria Pelentritou > *Verzonden:* 10 mei 17 1:52 > *Aan:* fieldtrip at science.ru.nl > *Onderwerp:* [FieldTrip] combining gradiometer/magnetometer sensors - > neuromag data > > Greetings from Melbourne! > > We've been using fieldtrip (v-20160801) for a while now and we are > having issues when it comes to combining magnetometer and gradiometer > MEG sensors types during (LCMV) beamforming for the Elekta Neuromag > Triux 306-channel system. Beamforming the magnetometers or > gradiometers separately on auditory evoked data works well, but we > cannot successfully combine the two sensor types. We've played with > the cfg.coilaccuracy variable as advised in one of the tutorials with > no luck as there seem to be no obvious effects on the output. The > documentation provides very little information on the topic. > > What strategies would you recommend when trying to combine the > Neuromag 306-channel system magnetometer/gradiometer data? > > Many thanks in advance for your help and many more thanks for > releasing such a valuable toolbox! > Warm regards > Andria > > ------------------------------------------------------------------------ > > /De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is > uitsluitend bestemd voor de geadresseerde. Indien u dit bericht > onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de > afzender direct te informeren door het bericht te retourneren. Het > Universitair Medisch Centrum Utrecht is een publiekrechtelijke > rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en > Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van > Koophandel voor Midden-Nederland onder nr. 30244197. / > > /Denk s.v.p aan het milieu voor u deze e-mail afdrukt. / > > ------------------------------------------------------------------------ > > /This message may contain confidential information and is intended > exclusively for the addressee. If you receive this message > unintentionally, please do not use the contents but notify the sender > immediately by return e-mail. University Medical Center Utrecht is a > legal person by public law and is registered at the Chamber of > Commerce for Midden-Nederland under no. 30244197. / > > /Please consider the environment before printing this e-mail. / > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Dr. Thomas Hartmann Centre for Cognitive Neuroscience FB Psychologie Universität Salzburg Hellbrunnerstraße 34/II 5020 Salzburg Tel: +43 662 8044 5109 Email: thomas.hartmann at th-ht.de "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarang at cfin.au.dk Wed May 10 10:59:39 2017 From: sarang at cfin.au.dk (Sarang S. Dalal) Date: Wed, 10 May 2017 08:59:39 +0000 Subject: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data In-Reply-To: References: Message-ID: <8076147A-E73C-419C-9F07-79B0419EA05E@cfin.au.dk> Dear Andria and Nicole, Combining sensor types (gradiometers and magnetometers, or MEG and EEG) is indeed something that is not documented, and there is not yet a unanimous agreement in the community about how to do this best. But, I can suggest one simple solution that was discussed at a recent beamformer workshop hosted by the Aston MEG Centre in February. (I believe John Mosher made the initial suggestion.) As you probably know, the covariance matrix is an essential ingredient to constructing beamformer solutions. Different sensor types will have different scales and different noise properties, which then complicates the covariance between channels of different types. So, one way around this is to zero out the ‘cross’ terms of the covariance matrix, i.e., set to 0 the elements of the covariance matrix that result from the product of a magnetometer channel and a gradiometer channel. This can be accomplished with something like the following code: timelock = ft_timelockanalysis(cfg, data); [~,megmagidx]=intersect(data.label,ft_channelselection('MEGMAG',data.label)); [~,meggradidx]=intersect(data.label,ft_channelselection('MEGGRAD',data.label)); timelock.cov(meggradidx,megmagidx)=0; timelock.cov(megmagidx,meggradidx)=0; In my experience, this allows source reconstruction using all channels, with results at least as good as analyzing the channels separately. This is not to say that is the best possible solution, but it is a simple one that should work well! Best wishes, Sarang On 10 May 2017, at 09:33, Klink-3, N.E.C. van > wrote: Hi Andria, We have been struggling with the same problem, also using a 306-channel Neuromag system. We ended up correcting for the scale difference between magnetometer and gradiometer signals (i.e. noise 5e-15T vs 5e-13T/m). So we multiplied the signals of the magnetometers and the leadfield values of the magnetometers by a factor 100. This gave us the best result. Kind regards, Nicole Van: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] Namens Andria Pelentritou Verzonden: 10 mei 17 1:52 Aan: fieldtrip at science.ru.nl Onderwerp: [FieldTrip] combining gradiometer/magnetometer sensors - neuromag data Greetings from Melbourne! We've been using fieldtrip (v-20160801) for a while now and we are having issues when it comes to combining magnetometer and gradiometer MEG sensors types during (LCMV) beamforming for the Elekta Neuromag Triux 306-channel system. Beamforming the magnetometers or gradiometers separately on auditory evoked data works well, but we cannot successfully combine the two sensor types. We've played with the cfg.coilaccuracy variable as advised in one of the tutorials with no luck as there seem to be no obvious effects on the output. The documentation provides very little information on the topic. What strategies would you recommend when trying to combine the Neuromag 306-channel system magnetometer/gradiometer data? Many thanks in advance for your help and many more thanks for releasing such a valuable toolbox! Warm regards Andria ________________________________ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ________________________________ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail. _______________________________________________ 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 maurice.goeldi at uzh.ch Wed May 10 11:24:30 2017 From: maurice.goeldi at uzh.ch (maurice.goeldi at uzh.ch) Date: Wed, 10 May 2017 11:24:30 +0200 Subject: [FieldTrip] Unwanted behavior of matlabs randomization functions? Message-ID: Dear Fieldtrippers I have just become aware of a 'feature' in matlabs randomization functions (rand, randi, randn and randperm). Every time matlab is restarted, the seed for the random number generator is reset. Therefore these functions always produce the same number sequence after a restart. This seems a very unintuitive use of these functions. I would think that people who need this reproducability should manually set a seed for their random number generator. Is this behaviour really wanted in FT? I did a quick check and ran ft_freqstatistics with montecarlo method. The stat.posdistribution is obviously different when i run it consecutive times.  However when I restart matlab I get exactly the same distributions again each time. I realize that in a standard analysis pipeline this is probably of absolutely no consequence.  But I still think it should not be that way and one should at least be aware of the fact. Even if it is not an issue for FT-analyses, this might very well be so for experimental procedures. E.g. some experimental stimuli are randomized for each subject. Then they are presented in randomized order. By the time the next subject comes in, chances are high that the computer or at least matlab has been restarted.  This subject will therefore recieve exactly the same 'randomized' list. Mostly these stimuli randomizations are checked by running the randomization script multiple times. So everything seems to work. Up to now at least I have never tested my scripts by restarting matlab after every run. And to catch this within the experiment is potentially impossible, depending on the procedure. Fortunately there is an easy fix for this. rng('shuffle');  before using the randomization function shuffles the seed for the random number generator (hopefully randomly). Even if this is not an issue for FT directly, I think many people do not know about this suboptimal (in my opinion) behaviour of the randomization functions and run into trouble. Appologies if this is an obvious and long known 'feature' to most of you. I hope it still helps some people getting strange results. Cheers Maurice --- University of Zürich Maurice Göldi, MSc Department of Psychology Biopsychology maurice.goeldi at uzh.ch -------------- next part -------------- An HTML attachment was scrubbed... URL: From dimitri.bayle at gmail.com Wed May 10 13:52:57 2017 From: dimitri.bayle at gmail.com (Dimitri Bayle) Date: Wed, 10 May 2017 13:52:57 +0200 Subject: [FieldTrip] Active versus Baseline statisitic on time-domain data Message-ID: <847a589e-b2ec-660b-90d8-7e01ae99fb0e@gmail.com> Hello, I want to do a test in time-domain data, to statistically compare each sample of an active time-windows with an average of the signal in a baseline time-windows. It work perfectly in frequency-domain data with the ft_statfun_actvsblT.m. However, when i try to apply the same test in my time-domain data (dimord = rpt_chan_time), it doesn't work and a realized that the function contain: switch cfg.dimord case 'chan_freq_time' nchan = cfg.dim(1); nfreq = cfg.dim(2); ntime = cfg.dim(3); [nsmpls,nrepl] = size(dat); nsmplsdivntime = floor(nsmpls/ntime); otherwise error('Inappropriate dimord for the statistics function STATFUN_ACTVSBLT.'); end; Is the ft_statfun_actvsblt.m only for time-frequency data? Does anyone has an other statfun function to compare active versus baseline windows in time-domain data. Thanks From v.piai.research at gmail.com Wed May 10 18:37:28 2017 From: v.piai.research at gmail.com (=?UTF-8?Q?Vit=c3=b3ria_Piai?=) Date: Wed, 10 May 2017 18:37:28 +0200 Subject: [FieldTrip] One or more output arguments not assigned during call to "read_16bit" Message-ID: <2c0a0f56-0466-3767-0e5c-f706f77e2677@gmail.com> Hi FT-ers, I'm trying to read a big .edf file (2.16GB), using a recent version, fieldtrip-20170401. I can read the header (attached, if it's of any use). However, when reading the data, I'm getting the following errors. _- If I specify begin and end sample:_ /X = ft_read_data(cfg.dataset,'begsample', 1, 'endsample', 30); /error opening file: /MaterSEEG04-17.edf One or more output arguments not assigned during call to "read_16bit". Error in read_edf>readLowLevel (line 449) buf = read_16bit(filename, offset, numwords); Error in read_edf (line 401) buf = readLowLevel(filename, offset, blocksize); % see below in subfunction Error in ft_read_data (line 683) dat = read_edf(filename, hdr, begsample, endsample, chanindx); _- If I specify channel index:_ /X = ft_read_data(cfg.dataset,'chanindx',chanindx); /Attempted to access EDF.chansel(34); index out of bounds because numel(EDF.chansel)=1. Error in read_edf (line 356) chanindx = EDF.chansel(chanindx); Error in ft_read_data (line 683) dat = read_edf(filename, hdr, begsample, endsample, chanindx);/ / I can then "fix" this error by commenting out line 356 in read_edf, which brings me back to the first error of "read_16bit". This happens on a PC and on a Mac. Something tells me the data isn't being read properly but I can't figure out why. Something with mex files maybe? I couldn't find anything similar in previous threads nor in Bugzilla, for as far as I could see. Any thoughts anyone? I have the data on Dropbox and can send the link if needed. Thanks loads, Vitoria -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hdr.mat Type: application/octet-stream Size: 67215 bytes Desc: not available URL: From a.stolk8 at gmail.com Wed May 10 18:50:34 2017 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Wed, 10 May 2017 09:50:34 -0700 Subject: [FieldTrip] One or more output arguments not assigned during call to "read_16bit" In-Reply-To: <2c0a0f56-0466-3767-0e5c-f706f77e2677@gmail.com> References: <2c0a0f56-0466-3767-0e5c-f706f77e2677@gmail.com> Message-ID: Hey Vitoria, Quick thoughts: what is cfg.dataset here? Is it '/MaterSEEG04-17.edf'? If so, please try without the '/', or specifying the full path location. Vaguely recalling here that read_16bit fails on statements such as '~', and perhaps also '/'. Hoping this was a good gamble. Best, Arjen 2017-05-10 9:37 GMT-07:00 Vitória Piai : > Hi FT-ers, > > I'm trying to read a big .edf file (2.16GB), using a recent version, > fieldtrip-20170401. > I can read the header (attached, if it's of any use). However, when > reading the data, I'm getting the following errors. > > *- If I specify begin and end sample:* > > > *X = ft_read_data(cfg.dataset,'begsample', 1, 'endsample', 30); *error > opening file: /MaterSEEG04-17.edf > One or more output arguments not assigned during call to "read_16bit". > > Error in read_edf>readLowLevel (line 449) > buf = read_16bit(filename, offset, numwords); > > Error in read_edf (line 401) > buf = readLowLevel(filename, offset, blocksize); % see below in > subfunction > > Error in ft_read_data (line 683) > dat = read_edf(filename, hdr, begsample, endsample, chanindx); > > *- If I specify channel index:* > > *X = ft_read_data(cfg.dataset,'chanindx',chanindx); *Attempted to access > EDF.chansel(34); index out of bounds because numel(EDF.chansel)=1. > > Error in read_edf (line 356) > chanindx = EDF.chansel(chanindx); > > Error in ft_read_data (line 683) > dat = read_edf(filename, hdr, begsample, endsample, chanindx); > > I can then "fix" this error by commenting out line 356 in read_edf, which > brings me back to the first error of "read_16bit". This happens on a PC and > on a Mac. Something tells me the data isn't being read properly but I can't > figure out why. Something with mex files maybe? I couldn't find anything > similar in previous threads nor in Bugzilla, for as far as I could see. > > Any thoughts anyone? I have the data on Dropbox and can send the link if > needed. > > Thanks loads, > Vitoria > > _______________________________________________ > 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 v.piai.research at gmail.com Thu May 11 08:08:46 2017 From: v.piai.research at gmail.com (=?UTF-8?Q?Vit=c3=b3ria_Piai?=) Date: Thu, 11 May 2017 08:08:46 +0200 Subject: [FieldTrip] One or more output arguments not assigned during call to "read_16bit" In-Reply-To: References: <2c0a0f56-0466-3767-0e5c-f706f77e2677@gmail.com> Message-ID: <056f91e6-4a9b-999a-3763-c1d9b372d340@gmail.com> Hey Arjen, Brilliant!! Thanks so much for the suggestion, it worked... I'm still having to comment out line 356 (chanindx = EDF.chansel;%(chanindx);), so something is going on but at least now I can work with the data! Thanks again, Vitória On 5/10/2017 6:50 PM, Arjen Stolk wrote: > Hey Vitoria, > > Quick thoughts: what is cfg.dataset here? Is it '/MaterSEEG04-17.edf'? > If so, please try without the '/', or specifying the full path > location. Vaguely recalling here that read_16bit fails on statements > such as '~', and perhaps also '/'. Hoping this was a good gamble. > > Best, > Arjen > > > > > > 2017-05-10 9:37 GMT-07:00 Vitória Piai >: > > Hi FT-ers, > > I'm trying to read a big .edf file (2.16GB), using a recent > version, fieldtrip-20170401. > I can read the header (attached, if it's of any use). However, > when reading the data, I'm getting the following errors. > > _- If I specify begin and end sample:_ > /X = ft_read_data(cfg.dataset,'begsample', 1, 'endsample', 30); > > /error opening file: /MaterSEEG04-17.edf > One or more output arguments not assigned during call to "read_16bit". > > Error in read_edf>readLowLevel (line 449) > buf = read_16bit(filename, offset, numwords); > > Error in read_edf (line 401) > buf = readLowLevel(filename, offset, blocksize); % see below > in subfunction > > Error in ft_read_data (line 683) > dat = read_edf(filename, hdr, begsample, endsample, chanindx); > > _- If I specify channel index:_ > /X = ft_read_data(cfg.dataset,'chanindx',chanindx); > /Attempted to access EDF.chansel(34); index out of bounds because > numel(EDF.chansel)=1. > > Error in read_edf (line 356) > chanindx = EDF.chansel(chanindx); > > Error in ft_read_data (line 683) > dat = read_edf(filename, hdr, begsample, endsample, chanindx);/ > / > I can then "fix" this error by commenting out line 356 in > read_edf, which brings me back to the first error of "read_16bit". > This happens on a PC and on a Mac. Something tells me the data > isn't being read properly but I can't figure out why. Something > with mex files maybe? I couldn't find anything similar in previous > threads nor in Bugzilla, for as far as I could see. > > Any thoughts anyone? I have the data on Dropbox and can send the > link if needed. > > Thanks loads, > Vitoria > > _______________________________________________ > 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 francois.tadel at mcgill.ca Thu May 11 12:26:31 2017 From: francois.tadel at mcgill.ca (=?UTF-8?Q?Fran=c3=a7ois_Tadel?=) Date: Thu, 11 May 2017 12:26:31 +0200 Subject: [FieldTrip] Correspondence channels-coils in HCP files Message-ID: <09bb7e15-f314-607c-e7e7-480f5a9d914e@mcgill.ca> Hello, I wrote a FieldTrip>Brainstorm import function based on Elekta files, and I was using the .tra matrix to get the correspondence between the channels and the coils: https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/io/in_data_fieldtrip.m#L107 I based this code on your description of the .tra field: "NxM matrix with the weight of each coil into each channel": http://www.fieldtriptoolbox.org/faq/how_are_electrodes_magnetometers_or_gradiometers_described This doesn't work with the processed 4D recordings from the HCP dataset because the .tra matrix is dense. Is this because the 4D compensation matrix is integrated in this .tra matrix? Or because there is some additional PCA/ICA projection done during the preprocessing? How do I recover the sparse .tra information that simply contains the weights channels-coils from the HCP processed files? Thanks, François -- François Tadel, MSc MEG / McConnell Brain Imaging Center / MNI / McGill University 3801 rue University, Montreal, QC H3A2B4, Canada From stefanwiens at gmail.com Thu May 11 16:17:13 2017 From: stefanwiens at gmail.com (Stefan Wiens) Date: Thu, 11 May 2017 16:17:13 +0200 Subject: [FieldTrip] reading offsets from Biosemi bdf file Message-ID: Hi! I am Stefan Wiens and am working with EEG in Stockholm, Sweden. ( people.su.se/~swiens/) I use a Cedrus Stimtracker to track visual events with a light diode and a TTL output to the Biosemi system. The onsets are save nicely in the bdf. I would also like to check duration by tracking not only onsets but also offsets. I tried the following but received a warning. event = ft_read_event(cfg.dataset, 'detectflank', 'both'); Warning: only up-going flanks are supported for Biosemi Do I understand correctly that there is not (reasonable) way to extract offsets? (I already have a work around by having a different picture at the offset of the first. This work but a direct approach with onset and offset might be better. Thanks for your input! Stefan -------------- next part -------------- An HTML attachment was scrubbed... URL: From u.pomper at ucl.ac.uk Thu May 11 19:21:42 2017 From: u.pomper at ucl.ac.uk (Pomper, Ulrich) Date: Thu, 11 May 2017 17:21:42 +0000 Subject: [FieldTrip] Rotating sensors using ft_transform_sens Message-ID: Dear Listmembers, Could someone please explain how to use ft_transform_sens in order to rotate sensors around a given axis? For example, how would the input variable 'transform' need to look like in order to perform a 90 degree rotation around the z-axis? Many thanks, Ulrich -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Fri May 12 09:44:01 2017 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 12 May 2017 09:44:01 +0200 Subject: [FieldTrip] Rotating sensors using ft_transform_sens In-Reply-To: References: Message-ID: Dear Ulrich, could you use ft_electroderealign with the interactive-option instead? Here you have an graphic interface that lets you rotate the electrodes in all directions to match your headshape. ft_transform_sens is used in this function, so the output should be the same. Moreover, if you check the code of ft_electroderealign, it can give you a hint to what the transform-matrix should look like: I think it should be a 3x3-matrix with scale, transform and rotate xyz-vectors. I hope this helps, Julian Am 11.05.2017 um 19:21 schrieb Pomper, Ulrich: > Dear Listmembers, > > Could someone please explain how to use ft_transform_sens in order to rotate sensors around a given axis? > For example, how would the input variable 'transform' need to look like in order to perform a 90 degree rotation around the z-axis? > > Many thanks, > Ulrich > > _______________________________________________ > 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: signature.asc Type: application/pgp-signature Size: 495 bytes Desc: Message signed with OpenPGP using GPGMail URL: From cornelia.quaedflieg at uni-hamburg.de Fri May 12 23:47:08 2017 From: cornelia.quaedflieg at uni-hamburg.de (cornelia.quaedflieg at uni-hamburg.de) Date: Fri, 12 May 2017 23:47:08 +0200 Subject: [FieldTrip] cluster based permutation tests - grandaverage - grad structure Message-ID: <20170512214709.BDD13F2D44@mailhost.uni-hamburg.de> Dear fieldtrip users,    we are having troubles running the cluster based permutation tests for MEG data analysis. We tried to run ft_freqstatistics for previously calculated grandaverages over subjects in two conditions. However, we are not sure how to specify cfg.neighbours. The grandaverage datasets in the fieldtrip tutorial contain a gradiometer structure, which is probably used to prepare neighbouring channels. When we run ft_freqgrandaverages on our data, this grad structure disappears because it cannot be averaged over subjects. Thus, we were wondering if there is a way to keep the gradiometer information in the averaged data or to append an example grad structure later on?   We appreciate any suggestions on that matter. Thank you in advance!   Best Dr Conny Quaedflieg & Hanna Stoffregen Hamburg University -------------- next part -------------- An HTML attachment was scrubbed... URL: From mailtome.2113 at gmail.com Sat May 13 16:18:27 2017 From: mailtome.2113 at gmail.com (Arti Abhishek) Date: Sun, 14 May 2017 00:18:27 +1000 Subject: [FieldTrip] Alternatives to cluster based permutation test Message-ID: Dear list, I was wondering whether it is appropriate to use cluster permutation tests on 32 channel ERP data. I am working on visual ERP response to text stimuli, and since there are only few electrodes I am expecting a focal effect (on P7 and P8). I was wondering whether it is appropriate to use cluster statistics here. If not, what test do you suggest? Thank you, Arti -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Sat May 13 18:10:08 2017 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Sat, 13 May 2017 17:10:08 +0100 Subject: [FieldTrip] randsample.m from fieldtrip toolbox does not work properly In-Reply-To: <3768651157128871.WA.violinist811googlemail.com@www.jiscmail.ac.uk> References: <3768651157128871.WA.violinist811googlemail.com@www.jiscmail.ac.uk> Message-ID: Dear Yuan-hao, I'm not sure whether what you found is a bug but the best way to report it is via http://bugzilla.fieldtriptoolbox.org . I also CC your e-mail to Fieldtrip mailing list. Best, Vladimir On Fri, May 12, 2017 at 9:18 PM, Yuan-hao Wu <00000a54691459fb-dmarc- request at jiscmail.ac.uk> wrote: > Dear all, > > I just want to inform you that the randsample.m function that is included > in the spm12/fieldtrip toolbox does not work properly. > It only draw samples WITH replacement. > > Best, > Yuan-hao > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanwiens at gmail.com Sun May 14 10:31:34 2017 From: stefanwiens at gmail.com (Stefan Wiens) Date: Sun, 14 May 2017 10:31:34 +0200 Subject: [FieldTrip] bug in ft_rejectvisual()? Message-ID: Hi! I downloaded a new version of ft last week (fieldtrip-20170511). I run these simple commands: cfg = []; cfg.layout = 'biosemi64.lay'; cfg.metric = 'range'; cfg.latency = [-.1 .6]; ft_rejectvisual(cfg, data); The plot seems to work, but when I want to plot a specific trial ("Plot trial", to the left of the quit button), ft does not plot the trial number I entered; instead, it plots the LAST trial. The matlab output actually states that whereas the figure title states the trial number that I entered. I remember that this worked well before, so maybe I am doing something wrong? Best Stefan Wiens people.su.se/~swiens/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From u.pomper at ucl.ac.uk Sun May 14 13:36:13 2017 From: u.pomper at ucl.ac.uk (Pomper, Ulrich) Date: Sun, 14 May 2017 11:36:13 +0000 Subject: [FieldTrip] Rotating sensors using ft_transform_sens In-Reply-To: References: , Message-ID: Dear Julian, Thanks a lot for your help! >From looking into the function as you suggested, it seems the transformation matrix is actually 4 dimensional, with one extra dimension for scaling. I managed to rotate the sensors but they are still quite far away from the headvolume. I tried using ft_sensorrealign (MEG equivalent of ft_electroderealign) but am getting an errormessage Undefined function or variable "pnt". Error in channelposition (line 327) pnt = pnt(sel2, :); which I haven't had time to follow up yet. I will post more once I have looked into it. Anyway, thanks again for the help so far. Cheers, Ulrich ________________________________ From: fieldtrip-bounces at science.ru.nl on behalf of Julian Keil Sent: 12 May 2017 08:44 To: FieldTrip discussion list Subject: Re: [FieldTrip] Rotating sensors using ft_transform_sens Dear Ulrich, could you use ft_electroderealign with the interactive-option instead? Here you have an graphic interface that lets you rotate the electrodes in all directions to match your headshape. ft_transform_sens is used in this function, so the output should be the same. Moreover, if you check the code of ft_electroderealign, it can give you a hint to what the transform-matrix should look like: I think it should be a 3x3-matrix with scale, transform and rotate xyz-vectors. I hope this helps, Julian Am 11.05.2017 um 19:21 schrieb Pomper, Ulrich: Dear Listmembers, Could someone please explain how to use ft_transform_sens in order to rotate sensors around a given axis? For example, how would the input variable 'transform' need to look like in order to perform a 90 degree rotation around the z-axis? Many thanks, Ulrich _______________________________________________ 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 laxmi.shaw22 at gmail.com Mon May 15 13:17:42 2017 From: laxmi.shaw22 at gmail.com (Laxmi Shaw) Date: Mon, 15 May 2017 16:47:42 +0530 Subject: [FieldTrip] fieldtrip Digest, Vol 78, Issue 13 In-Reply-To: References: Message-ID: Dear Fieldtrip Users, I am using fieldtrip plot function, and it was running fine. Last two days back the code is showing some error, and I am not able to figure it out. Could you please help me in this regard. I have attached the screen shot of that error window. Please find the screenshot. Thanks and Regards[image: Inline image 1] On Mon, May 15, 2017 at 3:30 PM, wrote: > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: Rotating sensors using ft_transform_sens (Pomper, Ulrich) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 14 May 2017 11:36:13 +0000 > From: "Pomper, Ulrich" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Rotating sensors using ft_transform_sens > Message-ID: > eurprd01.prod.exchangelabs.com> > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Julian, > > > Thanks a lot for your help! > > >From looking into the function as you suggested, it seems the > transformation matrix is actually 4 dimensional, with one extra dimension > for scaling. I managed to rotate the sensors but they are still quite far > away from the headvolume. > > I tried using ft_sensorrealign (MEG equivalent of ft_electroderealign) but > am getting an errormessage > > > Undefined function or variable "pnt". > > Error in channelposition (line 327) > pnt = pnt(sel2, :); > > > > which I haven't had time to follow up yet. I will post more once I have > looked into it. > > Anyway, thanks again for the help so far. > > > Cheers, > > Ulrich > > > > ________________________________ > From: fieldtrip-bounces at science.ru.nl > on behalf of Julian Keil > Sent: 12 May 2017 08:44 > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Rotating sensors using ft_transform_sens > > Dear Ulrich, > > could you use ft_electroderealign with the interactive-option instead? > Here you have an graphic interface that lets you rotate the electrodes in > all directions to match your headshape. > ft_transform_sens is used in this function, so the output should be the > same. > Moreover, if you check the code of ft_electroderealign, it can give you a > hint to what the transform-matrix should look like: I think it should be a > 3x3-matrix with scale, transform and rotate xyz-vectors. > > I hope this helps, > > Julian > > > Am 11.05.2017 um 19:21 schrieb Pomper, Ulrich: > > Dear Listmembers, > > Could someone please explain how to use ft_transform_sens in order to > rotate sensors around a given axis? > For example, how would the input variable 'transform' need to look like in > order to perform a 90 degree rotation around the z-axis? > > Many thanks, > Ulrich > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20170514/c4c91a75/attachment-0001.html> > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 78, Issue 13 > ***************************************** > -- Laxmi Shaw Research Scholar(PhD) IIT Kharagpur West Bengal Ph no-08388837821 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Error_fig.png Type: image/png Size: 130728 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Error_fig.png Type: image/png Size: 130728 bytes Desc: not available URL: From david.m.groppe at gmail.com Mon May 15 16:24:20 2017 From: david.m.groppe at gmail.com (David Groppe) Date: Mon, 15 May 2017 10:24:20 -0400 Subject: [FieldTrip] Alternatives to cluster based permutation test In-Reply-To: References: Message-ID: Hi Arti, For very focal effects, the tmax permutation test and Benjamini & Hochberg false discovery rate (FDR) control algorithm are more powerful than cluster-based permutation tests: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4059014/ cheers, -David On Sat, May 13, 2017 at 10:18 AM, Arti Abhishek wrote: > Dear list, > > I was wondering whether it is appropriate to use cluster permutation tests > on 32 channel ERP data. I am working on visual ERP response to text > stimuli, and since there are only few electrodes I am expecting a focal > effect (on P7 and P8). I was wondering whether it is appropriate to use > cluster statistics here. If not, what test do you suggest? > > Thank you, > 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 HEROBINSON at augusta.edu Mon May 15 16:30:37 2017 From: HEROBINSON at augusta.edu (Robinson, Heath) Date: Mon, 15 May 2017 14:30:37 +0000 Subject: [FieldTrip] [EXTERNAL] Re: Alternatives to cluster based permutation test In-Reply-To: References: Message-ID: I tried to save my profile and it is sying that I am logged in as Anonymous. I logged out and logged back in and it did the same thing. From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of David Groppe Sent: Monday, May 15, 2017 10:24 AM To: FieldTrip discussion list Subject: [EXTERNAL] Re: [FieldTrip] Alternatives to cluster based permutation test This is an external email. Use caution responding, opening attachments and following links. Hi Arti, For very focal effects, the tmax permutation test and Benjamini & Hochberg false discovery rate (FDR) control algorithm are more powerful than cluster-based permutation tests: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4059014/ cheers, -David On Sat, May 13, 2017 at 10:18 AM, Arti Abhishek > wrote: Dear list, I was wondering whether it is appropriate to use cluster permutation tests on 32 channel ERP data. I am working on visual ERP response to text stimuli, and since there are only few electrodes I am expecting a focal effect (on P7 and P8). I was wondering whether it is appropriate to use cluster statistics here. If not, what test do you suggest? Thank you, 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 elam4hcp at gmail.com Mon May 15 19:37:09 2017 From: elam4hcp at gmail.com (Jennifer Elam) Date: Mon, 15 May 2017 12:37:09 -0500 Subject: [FieldTrip] Reminder to Register for HCP Course 2017 Message-ID: Only a few spaces remain for the *2017 HCP Course: "Exploring the Human Connectome"*. For more info and to register: https://store.humanconnectome. org/courses/2017/exploring-the-human-connectome.php Don't forget to also reserve your accommodation for the course by May 17, 2017 to be sure of securing a room on the UBC campus in the HCP Course room block. Before or after May 17, 2017, please use this link to make a reservation: https://reserve.ubcconferences.com/vancouver/availability.asp?hotelCode=%2A&startDate=06%2F18%2F2017&endDate=06%2F23%2F2017&adults=1&children=&rooms=1&requesttype=invBlockCode&code=G170618A HCP Course 2017 will be held June 19-23 (week before OHBM) at the Djavad Mowafagian Centre for Brain Health at University of British Columbia (UBC) in Vancouver, BC, Canada. The 5-day intensive course of lectures and hands-on practicals is a great opportunity to learn directly from HCP investigators about using HCP data, acquisition, processing methods, and software tools in your own studies. If you have any questions, please contact us at: hcpcourse at humanconnectome. org We look forward to seeing you in Vancouver! Best, 2017 HCP Course Staff -- 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 laxmi.shaw22 at gmail.com Tue May 16 05:48:00 2017 From: laxmi.shaw22 at gmail.com (Laxmi Shaw) Date: Tue, 16 May 2017 09:18:00 +0530 Subject: [FieldTrip] Some plotting error Message-ID: * Dear community, **I have a data such that every channel has 1 value that is result of some **calculation(I mean I have 14 channel thus a data vector of length14).I want **to plot map of head how? every channel has a color corresponding its? **value... **I tried using? ft_topoplotER to assess my data and I made the true layout ** but when I want to use ft_topoplotER receive the following error message:? **Subscript indices must either be real positive integers or logicals. ** Error in topoplot_common (line 79) ** data = varargin{indx}; **Error in ft_topoplotER (line 169) ** cfg = topoplot_common(cfg, varargin{:}); ** Error in top (line 19) **figure; ft_topoplotER(cfg,data); colorbar;? ** Could you please help to fix this problem How to remove this error.* *Thanks and Regards * Laxmi Shaw Research Scholar(PhD) IIT Kharagpur West Bengal Ph no-08388837821 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Patrick.Rollo at uth.tmc.edu Tue May 16 18:24:24 2017 From: Patrick.Rollo at uth.tmc.edu (Rollo, Patrick) Date: Tue, 16 May 2017 16:24:24 +0000 Subject: [FieldTrip] Job posting on FieldTrip message board Message-ID: FieldTrip, I have a job posting that I would like to make on this message board, our lab, Tandon Lab, has posted in the past. The advert is attached here. Please let me know if you have any questions, Thank you, Patrick Rollo -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Postdocs_U01_updated 5:17.pdf Type: application/pdf Size: 236167 bytes Desc: Postdocs_U01_updated 5:17.pdf URL: From stephen.whitmarsh at gmail.com Wed May 17 16:46:53 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Wed, 17 May 2017 16:46:53 +0200 Subject: [FieldTrip] source pos dimensions ft_sourcestatistics Message-ID: Hi there, After beamformer sourceanalysis I end up with datastructures looking like: struct with fields: freq: 10.5000 cfg: [1×1 struct] pos: [2982×3 double] pow: [2982×1 double] inside: [2982×1 logical] powdimord: 'pos' The .inside field is created by ft_selectdata used to average across frequencies, and contains all 1s. Running sourceanalysis with this data trows the following error: Error using spm_bwlabel spm_bwlabel: CONN must be 6, 18 or 26 Error in clusterstat (line 222) [negclusobs, negnum] = spm_bwlabel(tmp, 2*numdims); Error in ft_statistics_montecarlo (line 347) [stat, cfg] = clusterstat(cfg, statrand, statobs); Error in ft_sourcestatistics (line 205) [stat, cfg] = statmethod(cfg, dat, design); *222 * [negclusobs, negnum] = spm_bwlabel(tmp, 2*numdims); I think this results because of a wrong estimate of the dimensionality, resulting from the fact that the data is represented in an array rather than a 3-dimensional matrix, which it seems to expect. I think therefor that I might need to convert my data back into a 3-d representation, i..e not a sparse but full representation. I have tried using ft_source2full, but that is not straightforward as I only have inside voxels/positions. In other words, I would need to do exactly the same as ft_source_statistics seems to want to do with spm_bwlabel. So I guess I might just have put FieldTrip on the wrong leg, to use a Dutch expression. Any suggestions? Best, Stephen -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu May 18 21:35:38 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 18 May 2017 19:35:38 +0000 Subject: [FieldTrip] source pos dimensions ft_sourcestatistics In-Reply-To: References: Message-ID: <4EF37F95-710B-4EAC-8FE5-786964346094@donders.ru.nl> Hi Stephen, source2full and source2sparse are probably quite outdated, and do not seem to work well anymore with the latest type of source-level data structures. Most relevantly, the inside field these days is by default a boolean vector of size nposx1, whereas once upon a time the inside and outside fields together contained the indices of the dipole positions, indicating which positions are on the in-/outside. Do you need the source2sparse step to begin with? Best, JM On 17 May 2017, at 16:46, Stephen Whitmarsh > wrote: Hi there, After beamformer sourceanalysis I end up with datastructures looking like: struct with fields: freq: 10.5000 cfg: [1×1 struct] pos: [2982×3 double] pow: [2982×1 double] inside: [2982×1 logical] powdimord: 'pos' The .inside field is created by ft_selectdata used to average across frequencies, and contains all 1s. Running sourceanalysis with this data trows the following error: Error using spm_bwlabel spm_bwlabel: CONN must be 6, 18 or 26 Error in clusterstat (line 222) [negclusobs, negnum] = spm_bwlabel(tmp, 2*numdims); Error in ft_statistics_montecarlo (line 347) [stat, cfg] = clusterstat(cfg, statrand, statobs); Error in ft_sourcestatistics (line 205) [stat, cfg] = statmethod(cfg, dat, design); 222 [negclusobs, negnum] = spm_bwlabel(tmp, 2*numdims); I think this results because of a wrong estimate of the dimensionality, resulting from the fact that the data is represented in an array rather than a 3-dimensional matrix, which it seems to expect. I think therefor that I might need to convert my data back into a 3-d representation, i..e not a sparse but full representation. I have tried using ft_source2full, but that is not straightforward as I only have inside voxels/positions. In other words, I would need to do exactly the same as ft_source_statistics seems to want to do with spm_bwlabel. So I guess I might just have put FieldTrip on the wrong leg, to use a Dutch expression. Any suggestions? Best, Stephen _______________________________________________ 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 D.C.W.Klooster at tue.nl Thu May 18 22:10:20 2017 From: D.C.W.Klooster at tue.nl (Klooster, D.C.W.) Date: Thu, 18 May 2017 20:10:20 +0000 Subject: [FieldTrip] Error loreta2fieldtrip Message-ID: <94D6E99297013F46990EEBA320449F617D02D71A@xserver30b.campus.tue.nl> Dear fieldtrip users, Hopefully this is an easy to solve issue for some of you... If I run loreta2fieldtrip I get an accute error that ft_preamble_callinfo is not known. Indeed, I can not find this anywhere within my fieldtrip folder. Am I doing something wrong or do I really need these files (same holds for ft_postamble_callinfo). If so, can anybody provide me the files? Thank you! Best regards, Debby -------------- next part -------------- An HTML attachment was scrubbed... URL: From seymourr at aston.ac.uk Fri May 19 08:46:08 2017 From: seymourr at aston.ac.uk (Seymour, Robert (Research Student)) Date: Fri, 19 May 2017 06:46:08 +0000 Subject: [FieldTrip] Inter-trial Coherence Stats Message-ID: Dear Fieldtrippers, I am trying to statistically evaluate inter-trial coherence on a virtual electrode, comparing an active to baseline period. However I get the following error when using 'diff_ITC' and ft_freqstatistics: Subscripted assignment dimension mismatch. Error in ft_freqstatistics (line 141) dat(:,i) = tmp(:); I can't seem to figure out what's going wrong... (code below). Has anyone else come across this error? Many thanks, Robert %% Script to calculate inter-trial coherence for the alien clicktrain data subject = sort({'RS','DB','MP','GR','DS','EC','VS','LA','AE','SY','GW',... 'SW','DK','LH','KM','FL','AN'}); grandavgA = zeros(1,length(subject)); grandavgB = zeros(1,length(subject)); for i = 1:length(subject) load(['D:\Pilot\' subject{i} '\auditory\sourceloc\VE_A1_RH.mat']); cfg = []; cfg.foi = [30:1:80]; cfg.method = 'mtmconvol'; cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; cfg.tapsmofrq = ones(length(cfg.foi),1).*8; cfg.toi = 0:0.01:1.5; cfg.output = 'fourier'; freq_post = (ft_freqanalysis(cfg, VE_A1_RH)); freq_post.fourierspctrm = (freq_post.fourierspctrm); grandavgA{i} = freq_post; cfg.toi = -1.5:0.01:0; freq_pre = (ft_freqanalysis(cfg, VE_A1_RH)); freq_pre.fourierspctrm = (freq_pre.fourierspctrm); grandavgB{i} = freq_pre; end cfg = []; cfg.latency = [0 1.5]; cfg.parameter = 'fourierspctrm'; cfg.frequency = [30 80]; cfg.method = 'montecarlo'; cfg.statistic = 'diff_ITC' cfg.clusterstatistic = 'maxsum'; cfg.tail = 0; cfg.alpha = 0.05; cfg.numrandomization = 1000; % Create design matrix based on specific number of trials from each % participant nsubj=numel(grandavgA); cfg.design(1,:) = [1:nsubj 1:nsubj]; cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2]; cfg.uvar = 1; % row of design matrix that contains unit variable (in this case: subjects) cfg.ivar = 2; % row of design matrix that contains independent variable (the conditions) [stat] = ft_freqstatistics(cfg, grandavgA{:}, grandavgB{:}); -------------- next part -------------- An HTML attachment was scrubbed... URL: From CXK699 at student.bham.ac.uk Fri May 19 09:36:43 2017 From: CXK699 at student.bham.ac.uk (Casper Kerren) Date: Fri, 19 May 2017 07:36:43 +0000 Subject: [FieldTrip] Inter-trial Coherence Stats In-Reply-To: References: Message-ID: <817B246999EC6E49AFEEDFCEC604EED83C5111E7@EX11.adf.bham.ac.uk> Dear Robert, Not sure whether I will give an appropriate answer to your question, but it seems like Fieldtrip doesn't like .fourierspctrm, and you could change it to powerspctrm yourself. Like this: For each participant run the ft_freqanalysis with your specified parameters. Get the output 'freq' and then a = freq.fourierspctrm; tmpli = abs(mean(a./abs(a),1)); % "manually" compute PLI freq.powspctrm = squeeze(tmpli); freq.dimord = 'chan_freq_time'; freq = rmfield(freq, 'fourierspctrm'); % remove field "fourierspctrm" because it confuses Fieldtrip freq = rmfield(freq, 'trialinfo'); % trialinfo no longer valid Of course, when you later run statistics use cfg.parameter = 'powspctrm' If this wasn't what you were looking for, let me know. Kind regards, Casper From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Seymour, Robert (Research Student) Sent: 19 May 2017 07:46 To: fieldtrip at science.ru.nl Subject: [FieldTrip] Inter-trial Coherence Stats Dear Fieldtrippers, I am trying to statistically evaluate inter-trial coherence on a virtual electrode, comparing an active to baseline period. However I get the following error when using 'diff_ITC' and ft_freqstatistics: Subscripted assignment dimension mismatch. Error in ft_freqstatistics (line 141) dat(:,i) = tmp(:); I can't seem to figure out what's going wrong... (code below). Has anyone else come across this error? Many thanks, Robert %% Script to calculate inter-trial coherence for the alien clicktrain data subject = sort({'RS','DB','MP','GR','DS','EC','VS','LA','AE','SY','GW',... 'SW','DK','LH','KM','FL','AN'}); grandavgA = zeros(1,length(subject)); grandavgB = zeros(1,length(subject)); for i = 1:length(subject) load(['D:\Pilot\' subject{i} '\auditory\sourceloc\VE_A1_RH.mat']); cfg = []; cfg.foi = [30:1:80]; cfg.method = 'mtmconvol'; cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; cfg.tapsmofrq = ones(length(cfg.foi),1).*8; cfg.toi = 0:0.01:1.5; cfg.output = 'fourier'; freq_post = (ft_freqanalysis(cfg, VE_A1_RH)); freq_post.fourierspctrm = (freq_post.fourierspctrm); grandavgA{i} = freq_post; cfg.toi = -1.5:0.01:0; freq_pre = (ft_freqanalysis(cfg, VE_A1_RH)); freq_pre.fourierspctrm = (freq_pre.fourierspctrm); grandavgB{i} = freq_pre; end cfg = []; cfg.latency = [0 1.5]; cfg.parameter = 'fourierspctrm'; cfg.frequency = [30 80]; cfg.method = 'montecarlo'; cfg.statistic = 'diff_ITC' cfg.clusterstatistic = 'maxsum'; cfg.tail = 0; cfg.alpha = 0.05; cfg.numrandomization = 1000; % Create design matrix based on specific number of trials from each % participant nsubj=numel(grandavgA); cfg.design(1,:) = [1:nsubj 1:nsubj]; cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2]; cfg.uvar = 1; % row of design matrix that contains unit variable (in this case: subjects) cfg.ivar = 2; % row of design matrix that contains independent variable (the conditions) [stat] = ft_freqstatistics(cfg, grandavgA{:}, grandavgB{:}); -------------- next part -------------- An HTML attachment was scrubbed... URL: From Simon.VanEyndhoven at esat.kuleuven.be Fri May 19 13:51:10 2017 From: Simon.VanEyndhoven at esat.kuleuven.be (Simon Van Eyndhoven) Date: Fri, 19 May 2017 13:51:10 +0200 Subject: [FieldTrip] Interpretation of Granger spectrum and link with directed coherence Message-ID: <99d3059295300fb8c2d53e4f1ae6f145@esat.kuleuven.be> Dear FieldTrip community, As a novice in EEG connectivity analysis, I am trying to reproduce and understand the connectivity tutorial of the website (http://www.fieldtriptoolbox.org/tutorial/connectivity). I was hoping that someone could shed light on the computation of the Granger frequency spectrum: cfg = []; cfg.method = 'granger'; granger = ft_connectivityanalysis(cfg, mfreq); More specifically, I would like to know which computations are done to obtain the values in granger.grangerspctrm. (Unfortunately, inspecting the paper by Brovelli et al. PNAS (2004), as indicated in ft_connectivity_granger did not clear this up...) Moreover, I wonder what the relationship is between the Granger spectrum and other metrics such as (partial) directed coherence (DC / PDC) and directed transfer function (DTF), which also provide connectivity information in the form channels x channels x frequencies? In the appendix in Van Mierlo et al., "Functional brain connectivity from EEG in epilepsy: Seizure prediction and epileptogenic focus localization" and in Baccala and Sameshima, "Partial directed coherence: a new concept in neural structure determination", it is explained that both DC and DTF are computed using the transfer function matrix H(f), while PDC is computed using the A(f) matrix. Is this the reason why only PDC is termed 'partial', and the others not (even though they are also computed in a multivariate framework, i.e. taking all available variables into account)? Although I could not find an answer to my questions in the mailing archives, I apologize if this question has been asked before. Thank you in advance for your help! Best regards, Simon From jan.schoffelen at donders.ru.nl Fri May 19 14:12:48 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 19 May 2017 12:12:48 +0000 Subject: [FieldTrip] Interpretation of Granger spectrum and link with directed coherence In-Reply-To: <99d3059295300fb8c2d53e4f1ae6f145@esat.kuleuven.be> References: <99d3059295300fb8c2d53e4f1ae6f145@esat.kuleuven.be> Message-ID: <0E539AF5-0DC8-4D03-A4EB-4B0ED7255E6D@donders.ru.nl> Hi Simon, You may want to check the ‘connectivity’ section in the following link: http://www.fieldtriptoolbox.org/references_to_implemented_methods It contains links to papers that might be relevant for you. I’d start from the first one, sorry for the shameless self-promotion. Best, Jan-Mathijs > On 19 May 2017, at 13:51, Simon Van Eyndhoven wrote: > > Dear FieldTrip community, > > As a novice in EEG connectivity analysis, I am trying to reproduce and understand the connectivity tutorial of the website (http://www.fieldtriptoolbox.org/tutorial/connectivity). > > I was hoping that someone could shed light on the computation of the Granger frequency spectrum: > > cfg = []; > cfg.method = 'granger'; > granger = ft_connectivityanalysis(cfg, mfreq); > > More specifically, I would like to know which computations are done to obtain the values in granger.grangerspctrm. (Unfortunately, inspecting the paper by Brovelli et al. PNAS (2004), as indicated in ft_connectivity_granger did not clear this up...) > > Moreover, I wonder what the relationship is between the Granger spectrum and other metrics such as (partial) directed coherence (DC / PDC) and directed transfer function (DTF), which also provide connectivity information in the form channels x channels x frequencies? > > In the appendix in Van Mierlo et al., "Functional brain connectivity from EEG in epilepsy: Seizure prediction and epileptogenic focus localization" and in Baccala and Sameshima, "Partial directed coherence: a new concept in neural structure determination", it is explained that both DC and DTF are computed using the transfer function matrix H(f), while PDC is computed using the A(f) matrix. Is this the reason why only PDC is termed 'partial', and the others not (even though they are also computed in a multivariate framework, i.e. taking all available variables into account)? > > Although I could not find an answer to my questions in the mailing archives, I apologize if this question has been asked before. > > Thank you in advance for your help! > Best regards, > > Simon > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From laxmi.shaw22 at gmail.com Fri May 19 16:56:51 2017 From: laxmi.shaw22 at gmail.com (Laxmi Shaw) Date: Fri, 19 May 2017 20:26:51 +0530 Subject: [FieldTrip] Error_while using ft_freqanalysis for non parametric computation Message-ID: Dear Fieldtrip users, I am getting an error while using frequency analysis using ft_connectivity analysis. Could you please help me by looking at the screenshot of the error. The error in the dpss.m file. Any help will always be appreciated. Thanks and Regards -- Laxmi Shaw Research Scholar(Ph.D.) IIT Kharagpur West Bengal Ph no-08388837821 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2017-05-19.png Type: image/png Size: 355204 bytes Desc: not available URL: From ty.mckinney.412 at gmail.com Fri May 19 18:16:15 2017 From: ty.mckinney.412 at gmail.com (Ty McKinney) Date: Fri, 19 May 2017 10:16:15 -0600 Subject: [FieldTrip] ft_preprocessing error Message-ID: Hi, I am having some trouble getting the ft_preprocessing function to work. The ft_definetrial function works and gives the trl matrix in the cfg output. As best as I can tell the read data function is returning a matrix that is smaller than the dimensions of the event sample indexes (by several orders of magnitude) from the read event function. I confirmed with EEG lab's loading function that the data matrix is thee same size. What is odd is that this script was working several weeks ago... I get this error: Error using ft_read_data (line 221) cannot read data after the end of the file Error in ft_preprocessing (line 576) dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) Posted below is my code leading up to the execution of the function. Any and all helps you can give me would be greatly appreciated %% Set up fieldtrip path ft_dir = 'C:\Users\Public\Documents\Euler_electrophys (Not backed up)\EEG_scripts\fieldtrip-master'; addpath(ft_dir); ft_defaults; % run this line ft needs it clc %% Load data datainfo.origdir = input('Please copy and paste the filepath for the .CNT file ', 's'); %datainfo.savdir = input('Please copy and paste the filepath for save directory ', 's'); datainfo.SID = input('Enter the Subject Name, e.g., Hick99 use lowercase!!', 's'); datainfo.hp = input('Was the data highpass filtered at 0.1Hz? (y/n)', 's'); cd(datainfo.origdir); % cd into the S's directory wrkdir = pwd; %go get the scalp maps % use the line below on MJE's computer upstairs %chanlocdir = 'C:\Users\u0850304.ADCSBS\Documents\MATLAB\euler_ electrophys\All_purpose_fxs'; % use the line below on the downstairs lab computer chanlocdir = 'C:\Users\Public\Documents\Euler_electrophys (Not backed up)\EEG_scripts\All_purpose_fxs\Waveguard_scalp_coordinates'; cd(chanlocdir); load WG64_4topoplot.mat cd(wrkdir); %find the exact file we need myfname = dir(strcat(datainfo.SID, '*', 'hick', '*','.cnt')); %Note that the file needs to end in ft.cnt/ft.trg exactname = myfname.name; datainfo.sourcepth = strcat(datainfo.origdir, '\', exactname); %set file path for the data cfg.trialfun='trialfun_Hick_tm2'; cfg.datainfo=datainfo; cfg.padding=0; cfg.padtype='data'; cfg.continuous='yes'; cfg.datafile=datainfo.sourcepth; cfg.headerfile=datainfo.sourcepth; cfg.dataset=datainfo.sourcepth; cfg.fsample=512; cd(cfg.datainfo.origdir); fileattrib; savep=ans.Name; newfolder = strcat(datainfo.SID, '_FT'); mkdir(newfolder); % Create new folder in Current Subject folder for FT output cfg.datainfo.savepath = strcat(savep,'\', newfolder); %create save path to new folder cfg.hdr = ft_read_header(cfg.datafile); %things I think fieldtrip needs according to site cfg.event = ft_read_event(cfg.datafile); cfg.data = ft_read_data(cfg.datafile); %% Define Trial Stuff % How much time, in seconds, is retained on either side of trigger codes %cfg.trialdef.eventtype= 'backpanel trigger'; %cfg.trialdef.eventvalue= '55 '; cfg.trialdef.pre= 1; % in seconds cfg.trialdef.post= 1; % in seconds %% read the header (needed for the samping rate) and the events evtsamps = [cfg.event.sample]';% for the events of interest, find the sample numbers (these are integers) Evtypes = {cfg.event.value}';% for the events of interest, find the trigger values (these are strings in the case of BrainVision) evtsamps=evtsamps(2:end); %Trim off first event that crashes script Evtypes =Evtypes (2:end); evtypes=zeros(length(Evtypes),1); for kk=1:length(evtsamps); %Convert string to numbers evtypes(kk) = str2double(Evtypes{kk}); % end pretrig = -round(cfg.trialdef.pre * cfg.hdr.Fs); % pre-stimulus boundary in samples posttrig = round(cfg.trialdef.post * cfg.hdr.Fs); % post-STIMULUS boundary in samples %% Trial definition [cfg]=ft_definetrial(cfg); data=ft_preprocessing(cfg); Ty McKinney Graduate Student-University of Utah ty.mckinney.412 at gmail.com 385.321.4061 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nicolas.abichacra at gmail.com Fri May 19 20:20:19 2017 From: nicolas.abichacra at gmail.com (Nicolas Abichacra) Date: Fri, 19 May 2017 19:20:19 +0100 Subject: [FieldTrip] Problem Matlab Path Message-ID: Dear Filedtrip list, I am currently pre processing EEG data. I recently moved my data from a hard drive to another (cut and paste). After resetting the path to fieldtrip, I get this kind or response when I run any of my scripts : When I run startup.m it gives me a list of warning messages like this one : Warning: Function iscolumn has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. > In path (line 109) In addpath (line 88) In startup (line 1) Then if I run one of the prepro scripts, I get this kind of response : Error using nargin You can only call nargin/nargout from within a MATLAB function. Error in ft_preamble_init (line 34) if nargin==0 Error in ft_preamble (line 56) evalin('caller', ['ft_preamble_' cmd]); Error in ft_rejectvisual (line 125) ft_preamble init Error in FT_prepro_2_sus (line 68) data = ft_rejectvisual(cfg, data); Does anyone have any idea where it might come from ? Thank you very much for the help. Best, Nicolas -------------- next part -------------- An HTML attachment was scrubbed... URL: From frsantos at fpce.up.pt Fri May 19 20:39:05 2017 From: frsantos at fpce.up.pt (Fernando Ferreira-Santos) Date: Fri, 19 May 2017 18:39:05 +0000 Subject: [FieldTrip] 2017 Porto EEG/ERP Summer School Message-ID: <2BAB036A9BAEA44984A131DFCE446108020C0A4975@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 6th 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 event will take place from 4-8 of September 2017 in the lovely city of Porto. In last year's edition the course was fully booked and, as such, we recommend early registration (course places are attributed by order of registration). For additional details and instructions on how to register, please 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, PhD Lecturer Laboratory of Neuropsychophysiology Faculty of Psychology and Education Sciences University of Porto Rua Alfredo Allen, 4200-135 Porto (Portugal) Tel.: +351 226079700 (ext. 409) E-mail: frsantos at fpce.up.pt Lab: http://www.fpce.up.pt/labpsi/ Personal: https://sites.google.com/view/ferreira-santos -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikexcohen at gmail.com Mon May 22 17:58:33 2017 From: mikexcohen at gmail.com (Mike X Cohen) Date: Mon, 22 May 2017 17:58:33 +0200 Subject: [FieldTrip] New book on MATLAB programming techniques for neuroscience data analysis Message-ID: Dear colleagues, There is a new book on MATLAB programming that is designed for masters/PhD/postdoc level researchers. The book is called "MATLAB for Brain and Cognitive Scientists" and is published by MIT Press. The goal of this book is to teach programming skills from beginner to intermediate/advanced levels (many other learning resources provide only beginner-level training), with a specific focus on the myriad analysis approaches often applied in neuroscience and cognitive neuroscience. Chapters end with many exercises to test and develop programming skills, and there are >9000 lines of MATLAB code to learn from on the accompanying website. An important feature of the book is that it teaches not only how to write good code, but also how to recognize and avoid writing bad or error-prone code. More information about the book can be obtained from the following websites: mikexcohen.com/book/#mbcs mitpress.mit.edu/books/matlab-brain-and-cognitive-scientists amazon.com/MATLAB-Brain-Cognitive-Scientists-Press/dp/0262035820/ Mike -------------- next part -------------- An HTML attachment was scrubbed... URL: From malgorzata.wislowska at gmail.com Wed May 24 16:34:17 2017 From: malgorzata.wislowska at gmail.com (Malgorzata Wislowska) Date: Wed, 24 May 2017 16:34:17 +0200 Subject: [FieldTrip] source statistics - spm_bwlabel error Message-ID: Dear FT-community, when calculating cluster permutation statistics on the source level, I receive the following error: Error using spm_bwlabel spm_bwlabel: CONN must be 6, 18 or 26 Error in clusterstat (line 319) [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use spm_bwlabel for 2D/3D to avoid usage of image toolbox Error in ft_statistics_montecarlo (line 347) [stat, cfg] = clusterstat(cfg, statrand, statobs); Error in ft_sourcestatistics (line 218) [stat, cfg] = statmethod(cfg, dat, design); I used MNE method for the inverse problem. I have 8196 grid points 1555 time points. But the error occurs also when I average across the time. Here is my configuration structure for the source analysis: design = zeros(2, nb_of_sbj*2); design(1,:) = [1:nb_of_sbj 1:nb_of_sbj]; design(2,:) = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2]; cfg = []; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_depsamplesT'; cfg.parameter = 'pow'; cfg.correctm = 'cluster'; cfg.clusterstatistic = 'maxsum'; cfg.design = design; cfg.ivar = 2; cfg.uvar = 1; cfg.numrandomization = 5000; cfg.tail = 0; cfg.alpha = 0.025; [stat] = ft_sourcestatistics(cfg,avg_con_sel{:},avg_incon_sel{:}); As far as I can see somebody had asked the same question last year, but the post doesn't seem to have been addressed: https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html Thank you for your help in advance. Best regards, Malgorzata Wislowska, University of Salzburg -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed May 24 16:42:26 2017 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 24 May 2017 16:42:26 +0200 Subject: [FieldTrip] source statistics - spm_bwlabel error In-Reply-To: References: Message-ID: <849BF19E-E573-4781-9B9D-800EB2DDB083@gmail.com> Dear Malgorzata, from a quick glance, it appears that in the call to spm_bwlabel "numdims" should be 3 to give you 2*numdims = 6. So, could you check what numdims is in your case? I suspect that you have 4-dimensional data (time by 3 spatial dimensions), so it might help to check where the dimensions are coming from and what happens if you average over time. Good luck, Julian Am 24.05.2017 um 16:34 schrieb Malgorzata Wislowska: > Dear FT-community, > > > when calculating cluster permutation statistics on the source level, I receive the following error: > Error using spm_bwlabel > spm_bwlabel: CONN must be 6, 18 or 26 > > Error in clusterstat (line 319) > [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use spm_bwlabel for 2D/3D to avoid usage of image toolbox > > Error in ft_statistics_montecarlo (line 347) > [stat, cfg] = clusterstat(cfg, statrand, statobs); > > Error in ft_sourcestatistics (line 218) > [stat, cfg] = statmethod(cfg, dat, design); > > I used MNE method for the inverse problem. I have 8196 grid points 1555 time points. > But the error occurs also when I average across the time. > > Here is my configuration structure for the source analysis: > > design = zeros(2, nb_of_sbj*2); > design(1,:) = [1:nb_of_sbj 1:nb_of_sbj]; > design(2,:) = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2]; > > cfg = []; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_depsamplesT'; > cfg.parameter = 'pow'; > cfg.correctm = 'cluster'; > cfg.clusterstatistic = 'maxsum'; > cfg.design = design; > cfg.ivar = 2; > cfg.uvar = 1; > cfg.numrandomization = 5000; > cfg.tail = 0; > cfg.alpha = 0.025; > > [stat] = ft_sourcestatistics(cfg,avg_con_sel{:},avg_incon_sel{:}); > > As far as I can see somebody had asked the same question last year, but the post doesn't seem to have been addressed: > https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html > > > Thank you for your help in advance. > > Best regards, > Malgorzata Wislowska, > University of Salzburg > _______________________________________________ > 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: signature.asc Type: application/pgp-signature Size: 495 bytes Desc: Message signed with OpenPGP using GPGMail URL: From jiversen at ucsd.edu Thu May 25 23:03:08 2017 From: jiversen at ucsd.edu (John Iversen) Date: Thu, 25 May 2017 14:03:08 -0700 Subject: [FieldTrip] ft_sourceanalysis of component data In-Reply-To: <849BF19E-E573-4781-9B9D-800EB2DDB083@gmail.com> References: <849BF19E-E573-4781-9B9D-800EB2DDB083@gmail.com> Message-ID: <74026E48-8F22-4140-AB9D-304F91FD4F32@ucsd.edu> Dear Fieldtrip development team, I’m doing a long-delayed upgrade of my fieldtrip installation and came across this error. I’m not sure how long this has / will be the case, but I’d like to know your plans. I am available to help re-enable it if that would make a difference. It’s not a really critical feature for me, but it is something I’d relied on in my analysis. For now, I suppose I can revert to the old version, which I recall did have to massage things to work (it mapped components onto time if I remember correctly). elseif iscomp % FIXME, select the components here % FIXME, add the component numbers to the output error('the use of component data in ft_sourceanalysis is disabled for the time being: if you encounter this error message and you need this functionality please contact the FieldTrip development team'); end Thanks, John John R. Iversen, PhD University of California, San Diego Swartz Center for Computational Neuroscience Institute for Neural Computation 9500 Gilman Dr #0559 La Jolla, CA 92093 jiversen at ucsd.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From malgorzata.wislowska at gmail.com Fri May 26 11:52:20 2017 From: malgorzata.wislowska at gmail.com (Malgorzata Wislowska) Date: Fri, 26 May 2017 11:52:20 +0200 Subject: [FieldTrip] source statistics - spm_bwlabel error Message-ID: Dear Julian, thank you very much for your prompt response. Yes, my numdims == 2 because my cfg.dim == [8196 1] which comes from ft_sourcestatistics.m (code lines 131-132) datdim = find(~strcmp(dimtok, 'subj') & ~strcmp(dimtok, 'rpt') & ~strcmp(dimtok, 'rpttap')); datsiz = dimsiz(datdim); calculated on the following input data: varargin{1}: cfg: [1x1 struct] inside: [8196x1 logical] pos: [8196x3 double] time: 0.1750 pow: [8196x1 double] dimord: 'chan_time' The above source level structure comes from ft_sourceanalysis calculated with cfg.method = 'mne'. Averaging over time unfortunately doesn't help - the same error continues to occur: But data that is not averaged over time has numdims == 2 too, because length(cfg.dim) == 2, even though that cfg.dim itself is different (for not averaged data it's e.g cfg.dim == [8196 61], whereas for averaged data it's cfg.dim == [8196 1]), It helps (well, the function runs through without errors and produces some output) if the line: if numdims == 2 || numdims == 3 % if 2D or 3D data gets replaced with: if numdims == 3 In clusterstat.m, code line: 318 (and also 269, 215, 184) Do you (or anybody else) have maybe any better idea how to fix it? Thanks and best regards, Malgorzata, University Salzburg > Subject: Re: [FieldTrip] source statistics - spm_bwlabel error > Dear Malgorzata, > > from a quick glance, it appears that in the call to spm_bwlabel "numdims" > should be 3 to give you 2*numdims = 6. > So, could you check what numdims is in your case? > I suspect that you have 4-dimensional data (time by 3 spatial dimensions), > so it might help to check where the dimensions are coming from and what > happens if you average over time. > > Good luck, > > Julian > > Am 24.05.2017 um 16:34 schrieb Malgorzata Wislowska: > > Dear FT-community, > > > when calculating cluster permutation statistics on the source level, I > receive the following error: > > Error using spm_bwlabel > spm_bwlabel: CONN must be 6, 18 or 26 > > Error in clusterstat (line 319) > [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use > spm_bwlabel for 2D/3D to avoid usage of image toolbox > > Error in ft_statistics_montecarlo (line 347) > [stat, cfg] = clusterstat(cfg, statrand, statobs); > > Error in ft_sourcestatistics (line 218) > [stat, cfg] = statmethod(cfg, dat, design); > > > I used MNE method for the inverse problem. I have 8196 grid points 1555 > time points. > But the error occurs also when I average across the time. > > Here is my configuration structure for the source analysis: > > > design = zeros(2, nb_of_sbj*2); > design(1,:) = [1:nb_of_sbj 1:nb_of_sbj]; > design(2,:) = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2]; > > cfg = []; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_depsamplesT'; > cfg.parameter = 'pow'; > cfg.correctm = 'cluster'; > cfg.clusterstatistic = 'maxsum'; > cfg.design = design; > cfg.ivar = 2; > cfg.uvar = 1; > cfg.numrandomization = 5000; > cfg.tail = 0; > cfg.alpha = 0.025; > > [stat] = ft_sourcestatistics(cfg,avg_co > n_sel{:},avg_incon_sel{:}); > > > As far as I can see somebody had asked the same question last year, but > the post doesn't seem to have been addressed: > https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html > > > Thank you for your help in advance. > > Best regards, > Malgorzata Wislowska, > University of Salzburg > _______________________________________________ > 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 craiggrichter at gmail.com Sun May 28 10:34:48 2017 From: craiggrichter at gmail.com (Craig Richter) Date: Sun, 28 May 2017 11:34:48 +0300 Subject: [FieldTrip] Peercellfun on systems after R2013 Message-ID: <3E539B83-5BB0-49B8-A41C-12409B7F4B19@gmail.com> Dear Fieldtrip development team, I’m having trouble getting peercellfun to function on a Matlab system post R2013. The issue stems from new handling of Mx[De]Serialize.m after R2013. This issue is covered in bug 2452, http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2452 and emerged for the peer system in bug 2598. http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2598 For newer versions of Matlab, peercompile must run to update the mex files, but this fails when trying to compile peer.c. This file calls the mx[De]Serialize functions internally, which are now must be c++ files. I have successfully compiled the c++ versions of these files to mex, but it seems the calls in peer.c must be modified in some way since these must now be c++ files, whereas they were c before. I’m not sure how to make these modifications to peer.c, or if peer.c must be updated to a c++ file. If anyone has any expertise how to do this, and get the peer system operating on systems above R2013, I’d greatly appreciate it!! Thanks! Craig -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon May 29 09:51:30 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 29 May 2017 07:51:30 +0000 Subject: [FieldTrip] ft_sourceanalysis of component data References: Message-ID: Dear John, Sorry about this. I think that we disabled this feature at some point, because the original implementation was a bit hacky (and unpredictable in its behavior). In a bout of quality-of-code-perfectionism we probably cleaned up the code, disabled the feature, agreed that we should address it at some point, even remembered to put in an error message … and subsequently forgot about it. Anyway, after these lame excuses I suggest to try and get this fixed. Thanks for your willingness to contribute. These days our development workflow lives on github, which should make external contributions to the code much more straightforward (github.com/fieldtrip.git is where the main repo is located). Perhaps you could check out this chunk of documentation, to get on the road: http://www.fieldtriptoolbox.org/development/git). For this specific issue, I think it would be best to first discuss a bit the requested features before we start changing the code, so I suggest that you create a local fork of the repository, and within it a new branch, which I think you can subsequently 'pull-request’. This allows us to have a location where we can discuss stuff (for now the ‘issues’ feature for the fieldtrip repo is disabled, yet this would be a more natural way for discussing things). Does that sound like a plan? Best, JM On 25 May 2017, at 23:03, John Iversen > wrote: Dear Fieldtrip development team, I’m doing a long-delayed upgrade of my fieldtrip installation and came across this error. I’m not sure how long this has / will be the case, but I’d like to know your plans. I am available to help re-enable it if that would make a difference. It’s not a really critical feature for me, but it is something I’d relied on in my analysis. For now, I suppose I can revert to the old version, which I recall did have to massage things to work (it mapped components onto time if I remember correctly). elseif iscomp % FIXME, select the components here % FIXME, add the component numbers to the output error('the use of component data in ft_sourceanalysis is disabled for the time being: if you encounter this error message and you need this functionality please contact the FieldTrip development team'); end Thanks, John John R. Iversen, PhD University of California, San Diego Swartz Center for Computational Neuroscience Institute for Neural Computation 9500 Gilman Dr #0559 La Jolla, CA 92093 jiversen at ucsd.edu _______________________________________________ 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 Mon May 29 09:52:04 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 29 May 2017 07:52:04 +0000 Subject: [FieldTrip] source statistics - spm_bwlabel error References: Message-ID: Hi Malgorzata, Could you try to add the original ‘tri’ field to each of your varargins, and check whether the problem persists? Thanks, Jan-Mathijs On 26 May 2017, at 11:52, Malgorzata Wislowska > wrote: Dear Julian, thank you very much for your prompt response. Yes, my numdims == 2 because my cfg.dim == [8196 1] which comes from ft_sourcestatistics.m (code lines 131-132) datdim = find(~strcmp(dimtok, 'subj') & ~strcmp(dimtok, 'rpt') & ~strcmp(dimtok, 'rpttap')); datsiz = dimsiz(datdim); calculated on the following input data: varargin{1}: cfg: [1x1 struct] inside: [8196x1 logical] pos: [8196x3 double] time: 0.1750 pow: [8196x1 double] dimord: 'chan_time' The above source level structure comes from ft_sourceanalysis calculated with cfg.method = 'mne'. Averaging over time unfortunately doesn't help - the same error continues to occur: But data that is not averaged over time has numdims == 2 too, because length(cfg.dim) == 2, even though that cfg.dim itself is different (for not averaged data it's e.g cfg.dim == [8196 61], whereas for averaged data it's cfg.dim == [8196 1]), It helps (well, the function runs through without errors and produces some output) if the line: if numdims == 2 || numdims == 3 % if 2D or 3D data gets replaced with: if numdims == 3 In clusterstat.m, code line: 318 (and also 269, 215, 184) Do you (or anybody else) have maybe any better idea how to fix it? Thanks and best regards, Malgorzata, University Salzburg Subject: Re: [FieldTrip] source statistics - spm_bwlabel error Dear Malgorzata, from a quick glance, it appears that in the call to spm_bwlabel "numdims" should be 3 to give you 2*numdims = 6. So, could you check what numdims is in your case? I suspect that you have 4-dimensional data (time by 3 spatial dimensions), so it might help to check where the dimensions are coming from and what happens if you average over time. Good luck, Julian Am 24.05.2017 um 16:34 schrieb Malgorzata Wislowska: Dear FT-community, when calculating cluster permutation statistics on the source level, I receive the following error: Error using spm_bwlabel spm_bwlabel: CONN must be 6, 18 or 26 Error in clusterstat (line 319) [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use spm_bwlabel for 2D/3D to avoid usage of image toolbox Error in ft_statistics_montecarlo (line 347) [stat, cfg] = clusterstat(cfg, statrand, statobs); Error in ft_sourcestatistics (line 218) [stat, cfg] = statmethod(cfg, dat, design); I used MNE method for the inverse problem. I have 8196 grid points 1555 time points. But the error occurs also when I average across the time. Here is my configuration structure for the source analysis: design = zeros(2, nb_of_sbj*2); design(1,:) = [1:nb_of_sbj 1:nb_of_sbj]; design(2,:) = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2]; cfg = []; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_depsamplesT'; cfg.parameter = 'pow'; cfg.correctm = 'cluster'; cfg.clusterstatistic = 'maxsum'; cfg.design = design; cfg.ivar = 2; cfg.uvar = 1; cfg.numrandomization = 5000; cfg.tail = 0; cfg.alpha = 0.025; [stat] = ft_sourcestatistics(cfg,avg_con_sel{:},avg_incon_sel{:}); As far as I can see somebody had asked the same question last year, but the post doesn't seem to have been addressed: https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html Thank you for your help in advance. Best regards, Malgorzata Wislowska, University of Salzburg _______________________________________________ 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 angelika.lingnau at gmail.com Mon May 29 13:09:47 2017 From: angelika.lingnau at gmail.com (Angelika Lingnau) Date: Mon, 29 May 2017 12:09:47 +0100 Subject: [FieldTrip] 1-Year fMRI/ MEG Postdoc, Center for Mind/Brain Sciences, University of Trento, Italy Message-ID: At the Center for Mind/ Brain Sciences (CIMeC, http://www.cimec.unitn.it/en) at the University of Trento, Italy, there will soon be an opening for a one-year postdoctoral fellowship to work with Dr. Angelika Lingnau to examine the neural basis of visual imagery in normal sighted participants and hemianopic patients. Further descriptions of our ongoing research projects can be found under the following link: https://sites.google.com/site/angelikalingnau/. The postdoc will be responsible for the design of fMRI and/ or MEG studies, conducting data analysis and leading the write-up of scientific work. The ideal applicant is highly motivated and creative and is capable of working both independently as well as in a young, dynamic group. The applicant furthermore should have experience with functional magnetic resonance imaging and/ or magnetoencephalography and a solid background in Cognitive Neuroscience. Programming experience with MATLAB or C is very desirable. The Center offers an international and vibrant research setting with access to state-of-the-art neuroimaging methodologies, including a research-only 4T MRI scanner, MEG, EEG and TMS, as well as behavioral, eye tracking and motion tracking laboratories. The 2011-2014 ANVUR Report ranked CIMeC first among Italian universities in the field of psychological sciences. English is the official language of the CIMeC, where a large proportion of the faculty, postdocs and students come from a wide range of countries outside of Italy. Informal inquiries should be sent to Angelika Lingnau ( angelika.lingnau at rhul.ac.uk or angelika.lingnau at gmail.com). -------------- next part -------------- An HTML attachment was scrubbed... URL: From malgorzata.wislowska at gmail.com Mon May 29 18:30:40 2017 From: malgorzata.wislowska at gmail.com (Malgorzata Wislowska) Date: Mon, 29 May 2017 18:30:40 +0200 Subject: [FieldTrip] source statistics - spm_bwlabel error Message-ID: Dear Jan-Mathijs, thank you for your message. when I add the 'tri' field to the input data, FT recognizes that data is a mesh (*the input is mesh data with 8196 vertices and 16384 triangles*), but it keep throwing the same *spm_bwlabel* error message. This is the current input data (that's what you meant, right?): varargin{1}: cfg: [1x1 struct] inside: [8196x1 logical] pos: [8196x3 double] time: 0.1000 pow: [8196x1 double] tri: [16384x3 uint16] dimord: 'chan_time' If I don't average over time, and the size of varargin{1}.pow equals e.g., [8196 73], then datsiz == 8196. That's because dimsiz == [8196 73], but datdim == 1 (ft_sourcestatistics, lines 131-132). That leads to the following error: Error using ft_sourcestatistics (line 205) the length of the design matrix (2) does not match the number of observations in the data (3358) Best regards, Malgorzata > Subject: Re: [FieldTrip] source statistics - spm_bwlabel error > Hi Malgorzata, > > Could you try to add the original ‘tri’ field to each of your varargins, > and check whether the problem persists? > > Thanks, > Jan-Mathijs > > > > On 26 May 2017, at 11:52, Malgorzata Wislowska < > malgorzata.wislowska at gmail.com> wrote: > > Dear Julian, > > > thank you very much for your prompt response. > > Yes, my numdims == 2 because my cfg.dim == [8196 1] > which comes from ft_sourcestatistics.m (code lines 131-132) > > datdim = find(~strcmp(dimtok, 'subj') & ~strcmp(dimtok, 'rpt') & > ~strcmp(dimtok, 'rpttap')); > datsiz = dimsiz(datdim); > > calculated on the following input data: > > varargin{1}: > cfg: [1x1 struct] > inside: [8196x1 logical] > pos: [8196x3 double] > time: 0.1750 > pow: [8196x1 double] > dimord: 'chan_time' > > The above source level structure comes from ft_sourceanalysis calculated > with cfg.method = 'mne'. > > Averaging over time unfortunately doesn't help - the same error continues > to occur: > But data that is not averaged over time has numdims == 2 too, because > length(cfg.dim) == 2, even though that cfg.dim itself is different (for not > averaged data it's e.g cfg.dim == [8196 61], whereas for averaged data it's > cfg.dim == [8196 1]), > > It helps (well, the function runs through without errors and produces some > output) if the line: > > if numdims == 2 || numdims == 3 % if 2D or 3D data > > gets replaced with: > > if numdims == 3 > > In clusterstat.m, code line: 318 (and also 269, 215, 184) > > Do you (or anybody else) have maybe any better idea how to fix it? > > > Thanks and best regards, > Malgorzata, > University Salzburg > > > > >> Subject: Re: [FieldTrip] source statistics - spm_bwlabel error >> > > > Dear Malgorzata, >> >> from a quick glance, it appears that in the call to spm_bwlabel "numdims" >> should be 3 to give you 2*numdims = 6. >> So, could you check what numdims is in your case? >> I suspect that you have 4-dimensional data (time by 3 spatial >> dimensions), so it might help to check where the dimensions are coming from >> and what happens if you average over time. >> >> Good luck, >> >> Julian >> >> Am 24.05.2017 um 16:34 schrieb Malgorzata Wislowska: >> >> Dear FT-community, >> >> >> when calculating cluster permutation statistics on the source level, I >> receive the following error: >> >> Error using spm_bwlabel >> spm_bwlabel: CONN must be 6, 18 or 26 >> >> Error in clusterstat (line 319) >> [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use >> spm_bwlabel for 2D/3D to avoid usage of image toolbox >> >> Error in ft_statistics_montecarlo (line 347) >> [stat, cfg] = clusterstat(cfg, statrand, statobs); >> >> Error in ft_sourcestatistics (line 218) >> [stat, cfg] = statmethod(cfg, dat, design); >> >> >> I used MNE method for the inverse problem. I have 8196 grid points 1555 >> time points. >> But the error occurs also when I average across the time. >> >> Here is my configuration structure for the source analysis: >> >> >> design = zeros(2, nb_of_sbj*2); >> design(1,:) = [1:nb_of_sbj 1:nb_of_sbj]; >> design(2,:) = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2]; >> >> cfg = []; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'ft_statfun_depsamplesT'; >> cfg.parameter = 'pow'; >> cfg.correctm = 'cluster'; >> cfg.clusterstatistic = 'maxsum'; >> cfg.design = design; >> cfg.ivar = 2; >> cfg.uvar = 1; >> cfg.numrandomization = 5000; >> cfg.tail = 0; >> cfg.alpha = 0.025; >> >> [stat] = ft_sourcestatistics(cfg,avg_co >> n_sel{:},avg_incon_sel{:}); >> >> >> As far as I can see somebody had asked the same question last year, but >> the post doesn't seem to have been addressed: >> https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html >> >> >> Thank you for your help in advance. >> >> Best regards, >> Malgorzata Wislowska, >> University of Salzburg >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.papen at uni-koeln.de Tue May 30 09:35:37 2017 From: m.papen at uni-koeln.de (Michael von Papen) Date: Tue, 30 May 2017 09:35:37 +0200 Subject: [FieldTrip] Extended Deadline: Coupling & Causality in Complex Systems, Sep 25-27, Cologne, Germany Message-ID: ============================================================== CALL FOR PAPERS (*Extended Deadline June 15*, 2017) http://c3s.uni-koeln.de ============================================================== INTERNATIONAL CONFERENCE: *Coupling and Causality in Complex Systems* September 25-27, 2017, Cologne, Germany -------------------------------------------------------------- The interdisciplinary conference Coupling and Causality in Complex Systems (C3S) is hosted by the Competence Area 3: Quantitative Modeling of Complex Systems of the University of Cologne (UoC), Germany. It is organized by the Institute of Geophysics & Meteorology, UoC, the Institute of Clinical Neuroscience and Psychology, Heinrich-Heine University Düsseldorf and the Department of Cognitive Neuroscience at the Research Center Juelich. -------------------------------------------------- *Invited Speakers* Jörg Breitung - Macroeconomic Policy Institute, University of Cologne, Germany David Gross - Institute of Theoretical Physics, University of Cologne, Germany Philip Holmes - Mechanical and Aerospace Engineering / Princeton Neuroscience Institute, Princeton, USA Ankit Khambhati - Department of Bioengineering, University of Pennsylvania, USA Laura Marzetti - Department of Neuroscience, Università degli Studi "G. d'Annunzio" Chieti - Pescara Arkady Pikovsky - Institute of Physics and Astronomy, University Potsdam, Germany Michael Rosenblum - Institute of Physics and Astronomy, University Potsdam, Germany Jakob Runge - The Grantham Institute for Climate Change, Imperial College London -------------------------------------------------- *Preliminary Session Program* We will have different sessions with differing topics and each session will be opened by one of the invited speakers. Here is a preliminary version of our program: Session 1 Synchronization I Arkady Pikovsky Session 2 Synchronization II Silvia Daun Session 3 Coupled oscillators I Phil Holmes Session 4 Coupled oscillators II Michael Rosenblum Session 5 Phase coupling Laura Marzetti Session 6 Network structures Ankit Khambati Session 7 Bayesian networks David Gross Session 8 Granger causality I Jörg Breitung Session 9 Granger causality II Esther Florin Session 10 Causal network measures Jakob Runge Further topics of interest for the conference include, amongst others, research and methods development on: functional connectivity, (partial directed) coherence, network topology, graph-theoretic measures, directed graphs, nonlinear dynamics of complex systems, complex spatio-temporal systems, mutual information and transfer entropy. -------------------------------------------------------------- *Scientific Organizing Committee* Silvia Daun - Institute of Zoology, University of Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany Esther Florin - Institute of Clinical Neuroscience and Psychology, Düsseldorf, Germany Joachim Gross - Center for Cognitive Neuroimaging, Glasgow, UK Michael von Papen - Institute of Geophysics & Meteorology, Cologne, Germany; Institute of Neuroscience and Medicine, Research Center Jülich, Germany -------------------------------------------------------------- *Abstract* Complex systems such as the human brain, Earth’s climate and economy are characterized by a multitude of coupled processes on different spatial and temporal scales. In order to better understand the dynamics of the system at hand each scientific area has developed specific tools to identify, model and quantify these processes. The conference Coupling and Causality in Complex Systems (C3S) will present a collection of these approaches with the aim to provide scientists with new analysis strategies for their field. The conference focuses on how to characterize a complex system and on the methods for estimating and modeling of statistical coupling (e.g. network coherence, creation and modulation of small networks and local or long-range synchronization by cross frequency phase-phase and phase-amplitude coupling) and causality (e.g. Granger causality, transfer entropy). Therefore, data analysts from different study fields including neuroscience, mathematics, physics, biology, and economy will present their approaches with a particular focus on the methods they use. The aim of this conference is to foster discussions and the transdisciplinary exchange of advanced techniques, methods, and algorithms, thereby stimulating potential future collaborations. -------------------------------------------------------------- *PAPER SUBMISSION AND REGISTRATION* Authors are invited to submit conference abstracts with up to 400 words. Authors of exceptional abstracts will be given the opportunity to present their research in a talk. However, poster sessions will be provided with ample time for discussions. For your submission, please use the conference website c3s.uni-koeln.de. To register, please send an email with the subject "registration" to c3s-conference at uni-koeln.de. Please be sure to include your full name, your affiliation and whether you qualify as student (also PhD candidates) or not. The registration fee will cover snacks and refreshments during coffee breaks, lunch and a dinner with all participants. Early-bird registration is available until July 10 with a reduced fee of 100 EUR (50 EUR for students), after July 10 the registration fee will be 200 EUR (100 EUR for students). -------------------------------------------------------------- IMPORTANT DATES Paper Submission deadline: June 15, 2017 Author Notification: end June, 2017 Early-bird registration: July 10, 2017 Conference: September 25-27, 2017 ============================================================== Please find the call for papers and more information at the conference website: http://c3s.uni-koeln.de. For questions regarding the conference feel free to contact us via c3s-conference at uni-koeln.de. -- ------------------------------------------ UNIVERSITY OF COLOGNE Institute of Geophysics & Meteorology Coordinator of Competence Area III: Quantitative Modeling of Complex Systems Dr. Michael von Papen Email: m.papen at uni-koeln.de http://www.uni-koeln.de/~vpapenm http://complexsystems.uni-koeln.de From l.roeder at qut.edu.au Wed May 31 04:28:11 2017 From: l.roeder at qut.edu.au (Luisa Roeder) Date: Wed, 31 May 2017 02:28:11 +0000 Subject: [FieldTrip] input data structure ft_freqstatistics Message-ID: Dear Fieldtrip users, I am part of a research team at the Institute of Health and Biomedical Innovation at Queensland University of Technology in Brisbane, Australia. I am currently working on time-frequency analyses of EEG and EMG signals. I would like to use ft_freqstatistics for a cluster-based permutation test on my time-frequency data. In the function itself and in the online documentation I read that the input data into ft_freqstatistics should be the result/output from either FT_FREQANALYSIS, FT_FREQDESCRIPTIVES or from FT_FREQGRANDAVERAGE. I have not completed my time-frequency analysis via fieldtrip; hence, I am wondering if it is also possible to create my own input data structure to make it fit for ft_freqstatistics? (Basically, I would like to skip ft_freqanalysis and directly start with cluster-based permutation testing via ft_freqstatistics, and for that I need to adapt my data structure.) If it is possible, which fields have to be created in my variable to be fed into ft_freqstatistics, so it fulfils all requirements to make the function run? Are there any fields from the output of, for example, FT_FREQANALYSIS that are not needed for ft_freqstatistics? For example, [stat] = ft_freqstatistics(cfg, coh1, coh2, ...) What fields do coh1, coh2, ... have to have? E.g. >> display(coh1) labelcmb: {8×2 cell} dimord: 'chancmb_freq_time' cohspctrm: [8×80×2049 double] time: [1×2049 double] freq: [1×80 double] elec: [1×1 struct] cfg: [1×1 struct] Can I leave out some of these fields (particularly coh1.cfg), and it will still work for ft_freqstatistics? Would it be enough to only have coh1.cohspctrm, coh1.time and coh1.freq? I am still relatively new to Fieldtrip, and working my way through the tutorials etc., but I definitely having trouble to create an appropriate data structure as input into ft_freqstatistics (without using ft_freqanalysis or other functions alike beforehand). I would very much appreciate your help with this. Thank you, Kind regards Luisa Luisa Roeder, PhD | Research Associate | Movement Neuroscience Institute of Health and Biomedical Innovation | School of Exercise and Nutrition Science Queensland University of Technology | 60 Musk Ave, Kelvin Grove, Brisbane, QLD 4059, Australia. t: +61 7 3138 6428 | e: l.roeder at qut.edu.au | w: www.ihbi.qut.edu.au CRICOS No. 00213J -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed May 31 08:58:12 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 31 May 2017 06:58:12 +0000 Subject: [FieldTrip] input data structure ft_freqstatistics In-Reply-To: References: Message-ID: Hi Luisa, The minimum requirement for a data structure that fieldtrip can work with should contain at least the following fields: - a field with the data matrix, in your case it can be cohspctrm - a bunch of fields that indicate how to interpret the dimensions of the input data matrix: * dimord, a descriptor in the style of ‘chancmb_freq_time’ * freq * time * labelcmb (for univariate data, it should be label) The cfg should be optional. Anyway, this being said, probably you may want to try and fool fieldtrip into getting a univariate data-field, i.e. rename cohspctrm into powspctrm, and labelcmb into label. This should work under the assumption that you are cohering 8 different EEG electrodes with a single EMG (for the label you could just take the column of labelcmb that represents the EEG). Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 31 May 2017, at 04:28, Luisa Roeder > wrote: Dear Fieldtrip users, I am part of a research team at the Institute of Health and Biomedical Innovation at Queensland University of Technology in Brisbane, Australia. I am currently working on time-frequency analyses of EEG and EMG signals. I would like to use ft_freqstatistics for a cluster-based permutation test on my time-frequency data. In the function itself and in the online documentation I read that the input data into ft_freqstatistics should be the result/output from either FT_FREQANALYSIS, FT_FREQDESCRIPTIVES or from FT_FREQGRANDAVERAGE. I have not completed my time-frequency analysis via fieldtrip; hence, I am wondering if it is also possible to create my own input data structure to make it fit for ft_freqstatistics? (Basically, I would like to skip ft_freqanalysis and directly start with cluster-based permutation testing via ft_freqstatistics, and for that I need to adapt my data structure.) If it is possible, which fields have to be created in my variable to be fed into ft_freqstatistics, so it fulfils all requirements to make the function run? Are there any fields from the output of, for example, FT_FREQANALYSIS that are not needed for ft_freqstatistics? For example, [stat] = ft_freqstatistics(cfg, coh1, coh2, ...) What fields do coh1, coh2, … have to have? E.g. >> display(coh1) labelcmb: {8×2 cell} dimord: 'chancmb_freq_time' cohspctrm: [8×80×2049 double] time: [1×2049 double] freq: [1×80 double] elec: [1×1 struct] cfg: [1×1 struct] Can I leave out some of these fields (particularly coh1.cfg), and it will still work for ft_freqstatistics? Would it be enough to only have coh1.cohspctrm, coh1.time and coh1.freq? I am still relatively new to Fieldtrip, and working my way through the tutorials etc., but I definitely having trouble to create an appropriate data structure as input into ft_freqstatistics (without using ft_freqanalysis or other functions alike beforehand). I would very much appreciate your help with this. Thank you, Kind regards Luisa Luisa Roeder, PhD | Research Associate | Movement Neuroscience Institute of Health and Biomedical Innovation | School of Exercise and Nutrition Science Queensland University of Technology | 60 Musk Ave, Kelvin Grove, Brisbane, QLD 4059, Australia. t: +61 7 3138 6428 | e: l.roeder at qut.edu.au | w: www.ihbi.qut.edu.au CRICOS No. 00213J _______________________________________________ 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 kash.kgp at gmail.com Wed May 31 12:50:41 2017 From: kash.kgp at gmail.com (Kasturi Barik) Date: Wed, 31 May 2017 16:20:41 +0530 Subject: [FieldTrip] Fwd: Source Analysis from EEG data In-Reply-To: References: Message-ID: *Dear all, **I am trying to perform source localization in the frequency domain * *from EEG data using 'DICS' . As I have no mri data of the participants, * *I am using **'Subject01.mri' to read the anatomical data with ft_read_mri. * *The **head model created with 'bemcp'.* *Code:* *%% **Read the anatomical data* *mri = ft_read_mri('Subject01.mri');* *%% **Segment the anatomical information & triangulate the surfaces* *load segmentedmri % load from *ftp server (segmentedmri.mat). *load bnd* *%% **Create the headmodel* *cfg = [];cfg.method = 'bemcp'; vol = ft_prepare_headmodel(cfg, bnd);%% Position of the electrodesload('Face_sub.mat'); % data of participants' electrode positions electrodes = Face_sub.elec;%% Interactive alignmentcfg = [];cfg.method = 'interactive';cfg.elec = electrodes;cfg.headshape = vol.bnd(3); % scalpelec_aligned = ft_electroderealign(cfg);%% Compute leadfield:cfg = [];cfg.elec = elec_aligned;cfg.vol = vol;cfg.channel = {'EEG'};[grid] = ft_prepare_leadfield(cfg);%% Source Analysiscfg = []; cfg.method = 'dics';cfg.frequency = 10; cfg.grid = grid;cfg.vol = vol;cfg.dics.projectnoise = 'yes';cfg.dics.lambda = 0;sourceFace = ft_sourceanalysis(cfg, face_data); % face_data is obtained from the FT_FREQANALYSIS % [%% time frequency analysis || cfg = []; || cfg.channel = 'EEG'; || cfg.method = 'mtmfft'; || cfg.output = 'powandcsd'; || cfg.tapsmofrq = 4; || cfg.foi = 1:1:40; || face_data = ft_freqanalysis(cfg, Face_sub); ]* *When running DICS with these settings **I am getting the following error message:* *Error using svd Input to SVD must not contain NaN or Inf. Error in beamformer_dics>pinv (line 650) [U,S,V] = svd(A,0); Error in beamformer_dics (line 339) filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ft_sourceanalysis (line 568) dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); Error in SourceAnalysis (line 133) sourceFace = ft_sourceanalysis(cfg, face_data);* * I am not able to detect, where is the problem. Another issue I have found that 'vol.mat' or 'grid.leadfield' are all NaN value. I cannot understand how to solve it. I would be very thankful if you can help me in this regard. * -- Thanks & Regards *Kasturi Barik* MS Research Scholar Audio and Bio-signal Processing Lab Department of Electronics and Electrical Engineering Indian Institute of Technology Kharagpur Mob: +91-8902400644 -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Wed May 31 13:49:35 2017 From: michelic72 at gmail.com (Cristiano Micheli) Date: Wed, 31 May 2017 13:49:35 +0200 Subject: [FieldTrip] Fwd: Source Analysis from EEG data In-Reply-To: References: Message-ID: Dear Kastouri, My hunch is that either ft_prepare_headmodel or ft_prepare_leadfield fail in generating a proper forward model for localization purposes. I would check that ft_prepare_headmodel's vol structure contains sensible data by plotting both the 'bnd' triangulated surface and the EEG electrodes together (you should be able to find instructions on the wiki) in the same image. Sometimes units (mm,cm) or coregistration (left/right swap) might influence a good outcome. Accordingly the grid.leadfield structure will not make sense because it uses the incorrect outcome of the vol structure. So if you manage to solve the 1st problem you'll kill two bird with a stone Good luck! Cris On Wed, May 31, 2017 at 12:50 PM, Kasturi Barik wrote: > *Dear all, > **I am trying to perform source localization in the frequency domain * > > *from EEG data using 'DICS' . As I have no mri data of the participants, * > > *I am using **'Subject01.mri' to read the anatomical data with ft_read_mri. * > > *The **head model created with 'bemcp'.* > > *Code:* > > *%% **Read the anatomical data* > > *mri = ft_read_mri('Subject01.mri');* > > *%% **Segment the anatomical information & triangulate the surfaces* > > *load segmentedmri % load from *ftp > server > > (segmentedmri.mat). > *load bnd* > > *%% **Create the headmodel* > > > > > > > > > > *cfg = [];cfg.method = 'bemcp'; vol = > ft_prepare_headmodel(cfg, bnd);%% Position of the > electrodesload('Face_sub.mat'); % data of > participants' electrode positions electrodes = Face_sub.elec;%% Interactive > alignmentcfg = [];cfg.method = 'interactive';cfg.elec = > electrodes;cfg.headshape = vol.bnd(3); % > scalpelec_aligned = ft_electroderealign(cfg);%% Compute leadfield:cfg > = [];cfg.elec = elec_aligned;cfg.vol = > vol;cfg.channel = {'EEG'};[grid] = ft_prepare_leadfield(cfg);%% > Source Analysiscfg = []; cfg.method = > 'dics';cfg.frequency = 10; cfg.grid = grid;cfg.vol = > vol;cfg.dics.projectnoise = 'yes';cfg.dics.lambda = 0;sourceFace = > ft_sourceanalysis(cfg, face_data); % face_data is obtained from the > FT_FREQANALYSIS % [%% time frequency analysis > || cfg = []; > || cfg.channel = 'EEG'; || > cfg.method = 'mtmfft'; || > cfg.output = 'powandcsd'; || > cfg.tapsmofrq = 4; || > cfg.foi = 1:1:40; || > face_data = ft_freqanalysis(cfg, Face_sub); ]* > > *When running DICS with these settings **I am getting the following error message:* > > > *Error using svd > Input to SVD must not contain NaN or Inf. > > Error in beamformer_dics>pinv (line 650) > [U,S,V] = svd(A,0); > > Error in beamformer_dics (line 339) > filt = pinv(lf' * invCf * lf) * lf' * invCf; > % Gross eqn. 3, use PINV/SVD to cover rank > deficient leadfield > > Error in ft_sourceanalysis (line 568) > dip(i) = beamformer_dics(grid, sens, vol, [], > squeeze(Cf(i,:,:)), optarg{:}); > > Error in SourceAnalysis (line 133) > sourceFace = ft_sourceanalysis(cfg, face_data);* > > > * I am not able to detect, where is the problem. Another issue I have found that 'vol.mat' or 'grid.leadfield' are all NaN value. I cannot understand how to solve it. I would be very thankful if you can help me in this regard. * > > > > > > -- > Thanks & Regards > > *Kasturi Barik* > > MS Research Scholar > Audio and Bio-signal Processing Lab > Department of Electronics and Electrical Engineering > Indian Institute of Technology Kharagpur > Mob: +91-8902400644 <+91%2089024%2000644> > > _______________________________________________ > 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 roycox.roycox at gmail.com Wed May 31 20:57:47 2017 From: roycox.roycox at gmail.com (Roy Cox) Date: Wed, 31 May 2017 14:57:47 -0400 Subject: [FieldTrip] cluster statistics on subset of channels Message-ID: hello, Does anyone know if it's possible to run ft_freqstatistics on only a subset of channels? Per my hypothesis, I'm only interested in the posterior half of the scalp. I know I could remove the channels entirely from the data, but for plotting purposes I'd like to retain the full set of data, and it would be cumbersome to stitch data and clusters back together. Alternatively, I could change the channel neighborhood structure for the frontal channels such that they don't enter the cluster formation procedure at all, but I'm not sure if this is valid. Maybe ft_freqstatistics already supports channel selection? Can't seem to find it in the documentation or tutorials, though. Thanks for any insights, Roy -------------- next part -------------- An HTML attachment was scrubbed... URL: From elmeri.syrjanen at gmail.com Wed May 31 21:24:07 2017 From: elmeri.syrjanen at gmail.com (=?UTF-8?Q?Elmeri_Syrj=C3=A4nen?=) Date: Wed, 31 May 2017 21:24:07 +0200 Subject: [FieldTrip] cluster statistics on subset of channels In-Reply-To: References: Message-ID: Hi Roy, I have pasted the relevant section from http://www.fieldtriptoolbox.org/reference/ft_freqstatistics the lines that would be applicable in your situation. The configuration can contain the following options for data selection *cfg.channel = Nx1 cell-array with selection of channels (default = 'all'), see FT_CHANNELSELECTION for details* *cfg.avgoverchan = 'yes'* or 'no' (default = 'no') /elmeri On Wed, May 31, 2017 at 8:57 PM, Roy Cox wrote: > hello, > > Does anyone know if it's possible to run ft_freqstatistics on only a > subset of channels? > > Per my hypothesis, I'm only interested in the posterior half of the scalp. > > I know I could remove the channels entirely from the data, but for > plotting purposes I'd like to retain the full set of data, and it would be > cumbersome to stitch data and clusters back together. Alternatively, I > could change the channel neighborhood structure for the frontal channels > such that they don't enter the cluster formation procedure at all, but I'm > not sure if this is valid. > > Maybe ft_freqstatistics already supports channel selection? Can't seem to > find it in the documentation or tutorials, though. > > Thanks for any insights, > > Roy > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: