From son.ta.dinh at tum.de Tue Apr 3 11:05:51 2018 From: son.ta.dinh at tum.de (Ta Dinh, Son) Date: Tue, 3 Apr 2018 09:05:51 +0000 Subject: [FieldTrip] FDR correction of multiple cluster-based permutation tests Message-ID: Dear FieldTrip list, I would like to correct the results of multiple cluster-based permutation tests using FDR. This is obviously trivial when I have a single cluster for every single test. However, this does not happen in general. My biggest problem is when I have no cluster at all because I also don't have a p value then. Is there a reasonable way to extract a p value from the cluster-statistics when no cluster can be found? I have thought about just using p = 1 in these cases, but that seems very arbitrary and intuitively wrong. Can anybody think of a different way of FDR-correcting multiple cluster-based permutation tests? Obviously, I could also just use Bonferroni to adjust the alpha level, but that is simply too restrictive in general. But maybe someone knows a different way of correcting for multiple comparisons for this case that is neither Bonferroni nor FDR? Any help and/or references would be greatly appreciated! Best, Son Son Ta Dinh, M.Sc. PhD student in Human Pain Research Klinikum rechts der Isar Technische Universität München Munich, Germany Phone: +49 89 4140 7664 http://www.painlabmunich.de/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.blume at sbg.ac.at Tue Apr 3 11:31:35 2018 From: christine.blume at sbg.ac.at (Blume Christine) Date: Tue, 3 Apr 2018 09:31:35 +0000 Subject: [FieldTrip] FDR correction of multiple cluster-based permutation tests In-Reply-To: References: Message-ID: Dear Son, I had a similar issue and had talked to our mathematicians/statisticians. They recommended to use Bonferroni...although that is not the answer you were looking for and other people might have better ideas, I though the info might still be valuable. Best, Christine Von: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] Im Auftrag von Ta Dinh, Son Gesendet: Dienstag, 03. April 2018 11:06 An: fieldtrip at science.ru.nl Betreff: [FieldTrip] FDR correction of multiple cluster-based permutation tests Dear FieldTrip list, I would like to correct the results of multiple cluster-based permutation tests using FDR. This is obviously trivial when I have a single cluster for every single test. However, this does not happen in general. My biggest problem is when I have no cluster at all because I also don't have a p value then. Is there a reasonable way to extract a p value from the cluster-statistics when no cluster can be found? I have thought about just using p = 1 in these cases, but that seems very arbitrary and intuitively wrong. Can anybody think of a different way of FDR-correcting multiple cluster-based permutation tests? Obviously, I could also just use Bonferroni to adjust the alpha level, but that is simply too restrictive in general. But maybe someone knows a different way of correcting for multiple comparisons for this case that is neither Bonferroni nor FDR? Any help and/or references would be greatly appreciated! Best, Son Son Ta Dinh, M.Sc. PhD student in Human Pain Research Klinikum rechts der Isar Technische Universität München Munich, Germany Phone: +49 89 4140 7664 http://www.painlabmunich.de/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From TaylorBealeR at cardiff.ac.uk Tue Apr 3 17:21:33 2018 From: TaylorBealeR at cardiff.ac.uk (Rosa Taylor Beale) Date: Tue, 3 Apr 2018 15:21:33 +0000 Subject: [FieldTrip] Empty array in coherence connectivity analysis In-Reply-To: <90B1A8AF-87AA-480B-BEE7-DC9A7148780E@donders.ru.nl> References: <90B1A8AF-87AA-480B-BEE7-DC9A7148780E@donders.ru.nl> Message-ID: Hi Tobias & Jan-Mathis, Changing the cfg.output worked! Many thanks Rosa From: fieldtrip-bounces at science.ru.nl On Behalf Of Schoffelen, J.M. (Jan Mathijs) Sent: 30 March 2018 19:34 To: FieldTrip discussion list Subject: Re: [FieldTrip] Empty array in coherence connectivity analysis Yes, and be sure that cfg.channelcmb is an Nx2 cell-array: {‘somechannel’ ‘someotherchannel’; ‘againsomechannel’ ‘someotherchannelaswell’; ‘etc’ ‘etc’} Best wishes, Jan-Mathijs On 30 Mar 2018, at 18:00, Tobias Staudigl > wrote: Hi Taylor, First specify cfg.output = 'fourier' Or cfg.output ='powandcsd' in your ft_freqanalysis. Then try ft_connectivityanalysis again. Best, Tobias Am 30.03.2018 17:53 schrieb "Rosa Taylor Beale" >: Hi all, I’m a final year undergraduate in Cardiff working on pain networks. I have been trying to calculate coherence between 3 seed regions, however when I run the ft_connectivityanalysis, the labelcmb and cohspctrm arrays are empty (the channel labels don’t look like they were read?). There is no error or warning messages that occur when running the command, so I am unsure why it is not running correctly. First, I run ft_freqanalysis which seems to run fine: cfg = [] cfg.method = 'wavelet'; cfg.output = 'pow'; cfg.toi = 0:0.05:2; cfg.foi = [30:1:100]; time_freq= ft_freqanalysis(cfg, virtualchannel_raw); time_freq = label: {3x1 cell} dimord: 'chan_freq_time' freq: [1x71 double] time: [1x41 double] powspctrm: [3x71x41 double] cfg: [1x1 struct] Then I run the connectivity analysis and up with the empty output: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'pfcCont_seed' 'smc_seed' 'pfcIps_seed' 'smc_seed' 'pfcCont_seed' 'pfcIps_seed'}; coherence = ft_connectivityanalysis(cfg, time_freq); coherence = labelcmb: {0x2 cell} dimord: 'chancmb_freq_time' cohspctrm: [0x71x41 double] time: [1x41 double] freq: [1x71 double] cfg: [1x1 struct] >> coherence.labelcmb ans = Empty cell array: 0-by-2 >> coherence.cohspctrm ans = Empty array: 0-by-71-by-41 I have tried with fieldtrip versions 20161011 and 20171015 on matlab r2015a. I’ve shown this to various people much more experienced at fieldtrip than I and we’ve all been a bit stumped! Any ideas? Many thanks Rosa Taylor Beale _______________________________________________ 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 s.nara at bcbl.eu Thu Apr 5 14:38:00 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Thu, 5 Apr 2018 14:38:00 +0200 (CEST) Subject: [FieldTrip] Abstract submission deadline extended - 1st International Workshop on Predictive Processing In-Reply-To: <2078083467.10234189.1522931807461.JavaMail.zimbra@bcbl.eu> References: <293623353.10226685.1522918393461.JavaMail.zimbra@bcbl.eu> <902547454.10232978.1522928065669.JavaMail.zimbra@bcbl.eu> <2076980298.10234035.1522931448115.JavaMail.zimbra@bcbl.eu> <1103871096.10234078.1522931543036.JavaMail.zimbra@bcbl.eu> <2078083467.10234189.1522931807461.JavaMail.zimbra@bcbl.eu> Message-ID: <2121194270.10234238.1522931880542.JavaMail.zimbra@bcbl.eu> Hello Researchers, We have received request from lot of researchers to extend the deadline for abstract submission, We are happy to announce that the deadline for abstract submission for 1st International Workshop on Predictive Processing (WoPP) has been extended upto 16th April 2018. Hope to see you in San Sebastian. on behalf of Organisers Sanjeev Nara Predoctoral Researcher BCBL www.bcbl.eu https://sites.google.com/view/sanjeev-nara/ Tel: +34 943 309 300 (ext 314) Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer Abstract submission deadline extended - 1st International Workshop on Predictive Processing We would like to inform you that the abstract submission deadline to PREDICTIVE PROCESSING has been extended. The new deadline is April 16th. The conference dates are June 20-22, 2018 Dear Researcher, We are happy to announce the new discussion arena fully centred on predictive processing. The Workshop on Predictive Processing (WoPP) will take place in San Sebastian (Spain) on June 20-22, 2018. The goal of the workshop is to address the role of predictive processing in cognition. Some of the crucial issues in this timely research topic are the extent to which prediction is a fundamental mechanism of brain function, the role of prediction in learning, and, how predictive processing is expressed across distinct cognitive domains. This workshop will gather experts from different fields in cognitive neuroscience including sensory processing, attention and memory, to work alongside the community of language processing, with the aim of furthering our understanding of the role of predictive processing in cognition. We invite submissions from researchers genuinely interested in discussing their data within the framework of the prediction view on neurocognition and brain functioning. The conference will include keynote speakers, regular talks, symposiums and poster sessions. Keynote speakers will be the main sources of discussion: Sophie Scott , University College London Moshe Bar , Bar-Ilan University Pascal Fries, Ernst Strüngmann Institute (ESI) Each keynote will be followed by a symposium on a related topic. Each symposium will be co-organized by two experts in the field, and will last 2 hours. Symposium organizers are Gina Kuperberg, Matt Davis, Craig Richter, Julien Vezoli, Lucia Amoruso and Ruth De Diego Balaguer. For further information please visit: http://www.bcbl.eu/events/prediction-2018/en/ We look forward to seeing you at the conference. Yours sincerely, The Organizing Committee Manuel Carreiras, Clara Martin, Nicola Molinaro & David Soto IMPORTANT DATES TO REMEMBER: Abstract submission and Registration OPEN Abstract deadline: April, 6th, 2018. Extended until April 16th, 2018. Notification of abstract acceptance : April 24th, 2018. Early registration deadline: May 11th, 2018. Online registration deadline: May 30th, 2018. Conference dates: June 20-22, 2018. BQ_BEGIN BQ_END -------------- next part -------------- An HTML attachment was scrubbed... URL: From johnnguyen.education at gmail.com Thu Apr 5 23:11:19 2018 From: johnnguyen.education at gmail.com (John Nguyen) Date: Thu, 5 Apr 2018 17:11:19 -0400 Subject: [FieldTrip] Possibly speeding Up Preprocessing. Message-ID: Hi all, I was running a lot of preprocessing and was finding that it was running slower than I wanted despite good amount CPU/GPUS on board so I decided to look more into the code. I think I found a way to improve the speed but I'm not familiar with Github and pull requests so I just wanted to throw it out there and get people's opinion. In read_brainvision_eeg there is a for loop at line 79 using fseek and fread to reposition the pointer and read the channel-specfic data. Using tic-toc, I'm finding that it takes some time, around ~.27 secs for the loop to finish. When no channels are found, the same script runs fseek and fread only once and I feel like this is the better way to go. if 64-65 is replaced with " fseek(fid, hdr.NumberOfChannels*samplesize*(begsample-1), *'bof'*); dat = fread(fid, [hdr.NumberOfChannels, (endsample-begsample+1)], sampletype) *dat = dat(chanindx,:)*;" where underlined are the changes. the code should run whether or not chanindx is empty. tic-toc says it takes ~.05 sec and isequal says the two dat to be exactly the same. This could makes sense because it is not running fseek and fread constantly which relies on hard drive speeds? Though the timing seems to negligible, .27 sec per trial vs .05 per trial comes out to be a lot in large number of trials. [29 minutes vs 4 mins at 216 trls for 30 subs] Is my assumption correct? why is the for-loop at line 78 running though the channels backwards? Best regards, John Nguyen -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Wed Apr 11 14:49:09 2018 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Wed, 11 Apr 2018 14:49:09 +0200 Subject: [FieldTrip] Neuralynx support on OSX Message-ID: Dear FieldTrippers, I just started with intracranial data for the first time (yeah!), recorded to .ncs-files with Neuralynx' Cheetah (okay...), while also starting working on an Apple Mac (hmmm...). My first step was to try to load the header of the .ncs files, which gives me the warning: *Warning: the NEURALYNX_V6 toolbox is not installed, see http://neuralynx.com/research_software/file_converters_and_utilities/ and take the* *version from Neuralynx (windows only) * I see that previously there was a V3 which supported Mac, but not anymore. So I am afraid to ask ... can I really not read Neuralynx .ncs files with FieldTrip *on OSX*? Best, Stephen -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.nara at bcbl.eu Thu Apr 12 15:11:43 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Thu, 12 Apr 2018 15:11:43 +0200 (CEST) Subject: [FieldTrip] Non-parametric statistics for TFR data Message-ID: <302195760.10422434.1523538703510.JavaMail.zimbra@bcbl.eu> Hello, I am trying to implement parametric test on TFR data. I have 20 participant's data with 4 different conditions. I am interested in compairing theses conditions. After preprocessing and TFR computation i have one variable with (subjects * channels * freq * time ). The tutorial given on the website is using ERF data. Can i use it for TFR as well. cfg = []; cfg.channel = 'MEG'; cfg.latency = [0.3 0.7]; cfg.avgovertime = 'yes'; cfg.parameter = 'avg'; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_depsamplesT' cfg.alpha = 0.05; cfg.correctm = 'no'; cfg.correcttail = 'prob'; cfg.numrandomization = 1000; Nsub = 10; cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; cfg.ivar = 1; % the 1st row in cfg.design contains the independent variable cfg.uvar = 2; % the 2nd row in cfg.design contains the subject number stat = ft_timelockstatistics(cfg,allsubjFIC{:},allsubjFC{:}) % make the plot cfg = []; cfg.style = 'blank'; cfg.layout = 'CTF151_helmet.mat'; cfg.highlight = 'on'; cfg.highlightchannel = find(stat.mask); cfg.comment = 'no'; figure; ft_topoplotER(cfg, GA_FC) title('Nonparametric: significant without multiple comparison correction') Best regards Sanjeev Sanjeev Nara Predoctoral Researcher BCBL www.bcbl.eu https://sites.google.com/view/sanjeev-nara/ Tel: +34 943 309 300 (ext 314) Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From julian.keil at gmail.com Thu Apr 12 15:18:54 2018 From: julian.keil at gmail.com (Julian Keil) Date: Thu, 12 Apr 2018 15:18:54 +0200 Subject: [FieldTrip] Non-parametric statistics for TFR data In-Reply-To: <302195760.10422434.1523538703510.JavaMail.zimbra@bcbl.eu> References: <302195760.10422434.1523538703510.JavaMail.zimbra@bcbl.eu> Message-ID: Dear Sanjeev, take a look at this tutorial: http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_freq You need to use the ft_freqstatistics-function for TFR data. Best, Julian ________________ Prof. Dr. Julian Keil Biologische Psychologie Olshausenstraße 62 - R. 306 24118 Kiel 0431 / 880 - 4872 http://www.biopsych.uni-kiel.de/ Klinik für Psychiatrie und Psychotherapie der Charité im St. Hedwig-Krankenhaus Große Hamburger Straße 5-11 10115 Berlin 030 / 2311 - 1879 www.multisensorymind.com > Am 12.04.2018 um 15:11 schrieb Sanjeev Nara : > > Hello, > > I am trying to implement parametric test on TFR data. I have 20 participant's data with 4 different conditions. I am interested in compairing theses conditions. After preprocessing and TFR computation i have one variable with (subjects * channels * freq * time ). The tutorial given on the website is using ERF data. Can i use it for TFR as well. > > > cfg = []; > cfg.channel = 'MEG'; > cfg.latency = [0.3 0.7]; > cfg.avgovertime = 'yes'; > cfg.parameter = 'avg'; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_depsamplesT' > cfg.alpha = 0.05; > cfg.correctm = 'no'; > cfg.correcttail = 'prob'; > cfg.numrandomization = 1000; > > Nsub = 10; > cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; > cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; > cfg.ivar = 1; % the 1st row in cfg.design contains the independent variable > cfg.uvar = 2; % the 2nd row in cfg.design contains the subject number > > stat = ft_timelockstatistics(cfg,allsubjFIC{:},allsubjFC{:}) > > % make the plot > cfg = []; > cfg.style = 'blank'; > cfg.layout = 'CTF151_helmet.mat'; > cfg.highlight = 'on'; > cfg.highlightchannel = find(stat.mask); > cfg.comment = 'no'; > figure; ft_topoplotER(cfg, GA_FC) > title('Nonparametric: significant without multiple comparison correction') > > > > > > Best regards > Sanjeev > > > > Sanjeev Nara > Predoctoral Researcher BCBL > www.bcbl.eu > https://sites.google.com/view/sanjeev-nara/ > Tel: +34 943 309 300 (ext 314) > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > _______________________________________________ > 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: 833 bytes Desc: Message signed with OpenPGP URL: From stephen.whitmarsh at gmail.com Thu Apr 12 15:28:03 2018 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 12 Apr 2018 15:28:03 +0200 Subject: [FieldTrip] Neuralynx support on OSX In-Reply-To: References: Message-ID: Hello again, It just needed a second look - on the neurolynx website there is also a Linux/OSX (compiled) library, which seems to work fine. So as far I can tell now, the 'windows only' part of the warning message can be removed :-) Best wishes, Stephen On 11 April 2018 at 14:49, Stephen Whitmarsh wrote: > Dear FieldTrippers, > > I just started with intracranial data for the first time (yeah!), recorded > to .ncs-files with Neuralynx' Cheetah (okay...), while also starting > working on an Apple Mac (hmmm...). > > My first step was to try to load the header of the .ncs files, which gives > me the warning: > > *Warning: the NEURALYNX_V6 toolbox is not installed, see > http://neuralynx.com/research_software/file_converters_and_utilities/ > and > take the* > *version from Neuralynx (windows only) * > > I see that previously there was a V3 which supported Mac, but not anymore. > So I am afraid to ask ... can I really not read Neuralynx .ncs files with > FieldTrip *on OSX*? > > Best, > Stephen > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From roycox.roycox at gmail.com Thu Apr 12 20:54:40 2018 From: roycox.roycox at gmail.com (Roy Cox) Date: Thu, 12 Apr 2018 14:54:40 -0400 Subject: [FieldTrip] excessive channel correlations Message-ID: hello EEG community, We have a rather peculiar problem that we're hoping to get some input on. In reviewing some existing 64-channel recordings, we noticed that some records show near-identical signals across al channels, with median channel-by-channel correlations of >0.99. This suggests some kind of electrical shorting, somewhere in the cap-cable-amplifier-montage-recording-exporting chain. The problem appears to be infrequent (most records have more acceptable R values of 0.6-0.9), but common enough that we'll need to review several hundred records. We haven't been able to identify the cause of the problem yet, and it affects ongoing data collection. Some details: - we use Grass AURA amplifiers and TWin software with the Easycap system - the problem has been observed with different amplifiers, different caps, different pcs, and at different sites - the problem is there regardless of reference montage (e.g., forehead and averaged mastoids) - gel bridging, while theoretically possible, seems unlikely given that literally all EEG channels are (almost) identical We're still investigating but wanted to hear if anyone ever observed anything like this? Were they able to solve it? Thanks, Roy -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.spaak at donders.ru.nl Fri Apr 13 08:45:23 2018 From: e.spaak at donders.ru.nl (Eelke Spaak) Date: Fri, 13 Apr 2018 08:45:23 +0200 Subject: [FieldTrip] excessive channel correlations In-Reply-To: References: Message-ID: Hi Roy, I have no suggestion as to what might be causing this, but one suggestion on how to pragmatically deal with it, or at least maybe get some more insight. > - the problem is there regardless of reference montage (e.g., forehead and > averaged mastoids) Have you tried common average reference? If the signal is there on all channels, subtracting the common average should get rid of it. Cheers, Eelke > - gel bridging, while theoretically possible, seems unlikely given that > literally all EEG channels are (almost) identical > > We're still investigating but wanted to hear if anyone ever observed > anything like this? Were they able to solve it? > > Thanks, > > Roy > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From maximilien.chaumon at gmail.com Fri Apr 13 16:16:35 2018 From: maximilien.chaumon at gmail.com (Maximilien Chaumon) Date: Fri, 13 Apr 2018 14:16:35 +0000 Subject: [FieldTrip] extracting a continuous patch on a mesh Message-ID: Dear all, I'm trying to extract a connected patch of vertices at most say 2 cm away from a given seed. Is there an easy way to do this in FieldTrip? Many thanks, Max -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.smulders at maastrichtuniversity.nl Fri Apr 13 16:45:50 2018 From: f.smulders at maastrichtuniversity.nl (Smulders, F (PSYCHOLOGY)) Date: Fri, 13 Apr 2018 14:45:50 +0000 Subject: [FieldTrip] excessive channel correlations In-Reply-To: References: , Message-ID: I have seen this occasionally, also on Brainvision's BrainAmp. I find it worrying, and would also like a good explanation. I have seen before that open channels on an AD converter just pass a copy of an occupied channel. So if you have a bad connection, that might explain it. Subtracting the channel-average would possibly 'hide' a serious hardware problem, it seems to me that you just might end up with pure noise. kind regards, Fren > On 13 Apr 2018, at 08:56, Eelke Spaak wrote: > > Hi Roy, > > I have no suggestion as to what might be causing this, but one > suggestion on how to pragmatically deal with it, or at least maybe get > some more insight. > >> - the problem is there regardless of reference montage (e.g., forehead and >> averaged mastoids) > > Have you tried common average reference? If the signal is there on all > channels, subtracting the common average should get rid of it. > > Cheers, > Eelke > >> - gel bridging, while theoretically possible, seems unlikely given that >> literally all EEG channels are (almost) identical >> >> We're still investigating but wanted to hear if anyone ever observed >> anything like this? Were they able to solve it? >> >> Thanks, >> >> Roy >> >> _______________________________________________ >> 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 From thomas.bancel at icm-institute.org Wed Apr 18 11:17:01 2018 From: thomas.bancel at icm-institute.org (BANCEL Thomas) Date: Wed, 18 Apr 2018 09:17:01 +0000 Subject: [FieldTrip] Opening .smr file with ft Message-ID: <28FC02000FAE4C418B74665EF5E368BA8A6E02@SRVMAIL-ICM.icm-institute.org> Hi everyone, My name is Thomas Bancel, I am working on epilepsy at ICM and we have recordings from the Spike2 (v 9.02) software (CED, .smr file) that I would like to put into Matlab using Fieldtrip (and not the SONLibrary). When I call the following script: addpath('C:\Users\thomas.bancel\Documents\MATLAB\fieldtrip-20180228\'); ft_defaults smr_filepath = 'C:\Users\thomas.bancel\Documents\Crises annotées Mark\557 GAERS S1 2015_10_19\557 GAERS S1 2015_10_19 _M.smr'; smrx_filepath = 'C:\Users\thomas.bancel\Documents\Crises annotées Mark\557 GAERS S1 2015_10_19\smrx557 GAERS S1 2015_10_19.smrx'; dll_name = 'C:\Users\thomas.bancel\Documents\MATLAB\nsMCDLibrary_3.7b\Matlab\Matlab-Import-Filter\Matlab_Interface\nsMCDLibrary64.dll'; [result] = ns_SetLibrary(dll_name) % give 0 ft_read_data(smr_filepath) I get the following message: Call ns_SetLibrary first! Process interrupted! Error using read_ced_son (line 97) Could not get NeuroShare library info, please use the NS_SETLIBRARY function. Can someone help me ? I work on Matlab R2017b, fieldtrip release 2018/02/28, windows 7 professional, 64 bit. Thank you in advance, Thomas PS: this is my first message in the discussion list, sorry if it lacks info or if it is unclear, I can update if needed. Thomas Bancel ICM - Equipe Charpier thomas.bancel at icm-institute.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From R.Mehraram2 at newcastle.ac.uk Wed Apr 18 11:28:36 2018 From: R.Mehraram2 at newcastle.ac.uk (Ramtin Mehraram (Student)) Date: Wed, 18 Apr 2018 09:28:36 +0000 Subject: [FieldTrip] Not timefrequency data on fieldtrip: cluster-based statistics References: Message-ID: Hi all! I need to run a statistical analysis across four independent groups for some network measure I obtained with the brain connectivity toolbox (degree, clustering coefficient, etc.) from EEG data. I am dealing with the multiple comparison issue. Since I am using a high density cap, nothing survives the Bonferroni correction (and variants), nor the FDR. I am trying to perform a cluster-based (montecarlo) analysis as implemented in Fieldtrip, but the toolbox needs the input to be organized as a time-frequency structure. I tried to rebuild a similar structure (degree values instead of power spectrum values), but it seems that I am being unsuccessful. Indeed: if I run a "cfg.statistic = indepsamplesF" across the groups I get NaNs in the probability output matrix. If I just perform a "cfg.statistic = indepsamplesT" between two random groups, I get a couple of channels or so with p<0.05. In all the cases, any form of fieldtrip plotting (such as ft_clusterplot) shows as output the message "Argument to mbscalar must be scalar". Any idea? Is it actually sensible to proceed in this way or is there any smarter way to work with not time-frequency data on fieldtrip? Many thanks in advance for your help. Ramtin Mehraram PhD Student @ramtinTVT Biomedical Research Building 3rd floor Institute of Neuroscience Newcastle University NE4 5PL, United Kingdom www.lewybodylab.org https://www.newcastlebrc.nihr.ac.uk/research-themes/dementia/ From e.maris at donders.ru.nl Wed Apr 18 13:39:45 2018 From: e.maris at donders.ru.nl (Maris, E.G.G. (Eric)) Date: Wed, 18 Apr 2018 11:39:45 +0000 Subject: [FieldTrip] PhD position at the Donders Institute on competition between internal and external attention states In-Reply-To: References: Message-ID: PhD position at the Donders Institute for Brain, Cognition and Behaviour: Watch out! Competition between internal and external attention states in brain and behavior Supervisors: Eric Maris & Marius Peelen Summary: Attention can be directed externally (to the outside world) or internally (to representations in the mind). While this distinction features prominently in current models of attention, there are surprisingly few empirical studies directly investigating this distinction. This project provides a comprehensive investigation of the external-internal attention distinction, its neurophysiological characteristics, and its relation to behavior. Using advanced analysis of both ongoing and evoked EEG/MEG data we will classify spontaneous brain states as corresponding to external versus internal attention states. We will link these brain states to perceptual performance in naturalistic object recognition tasks, testing the hypothesis that an external attention state leads to better perceptual performance. In addition, we will induce attention states by having participants perform externally and internally directed tasks. Finally, we will test the hypothesis that shifting gaze, even in complete darkness, directs attention externally, leading to better perceptual performance. Results of these studies will: (1) provide empirical evidence for the proposed distinction between external and internal attention, (2) provide a neurophysiological characterization of these attention states, and (3) shed light on the feasibility to improve perceptual performance by biasing attention towards the external state. Contact: e.maris at donders.ru.nl or m.peelen at donders.ru.nl Eric Maris | Donders Institute for Brain, Cognition, and Behaviour & Faculty of Social Sciences | Radboud University | PO Box 9104, 6500 HE Nijmegen | (024) 3612651 | www.ru.nl This message (and any attachments) is intended solely for the addressee(s) and may contain confidential information. If you are not the addressee, do not copy this message (and any attachments), forward or share this message with third parties. You are requested to notify the sender immediately and delete this message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.stoica at uke.de Wed Apr 18 15:32:51 2018 From: m.stoica at uke.de (Mircea Stoica) Date: Wed, 18 Apr 2018 15:32:51 +0200 Subject: [FieldTrip] Social cognition in humans and robots (Hamburg, September 27-28, 2018) Message-ID: Dear all, we are pleased to invite you to the "Social cognition in humans and robots" conference that will take place in Hamburg between the 27th and 28th of September, 2018. Over decades, a range of theories and concepts for explaining how we understand others have been developed. This conference turns the spotlight on the idea that social cognition is grounded in sensorimotor and informational dynamic coupling of agents. According to this view, interaction dynamics is one of the keys to understand the mechanisms of successful social interaction because it provides substantial clues to social understanding and gives rise to high-level capabilities such as joint shared intentionality and joint action. Moreover it suggests that many disturbances of social cognition may be rooted in the impaired capacity for entraining and sustaining sensorimotor and informational coupling. The conference will provide an interdisciplinary podium which overviews trends and recent developments of concepts, methods, basic research and applications of sensorimotor approaches in social cognitive science, neuroscience, and robotic research. A particularly interesting question will be how concepts and methods from social cognitive and neuroscience transfer to human-robot interaction. The meeting will also gauge the societal impact of progress in understanding dynamic coupling processes in human-human and human-robot interactions. The event is organized by the FET Proactive H2020 project "Socializing Sensorimotor Contingencies - soSMCs" (socSMCs.eu) in partner alliance with the European Society for Cognitive Systems - EUCog (eucognition.org). Keynote speakers - Natalie Sebanz (Central European University, Hungary) - Antonia Hamilton (University College London, UK) - Scott Kelso (Florida Atlantic University, USA) - Luciano Fadiga (University of Ferrara and IIT, Italy) - Iain Couzin (University of Konstanz, Germany) - Paul Verschure (Institute for Bioengineering of Catalonia, Spain) Submissions - Conference contributions (talks, posters) - Research articles (to be published in a Frontiers Research Topic) - Venues for the EUCognition meeting in 2019 For all submission types, please send an abstract of no more than 1.000 words to conference2018 at socSMCs.eu and indicate the type of your contribution (poster|talk|article|venue), the title (500 characters max.), all author names and affiliations. Important dates - May 25, 2018: Deadline for submission of abstracts - June 29, 2018: Registration closes - Decemnaber 3, 2018: Submission of research articles Fee The registration fee of 110€ includes coffee, soft drinks and snacks on both days. On September 27th, a social dinner at an extra charge of 20€ will be hosted at the MS Cap San Diego (http://www.capsandiego.de/in- brief.html).Booking of the social dinner is only possible in combination with a conference registration. Register today at https://en.xing-events.com/TEHHWXM More info at https://www.socsmcs.eu/conference2018 Best regards, Mircea Stoica -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Martina Saurin (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING -------------- next part -------------- An HTML attachment was scrubbed... URL: From elam4hcp at gmail.com Wed Apr 18 18:55:25 2018 From: elam4hcp at gmail.com (Jennifer Elam) Date: Wed, 18 Apr 2018 11:55:25 -0500 Subject: [FieldTrip] HCP Course 2018 at Oxford: Final Course Schedule posted -- Register Now! Message-ID: Faculty listings and the full schedule of covered topics are now available for the *2018 HCP Course: "Exploring the Human Connectome" *, to be held *June 25 – 29, 2018* at the Blavatnik School of Government , at the University of Oxford , in Oxford, UK! The 5-day intensive course is a great opportunity to learn directly from HCP investigators and gain practical experience with the Human Connectome Project's approach to multimodal whole brain imaging acquisition, processing, analysis, visualization, and sharing of data and results. For more info and to register visit the HCP Course 2018 website . Don't delay, registration is limited, and the course is filling up fast! Nearby affordable accommodations are available at Worcester College at Oxford by selecting registration with accommodations on the site. If you have any questions, please contact us at: hcpcourse at humanconnectome. org We look forward to seeing you in Oxford! Best, 2018 HCP Course Staff -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam at wustl.edu www.humanconnectome.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.nara at bcbl.eu Thu Apr 19 23:15:13 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Thu, 19 Apr 2018 23:15:13 +0200 (CEST) Subject: [FieldTrip] Brainhack Donostia 2018 In-Reply-To: <2051471137.10611732.1524143917106.JavaMail.zimbra@bcbl.eu> References: <2051471137.10611732.1524143917106.JavaMail.zimbra@bcbl.eu> Message-ID: <1069339273.10622399.1524172513356.JavaMail.zimbra@bcbl.eu> Hello Everyone The Basque Center on Cognition Brain and Language (BCBL) will host the first edition of the BrainhackDonostia2018. The event aims at bringing together students and scientists at all levels of their careers to enjoy science and a couple of Cider glasses together. This year's edition will focus on Neuroimaging techniques, in particular fMRI (functional magnetic resonance) MEG (magnetoencephalography, EEG (electroencephalogaphy) and fNIRS (functional near infrared spectroscopy). Through a combination of lectures and tutorials, participants will be introduced on these techniques, and how they can be used to study the mind and brain. For those that have more experience, and have an interest in three days of project development, there is also the possibility to propose and develop a project related to neuroimaging and/or electrophysiology recruiting participants on site. The event is open to people from different disciplines and backgrounds, with a genuine interest in neuroimaging methods, psychology, neuroscience, and more generally interdisciplinary research. Feel free to explore our website for further information. http://www.bcbl.eu/events/BrainhackDonostia2018/en/ The event will be hosted on May 2nd-4th 2018 in the Basque Center on Cognition Brain and Language in San Sebastian, Spain. The cost is 10€ for Master Students, 15€ for PhD and PostDocs, 40€ for Seniors and "Industrials" + optional 13€ for the T-shirt. Registration to the event is needed and can be done on the website, until the 25th of April. A certificate of attendance will be provided to participants. If you have more questions, we remain at your disposal at the address info.bhg-donostia at bcbl.eu We look forward to see you in May! From s.nara at bcbl.eu Thu Apr 19 23:48:24 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Thu, 19 Apr 2018 23:48:24 +0200 (CEST) Subject: [FieldTrip] Common Baseline for uneven length trials Message-ID: <356285164.10622632.1524174504598.JavaMail.zimbra@bcbl.eu> Hello Researchers I am working on a dataset where i have some trials per subject which are time locked to target1. I computed the time frequency response by specifying first 400 miliseconds as Baseline. Then i redefine the trials to a different triggers by providing the pre calculated offset. The offset introduces the trials (pre trig) with different timings. I mean some trials start with say -2.5 seconds and some starts at say -2.4 (my offsets is varying). i have mainly two questions: 1. How can take a common baseline for both the cases. 2. is it possible to specify the samples in fieldtrip Baseline option. Thanks Best regards Sanjeev Sanjeev Nara Predoctoral Researcher BCBL www.bcbl.eu https://sites.google.com/view/sanjeev-nara/ Tel: +34 943 309 300 (ext 314) Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From zoran at nyu.edu Fri Apr 20 16:59:02 2018 From: zoran at nyu.edu (Zoran Josipovic) Date: Fri, 20 Apr 2018 10:59:02 -0400 Subject: [FieldTrip] fieldtrip Digest, Vol 89, Issue 9 In-Reply-To: References: Message-ID: Hello fieldtrip community, Does anyone know if the fieldtrip can run Matlab firpm filter, and if so, what is the correct script to do it? Here is the Matlab page for this filter: https://www.mathworks.com/help/signal/ref/firpm.html Thanks! Zoran On Fri, Apr 20, 2018 at 6:00 AM, 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. Brainhack Donostia 2018 (Sanjeev Nara) > 2. Common Baseline for uneven length trials (Sanjeev Nara) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 19 Apr 2018 23:15:13 +0200 (CEST) > From: Sanjeev Nara > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Brainhack Donostia 2018 > Message-ID: > <1069339273.10622399.1524172513356.JavaMail.zimbra at bcbl.eu> > Content-Type: text/plain; charset=utf-8 > > > Hello Everyone > > The Basque Center on Cognition Brain and Language (BCBL) will host the > first edition of the BrainhackDonostia2018. The event aims at bringing > together students and scientists at all levels of their careers to enjoy > science and a couple of Cider glasses together. > > This year's edition will focus on Neuroimaging techniques, in particular > fMRI (functional magnetic resonance) MEG (magnetoencephalography, EEG > (electroencephalogaphy) and fNIRS (functional near infrared spectroscopy). > Through a combination of lectures and tutorials, participants will be > introduced on these techniques, and how they can be used to study the mind > and brain. > For those that have more experience, and have an interest in three days of > project development, there is also the possibility to propose and develop a > project related to neuroimaging and/or electrophysiology recruiting > participants on site. > > The event is open to people from different disciplines and backgrounds, > with a genuine interest in neuroimaging methods, psychology, neuroscience, > and more generally interdisciplinary research. Feel free to explore our > website for further information. > http://www.bcbl.eu/events/BrainhackDonostia2018/en/ > > The event will be hosted on May 2nd-4th 2018 in the Basque Center on > Cognition Brain and Language in San Sebastian, Spain. The cost is 10? for > Master Students, 15? for PhD and PostDocs, 40? for Seniors and > "Industrials" + optional 13? for the T-shirt. Registration to the event is > needed and can be done on the website, until the 25th of April. A > certificate of attendance will be provided to participants. > > If you have more questions, we remain at your disposal at the address > info.bhg-donostia at bcbl.eu > > We look forward to see you in May! > > > > > ------------------------------ > > Message: 2 > Date: Thu, 19 Apr 2018 23:48:24 +0200 (CEST) > From: Sanjeev Nara > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Common Baseline for uneven length trials > Message-ID: <356285164.10622632.1524174504598.JavaMail.zimbra at bcbl.eu> > Content-Type: text/plain; charset=utf-8 > > Hello Researchers > > I am working on a dataset where i have some trials per subject which are > time locked to target1. I computed the time frequency response by > specifying first 400 miliseconds as Baseline. Then i redefine the trials to > a different triggers by providing the pre calculated offset. The offset > introduces the trials (pre trig) with different timings. I mean some trials > start with say -2.5 seconds and some starts at say -2.4 (my offsets is > varying). i have mainly two questions: > > 1. How can take a common baseline for both the cases. > 2. is it possible to specify the samples in fieldtrip Baseline option. > > Thanks > > > Best regards > Sanjeev > > > > Sanjeev Nara > Predoctoral Researcher BCBL > www.bcbl.eu > https://sites.google.com/view/sanjeev-nara/ > Tel: +34 943 309 300 (ext 314) > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 89, Issue 9 > **************************************** > -- Zoran Josipovic, PhD Adjunct Assistant Professor Psychology Dept. Research Associate NYULMC New York University -------------- next part -------------- An HTML attachment was scrubbed... URL: From virginie.van.wassenhove at gmail.com Sat Apr 21 23:45:25 2018 From: virginie.van.wassenhove at gmail.com (Virginie van Wassenhove) Date: Sat, 21 Apr 2018 23:45:25 +0200 Subject: [FieldTrip] Fwd: [last call for a position in the Cognition & Brain Dynamics lab, NeuroSpin - Closing date: April 22nd 2018] In-Reply-To: References: Message-ID: Dear all, this is a last reminder for a previously advertised job opening in my lab, description available here: https://brainthemind.files.wordpress.com/2018/02/2018_vvw_ jobdescription_cea1.pdf **Deadline is tomorrow April 22nd at midnight (UTC-12)** Best wishes, Virginie -- Virginie van Wassenhove *https://brainthemind.com/ * -------------- next part -------------- An HTML attachment was scrubbed... URL: From luca.turella at unitn.it Sun Apr 22 21:41:14 2018 From: luca.turella at unitn.it (Luca Turella) Date: Sun, 22 Apr 2018 21:41:14 +0200 Subject: [FieldTrip] Call for 11 fully-funded PhD positions NOW OPEN @ CIMeC, UNITrento. Italy Message-ID: Dear all, We are pleased to announce the opening of a call for *11 fellowships* for our international PhD Program in Cognitive and Brain Sciences (CIMeC), commencing November 2018 at the University of Trento, Italy. As you will see from the links below, the PhD call is open to several fields of cognitive neuroscience research. Interested candidates should feel free to contact the PIs that might have topics of interest to them. - *Admissions*: http://www.unitn.it/drcimec/admission - PhD research areas outline: http://www.unitn.it/drcimec/research-topics - PhD Application *summary*: http://www.unitn.it/drcimec/node/118 - PhD *Application *link: https://webapps.unitn.it/Apply/en/MyUnitn/Home/669/dott/cbs34 - PhD Application *Deadline*:* Thursday May 31, 2018, at 4pm (Italian time)* - *CIMeC*: http://www.unitn.it/cimec This year’s research topics proposed by the Doctoral Program Committee for 5 UNITN grants are visible here: http://www.unitn.it/drcimec/research-topics, while the 6 topic-specific grants’ details can be found here: http://www.unitn.it/drcimec/topic-specific-grants *The CIMeC, it’s doctoral program and UNITN in numbers:* - 2018 UNITrento ranks among top Italian Universities in THE - Times Higher Education - *4-yr program* (Nov. 1, 2018- Oct. 31, 2022). - Why a 4-yr program - Courses are given in English - 11 positions, 100% funded - Salary: starting at approximately €1.200/mo., net - Winners receive a €4887 tax-free research/mobility budget - Why choose UNITRENTO Please feel free to browse the FAQ pages on our website for further information, or contact the Director of the Programme, Prof. Francesco Pavani phd.cimec at unitn.it. -- Luca Turella, PhD Assistant Professor CIMeC - Center for Mind/Brain Sciences University of Trento Mattarello (TN), Via Delle Regole 101 Tel.+39 0461-28 3098 http://www.unitn.it/cimec Legal Disclaimer This electronic message contains information that is confidential. The information is intended for the use of the addressee only. If you are not the addressee we would appreciate your notification in this respect. Please note that any disclosure, copy, distribution or use of the contents of this message is prohibited and may be unlawful. Avvertenza legale Questo messaggio Email contiene informazioni confidenziali riservate ai soli destinatari. Qualora veniate in possesso di tali informazioni senza essere definito come destinatario vi reghiamo di leggere le seguenti note. Ogni apertura, copia, distribuzione del contenuto del messaggio e dei suoi allegati è proibito e potrebbe violare le presenti leggi. -------------- next part -------------- An HTML attachment was scrubbed... URL: From maximilien.chaumon at gmail.com Mon Apr 23 14:15:19 2018 From: maximilien.chaumon at gmail.com (Maximilien Chaumon) Date: Mon, 23 Apr 2018 12:15:19 +0000 Subject: [FieldTrip] extracting a continuous patch on a mesh In-Reply-To: References: Message-ID: Hi all, So I coded something that could perhaps be useful to others. It grows a patch around a seed up to a certain distance. See below function [list] = mesh_patch(mesh,seed,dmax) % [list] = mesh_patch(mesh,seed,d) % % return the list of connected vertices that are at most d mesh.unit away % from seed. % % Maximilien Chaumon 2018 % measure distance to seed seedpos = mesh.pos(seed,:); distances = sqrt(sum(bsxfun(@minus,mesh.pos,seedpos).^2,2)); % crawl starting from seed list = crawl(mesh.tri,distances,dmax,seed); function final = crawl(tri,d,dmax,vert) % bookkeeping: the list of vertices persistent listi st = dbstack; level = sum(strcmp({st.name},'crawl')); if level == 1 listi = []; end % listi(end+1) = vert; % append this vertex to the list conn = tri(any(tri==vert,2),:);% connected vertices conn = unique(conn); conn(d(conn) > dmax) = []; % remove those that are too far. conn(ismember(conn,listi)) = [];%keep only vertices that have not been crawled yet for i = 1:numel(conn) crawl(tri,d,dmax,conn(i));% move to next end % bookkeeping: return the list at last if level == 1 final = listi; % return list if it's last call end Le ven. 13 avr. 2018 à 16:16, Maximilien Chaumon < maximilien.chaumon at gmail.com> a écrit : > Dear all, > > I'm trying to extract a connected patch of vertices at most say 2 cm away > from a given seed. > Is there an easy way to do this in FieldTrip? > > Many thanks, > Max > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ph442 at cam.ac.uk Mon Apr 23 14:48:06 2018 From: ph442 at cam.ac.uk (parham hashemzadeh) Date: Mon, 23 Apr 2018 13:48:06 +0100 Subject: [FieldTrip] extracting a continuous patch on a mesh In-Reply-To: References: Message-ID: Hi All Is there a Matlab implementation of openMEEG lying around somewhere? I was wondering, if openMEEG has a pure Matlab or python implementation. Pure form. Many of us (INCLUDING ME) are using code, without really digging deep into the details. I would be grateful, if it can be shared. Many thanks best regards parham On 2018-04-23 13:15, Maximilien Chaumon wrote: > Hi all, > > So I coded something that could perhaps be useful to others. It grows > a patch around a seed up to a certain distance. See below > > function [list] = mesh_patch(mesh,seed,dmax) > > % [list] = mesh_patch(mesh,seed,d) > % > % return the list of connected vertices that are at most d mesh.unit > away > % from seed. > % > % Maximilien Chaumon 2018 > > % measure distance to seed > seedpos = mesh.pos(seed,:); > distances = sqrt(sum(bsxfun(@minus,mesh.pos,seedpos).^2,2)); > > % crawl starting from seed > list = crawl(mesh.tri,distances,dmax,seed); > > function final = crawl(tri,d,dmax,vert) > > % bookkeeping: the list of vertices > persistent listi > st = dbstack; > level = sum(strcmp({st.name [1]},'crawl')); > if level == 1 > listi = []; > end > % > > listi(end+1) = vert; % append this vertex to the list > > conn = tri(any(tri==vert,2),:);% connected vertices > conn = unique(conn); > conn(d(conn) > dmax) = []; % remove those that are too far. > conn(ismember(conn,listi)) = [];%keep only vertices that have not been > crawled yet > for i = 1:numel(conn) > crawl(tri,d,dmax,conn(i));% move to next > end > > % bookkeeping: return the list at last > if level == 1 > final = listi; % return list if it's last call > end > > Le ven. 13 avr. 2018 à 16:16, Maximilien Chaumon > a écrit : > >> Dear all, >> >> I'm trying to extract a connected patch of vertices at most say 2 cm >> away from a given seed. >> Is there an easy way to do this in FieldTrip? >> >> Many thanks, >> Max > > > Links: > ------ > [1] http://st.name > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- best regards Parham Hashemzadeh Research Associate Department of Applied Mathematics and Theoretical Physics University of Cambridge, UK. email: hashemzadeh at damtp.cam.ac.uk From Joshua.Bear at childrenscolorado.org Wed Apr 25 19:07:13 2018 From: Joshua.Bear at childrenscolorado.org (Bear, Joshua) Date: Wed, 25 Apr 2018 17:07:13 +0000 Subject: [FieldTrip] ft_sourceinterpolate question Message-ID: <2E9B4D36-9330-49D1-8F3D-2EEAFA4E40B2@contoso.com> Dear FieldTrip Users: I am trying to apply the Network Analysis tutorial to my own data, and I have hit a stumbling block with the atlas and parcellation steps. Briefly, I am using a mesh exported from Brainstorm with 15002 vertices, so at the end of all steps through ft_connectivityanalysis I have a connectivity structure with pos = 15002. The atlas has pos = 8004. I tried to use ft_sourceinterpolate to make my connectivity structure match the atlas, but it is only seems to be interpolating the first dimension of the source data as shown below. My question: How can I make ft_sourceinterpolate apply to both dimensions of my cohspctrm parameter rather than only the first dimension? RESULTS from ft_connectivityanalysis: source_conn = struct with fields: inside: [15002×1 logical] pos: [15002×3 double] tri: [29989×3 double] cohspctrm: [15002×15002 double] dimord: 'pos_pos_freq' freq: 9.9340 cfg: [1×1 struct] INTERPOLATION commands: cfg = []; cfg.parameter = 'cohspctrm'; cfg.interpmethod = 'nearest'; source_conn_interp = ft_sourceinterpolate(cfg, source_conn, atlas); RESULTS from ft_sourceinterpolate: source_conn_interp = struct with fields: freq: 9.9340 pos: [8004×3 double] tri: [16000×3 double] unit: 'mm' inside: [8004×1 logical] cohspctrm: [8004×15002 double] cfg: [1×1 struct] Notice that the cohspctrm is interpolated from a [15002×15002 double] to a [8004×15002 double]. This then translates to the parcellation step where only the first dimension can be parcellated using the atlas. I’m sure I am missing something obvious and appreciate your thoughts and patience, Josh -- Joshua Bear, MD, MA Neuroscience Institute, Children’s Hospital Colorado ------------------------------------------------------------------------------ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ------------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.nara at bcbl.eu Wed Apr 25 21:52:39 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Wed, 25 Apr 2018 21:52:39 +0200 (CEST) Subject: [FieldTrip] Mismatch between cluster activation and * marks Message-ID: <158854153.10803185.1524685959460.JavaMail.zimbra@bcbl.eu> Hi Fieldtrip Experts Apologies for a long mail. I have a experiment where i have 20 subjects which have performed 2 different tasks. I want to implement a cluster based permutation test for compare the Time frequency analysis in two different conditions. I a following this tutorial for computing the stats http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_freq . I have computed the stats using ft_freqstatistics by providing input a 4 D matrix which has size (20 subjects * 102 channels * 70 frequency bins * 190 time points ). The analysis give me positive and negative clusters. I want to plot first positive and negative cluster in terms of channels which are significant during a specifies frequency range (say 12 - 30 ) in a specified time range. After that i use ft_descriptive on difference of powerspectrum in both conditions. I am plotting the cluster within a specified time and frequency duration computed from first positive and negative cluster. The problem is i am getting topoplots which have a difference in the colour activation and the ' * ' marks. I have attached few plots to show what is the issue. The image img1_correct and img2_correct shows the match between activations and ' * ' marks whereas the img1_incorrect and img2_incorrect shows the mismatch. I shall be thankful if you could please help me debugging the issue. Best regards Sanjeev Sanjeev Nara Predoctoral Researcher BCBL www.bcbl.eu https://sites.google.com/view/sanjeev-nara/ Tel: +34 943 309 300 (ext 314) Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer -------------- next part -------------- A non-text attachment was scrubbed... Name: img1_correct.png Type: image/png Size: 48736 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: img1_incorrect.png Type: image/png Size: 52018 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: img2_incorrect.png Type: image/png Size: 48615 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: img2_correct.png Type: image/png Size: 49975 bytes Desc: not available URL: From seymourr at aston.ac.uk Thu Apr 26 01:48:31 2018 From: seymourr at aston.ac.uk (Seymour, Robert (Research Student)) Date: Wed, 25 Apr 2018 23:48:31 +0000 Subject: [FieldTrip] ft_sourceinterpolate question Message-ID: Hi Josh, It seems like you are using the HCP Glasser atlas ('A multi-modal parcellation of human cerebral cortex')? The atlas presented as part of the network analysis tutorial is designed for a cortical mesh with 8004 vertices, rather than the 15002 you are using. I don’t believe ft_sourceinterpolate can currently cope with the surface-based transformation upwards from 8000—> 15000 vertices. To use the HCP atlas you will need to downsample the original 32k atlas in fs_LR space to 15000 space and transform to whichever standard-brain template you are using. This is non-trivial and requires some functions from the HCP project (e.g. wb_command which can be found here: https://www.humanconnectome.org/software/workbench-command). If your mesh is created using Freesurfer you can use this script here: https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh If the mesh is not constructed using Freesurfer it will be tricker & I would recommend contacting the HCP mailing list. Good luck! Robert Seymour (Aston Brain Centre & Department of Cognitive Science, Macquarie University). -------------- next part -------------- An HTML attachment was scrubbed... URL: From Joshua.Bear at childrenscolorado.org Thu Apr 26 04:14:09 2018 From: Joshua.Bear at childrenscolorado.org (Bear, Joshua) Date: Thu, 26 Apr 2018 02:14:09 +0000 Subject: [FieldTrip] ft_sourceinterpolate question In-Reply-To: References: Message-ID: Hi Robert, Thank you so much for the response! My ultimate intention is actually to use the parcellation scheme proposed by Gordon et al. (Cerebral Cortex, Volume 26, Issue 1, 1 January 2016, Pages 288–303, https://doi.org/10.1093/cercor/bhu239) though at this time I was using the atlas provided in the tutorial. The problem I ran into is that I am trying to interpolate my brain’s mesh DOWN from 15002 to 8004 (to match the atlas), not up. As you pointed out, I have had some problems with other high resolution meshes, but in this case ft_sourceinterpolate seemed to work — it just only worked for one of the two dimensions of my connectivity data. That is, it went from a [15002×15002 double] to a [8004×15002 double]. Of course it’s possible the interpolation for that first dimension was incorrect, but what confused me was that it did not interpolate the second dimension. (As I write this, I’m wondering if I should simply try transposing the matrix and running the interpolation again!). I will try, as you suggest, downsampling the mesh externally and trying again. I’m not able to match the 8004 vertices perfectly, but perhaps if I drop it slightly below this number it will be able to interpolate up correctly. Any other thoughts or suggestions are greatly appreciated as well. Best, Josh From: on behalf of "Seymour, Robert (Research Student)" Reply-To: FieldTrip discussion list Date: Wednesday, April 25, 2018 at 5:48 PM To: "fieldtrip at science.ru.nl" Subject: Re: [FieldTrip] ft_sourceinterpolate question Hi Josh, It seems like you are using the HCP Glasser atlas ('A multi-modal parcellation of human cerebral cortex')? The atlas presented as part of the network analysis tutorial is designed for a cortical mesh with 8004 vertices, rather than the 15002 you are using. I don’t believe ft_sourceinterpolate can currently cope with the surface-based transformation upwards from 8000—> 15000 vertices. To use the HCP atlas you will need to downsample the original 32k atlas in fs_LR space to 15000 space and transform to whichever standard-brain template you are using. This is non-trivial and requires some functions from the HCP project (e.g. wb_command which can be found here: https://www.humanconnectome.org/software/workbench-command). If your mesh is created using Freesurfer you can use this script here: https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh If the mesh is not constructed using Freesurfer it will be tricker & I would recommend contacting the HCP mailing list. Good luck! Robert Seymour (Aston Brain Centre & Department of Cognitive Science, Macquarie University). ------------------------------------------------------------------------------ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ------------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From Joshua.Bear at childrenscolorado.org Thu Apr 26 08:01:28 2018 From: Joshua.Bear at childrenscolorado.org (Bear, Joshua) Date: Thu, 26 Apr 2018 06:01:28 +0000 Subject: [FieldTrip] ft_sourceinterpolate question In-Reply-To: References: Message-ID: <271913CA-10AE-4E5B-8424-429132D272A7@childrenscolorado.org> Hi all, It occurs to me that using ft_sourceinterpolate to decrease, rather than increase, the dimensions is not intuitive, and I found that it was actually fairly easy to get the Gorden et al. atlas loaded in as they provide an MNI-registered form of the atlas. So I repeated my steps using the selected atlas and with a smaller headmodel and leadfield resulting in a source file that had to be interpolated in the more anticipated direction. The problem persists, however. I now have connectivity results with the following pertinent values: dim: [18 15 15] pos: [4050×3 double] cohspctrm: [4050×4050 double] dimord: 'pos_pos_freq' My atlas has the following pertinent values: dim: [61 73 61] transform: [4×4 double] brick0: [61×73×61 uint16] brick0label: {1×333 cell} The results of interpolating my connectivity source to the atlas lead to the same peculiar asymmetry in the cohspctrm results: dim: [61 73 61] transform: [4×4 double] inside: [61×73×61 logical] cohspctrm: [271633×4050 double] pos: [271633×3 double] And as the whole point is to then use ft_sourceparcellate, I found that this carries over the asymmetrical results of the interpolation with the following source values after parcellation: freq: 9.9340 label: {1×333 cell} cohspctrm: [333×4050 double] brainordinate: [1×1 struct] cfg: [1×1 struct] As you can see, the first dimension of the cohspctrm results increased from 4050 to 271633 with interpolation and then decreased to 333, the number of parcels in my chosen atlas, exactly as I would have expected. The second dimension, however, did not budge from its initial 4050. The interpolation step is necessary to ensure the source matches the atlas (FT throws an error otherwise). Could this be a bug in ft_sourceinterpolate and ft_sourceparcellate, or is there some crucial step such as converting everything into another format that I am missing? Thanks again and sorry for the serial messages, Josh From: on behalf of Joshua Bear Reply-To: FieldTrip discussion list Date: Wednesday, April 25, 2018 at 8:14 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] ft_sourceinterpolate question Hi Robert, Thank you so much for the response! My ultimate intention is actually to use the parcellation scheme proposed by Gordon et al. (Cerebral Cortex, Volume 26, Issue 1, 1 January 2016, Pages 288–303, https://doi.org/10.1093/cercor/bhu239) though at this time I was using the atlas provided in the tutorial. The problem I ran into is that I am trying to interpolate my brain’s mesh DOWN from 15002 to 8004 (to match the atlas), not up. As you pointed out, I have had some problems with other high resolution meshes, but in this case ft_sourceinterpolate seemed to work — it just only worked for one of the two dimensions of my connectivity data. That is, it went from a [15002×15002 double] to a [8004×15002 double]. Of course it’s possible the interpolation for that first dimension was incorrect, but what confused me was that it did not interpolate the second dimension. (As I write this, I’m wondering if I should simply try transposing the matrix and running the interpolation again!). I will try, as you suggest, downsampling the mesh externally and trying again. I’m not able to match the 8004 vertices perfectly, but perhaps if I drop it slightly below this number it will be able to interpolate up correctly. Any other thoughts or suggestions are greatly appreciated as well. Best, Josh From: on behalf of "Seymour, Robert (Research Student)" Reply-To: FieldTrip discussion list Date: Wednesday, April 25, 2018 at 5:48 PM To: "fieldtrip at science.ru.nl" Subject: Re: [FieldTrip] ft_sourceinterpolate question Hi Josh, It seems like you are using the HCP Glasser atlas ('A multi-modal parcellation of human cerebral cortex')? The atlas presented as part of the network analysis tutorial is designed for a cortical mesh with 8004 vertices, rather than the 15002 you are using. I don’t believe ft_sourceinterpolate can currently cope with the surface-based transformation upwards from 8000—> 15000 vertices. To use the HCP atlas you will need to downsample the original 32k atlas in fs_LR space to 15000 space and transform to whichever standard-brain template you are using. This is non-trivial and requires some functions from the HCP project (e.g. wb_command which can be found here: https://www.humanconnectome.org/software/workbench-command). If your mesh is created using Freesurfer you can use this script here: https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh If the mesh is not constructed using Freesurfer it will be tricker & I would recommend contacting the HCP mailing list. Good luck! Robert Seymour (Aston Brain Centre & Department of Cognitive Science, Macquarie University). ________________________________ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ________________________________ ------------------------------------------------------------------------------ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ------------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Apr 26 09:35:39 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 26 Apr 2018 07:35:39 +0000 Subject: [FieldTrip] ft_sourceinterpolate question In-Reply-To: <271913CA-10AE-4E5B-8424-429132D272A7@childrenscolorado.org> References: <271913CA-10AE-4E5B-8424-429132D272A7@childrenscolorado.org> Message-ID: <420D1830-F271-4955-9D48-B9F3E68F809E@donders.ru.nl> The most sensible approach to take here would be to interpolate the atlas onto the low-resolution grid that was used for the sourcereconstruction+connectivity analysis, and then parcellate. Be aware that the functional data should be defined in the same coordinate system as the anatomical data. For the interpolation set the parameter to ‘brick0’, and the interpolation method to ‘nearest’. Good luck, Jan-Mathijs On 26 Apr 2018, at 08:01, Bear, Joshua > wrote: Hi all, It occurs to me that using ft_sourceinterpolate to decrease, rather than increase, the dimensions is not intuitive, and I found that it was actually fairly easy to get the Gorden et al. atlas loaded in as they provide an MNI-registered form of the atlas. So I repeated my steps using the selected atlas and with a smaller headmodel and leadfield resulting in a source file that had to be interpolated in the more anticipated direction. The problem persists, however. I now have connectivity results with the following pertinent values: dim: [18 15 15] pos: [4050×3 double] cohspctrm: [4050×4050 double] dimord: 'pos_pos_freq' My atlas has the following pertinent values: dim: [61 73 61] transform: [4×4 double] brick0: [61×73×61 uint16] brick0label: {1×333 cell} The results of interpolating my connectivity source to the atlas lead to the same peculiar asymmetry in the cohspctrm results: dim: [61 73 61] transform: [4×4 double] inside: [61×73×61 logical] cohspctrm: [271633×4050 double] pos: [271633×3 double] And as the whole point is to then use ft_sourceparcellate, I found that this carries over the asymmetrical results of the interpolation with the following source values after parcellation: freq: 9.9340 label: {1×333 cell} cohspctrm: [333×4050 double] brainordinate: [1×1 struct] cfg: [1×1 struct] As you can see, the first dimension of the cohspctrm results increased from 4050 to 271633 with interpolation and then decreased to 333, the number of parcels in my chosen atlas, exactly as I would have expected. The second dimension, however, did not budge from its initial 4050. The interpolation step is necessary to ensure the source matches the atlas (FT throws an error otherwise). Could this be a bug in ft_sourceinterpolate and ft_sourceparcellate, or is there some crucial step such as converting everything into another format that I am missing? Thanks again and sorry for the serial messages, Josh From: > on behalf of Joshua Bear > Reply-To: FieldTrip discussion list > Date: Wednesday, April 25, 2018 at 8:14 PM To: FieldTrip discussion list > Subject: Re: [FieldTrip] ft_sourceinterpolate question Hi Robert, Thank you so much for the response! My ultimate intention is actually to use the parcellation scheme proposed by Gordon et al. (Cerebral Cortex, Volume 26, Issue 1, 1 January 2016, Pages 288–303, https://doi.org/10.1093/cercor/bhu239) though at this time I was using the atlas provided in the tutorial. The problem I ran into is that I am trying to interpolate my brain’s mesh DOWN from 15002 to 8004 (to match the atlas), not up. As you pointed out, I have had some problems with other high resolution meshes, but in this case ft_sourceinterpolate seemed to work — it just only worked for one of the two dimensions of my connectivity data. That is, it went from a [15002×15002 double] to a [8004×15002 double]. Of course it’s possible the interpolation for that first dimension was incorrect, but what confused me was that it did not interpolate the second dimension. (As I write this, I’m wondering if I should simply try transposing the matrix and running the interpolation again!). I will try, as you suggest, downsampling the mesh externally and trying again. I’m not able to match the 8004 vertices perfectly, but perhaps if I drop it slightly below this number it will be able to interpolate up correctly. Any other thoughts or suggestions are greatly appreciated as well. Best, Josh From: > on behalf of "Seymour, Robert (Research Student)" > Reply-To: FieldTrip discussion list > Date: Wednesday, April 25, 2018 at 5:48 PM To: "fieldtrip at science.ru.nl" > Subject: Re: [FieldTrip] ft_sourceinterpolate question Hi Josh, It seems like you are using the HCP Glasser atlas ('A multi-modal parcellation of human cerebral cortex')? The atlas presented as part of the network analysis tutorial is designed for a cortical mesh with 8004 vertices, rather than the 15002 you are using. I don’t believe ft_sourceinterpolate can currently cope with the surface-based transformation upwards from 8000—> 15000 vertices. To use the HCP atlas you will need to downsample the original 32k atlas in fs_LR space to 15000 space and transform to whichever standard-brain template you are using. This is non-trivial and requires some functions from the HCP project (e.g. wb_command which can be found here: https://www.humanconnectome.org/software/workbench-command). If your mesh is created using Freesurfer you can use this script here: https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh If the mesh is not constructed using Freesurfer it will be tricker & I would recommend contacting the HCP mailing list. Good luck! Robert Seymour (Aston Brain Centre & Department of Cognitive Science, Macquarie University). ________________________________ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ________________________________ ________________________________ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ________________________________ _______________________________________________ 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 yoniilevy at gmail.com Thu Apr 26 15:39:42 2018 From: yoniilevy at gmail.com (Yoni Levy) Date: Thu, 26 Apr 2018 16:39:42 +0300 Subject: [FieldTrip] Appending acquisition files Message-ID: Hi there, what is the way to append two acquisition files from the same experiment (say, in case I needed to stop recording and restart it during the experiment) ? >From my understanding, ft_appenddata doesnt work on acquisition files. p.s. I am using 4D system with files named "c,rfhp0.1Hz" Thank you, Yoni -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Apr 26 16:23:57 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 26 Apr 2018 14:23:57 +0000 Subject: [FieldTrip] Appending acquisition files In-Reply-To: References: Message-ID: Hi Yoni, In FieldTrip this is impossible. You may need to check the command line tools that come with the system. Jan-Mathijs On 26 Apr 2018, at 15:39, Yoni Levy > wrote: Hi there, what is the way to append two acquisition files from the same experiment (say, in case I needed to stop recording and restart it during the experiment) ? >From my understanding, ft_appenddata doesnt work on acquisition files. p.s. I am using 4D system with files named "c,rfhp0.1Hz" Thank you, Yoni _______________________________________________ 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 johnnguyen.education at gmail.com Fri Apr 27 05:13:16 2018 From: johnnguyen.education at gmail.com (John Nguyen) Date: Thu, 26 Apr 2018 23:13:16 -0400 Subject: [FieldTrip] ft_freqanalysis fourier rpttap to rpt conversion? Message-ID: Hi, I noticed that it's not an option to remove the tapers if the output is "fourier". Is this because the resulting output won't be a true Fourier if the tapers are removed, and is forced as a preventive measure? I was looking to reduce my fourier size by removing the tapers but not the trials, is there a danger to this? Thank you! John Nguyen -------------- next part -------------- An HTML attachment was scrubbed... URL: From dr.ritwik257 at gmail.com Mon Apr 30 03:00:10 2018 From: dr.ritwik257 at gmail.com (Ritwik Das) Date: Sun, 29 Apr 2018 21:00:10 -0400 Subject: [FieldTrip] Introduction and query regarding EEG file Message-ID: Dear all I am Ritwik Das, a faculty at St. George's University, Grenada, W.I. I am presently working with Dr. Thomas Thesen, from NYU, on the EEG analysis of children. The problem I am currently having is the format in which I am getting my EEG recordings. I have data in NEDF format and text documents. I want to ask two questions, 1. Is it possible to convert NEDF file format to EDF format? 2. Is it possible for Fieldtrip to use EEG data in formats other than EDF? Thank you so much for the help. Regards Ritwik Dr Ritwik Das, MBBS Department of Pathology St. George's University Grenada, W.I. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bernhard.spitzer at bccn-berlin.de Mon Apr 30 15:53:09 2018 From: bernhard.spitzer at bccn-berlin.de (Bernhard Spitzer) Date: Mon, 30 Apr 2018 15:53:09 +0200 Subject: [FieldTrip] Postdoc position in cognitive neuroscience at MPIB Berlin Message-ID: <096b6df3-0425-9012-45c5-f10e49160f56@bccn-berlin.de> We are looking for a postdoctoral researcher to work with us on the neural mechanisms of memory and decision making. For details, please see https://www.mpib-berlin.mpg.de/sites/default/files/download/jobs/16-2018_stellenanzeige_arc-ie.pdf or contact me if you have any questions: spitzer at mpib-berlin.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From son.ta.dinh at tum.de Tue Apr 3 11:05:51 2018 From: son.ta.dinh at tum.de (Ta Dinh, Son) Date: Tue, 3 Apr 2018 09:05:51 +0000 Subject: [FieldTrip] FDR correction of multiple cluster-based permutation tests Message-ID: Dear FieldTrip list, I would like to correct the results of multiple cluster-based permutation tests using FDR. This is obviously trivial when I have a single cluster for every single test. However, this does not happen in general. My biggest problem is when I have no cluster at all because I also don't have a p value then. Is there a reasonable way to extract a p value from the cluster-statistics when no cluster can be found? I have thought about just using p = 1 in these cases, but that seems very arbitrary and intuitively wrong. Can anybody think of a different way of FDR-correcting multiple cluster-based permutation tests? Obviously, I could also just use Bonferroni to adjust the alpha level, but that is simply too restrictive in general. But maybe someone knows a different way of correcting for multiple comparisons for this case that is neither Bonferroni nor FDR? Any help and/or references would be greatly appreciated! Best, Son Son Ta Dinh, M.Sc. PhD student in Human Pain Research Klinikum rechts der Isar Technische Universität München Munich, Germany Phone: +49 89 4140 7664 http://www.painlabmunich.de/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.blume at sbg.ac.at Tue Apr 3 11:31:35 2018 From: christine.blume at sbg.ac.at (Blume Christine) Date: Tue, 3 Apr 2018 09:31:35 +0000 Subject: [FieldTrip] FDR correction of multiple cluster-based permutation tests In-Reply-To: References: Message-ID: Dear Son, I had a similar issue and had talked to our mathematicians/statisticians. They recommended to use Bonferroni...although that is not the answer you were looking for and other people might have better ideas, I though the info might still be valuable. Best, Christine Von: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] Im Auftrag von Ta Dinh, Son Gesendet: Dienstag, 03. April 2018 11:06 An: fieldtrip at science.ru.nl Betreff: [FieldTrip] FDR correction of multiple cluster-based permutation tests Dear FieldTrip list, I would like to correct the results of multiple cluster-based permutation tests using FDR. This is obviously trivial when I have a single cluster for every single test. However, this does not happen in general. My biggest problem is when I have no cluster at all because I also don't have a p value then. Is there a reasonable way to extract a p value from the cluster-statistics when no cluster can be found? I have thought about just using p = 1 in these cases, but that seems very arbitrary and intuitively wrong. Can anybody think of a different way of FDR-correcting multiple cluster-based permutation tests? Obviously, I could also just use Bonferroni to adjust the alpha level, but that is simply too restrictive in general. But maybe someone knows a different way of correcting for multiple comparisons for this case that is neither Bonferroni nor FDR? Any help and/or references would be greatly appreciated! Best, Son Son Ta Dinh, M.Sc. PhD student in Human Pain Research Klinikum rechts der Isar Technische Universität München Munich, Germany Phone: +49 89 4140 7664 http://www.painlabmunich.de/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From TaylorBealeR at cardiff.ac.uk Tue Apr 3 17:21:33 2018 From: TaylorBealeR at cardiff.ac.uk (Rosa Taylor Beale) Date: Tue, 3 Apr 2018 15:21:33 +0000 Subject: [FieldTrip] Empty array in coherence connectivity analysis In-Reply-To: <90B1A8AF-87AA-480B-BEE7-DC9A7148780E@donders.ru.nl> References: <90B1A8AF-87AA-480B-BEE7-DC9A7148780E@donders.ru.nl> Message-ID: Hi Tobias & Jan-Mathis, Changing the cfg.output worked! Many thanks Rosa From: fieldtrip-bounces at science.ru.nl On Behalf Of Schoffelen, J.M. (Jan Mathijs) Sent: 30 March 2018 19:34 To: FieldTrip discussion list Subject: Re: [FieldTrip] Empty array in coherence connectivity analysis Yes, and be sure that cfg.channelcmb is an Nx2 cell-array: {‘somechannel’ ‘someotherchannel’; ‘againsomechannel’ ‘someotherchannelaswell’; ‘etc’ ‘etc’} Best wishes, Jan-Mathijs On 30 Mar 2018, at 18:00, Tobias Staudigl > wrote: Hi Taylor, First specify cfg.output = 'fourier' Or cfg.output ='powandcsd' in your ft_freqanalysis. Then try ft_connectivityanalysis again. Best, Tobias Am 30.03.2018 17:53 schrieb "Rosa Taylor Beale" >: Hi all, I’m a final year undergraduate in Cardiff working on pain networks. I have been trying to calculate coherence between 3 seed regions, however when I run the ft_connectivityanalysis, the labelcmb and cohspctrm arrays are empty (the channel labels don’t look like they were read?). There is no error or warning messages that occur when running the command, so I am unsure why it is not running correctly. First, I run ft_freqanalysis which seems to run fine: cfg = [] cfg.method = 'wavelet'; cfg.output = 'pow'; cfg.toi = 0:0.05:2; cfg.foi = [30:1:100]; time_freq= ft_freqanalysis(cfg, virtualchannel_raw); time_freq = label: {3x1 cell} dimord: 'chan_freq_time' freq: [1x71 double] time: [1x41 double] powspctrm: [3x71x41 double] cfg: [1x1 struct] Then I run the connectivity analysis and up with the empty output: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'pfcCont_seed' 'smc_seed' 'pfcIps_seed' 'smc_seed' 'pfcCont_seed' 'pfcIps_seed'}; coherence = ft_connectivityanalysis(cfg, time_freq); coherence = labelcmb: {0x2 cell} dimord: 'chancmb_freq_time' cohspctrm: [0x71x41 double] time: [1x41 double] freq: [1x71 double] cfg: [1x1 struct] >> coherence.labelcmb ans = Empty cell array: 0-by-2 >> coherence.cohspctrm ans = Empty array: 0-by-71-by-41 I have tried with fieldtrip versions 20161011 and 20171015 on matlab r2015a. I’ve shown this to various people much more experienced at fieldtrip than I and we’ve all been a bit stumped! Any ideas? Many thanks Rosa Taylor Beale _______________________________________________ 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 s.nara at bcbl.eu Thu Apr 5 14:38:00 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Thu, 5 Apr 2018 14:38:00 +0200 (CEST) Subject: [FieldTrip] Abstract submission deadline extended - 1st International Workshop on Predictive Processing In-Reply-To: <2078083467.10234189.1522931807461.JavaMail.zimbra@bcbl.eu> References: <293623353.10226685.1522918393461.JavaMail.zimbra@bcbl.eu> <902547454.10232978.1522928065669.JavaMail.zimbra@bcbl.eu> <2076980298.10234035.1522931448115.JavaMail.zimbra@bcbl.eu> <1103871096.10234078.1522931543036.JavaMail.zimbra@bcbl.eu> <2078083467.10234189.1522931807461.JavaMail.zimbra@bcbl.eu> Message-ID: <2121194270.10234238.1522931880542.JavaMail.zimbra@bcbl.eu> Hello Researchers, We have received request from lot of researchers to extend the deadline for abstract submission, We are happy to announce that the deadline for abstract submission for 1st International Workshop on Predictive Processing (WoPP) has been extended upto 16th April 2018. Hope to see you in San Sebastian. on behalf of Organisers Sanjeev Nara Predoctoral Researcher BCBL www.bcbl.eu https://sites.google.com/view/sanjeev-nara/ Tel: +34 943 309 300 (ext 314) Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer Abstract submission deadline extended - 1st International Workshop on Predictive Processing We would like to inform you that the abstract submission deadline to PREDICTIVE PROCESSING has been extended. The new deadline is April 16th. The conference dates are June 20-22, 2018 Dear Researcher, We are happy to announce the new discussion arena fully centred on predictive processing. The Workshop on Predictive Processing (WoPP) will take place in San Sebastian (Spain) on June 20-22, 2018. The goal of the workshop is to address the role of predictive processing in cognition. Some of the crucial issues in this timely research topic are the extent to which prediction is a fundamental mechanism of brain function, the role of prediction in learning, and, how predictive processing is expressed across distinct cognitive domains. This workshop will gather experts from different fields in cognitive neuroscience including sensory processing, attention and memory, to work alongside the community of language processing, with the aim of furthering our understanding of the role of predictive processing in cognition. We invite submissions from researchers genuinely interested in discussing their data within the framework of the prediction view on neurocognition and brain functioning. The conference will include keynote speakers, regular talks, symposiums and poster sessions. Keynote speakers will be the main sources of discussion: Sophie Scott , University College London Moshe Bar , Bar-Ilan University Pascal Fries, Ernst Strüngmann Institute (ESI) Each keynote will be followed by a symposium on a related topic. Each symposium will be co-organized by two experts in the field, and will last 2 hours. Symposium organizers are Gina Kuperberg, Matt Davis, Craig Richter, Julien Vezoli, Lucia Amoruso and Ruth De Diego Balaguer. For further information please visit: http://www.bcbl.eu/events/prediction-2018/en/ We look forward to seeing you at the conference. Yours sincerely, The Organizing Committee Manuel Carreiras, Clara Martin, Nicola Molinaro & David Soto IMPORTANT DATES TO REMEMBER: Abstract submission and Registration OPEN Abstract deadline: April, 6th, 2018. Extended until April 16th, 2018. Notification of abstract acceptance : April 24th, 2018. Early registration deadline: May 11th, 2018. Online registration deadline: May 30th, 2018. Conference dates: June 20-22, 2018. BQ_BEGIN BQ_END -------------- next part -------------- An HTML attachment was scrubbed... URL: From johnnguyen.education at gmail.com Thu Apr 5 23:11:19 2018 From: johnnguyen.education at gmail.com (John Nguyen) Date: Thu, 5 Apr 2018 17:11:19 -0400 Subject: [FieldTrip] Possibly speeding Up Preprocessing. Message-ID: Hi all, I was running a lot of preprocessing and was finding that it was running slower than I wanted despite good amount CPU/GPUS on board so I decided to look more into the code. I think I found a way to improve the speed but I'm not familiar with Github and pull requests so I just wanted to throw it out there and get people's opinion. In read_brainvision_eeg there is a for loop at line 79 using fseek and fread to reposition the pointer and read the channel-specfic data. Using tic-toc, I'm finding that it takes some time, around ~.27 secs for the loop to finish. When no channels are found, the same script runs fseek and fread only once and I feel like this is the better way to go. if 64-65 is replaced with " fseek(fid, hdr.NumberOfChannels*samplesize*(begsample-1), *'bof'*); dat = fread(fid, [hdr.NumberOfChannels, (endsample-begsample+1)], sampletype) *dat = dat(chanindx,:)*;" where underlined are the changes. the code should run whether or not chanindx is empty. tic-toc says it takes ~.05 sec and isequal says the two dat to be exactly the same. This could makes sense because it is not running fseek and fread constantly which relies on hard drive speeds? Though the timing seems to negligible, .27 sec per trial vs .05 per trial comes out to be a lot in large number of trials. [29 minutes vs 4 mins at 216 trls for 30 subs] Is my assumption correct? why is the for-loop at line 78 running though the channels backwards? Best regards, John Nguyen -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Wed Apr 11 14:49:09 2018 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Wed, 11 Apr 2018 14:49:09 +0200 Subject: [FieldTrip] Neuralynx support on OSX Message-ID: Dear FieldTrippers, I just started with intracranial data for the first time (yeah!), recorded to .ncs-files with Neuralynx' Cheetah (okay...), while also starting working on an Apple Mac (hmmm...). My first step was to try to load the header of the .ncs files, which gives me the warning: *Warning: the NEURALYNX_V6 toolbox is not installed, see http://neuralynx.com/research_software/file_converters_and_utilities/ and take the* *version from Neuralynx (windows only) * I see that previously there was a V3 which supported Mac, but not anymore. So I am afraid to ask ... can I really not read Neuralynx .ncs files with FieldTrip *on OSX*? Best, Stephen -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.nara at bcbl.eu Thu Apr 12 15:11:43 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Thu, 12 Apr 2018 15:11:43 +0200 (CEST) Subject: [FieldTrip] Non-parametric statistics for TFR data Message-ID: <302195760.10422434.1523538703510.JavaMail.zimbra@bcbl.eu> Hello, I am trying to implement parametric test on TFR data. I have 20 participant's data with 4 different conditions. I am interested in compairing theses conditions. After preprocessing and TFR computation i have one variable with (subjects * channels * freq * time ). The tutorial given on the website is using ERF data. Can i use it for TFR as well. cfg = []; cfg.channel = 'MEG'; cfg.latency = [0.3 0.7]; cfg.avgovertime = 'yes'; cfg.parameter = 'avg'; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_depsamplesT' cfg.alpha = 0.05; cfg.correctm = 'no'; cfg.correcttail = 'prob'; cfg.numrandomization = 1000; Nsub = 10; cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; cfg.ivar = 1; % the 1st row in cfg.design contains the independent variable cfg.uvar = 2; % the 2nd row in cfg.design contains the subject number stat = ft_timelockstatistics(cfg,allsubjFIC{:},allsubjFC{:}) % make the plot cfg = []; cfg.style = 'blank'; cfg.layout = 'CTF151_helmet.mat'; cfg.highlight = 'on'; cfg.highlightchannel = find(stat.mask); cfg.comment = 'no'; figure; ft_topoplotER(cfg, GA_FC) title('Nonparametric: significant without multiple comparison correction') Best regards Sanjeev Sanjeev Nara Predoctoral Researcher BCBL www.bcbl.eu https://sites.google.com/view/sanjeev-nara/ Tel: +34 943 309 300 (ext 314) Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From julian.keil at gmail.com Thu Apr 12 15:18:54 2018 From: julian.keil at gmail.com (Julian Keil) Date: Thu, 12 Apr 2018 15:18:54 +0200 Subject: [FieldTrip] Non-parametric statistics for TFR data In-Reply-To: <302195760.10422434.1523538703510.JavaMail.zimbra@bcbl.eu> References: <302195760.10422434.1523538703510.JavaMail.zimbra@bcbl.eu> Message-ID: Dear Sanjeev, take a look at this tutorial: http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_freq You need to use the ft_freqstatistics-function for TFR data. Best, Julian ________________ Prof. Dr. Julian Keil Biologische Psychologie Olshausenstraße 62 - R. 306 24118 Kiel 0431 / 880 - 4872 http://www.biopsych.uni-kiel.de/ Klinik für Psychiatrie und Psychotherapie der Charité im St. Hedwig-Krankenhaus Große Hamburger Straße 5-11 10115 Berlin 030 / 2311 - 1879 www.multisensorymind.com > Am 12.04.2018 um 15:11 schrieb Sanjeev Nara : > > Hello, > > I am trying to implement parametric test on TFR data. I have 20 participant's data with 4 different conditions. I am interested in compairing theses conditions. After preprocessing and TFR computation i have one variable with (subjects * channels * freq * time ). The tutorial given on the website is using ERF data. Can i use it for TFR as well. > > > cfg = []; > cfg.channel = 'MEG'; > cfg.latency = [0.3 0.7]; > cfg.avgovertime = 'yes'; > cfg.parameter = 'avg'; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_depsamplesT' > cfg.alpha = 0.05; > cfg.correctm = 'no'; > cfg.correcttail = 'prob'; > cfg.numrandomization = 1000; > > Nsub = 10; > cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; > cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; > cfg.ivar = 1; % the 1st row in cfg.design contains the independent variable > cfg.uvar = 2; % the 2nd row in cfg.design contains the subject number > > stat = ft_timelockstatistics(cfg,allsubjFIC{:},allsubjFC{:}) > > % make the plot > cfg = []; > cfg.style = 'blank'; > cfg.layout = 'CTF151_helmet.mat'; > cfg.highlight = 'on'; > cfg.highlightchannel = find(stat.mask); > cfg.comment = 'no'; > figure; ft_topoplotER(cfg, GA_FC) > title('Nonparametric: significant without multiple comparison correction') > > > > > > Best regards > Sanjeev > > > > Sanjeev Nara > Predoctoral Researcher BCBL > www.bcbl.eu > https://sites.google.com/view/sanjeev-nara/ > Tel: +34 943 309 300 (ext 314) > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > _______________________________________________ > 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: 833 bytes Desc: Message signed with OpenPGP URL: From stephen.whitmarsh at gmail.com Thu Apr 12 15:28:03 2018 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 12 Apr 2018 15:28:03 +0200 Subject: [FieldTrip] Neuralynx support on OSX In-Reply-To: References: Message-ID: Hello again, It just needed a second look - on the neurolynx website there is also a Linux/OSX (compiled) library, which seems to work fine. So as far I can tell now, the 'windows only' part of the warning message can be removed :-) Best wishes, Stephen On 11 April 2018 at 14:49, Stephen Whitmarsh wrote: > Dear FieldTrippers, > > I just started with intracranial data for the first time (yeah!), recorded > to .ncs-files with Neuralynx' Cheetah (okay...), while also starting > working on an Apple Mac (hmmm...). > > My first step was to try to load the header of the .ncs files, which gives > me the warning: > > *Warning: the NEURALYNX_V6 toolbox is not installed, see > http://neuralynx.com/research_software/file_converters_and_utilities/ > and > take the* > *version from Neuralynx (windows only) * > > I see that previously there was a V3 which supported Mac, but not anymore. > So I am afraid to ask ... can I really not read Neuralynx .ncs files with > FieldTrip *on OSX*? > > Best, > Stephen > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From roycox.roycox at gmail.com Thu Apr 12 20:54:40 2018 From: roycox.roycox at gmail.com (Roy Cox) Date: Thu, 12 Apr 2018 14:54:40 -0400 Subject: [FieldTrip] excessive channel correlations Message-ID: hello EEG community, We have a rather peculiar problem that we're hoping to get some input on. In reviewing some existing 64-channel recordings, we noticed that some records show near-identical signals across al channels, with median channel-by-channel correlations of >0.99. This suggests some kind of electrical shorting, somewhere in the cap-cable-amplifier-montage-recording-exporting chain. The problem appears to be infrequent (most records have more acceptable R values of 0.6-0.9), but common enough that we'll need to review several hundred records. We haven't been able to identify the cause of the problem yet, and it affects ongoing data collection. Some details: - we use Grass AURA amplifiers and TWin software with the Easycap system - the problem has been observed with different amplifiers, different caps, different pcs, and at different sites - the problem is there regardless of reference montage (e.g., forehead and averaged mastoids) - gel bridging, while theoretically possible, seems unlikely given that literally all EEG channels are (almost) identical We're still investigating but wanted to hear if anyone ever observed anything like this? Were they able to solve it? Thanks, Roy -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.spaak at donders.ru.nl Fri Apr 13 08:45:23 2018 From: e.spaak at donders.ru.nl (Eelke Spaak) Date: Fri, 13 Apr 2018 08:45:23 +0200 Subject: [FieldTrip] excessive channel correlations In-Reply-To: References: Message-ID: Hi Roy, I have no suggestion as to what might be causing this, but one suggestion on how to pragmatically deal with it, or at least maybe get some more insight. > - the problem is there regardless of reference montage (e.g., forehead and > averaged mastoids) Have you tried common average reference? If the signal is there on all channels, subtracting the common average should get rid of it. Cheers, Eelke > - gel bridging, while theoretically possible, seems unlikely given that > literally all EEG channels are (almost) identical > > We're still investigating but wanted to hear if anyone ever observed > anything like this? Were they able to solve it? > > Thanks, > > Roy > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From maximilien.chaumon at gmail.com Fri Apr 13 16:16:35 2018 From: maximilien.chaumon at gmail.com (Maximilien Chaumon) Date: Fri, 13 Apr 2018 14:16:35 +0000 Subject: [FieldTrip] extracting a continuous patch on a mesh Message-ID: Dear all, I'm trying to extract a connected patch of vertices at most say 2 cm away from a given seed. Is there an easy way to do this in FieldTrip? Many thanks, Max -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.smulders at maastrichtuniversity.nl Fri Apr 13 16:45:50 2018 From: f.smulders at maastrichtuniversity.nl (Smulders, F (PSYCHOLOGY)) Date: Fri, 13 Apr 2018 14:45:50 +0000 Subject: [FieldTrip] excessive channel correlations In-Reply-To: References: , Message-ID: I have seen this occasionally, also on Brainvision's BrainAmp. I find it worrying, and would also like a good explanation. I have seen before that open channels on an AD converter just pass a copy of an occupied channel. So if you have a bad connection, that might explain it. Subtracting the channel-average would possibly 'hide' a serious hardware problem, it seems to me that you just might end up with pure noise. kind regards, Fren > On 13 Apr 2018, at 08:56, Eelke Spaak wrote: > > Hi Roy, > > I have no suggestion as to what might be causing this, but one > suggestion on how to pragmatically deal with it, or at least maybe get > some more insight. > >> - the problem is there regardless of reference montage (e.g., forehead and >> averaged mastoids) > > Have you tried common average reference? If the signal is there on all > channels, subtracting the common average should get rid of it. > > Cheers, > Eelke > >> - gel bridging, while theoretically possible, seems unlikely given that >> literally all EEG channels are (almost) identical >> >> We're still investigating but wanted to hear if anyone ever observed >> anything like this? Were they able to solve it? >> >> Thanks, >> >> Roy >> >> _______________________________________________ >> 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 From thomas.bancel at icm-institute.org Wed Apr 18 11:17:01 2018 From: thomas.bancel at icm-institute.org (BANCEL Thomas) Date: Wed, 18 Apr 2018 09:17:01 +0000 Subject: [FieldTrip] Opening .smr file with ft Message-ID: <28FC02000FAE4C418B74665EF5E368BA8A6E02@SRVMAIL-ICM.icm-institute.org> Hi everyone, My name is Thomas Bancel, I am working on epilepsy at ICM and we have recordings from the Spike2 (v 9.02) software (CED, .smr file) that I would like to put into Matlab using Fieldtrip (and not the SONLibrary). When I call the following script: addpath('C:\Users\thomas.bancel\Documents\MATLAB\fieldtrip-20180228\'); ft_defaults smr_filepath = 'C:\Users\thomas.bancel\Documents\Crises annotées Mark\557 GAERS S1 2015_10_19\557 GAERS S1 2015_10_19 _M.smr'; smrx_filepath = 'C:\Users\thomas.bancel\Documents\Crises annotées Mark\557 GAERS S1 2015_10_19\smrx557 GAERS S1 2015_10_19.smrx'; dll_name = 'C:\Users\thomas.bancel\Documents\MATLAB\nsMCDLibrary_3.7b\Matlab\Matlab-Import-Filter\Matlab_Interface\nsMCDLibrary64.dll'; [result] = ns_SetLibrary(dll_name) % give 0 ft_read_data(smr_filepath) I get the following message: Call ns_SetLibrary first! Process interrupted! Error using read_ced_son (line 97) Could not get NeuroShare library info, please use the NS_SETLIBRARY function. Can someone help me ? I work on Matlab R2017b, fieldtrip release 2018/02/28, windows 7 professional, 64 bit. Thank you in advance, Thomas PS: this is my first message in the discussion list, sorry if it lacks info or if it is unclear, I can update if needed. Thomas Bancel ICM - Equipe Charpier thomas.bancel at icm-institute.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From R.Mehraram2 at newcastle.ac.uk Wed Apr 18 11:28:36 2018 From: R.Mehraram2 at newcastle.ac.uk (Ramtin Mehraram (Student)) Date: Wed, 18 Apr 2018 09:28:36 +0000 Subject: [FieldTrip] Not timefrequency data on fieldtrip: cluster-based statistics References: Message-ID: Hi all! I need to run a statistical analysis across four independent groups for some network measure I obtained with the brain connectivity toolbox (degree, clustering coefficient, etc.) from EEG data. I am dealing with the multiple comparison issue. Since I am using a high density cap, nothing survives the Bonferroni correction (and variants), nor the FDR. I am trying to perform a cluster-based (montecarlo) analysis as implemented in Fieldtrip, but the toolbox needs the input to be organized as a time-frequency structure. I tried to rebuild a similar structure (degree values instead of power spectrum values), but it seems that I am being unsuccessful. Indeed: if I run a "cfg.statistic = indepsamplesF" across the groups I get NaNs in the probability output matrix. If I just perform a "cfg.statistic = indepsamplesT" between two random groups, I get a couple of channels or so with p<0.05. In all the cases, any form of fieldtrip plotting (such as ft_clusterplot) shows as output the message "Argument to mbscalar must be scalar". Any idea? Is it actually sensible to proceed in this way or is there any smarter way to work with not time-frequency data on fieldtrip? Many thanks in advance for your help. Ramtin Mehraram PhD Student @ramtinTVT Biomedical Research Building 3rd floor Institute of Neuroscience Newcastle University NE4 5PL, United Kingdom www.lewybodylab.org https://www.newcastlebrc.nihr.ac.uk/research-themes/dementia/ From e.maris at donders.ru.nl Wed Apr 18 13:39:45 2018 From: e.maris at donders.ru.nl (Maris, E.G.G. (Eric)) Date: Wed, 18 Apr 2018 11:39:45 +0000 Subject: [FieldTrip] PhD position at the Donders Institute on competition between internal and external attention states In-Reply-To: References: Message-ID: PhD position at the Donders Institute for Brain, Cognition and Behaviour: Watch out! Competition between internal and external attention states in brain and behavior Supervisors: Eric Maris & Marius Peelen Summary: Attention can be directed externally (to the outside world) or internally (to representations in the mind). While this distinction features prominently in current models of attention, there are surprisingly few empirical studies directly investigating this distinction. This project provides a comprehensive investigation of the external-internal attention distinction, its neurophysiological characteristics, and its relation to behavior. Using advanced analysis of both ongoing and evoked EEG/MEG data we will classify spontaneous brain states as corresponding to external versus internal attention states. We will link these brain states to perceptual performance in naturalistic object recognition tasks, testing the hypothesis that an external attention state leads to better perceptual performance. In addition, we will induce attention states by having participants perform externally and internally directed tasks. Finally, we will test the hypothesis that shifting gaze, even in complete darkness, directs attention externally, leading to better perceptual performance. Results of these studies will: (1) provide empirical evidence for the proposed distinction between external and internal attention, (2) provide a neurophysiological characterization of these attention states, and (3) shed light on the feasibility to improve perceptual performance by biasing attention towards the external state. Contact: e.maris at donders.ru.nl or m.peelen at donders.ru.nl Eric Maris | Donders Institute for Brain, Cognition, and Behaviour & Faculty of Social Sciences | Radboud University | PO Box 9104, 6500 HE Nijmegen | (024) 3612651 | www.ru.nl This message (and any attachments) is intended solely for the addressee(s) and may contain confidential information. If you are not the addressee, do not copy this message (and any attachments), forward or share this message with third parties. You are requested to notify the sender immediately and delete this message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.stoica at uke.de Wed Apr 18 15:32:51 2018 From: m.stoica at uke.de (Mircea Stoica) Date: Wed, 18 Apr 2018 15:32:51 +0200 Subject: [FieldTrip] Social cognition in humans and robots (Hamburg, September 27-28, 2018) Message-ID: Dear all, we are pleased to invite you to the "Social cognition in humans and robots" conference that will take place in Hamburg between the 27th and 28th of September, 2018. Over decades, a range of theories and concepts for explaining how we understand others have been developed. This conference turns the spotlight on the idea that social cognition is grounded in sensorimotor and informational dynamic coupling of agents. According to this view, interaction dynamics is one of the keys to understand the mechanisms of successful social interaction because it provides substantial clues to social understanding and gives rise to high-level capabilities such as joint shared intentionality and joint action. Moreover it suggests that many disturbances of social cognition may be rooted in the impaired capacity for entraining and sustaining sensorimotor and informational coupling. The conference will provide an interdisciplinary podium which overviews trends and recent developments of concepts, methods, basic research and applications of sensorimotor approaches in social cognitive science, neuroscience, and robotic research. A particularly interesting question will be how concepts and methods from social cognitive and neuroscience transfer to human-robot interaction. The meeting will also gauge the societal impact of progress in understanding dynamic coupling processes in human-human and human-robot interactions. The event is organized by the FET Proactive H2020 project "Socializing Sensorimotor Contingencies - soSMCs" (socSMCs.eu) in partner alliance with the European Society for Cognitive Systems - EUCog (eucognition.org). Keynote speakers - Natalie Sebanz (Central European University, Hungary) - Antonia Hamilton (University College London, UK) - Scott Kelso (Florida Atlantic University, USA) - Luciano Fadiga (University of Ferrara and IIT, Italy) - Iain Couzin (University of Konstanz, Germany) - Paul Verschure (Institute for Bioengineering of Catalonia, Spain) Submissions - Conference contributions (talks, posters) - Research articles (to be published in a Frontiers Research Topic) - Venues for the EUCognition meeting in 2019 For all submission types, please send an abstract of no more than 1.000 words to conference2018 at socSMCs.eu and indicate the type of your contribution (poster|talk|article|venue), the title (500 characters max.), all author names and affiliations. Important dates - May 25, 2018: Deadline for submission of abstracts - June 29, 2018: Registration closes - Decemnaber 3, 2018: Submission of research articles Fee The registration fee of 110€ includes coffee, soft drinks and snacks on both days. On September 27th, a social dinner at an extra charge of 20€ will be hosted at the MS Cap San Diego (http://www.capsandiego.de/in- brief.html).Booking of the social dinner is only possible in combination with a conference registration. Register today at https://en.xing-events.com/TEHHWXM More info at https://www.socsmcs.eu/conference2018 Best regards, Mircea Stoica -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Martina Saurin (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING -------------- next part -------------- An HTML attachment was scrubbed... URL: From elam4hcp at gmail.com Wed Apr 18 18:55:25 2018 From: elam4hcp at gmail.com (Jennifer Elam) Date: Wed, 18 Apr 2018 11:55:25 -0500 Subject: [FieldTrip] HCP Course 2018 at Oxford: Final Course Schedule posted -- Register Now! Message-ID: Faculty listings and the full schedule of covered topics are now available for the *2018 HCP Course: "Exploring the Human Connectome" *, to be held *June 25 – 29, 2018* at the Blavatnik School of Government , at the University of Oxford , in Oxford, UK! The 5-day intensive course is a great opportunity to learn directly from HCP investigators and gain practical experience with the Human Connectome Project's approach to multimodal whole brain imaging acquisition, processing, analysis, visualization, and sharing of data and results. For more info and to register visit the HCP Course 2018 website . Don't delay, registration is limited, and the course is filling up fast! Nearby affordable accommodations are available at Worcester College at Oxford by selecting registration with accommodations on the site. If you have any questions, please contact us at: hcpcourse at humanconnectome. org We look forward to seeing you in Oxford! Best, 2018 HCP Course Staff -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam at wustl.edu www.humanconnectome.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.nara at bcbl.eu Thu Apr 19 23:15:13 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Thu, 19 Apr 2018 23:15:13 +0200 (CEST) Subject: [FieldTrip] Brainhack Donostia 2018 In-Reply-To: <2051471137.10611732.1524143917106.JavaMail.zimbra@bcbl.eu> References: <2051471137.10611732.1524143917106.JavaMail.zimbra@bcbl.eu> Message-ID: <1069339273.10622399.1524172513356.JavaMail.zimbra@bcbl.eu> Hello Everyone The Basque Center on Cognition Brain and Language (BCBL) will host the first edition of the BrainhackDonostia2018. The event aims at bringing together students and scientists at all levels of their careers to enjoy science and a couple of Cider glasses together. This year's edition will focus on Neuroimaging techniques, in particular fMRI (functional magnetic resonance) MEG (magnetoencephalography, EEG (electroencephalogaphy) and fNIRS (functional near infrared spectroscopy). Through a combination of lectures and tutorials, participants will be introduced on these techniques, and how they can be used to study the mind and brain. For those that have more experience, and have an interest in three days of project development, there is also the possibility to propose and develop a project related to neuroimaging and/or electrophysiology recruiting participants on site. The event is open to people from different disciplines and backgrounds, with a genuine interest in neuroimaging methods, psychology, neuroscience, and more generally interdisciplinary research. Feel free to explore our website for further information. http://www.bcbl.eu/events/BrainhackDonostia2018/en/ The event will be hosted on May 2nd-4th 2018 in the Basque Center on Cognition Brain and Language in San Sebastian, Spain. The cost is 10€ for Master Students, 15€ for PhD and PostDocs, 40€ for Seniors and "Industrials" + optional 13€ for the T-shirt. Registration to the event is needed and can be done on the website, until the 25th of April. A certificate of attendance will be provided to participants. If you have more questions, we remain at your disposal at the address info.bhg-donostia at bcbl.eu We look forward to see you in May! From s.nara at bcbl.eu Thu Apr 19 23:48:24 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Thu, 19 Apr 2018 23:48:24 +0200 (CEST) Subject: [FieldTrip] Common Baseline for uneven length trials Message-ID: <356285164.10622632.1524174504598.JavaMail.zimbra@bcbl.eu> Hello Researchers I am working on a dataset where i have some trials per subject which are time locked to target1. I computed the time frequency response by specifying first 400 miliseconds as Baseline. Then i redefine the trials to a different triggers by providing the pre calculated offset. The offset introduces the trials (pre trig) with different timings. I mean some trials start with say -2.5 seconds and some starts at say -2.4 (my offsets is varying). i have mainly two questions: 1. How can take a common baseline for both the cases. 2. is it possible to specify the samples in fieldtrip Baseline option. Thanks Best regards Sanjeev Sanjeev Nara Predoctoral Researcher BCBL www.bcbl.eu https://sites.google.com/view/sanjeev-nara/ Tel: +34 943 309 300 (ext 314) Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From zoran at nyu.edu Fri Apr 20 16:59:02 2018 From: zoran at nyu.edu (Zoran Josipovic) Date: Fri, 20 Apr 2018 10:59:02 -0400 Subject: [FieldTrip] fieldtrip Digest, Vol 89, Issue 9 In-Reply-To: References: Message-ID: Hello fieldtrip community, Does anyone know if the fieldtrip can run Matlab firpm filter, and if so, what is the correct script to do it? Here is the Matlab page for this filter: https://www.mathworks.com/help/signal/ref/firpm.html Thanks! Zoran On Fri, Apr 20, 2018 at 6:00 AM, 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. Brainhack Donostia 2018 (Sanjeev Nara) > 2. Common Baseline for uneven length trials (Sanjeev Nara) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 19 Apr 2018 23:15:13 +0200 (CEST) > From: Sanjeev Nara > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Brainhack Donostia 2018 > Message-ID: > <1069339273.10622399.1524172513356.JavaMail.zimbra at bcbl.eu> > Content-Type: text/plain; charset=utf-8 > > > Hello Everyone > > The Basque Center on Cognition Brain and Language (BCBL) will host the > first edition of the BrainhackDonostia2018. The event aims at bringing > together students and scientists at all levels of their careers to enjoy > science and a couple of Cider glasses together. > > This year's edition will focus on Neuroimaging techniques, in particular > fMRI (functional magnetic resonance) MEG (magnetoencephalography, EEG > (electroencephalogaphy) and fNIRS (functional near infrared spectroscopy). > Through a combination of lectures and tutorials, participants will be > introduced on these techniques, and how they can be used to study the mind > and brain. > For those that have more experience, and have an interest in three days of > project development, there is also the possibility to propose and develop a > project related to neuroimaging and/or electrophysiology recruiting > participants on site. > > The event is open to people from different disciplines and backgrounds, > with a genuine interest in neuroimaging methods, psychology, neuroscience, > and more generally interdisciplinary research. Feel free to explore our > website for further information. > http://www.bcbl.eu/events/BrainhackDonostia2018/en/ > > The event will be hosted on May 2nd-4th 2018 in the Basque Center on > Cognition Brain and Language in San Sebastian, Spain. The cost is 10? for > Master Students, 15? for PhD and PostDocs, 40? for Seniors and > "Industrials" + optional 13? for the T-shirt. Registration to the event is > needed and can be done on the website, until the 25th of April. A > certificate of attendance will be provided to participants. > > If you have more questions, we remain at your disposal at the address > info.bhg-donostia at bcbl.eu > > We look forward to see you in May! > > > > > ------------------------------ > > Message: 2 > Date: Thu, 19 Apr 2018 23:48:24 +0200 (CEST) > From: Sanjeev Nara > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Common Baseline for uneven length trials > Message-ID: <356285164.10622632.1524174504598.JavaMail.zimbra at bcbl.eu> > Content-Type: text/plain; charset=utf-8 > > Hello Researchers > > I am working on a dataset where i have some trials per subject which are > time locked to target1. I computed the time frequency response by > specifying first 400 miliseconds as Baseline. Then i redefine the trials to > a different triggers by providing the pre calculated offset. The offset > introduces the trials (pre trig) with different timings. I mean some trials > start with say -2.5 seconds and some starts at say -2.4 (my offsets is > varying). i have mainly two questions: > > 1. How can take a common baseline for both the cases. > 2. is it possible to specify the samples in fieldtrip Baseline option. > > Thanks > > > Best regards > Sanjeev > > > > Sanjeev Nara > Predoctoral Researcher BCBL > www.bcbl.eu > https://sites.google.com/view/sanjeev-nara/ > Tel: +34 943 309 300 (ext 314) > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 89, Issue 9 > **************************************** > -- Zoran Josipovic, PhD Adjunct Assistant Professor Psychology Dept. Research Associate NYULMC New York University -------------- next part -------------- An HTML attachment was scrubbed... URL: From virginie.van.wassenhove at gmail.com Sat Apr 21 23:45:25 2018 From: virginie.van.wassenhove at gmail.com (Virginie van Wassenhove) Date: Sat, 21 Apr 2018 23:45:25 +0200 Subject: [FieldTrip] Fwd: [last call for a position in the Cognition & Brain Dynamics lab, NeuroSpin - Closing date: April 22nd 2018] In-Reply-To: References: Message-ID: Dear all, this is a last reminder for a previously advertised job opening in my lab, description available here: https://brainthemind.files.wordpress.com/2018/02/2018_vvw_ jobdescription_cea1.pdf **Deadline is tomorrow April 22nd at midnight (UTC-12)** Best wishes, Virginie -- Virginie van Wassenhove *https://brainthemind.com/ * -------------- next part -------------- An HTML attachment was scrubbed... URL: From luca.turella at unitn.it Sun Apr 22 21:41:14 2018 From: luca.turella at unitn.it (Luca Turella) Date: Sun, 22 Apr 2018 21:41:14 +0200 Subject: [FieldTrip] Call for 11 fully-funded PhD positions NOW OPEN @ CIMeC, UNITrento. Italy Message-ID: Dear all, We are pleased to announce the opening of a call for *11 fellowships* for our international PhD Program in Cognitive and Brain Sciences (CIMeC), commencing November 2018 at the University of Trento, Italy. As you will see from the links below, the PhD call is open to several fields of cognitive neuroscience research. Interested candidates should feel free to contact the PIs that might have topics of interest to them. - *Admissions*: http://www.unitn.it/drcimec/admission - PhD research areas outline: http://www.unitn.it/drcimec/research-topics - PhD Application *summary*: http://www.unitn.it/drcimec/node/118 - PhD *Application *link: https://webapps.unitn.it/Apply/en/MyUnitn/Home/669/dott/cbs34 - PhD Application *Deadline*:* Thursday May 31, 2018, at 4pm (Italian time)* - *CIMeC*: http://www.unitn.it/cimec This year’s research topics proposed by the Doctoral Program Committee for 5 UNITN grants are visible here: http://www.unitn.it/drcimec/research-topics, while the 6 topic-specific grants’ details can be found here: http://www.unitn.it/drcimec/topic-specific-grants *The CIMeC, it’s doctoral program and UNITN in numbers:* - 2018 UNITrento ranks among top Italian Universities in THE - Times Higher Education - *4-yr program* (Nov. 1, 2018- Oct. 31, 2022). - Why a 4-yr program - Courses are given in English - 11 positions, 100% funded - Salary: starting at approximately €1.200/mo., net - Winners receive a €4887 tax-free research/mobility budget - Why choose UNITRENTO Please feel free to browse the FAQ pages on our website for further information, or contact the Director of the Programme, Prof. Francesco Pavani phd.cimec at unitn.it. -- Luca Turella, PhD Assistant Professor CIMeC - Center for Mind/Brain Sciences University of Trento Mattarello (TN), Via Delle Regole 101 Tel.+39 0461-28 3098 http://www.unitn.it/cimec Legal Disclaimer This electronic message contains information that is confidential. The information is intended for the use of the addressee only. If you are not the addressee we would appreciate your notification in this respect. Please note that any disclosure, copy, distribution or use of the contents of this message is prohibited and may be unlawful. Avvertenza legale Questo messaggio Email contiene informazioni confidenziali riservate ai soli destinatari. Qualora veniate in possesso di tali informazioni senza essere definito come destinatario vi reghiamo di leggere le seguenti note. Ogni apertura, copia, distribuzione del contenuto del messaggio e dei suoi allegati è proibito e potrebbe violare le presenti leggi. -------------- next part -------------- An HTML attachment was scrubbed... URL: From maximilien.chaumon at gmail.com Mon Apr 23 14:15:19 2018 From: maximilien.chaumon at gmail.com (Maximilien Chaumon) Date: Mon, 23 Apr 2018 12:15:19 +0000 Subject: [FieldTrip] extracting a continuous patch on a mesh In-Reply-To: References: Message-ID: Hi all, So I coded something that could perhaps be useful to others. It grows a patch around a seed up to a certain distance. See below function [list] = mesh_patch(mesh,seed,dmax) % [list] = mesh_patch(mesh,seed,d) % % return the list of connected vertices that are at most d mesh.unit away % from seed. % % Maximilien Chaumon 2018 % measure distance to seed seedpos = mesh.pos(seed,:); distances = sqrt(sum(bsxfun(@minus,mesh.pos,seedpos).^2,2)); % crawl starting from seed list = crawl(mesh.tri,distances,dmax,seed); function final = crawl(tri,d,dmax,vert) % bookkeeping: the list of vertices persistent listi st = dbstack; level = sum(strcmp({st.name},'crawl')); if level == 1 listi = []; end % listi(end+1) = vert; % append this vertex to the list conn = tri(any(tri==vert,2),:);% connected vertices conn = unique(conn); conn(d(conn) > dmax) = []; % remove those that are too far. conn(ismember(conn,listi)) = [];%keep only vertices that have not been crawled yet for i = 1:numel(conn) crawl(tri,d,dmax,conn(i));% move to next end % bookkeeping: return the list at last if level == 1 final = listi; % return list if it's last call end Le ven. 13 avr. 2018 à 16:16, Maximilien Chaumon < maximilien.chaumon at gmail.com> a écrit : > Dear all, > > I'm trying to extract a connected patch of vertices at most say 2 cm away > from a given seed. > Is there an easy way to do this in FieldTrip? > > Many thanks, > Max > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ph442 at cam.ac.uk Mon Apr 23 14:48:06 2018 From: ph442 at cam.ac.uk (parham hashemzadeh) Date: Mon, 23 Apr 2018 13:48:06 +0100 Subject: [FieldTrip] extracting a continuous patch on a mesh In-Reply-To: References: Message-ID: Hi All Is there a Matlab implementation of openMEEG lying around somewhere? I was wondering, if openMEEG has a pure Matlab or python implementation. Pure form. Many of us (INCLUDING ME) are using code, without really digging deep into the details. I would be grateful, if it can be shared. Many thanks best regards parham On 2018-04-23 13:15, Maximilien Chaumon wrote: > Hi all, > > So I coded something that could perhaps be useful to others. It grows > a patch around a seed up to a certain distance. See below > > function [list] = mesh_patch(mesh,seed,dmax) > > % [list] = mesh_patch(mesh,seed,d) > % > % return the list of connected vertices that are at most d mesh.unit > away > % from seed. > % > % Maximilien Chaumon 2018 > > % measure distance to seed > seedpos = mesh.pos(seed,:); > distances = sqrt(sum(bsxfun(@minus,mesh.pos,seedpos).^2,2)); > > % crawl starting from seed > list = crawl(mesh.tri,distances,dmax,seed); > > function final = crawl(tri,d,dmax,vert) > > % bookkeeping: the list of vertices > persistent listi > st = dbstack; > level = sum(strcmp({st.name [1]},'crawl')); > if level == 1 > listi = []; > end > % > > listi(end+1) = vert; % append this vertex to the list > > conn = tri(any(tri==vert,2),:);% connected vertices > conn = unique(conn); > conn(d(conn) > dmax) = []; % remove those that are too far. > conn(ismember(conn,listi)) = [];%keep only vertices that have not been > crawled yet > for i = 1:numel(conn) > crawl(tri,d,dmax,conn(i));% move to next > end > > % bookkeeping: return the list at last > if level == 1 > final = listi; % return list if it's last call > end > > Le ven. 13 avr. 2018 à 16:16, Maximilien Chaumon > a écrit : > >> Dear all, >> >> I'm trying to extract a connected patch of vertices at most say 2 cm >> away from a given seed. >> Is there an easy way to do this in FieldTrip? >> >> Many thanks, >> Max > > > Links: > ------ > [1] http://st.name > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- best regards Parham Hashemzadeh Research Associate Department of Applied Mathematics and Theoretical Physics University of Cambridge, UK. email: hashemzadeh at damtp.cam.ac.uk From Joshua.Bear at childrenscolorado.org Wed Apr 25 19:07:13 2018 From: Joshua.Bear at childrenscolorado.org (Bear, Joshua) Date: Wed, 25 Apr 2018 17:07:13 +0000 Subject: [FieldTrip] ft_sourceinterpolate question Message-ID: <2E9B4D36-9330-49D1-8F3D-2EEAFA4E40B2@contoso.com> Dear FieldTrip Users: I am trying to apply the Network Analysis tutorial to my own data, and I have hit a stumbling block with the atlas and parcellation steps. Briefly, I am using a mesh exported from Brainstorm with 15002 vertices, so at the end of all steps through ft_connectivityanalysis I have a connectivity structure with pos = 15002. The atlas has pos = 8004. I tried to use ft_sourceinterpolate to make my connectivity structure match the atlas, but it is only seems to be interpolating the first dimension of the source data as shown below. My question: How can I make ft_sourceinterpolate apply to both dimensions of my cohspctrm parameter rather than only the first dimension? RESULTS from ft_connectivityanalysis: source_conn = struct with fields: inside: [15002×1 logical] pos: [15002×3 double] tri: [29989×3 double] cohspctrm: [15002×15002 double] dimord: 'pos_pos_freq' freq: 9.9340 cfg: [1×1 struct] INTERPOLATION commands: cfg = []; cfg.parameter = 'cohspctrm'; cfg.interpmethod = 'nearest'; source_conn_interp = ft_sourceinterpolate(cfg, source_conn, atlas); RESULTS from ft_sourceinterpolate: source_conn_interp = struct with fields: freq: 9.9340 pos: [8004×3 double] tri: [16000×3 double] unit: 'mm' inside: [8004×1 logical] cohspctrm: [8004×15002 double] cfg: [1×1 struct] Notice that the cohspctrm is interpolated from a [15002×15002 double] to a [8004×15002 double]. This then translates to the parcellation step where only the first dimension can be parcellated using the atlas. I’m sure I am missing something obvious and appreciate your thoughts and patience, Josh -- Joshua Bear, MD, MA Neuroscience Institute, Children’s Hospital Colorado ------------------------------------------------------------------------------ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ------------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.nara at bcbl.eu Wed Apr 25 21:52:39 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Wed, 25 Apr 2018 21:52:39 +0200 (CEST) Subject: [FieldTrip] Mismatch between cluster activation and * marks Message-ID: <158854153.10803185.1524685959460.JavaMail.zimbra@bcbl.eu> Hi Fieldtrip Experts Apologies for a long mail. I have a experiment where i have 20 subjects which have performed 2 different tasks. I want to implement a cluster based permutation test for compare the Time frequency analysis in two different conditions. I a following this tutorial for computing the stats http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_freq . I have computed the stats using ft_freqstatistics by providing input a 4 D matrix which has size (20 subjects * 102 channels * 70 frequency bins * 190 time points ). The analysis give me positive and negative clusters. I want to plot first positive and negative cluster in terms of channels which are significant during a specifies frequency range (say 12 - 30 ) in a specified time range. After that i use ft_descriptive on difference of powerspectrum in both conditions. I am plotting the cluster within a specified time and frequency duration computed from first positive and negative cluster. The problem is i am getting topoplots which have a difference in the colour activation and the ' * ' marks. I have attached few plots to show what is the issue. The image img1_correct and img2_correct shows the match between activations and ' * ' marks whereas the img1_incorrect and img2_incorrect shows the mismatch. I shall be thankful if you could please help me debugging the issue. Best regards Sanjeev Sanjeev Nara Predoctoral Researcher BCBL www.bcbl.eu https://sites.google.com/view/sanjeev-nara/ Tel: +34 943 309 300 (ext 314) Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer -------------- next part -------------- A non-text attachment was scrubbed... Name: img1_correct.png Type: image/png Size: 48736 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: img1_incorrect.png Type: image/png Size: 52018 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: img2_incorrect.png Type: image/png Size: 48615 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: img2_correct.png Type: image/png Size: 49975 bytes Desc: not available URL: From seymourr at aston.ac.uk Thu Apr 26 01:48:31 2018 From: seymourr at aston.ac.uk (Seymour, Robert (Research Student)) Date: Wed, 25 Apr 2018 23:48:31 +0000 Subject: [FieldTrip] ft_sourceinterpolate question Message-ID: Hi Josh, It seems like you are using the HCP Glasser atlas ('A multi-modal parcellation of human cerebral cortex')? The atlas presented as part of the network analysis tutorial is designed for a cortical mesh with 8004 vertices, rather than the 15002 you are using. I don’t believe ft_sourceinterpolate can currently cope with the surface-based transformation upwards from 8000—> 15000 vertices. To use the HCP atlas you will need to downsample the original 32k atlas in fs_LR space to 15000 space and transform to whichever standard-brain template you are using. This is non-trivial and requires some functions from the HCP project (e.g. wb_command which can be found here: https://www.humanconnectome.org/software/workbench-command). If your mesh is created using Freesurfer you can use this script here: https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh If the mesh is not constructed using Freesurfer it will be tricker & I would recommend contacting the HCP mailing list. Good luck! Robert Seymour (Aston Brain Centre & Department of Cognitive Science, Macquarie University). -------------- next part -------------- An HTML attachment was scrubbed... URL: From Joshua.Bear at childrenscolorado.org Thu Apr 26 04:14:09 2018 From: Joshua.Bear at childrenscolorado.org (Bear, Joshua) Date: Thu, 26 Apr 2018 02:14:09 +0000 Subject: [FieldTrip] ft_sourceinterpolate question In-Reply-To: References: Message-ID: Hi Robert, Thank you so much for the response! My ultimate intention is actually to use the parcellation scheme proposed by Gordon et al. (Cerebral Cortex, Volume 26, Issue 1, 1 January 2016, Pages 288–303, https://doi.org/10.1093/cercor/bhu239) though at this time I was using the atlas provided in the tutorial. The problem I ran into is that I am trying to interpolate my brain’s mesh DOWN from 15002 to 8004 (to match the atlas), not up. As you pointed out, I have had some problems with other high resolution meshes, but in this case ft_sourceinterpolate seemed to work — it just only worked for one of the two dimensions of my connectivity data. That is, it went from a [15002×15002 double] to a [8004×15002 double]. Of course it’s possible the interpolation for that first dimension was incorrect, but what confused me was that it did not interpolate the second dimension. (As I write this, I’m wondering if I should simply try transposing the matrix and running the interpolation again!). I will try, as you suggest, downsampling the mesh externally and trying again. I’m not able to match the 8004 vertices perfectly, but perhaps if I drop it slightly below this number it will be able to interpolate up correctly. Any other thoughts or suggestions are greatly appreciated as well. Best, Josh From: on behalf of "Seymour, Robert (Research Student)" Reply-To: FieldTrip discussion list Date: Wednesday, April 25, 2018 at 5:48 PM To: "fieldtrip at science.ru.nl" Subject: Re: [FieldTrip] ft_sourceinterpolate question Hi Josh, It seems like you are using the HCP Glasser atlas ('A multi-modal parcellation of human cerebral cortex')? The atlas presented as part of the network analysis tutorial is designed for a cortical mesh with 8004 vertices, rather than the 15002 you are using. I don’t believe ft_sourceinterpolate can currently cope with the surface-based transformation upwards from 8000—> 15000 vertices. To use the HCP atlas you will need to downsample the original 32k atlas in fs_LR space to 15000 space and transform to whichever standard-brain template you are using. This is non-trivial and requires some functions from the HCP project (e.g. wb_command which can be found here: https://www.humanconnectome.org/software/workbench-command). If your mesh is created using Freesurfer you can use this script here: https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh If the mesh is not constructed using Freesurfer it will be tricker & I would recommend contacting the HCP mailing list. Good luck! Robert Seymour (Aston Brain Centre & Department of Cognitive Science, Macquarie University). ------------------------------------------------------------------------------ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ------------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From Joshua.Bear at childrenscolorado.org Thu Apr 26 08:01:28 2018 From: Joshua.Bear at childrenscolorado.org (Bear, Joshua) Date: Thu, 26 Apr 2018 06:01:28 +0000 Subject: [FieldTrip] ft_sourceinterpolate question In-Reply-To: References: Message-ID: <271913CA-10AE-4E5B-8424-429132D272A7@childrenscolorado.org> Hi all, It occurs to me that using ft_sourceinterpolate to decrease, rather than increase, the dimensions is not intuitive, and I found that it was actually fairly easy to get the Gorden et al. atlas loaded in as they provide an MNI-registered form of the atlas. So I repeated my steps using the selected atlas and with a smaller headmodel and leadfield resulting in a source file that had to be interpolated in the more anticipated direction. The problem persists, however. I now have connectivity results with the following pertinent values: dim: [18 15 15] pos: [4050×3 double] cohspctrm: [4050×4050 double] dimord: 'pos_pos_freq' My atlas has the following pertinent values: dim: [61 73 61] transform: [4×4 double] brick0: [61×73×61 uint16] brick0label: {1×333 cell} The results of interpolating my connectivity source to the atlas lead to the same peculiar asymmetry in the cohspctrm results: dim: [61 73 61] transform: [4×4 double] inside: [61×73×61 logical] cohspctrm: [271633×4050 double] pos: [271633×3 double] And as the whole point is to then use ft_sourceparcellate, I found that this carries over the asymmetrical results of the interpolation with the following source values after parcellation: freq: 9.9340 label: {1×333 cell} cohspctrm: [333×4050 double] brainordinate: [1×1 struct] cfg: [1×1 struct] As you can see, the first dimension of the cohspctrm results increased from 4050 to 271633 with interpolation and then decreased to 333, the number of parcels in my chosen atlas, exactly as I would have expected. The second dimension, however, did not budge from its initial 4050. The interpolation step is necessary to ensure the source matches the atlas (FT throws an error otherwise). Could this be a bug in ft_sourceinterpolate and ft_sourceparcellate, or is there some crucial step such as converting everything into another format that I am missing? Thanks again and sorry for the serial messages, Josh From: on behalf of Joshua Bear Reply-To: FieldTrip discussion list Date: Wednesday, April 25, 2018 at 8:14 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] ft_sourceinterpolate question Hi Robert, Thank you so much for the response! My ultimate intention is actually to use the parcellation scheme proposed by Gordon et al. (Cerebral Cortex, Volume 26, Issue 1, 1 January 2016, Pages 288–303, https://doi.org/10.1093/cercor/bhu239) though at this time I was using the atlas provided in the tutorial. The problem I ran into is that I am trying to interpolate my brain’s mesh DOWN from 15002 to 8004 (to match the atlas), not up. As you pointed out, I have had some problems with other high resolution meshes, but in this case ft_sourceinterpolate seemed to work — it just only worked for one of the two dimensions of my connectivity data. That is, it went from a [15002×15002 double] to a [8004×15002 double]. Of course it’s possible the interpolation for that first dimension was incorrect, but what confused me was that it did not interpolate the second dimension. (As I write this, I’m wondering if I should simply try transposing the matrix and running the interpolation again!). I will try, as you suggest, downsampling the mesh externally and trying again. I’m not able to match the 8004 vertices perfectly, but perhaps if I drop it slightly below this number it will be able to interpolate up correctly. Any other thoughts or suggestions are greatly appreciated as well. Best, Josh From: on behalf of "Seymour, Robert (Research Student)" Reply-To: FieldTrip discussion list Date: Wednesday, April 25, 2018 at 5:48 PM To: "fieldtrip at science.ru.nl" Subject: Re: [FieldTrip] ft_sourceinterpolate question Hi Josh, It seems like you are using the HCP Glasser atlas ('A multi-modal parcellation of human cerebral cortex')? The atlas presented as part of the network analysis tutorial is designed for a cortical mesh with 8004 vertices, rather than the 15002 you are using. I don’t believe ft_sourceinterpolate can currently cope with the surface-based transformation upwards from 8000—> 15000 vertices. To use the HCP atlas you will need to downsample the original 32k atlas in fs_LR space to 15000 space and transform to whichever standard-brain template you are using. This is non-trivial and requires some functions from the HCP project (e.g. wb_command which can be found here: https://www.humanconnectome.org/software/workbench-command). If your mesh is created using Freesurfer you can use this script here: https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh If the mesh is not constructed using Freesurfer it will be tricker & I would recommend contacting the HCP mailing list. Good luck! Robert Seymour (Aston Brain Centre & Department of Cognitive Science, Macquarie University). ________________________________ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ________________________________ ------------------------------------------------------------------------------ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ------------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Apr 26 09:35:39 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 26 Apr 2018 07:35:39 +0000 Subject: [FieldTrip] ft_sourceinterpolate question In-Reply-To: <271913CA-10AE-4E5B-8424-429132D272A7@childrenscolorado.org> References: <271913CA-10AE-4E5B-8424-429132D272A7@childrenscolorado.org> Message-ID: <420D1830-F271-4955-9D48-B9F3E68F809E@donders.ru.nl> The most sensible approach to take here would be to interpolate the atlas onto the low-resolution grid that was used for the sourcereconstruction+connectivity analysis, and then parcellate. Be aware that the functional data should be defined in the same coordinate system as the anatomical data. For the interpolation set the parameter to ‘brick0’, and the interpolation method to ‘nearest’. Good luck, Jan-Mathijs On 26 Apr 2018, at 08:01, Bear, Joshua > wrote: Hi all, It occurs to me that using ft_sourceinterpolate to decrease, rather than increase, the dimensions is not intuitive, and I found that it was actually fairly easy to get the Gorden et al. atlas loaded in as they provide an MNI-registered form of the atlas. So I repeated my steps using the selected atlas and with a smaller headmodel and leadfield resulting in a source file that had to be interpolated in the more anticipated direction. The problem persists, however. I now have connectivity results with the following pertinent values: dim: [18 15 15] pos: [4050×3 double] cohspctrm: [4050×4050 double] dimord: 'pos_pos_freq' My atlas has the following pertinent values: dim: [61 73 61] transform: [4×4 double] brick0: [61×73×61 uint16] brick0label: {1×333 cell} The results of interpolating my connectivity source to the atlas lead to the same peculiar asymmetry in the cohspctrm results: dim: [61 73 61] transform: [4×4 double] inside: [61×73×61 logical] cohspctrm: [271633×4050 double] pos: [271633×3 double] And as the whole point is to then use ft_sourceparcellate, I found that this carries over the asymmetrical results of the interpolation with the following source values after parcellation: freq: 9.9340 label: {1×333 cell} cohspctrm: [333×4050 double] brainordinate: [1×1 struct] cfg: [1×1 struct] As you can see, the first dimension of the cohspctrm results increased from 4050 to 271633 with interpolation and then decreased to 333, the number of parcels in my chosen atlas, exactly as I would have expected. The second dimension, however, did not budge from its initial 4050. The interpolation step is necessary to ensure the source matches the atlas (FT throws an error otherwise). Could this be a bug in ft_sourceinterpolate and ft_sourceparcellate, or is there some crucial step such as converting everything into another format that I am missing? Thanks again and sorry for the serial messages, Josh From: > on behalf of Joshua Bear > Reply-To: FieldTrip discussion list > Date: Wednesday, April 25, 2018 at 8:14 PM To: FieldTrip discussion list > Subject: Re: [FieldTrip] ft_sourceinterpolate question Hi Robert, Thank you so much for the response! My ultimate intention is actually to use the parcellation scheme proposed by Gordon et al. (Cerebral Cortex, Volume 26, Issue 1, 1 January 2016, Pages 288–303, https://doi.org/10.1093/cercor/bhu239) though at this time I was using the atlas provided in the tutorial. The problem I ran into is that I am trying to interpolate my brain’s mesh DOWN from 15002 to 8004 (to match the atlas), not up. As you pointed out, I have had some problems with other high resolution meshes, but in this case ft_sourceinterpolate seemed to work — it just only worked for one of the two dimensions of my connectivity data. That is, it went from a [15002×15002 double] to a [8004×15002 double]. Of course it’s possible the interpolation for that first dimension was incorrect, but what confused me was that it did not interpolate the second dimension. (As I write this, I’m wondering if I should simply try transposing the matrix and running the interpolation again!). I will try, as you suggest, downsampling the mesh externally and trying again. I’m not able to match the 8004 vertices perfectly, but perhaps if I drop it slightly below this number it will be able to interpolate up correctly. Any other thoughts or suggestions are greatly appreciated as well. Best, Josh From: > on behalf of "Seymour, Robert (Research Student)" > Reply-To: FieldTrip discussion list > Date: Wednesday, April 25, 2018 at 5:48 PM To: "fieldtrip at science.ru.nl" > Subject: Re: [FieldTrip] ft_sourceinterpolate question Hi Josh, It seems like you are using the HCP Glasser atlas ('A multi-modal parcellation of human cerebral cortex')? The atlas presented as part of the network analysis tutorial is designed for a cortical mesh with 8004 vertices, rather than the 15002 you are using. I don’t believe ft_sourceinterpolate can currently cope with the surface-based transformation upwards from 8000—> 15000 vertices. To use the HCP atlas you will need to downsample the original 32k atlas in fs_LR space to 15000 space and transform to whichever standard-brain template you are using. This is non-trivial and requires some functions from the HCP project (e.g. wb_command which can be found here: https://www.humanconnectome.org/software/workbench-command). If your mesh is created using Freesurfer you can use this script here: https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh If the mesh is not constructed using Freesurfer it will be tricker & I would recommend contacting the HCP mailing list. Good luck! Robert Seymour (Aston Brain Centre & Department of Cognitive Science, Macquarie University). ________________________________ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ________________________________ ________________________________ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ________________________________ _______________________________________________ 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 yoniilevy at gmail.com Thu Apr 26 15:39:42 2018 From: yoniilevy at gmail.com (Yoni Levy) Date: Thu, 26 Apr 2018 16:39:42 +0300 Subject: [FieldTrip] Appending acquisition files Message-ID: Hi there, what is the way to append two acquisition files from the same experiment (say, in case I needed to stop recording and restart it during the experiment) ? >From my understanding, ft_appenddata doesnt work on acquisition files. p.s. I am using 4D system with files named "c,rfhp0.1Hz" Thank you, Yoni -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Apr 26 16:23:57 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 26 Apr 2018 14:23:57 +0000 Subject: [FieldTrip] Appending acquisition files In-Reply-To: References: Message-ID: Hi Yoni, In FieldTrip this is impossible. You may need to check the command line tools that come with the system. Jan-Mathijs On 26 Apr 2018, at 15:39, Yoni Levy > wrote: Hi there, what is the way to append two acquisition files from the same experiment (say, in case I needed to stop recording and restart it during the experiment) ? >From my understanding, ft_appenddata doesnt work on acquisition files. p.s. I am using 4D system with files named "c,rfhp0.1Hz" Thank you, Yoni _______________________________________________ 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 johnnguyen.education at gmail.com Fri Apr 27 05:13:16 2018 From: johnnguyen.education at gmail.com (John Nguyen) Date: Thu, 26 Apr 2018 23:13:16 -0400 Subject: [FieldTrip] ft_freqanalysis fourier rpttap to rpt conversion? Message-ID: Hi, I noticed that it's not an option to remove the tapers if the output is "fourier". Is this because the resulting output won't be a true Fourier if the tapers are removed, and is forced as a preventive measure? I was looking to reduce my fourier size by removing the tapers but not the trials, is there a danger to this? Thank you! John Nguyen -------------- next part -------------- An HTML attachment was scrubbed... URL: From dr.ritwik257 at gmail.com Mon Apr 30 03:00:10 2018 From: dr.ritwik257 at gmail.com (Ritwik Das) Date: Sun, 29 Apr 2018 21:00:10 -0400 Subject: [FieldTrip] Introduction and query regarding EEG file Message-ID: Dear all I am Ritwik Das, a faculty at St. George's University, Grenada, W.I. I am presently working with Dr. Thomas Thesen, from NYU, on the EEG analysis of children. The problem I am currently having is the format in which I am getting my EEG recordings. I have data in NEDF format and text documents. I want to ask two questions, 1. Is it possible to convert NEDF file format to EDF format? 2. Is it possible for Fieldtrip to use EEG data in formats other than EDF? Thank you so much for the help. Regards Ritwik Dr Ritwik Das, MBBS Department of Pathology St. George's University Grenada, W.I. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bernhard.spitzer at bccn-berlin.de Mon Apr 30 15:53:09 2018 From: bernhard.spitzer at bccn-berlin.de (Bernhard Spitzer) Date: Mon, 30 Apr 2018 15:53:09 +0200 Subject: [FieldTrip] Postdoc position in cognitive neuroscience at MPIB Berlin Message-ID: <096b6df3-0425-9012-45c5-f10e49160f56@bccn-berlin.de> We are looking for a postdoctoral researcher to work with us on the neural mechanisms of memory and decision making. For details, please see https://www.mpib-berlin.mpg.de/sites/default/files/download/jobs/16-2018_stellenanzeige_arc-ie.pdf or contact me if you have any questions: spitzer at mpib-berlin.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From son.ta.dinh at tum.de Tue Apr 3 11:05:51 2018 From: son.ta.dinh at tum.de (Ta Dinh, Son) Date: Tue, 3 Apr 2018 09:05:51 +0000 Subject: [FieldTrip] FDR correction of multiple cluster-based permutation tests Message-ID: Dear FieldTrip list, I would like to correct the results of multiple cluster-based permutation tests using FDR. This is obviously trivial when I have a single cluster for every single test. However, this does not happen in general. My biggest problem is when I have no cluster at all because I also don't have a p value then. Is there a reasonable way to extract a p value from the cluster-statistics when no cluster can be found? I have thought about just using p = 1 in these cases, but that seems very arbitrary and intuitively wrong. Can anybody think of a different way of FDR-correcting multiple cluster-based permutation tests? Obviously, I could also just use Bonferroni to adjust the alpha level, but that is simply too restrictive in general. But maybe someone knows a different way of correcting for multiple comparisons for this case that is neither Bonferroni nor FDR? Any help and/or references would be greatly appreciated! Best, Son Son Ta Dinh, M.Sc. PhD student in Human Pain Research Klinikum rechts der Isar Technische Universität München Munich, Germany Phone: +49 89 4140 7664 http://www.painlabmunich.de/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.blume at sbg.ac.at Tue Apr 3 11:31:35 2018 From: christine.blume at sbg.ac.at (Blume Christine) Date: Tue, 3 Apr 2018 09:31:35 +0000 Subject: [FieldTrip] FDR correction of multiple cluster-based permutation tests In-Reply-To: References: Message-ID: Dear Son, I had a similar issue and had talked to our mathematicians/statisticians. They recommended to use Bonferroni...although that is not the answer you were looking for and other people might have better ideas, I though the info might still be valuable. Best, Christine Von: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] Im Auftrag von Ta Dinh, Son Gesendet: Dienstag, 03. April 2018 11:06 An: fieldtrip at science.ru.nl Betreff: [FieldTrip] FDR correction of multiple cluster-based permutation tests Dear FieldTrip list, I would like to correct the results of multiple cluster-based permutation tests using FDR. This is obviously trivial when I have a single cluster for every single test. However, this does not happen in general. My biggest problem is when I have no cluster at all because I also don't have a p value then. Is there a reasonable way to extract a p value from the cluster-statistics when no cluster can be found? I have thought about just using p = 1 in these cases, but that seems very arbitrary and intuitively wrong. Can anybody think of a different way of FDR-correcting multiple cluster-based permutation tests? Obviously, I could also just use Bonferroni to adjust the alpha level, but that is simply too restrictive in general. But maybe someone knows a different way of correcting for multiple comparisons for this case that is neither Bonferroni nor FDR? Any help and/or references would be greatly appreciated! Best, Son Son Ta Dinh, M.Sc. PhD student in Human Pain Research Klinikum rechts der Isar Technische Universität München Munich, Germany Phone: +49 89 4140 7664 http://www.painlabmunich.de/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From TaylorBealeR at cardiff.ac.uk Tue Apr 3 17:21:33 2018 From: TaylorBealeR at cardiff.ac.uk (Rosa Taylor Beale) Date: Tue, 3 Apr 2018 15:21:33 +0000 Subject: [FieldTrip] Empty array in coherence connectivity analysis In-Reply-To: <90B1A8AF-87AA-480B-BEE7-DC9A7148780E@donders.ru.nl> References: <90B1A8AF-87AA-480B-BEE7-DC9A7148780E@donders.ru.nl> Message-ID: Hi Tobias & Jan-Mathis, Changing the cfg.output worked! Many thanks Rosa From: fieldtrip-bounces at science.ru.nl On Behalf Of Schoffelen, J.M. (Jan Mathijs) Sent: 30 March 2018 19:34 To: FieldTrip discussion list Subject: Re: [FieldTrip] Empty array in coherence connectivity analysis Yes, and be sure that cfg.channelcmb is an Nx2 cell-array: {‘somechannel’ ‘someotherchannel’; ‘againsomechannel’ ‘someotherchannelaswell’; ‘etc’ ‘etc’} Best wishes, Jan-Mathijs On 30 Mar 2018, at 18:00, Tobias Staudigl > wrote: Hi Taylor, First specify cfg.output = 'fourier' Or cfg.output ='powandcsd' in your ft_freqanalysis. Then try ft_connectivityanalysis again. Best, Tobias Am 30.03.2018 17:53 schrieb "Rosa Taylor Beale" >: Hi all, I’m a final year undergraduate in Cardiff working on pain networks. I have been trying to calculate coherence between 3 seed regions, however when I run the ft_connectivityanalysis, the labelcmb and cohspctrm arrays are empty (the channel labels don’t look like they were read?). There is no error or warning messages that occur when running the command, so I am unsure why it is not running correctly. First, I run ft_freqanalysis which seems to run fine: cfg = [] cfg.method = 'wavelet'; cfg.output = 'pow'; cfg.toi = 0:0.05:2; cfg.foi = [30:1:100]; time_freq= ft_freqanalysis(cfg, virtualchannel_raw); time_freq = label: {3x1 cell} dimord: 'chan_freq_time' freq: [1x71 double] time: [1x41 double] powspctrm: [3x71x41 double] cfg: [1x1 struct] Then I run the connectivity analysis and up with the empty output: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'pfcCont_seed' 'smc_seed' 'pfcIps_seed' 'smc_seed' 'pfcCont_seed' 'pfcIps_seed'}; coherence = ft_connectivityanalysis(cfg, time_freq); coherence = labelcmb: {0x2 cell} dimord: 'chancmb_freq_time' cohspctrm: [0x71x41 double] time: [1x41 double] freq: [1x71 double] cfg: [1x1 struct] >> coherence.labelcmb ans = Empty cell array: 0-by-2 >> coherence.cohspctrm ans = Empty array: 0-by-71-by-41 I have tried with fieldtrip versions 20161011 and 20171015 on matlab r2015a. I’ve shown this to various people much more experienced at fieldtrip than I and we’ve all been a bit stumped! Any ideas? Many thanks Rosa Taylor Beale _______________________________________________ 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 s.nara at bcbl.eu Thu Apr 5 14:38:00 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Thu, 5 Apr 2018 14:38:00 +0200 (CEST) Subject: [FieldTrip] Abstract submission deadline extended - 1st International Workshop on Predictive Processing In-Reply-To: <2078083467.10234189.1522931807461.JavaMail.zimbra@bcbl.eu> References: <293623353.10226685.1522918393461.JavaMail.zimbra@bcbl.eu> <902547454.10232978.1522928065669.JavaMail.zimbra@bcbl.eu> <2076980298.10234035.1522931448115.JavaMail.zimbra@bcbl.eu> <1103871096.10234078.1522931543036.JavaMail.zimbra@bcbl.eu> <2078083467.10234189.1522931807461.JavaMail.zimbra@bcbl.eu> Message-ID: <2121194270.10234238.1522931880542.JavaMail.zimbra@bcbl.eu> Hello Researchers, We have received request from lot of researchers to extend the deadline for abstract submission, We are happy to announce that the deadline for abstract submission for 1st International Workshop on Predictive Processing (WoPP) has been extended upto 16th April 2018. Hope to see you in San Sebastian. on behalf of Organisers Sanjeev Nara Predoctoral Researcher BCBL www.bcbl.eu https://sites.google.com/view/sanjeev-nara/ Tel: +34 943 309 300 (ext 314) Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer Abstract submission deadline extended - 1st International Workshop on Predictive Processing We would like to inform you that the abstract submission deadline to PREDICTIVE PROCESSING has been extended. The new deadline is April 16th. The conference dates are June 20-22, 2018 Dear Researcher, We are happy to announce the new discussion arena fully centred on predictive processing. The Workshop on Predictive Processing (WoPP) will take place in San Sebastian (Spain) on June 20-22, 2018. The goal of the workshop is to address the role of predictive processing in cognition. Some of the crucial issues in this timely research topic are the extent to which prediction is a fundamental mechanism of brain function, the role of prediction in learning, and, how predictive processing is expressed across distinct cognitive domains. This workshop will gather experts from different fields in cognitive neuroscience including sensory processing, attention and memory, to work alongside the community of language processing, with the aim of furthering our understanding of the role of predictive processing in cognition. We invite submissions from researchers genuinely interested in discussing their data within the framework of the prediction view on neurocognition and brain functioning. The conference will include keynote speakers, regular talks, symposiums and poster sessions. Keynote speakers will be the main sources of discussion: Sophie Scott , University College London Moshe Bar , Bar-Ilan University Pascal Fries, Ernst Strüngmann Institute (ESI) Each keynote will be followed by a symposium on a related topic. Each symposium will be co-organized by two experts in the field, and will last 2 hours. Symposium organizers are Gina Kuperberg, Matt Davis, Craig Richter, Julien Vezoli, Lucia Amoruso and Ruth De Diego Balaguer. For further information please visit: http://www.bcbl.eu/events/prediction-2018/en/ We look forward to seeing you at the conference. Yours sincerely, The Organizing Committee Manuel Carreiras, Clara Martin, Nicola Molinaro & David Soto IMPORTANT DATES TO REMEMBER: Abstract submission and Registration OPEN Abstract deadline: April, 6th, 2018. Extended until April 16th, 2018. Notification of abstract acceptance : April 24th, 2018. Early registration deadline: May 11th, 2018. Online registration deadline: May 30th, 2018. Conference dates: June 20-22, 2018. BQ_BEGIN BQ_END -------------- next part -------------- An HTML attachment was scrubbed... URL: From johnnguyen.education at gmail.com Thu Apr 5 23:11:19 2018 From: johnnguyen.education at gmail.com (John Nguyen) Date: Thu, 5 Apr 2018 17:11:19 -0400 Subject: [FieldTrip] Possibly speeding Up Preprocessing. Message-ID: Hi all, I was running a lot of preprocessing and was finding that it was running slower than I wanted despite good amount CPU/GPUS on board so I decided to look more into the code. I think I found a way to improve the speed but I'm not familiar with Github and pull requests so I just wanted to throw it out there and get people's opinion. In read_brainvision_eeg there is a for loop at line 79 using fseek and fread to reposition the pointer and read the channel-specfic data. Using tic-toc, I'm finding that it takes some time, around ~.27 secs for the loop to finish. When no channels are found, the same script runs fseek and fread only once and I feel like this is the better way to go. if 64-65 is replaced with " fseek(fid, hdr.NumberOfChannels*samplesize*(begsample-1), *'bof'*); dat = fread(fid, [hdr.NumberOfChannels, (endsample-begsample+1)], sampletype) *dat = dat(chanindx,:)*;" where underlined are the changes. the code should run whether or not chanindx is empty. tic-toc says it takes ~.05 sec and isequal says the two dat to be exactly the same. This could makes sense because it is not running fseek and fread constantly which relies on hard drive speeds? Though the timing seems to negligible, .27 sec per trial vs .05 per trial comes out to be a lot in large number of trials. [29 minutes vs 4 mins at 216 trls for 30 subs] Is my assumption correct? why is the for-loop at line 78 running though the channels backwards? Best regards, John Nguyen -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Wed Apr 11 14:49:09 2018 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Wed, 11 Apr 2018 14:49:09 +0200 Subject: [FieldTrip] Neuralynx support on OSX Message-ID: Dear FieldTrippers, I just started with intracranial data for the first time (yeah!), recorded to .ncs-files with Neuralynx' Cheetah (okay...), while also starting working on an Apple Mac (hmmm...). My first step was to try to load the header of the .ncs files, which gives me the warning: *Warning: the NEURALYNX_V6 toolbox is not installed, see http://neuralynx.com/research_software/file_converters_and_utilities/ and take the* *version from Neuralynx (windows only) * I see that previously there was a V3 which supported Mac, but not anymore. So I am afraid to ask ... can I really not read Neuralynx .ncs files with FieldTrip *on OSX*? Best, Stephen -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.nara at bcbl.eu Thu Apr 12 15:11:43 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Thu, 12 Apr 2018 15:11:43 +0200 (CEST) Subject: [FieldTrip] Non-parametric statistics for TFR data Message-ID: <302195760.10422434.1523538703510.JavaMail.zimbra@bcbl.eu> Hello, I am trying to implement parametric test on TFR data. I have 20 participant's data with 4 different conditions. I am interested in compairing theses conditions. After preprocessing and TFR computation i have one variable with (subjects * channels * freq * time ). The tutorial given on the website is using ERF data. Can i use it for TFR as well. cfg = []; cfg.channel = 'MEG'; cfg.latency = [0.3 0.7]; cfg.avgovertime = 'yes'; cfg.parameter = 'avg'; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_depsamplesT' cfg.alpha = 0.05; cfg.correctm = 'no'; cfg.correcttail = 'prob'; cfg.numrandomization = 1000; Nsub = 10; cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; cfg.ivar = 1; % the 1st row in cfg.design contains the independent variable cfg.uvar = 2; % the 2nd row in cfg.design contains the subject number stat = ft_timelockstatistics(cfg,allsubjFIC{:},allsubjFC{:}) % make the plot cfg = []; cfg.style = 'blank'; cfg.layout = 'CTF151_helmet.mat'; cfg.highlight = 'on'; cfg.highlightchannel = find(stat.mask); cfg.comment = 'no'; figure; ft_topoplotER(cfg, GA_FC) title('Nonparametric: significant without multiple comparison correction') Best regards Sanjeev Sanjeev Nara Predoctoral Researcher BCBL www.bcbl.eu https://sites.google.com/view/sanjeev-nara/ Tel: +34 943 309 300 (ext 314) Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From julian.keil at gmail.com Thu Apr 12 15:18:54 2018 From: julian.keil at gmail.com (Julian Keil) Date: Thu, 12 Apr 2018 15:18:54 +0200 Subject: [FieldTrip] Non-parametric statistics for TFR data In-Reply-To: <302195760.10422434.1523538703510.JavaMail.zimbra@bcbl.eu> References: <302195760.10422434.1523538703510.JavaMail.zimbra@bcbl.eu> Message-ID: Dear Sanjeev, take a look at this tutorial: http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_freq You need to use the ft_freqstatistics-function for TFR data. Best, Julian ________________ Prof. Dr. Julian Keil Biologische Psychologie Olshausenstraße 62 - R. 306 24118 Kiel 0431 / 880 - 4872 http://www.biopsych.uni-kiel.de/ Klinik für Psychiatrie und Psychotherapie der Charité im St. Hedwig-Krankenhaus Große Hamburger Straße 5-11 10115 Berlin 030 / 2311 - 1879 www.multisensorymind.com > Am 12.04.2018 um 15:11 schrieb Sanjeev Nara : > > Hello, > > I am trying to implement parametric test on TFR data. I have 20 participant's data with 4 different conditions. I am interested in compairing theses conditions. After preprocessing and TFR computation i have one variable with (subjects * channels * freq * time ). The tutorial given on the website is using ERF data. Can i use it for TFR as well. > > > cfg = []; > cfg.channel = 'MEG'; > cfg.latency = [0.3 0.7]; > cfg.avgovertime = 'yes'; > cfg.parameter = 'avg'; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_depsamplesT' > cfg.alpha = 0.05; > cfg.correctm = 'no'; > cfg.correcttail = 'prob'; > cfg.numrandomization = 1000; > > Nsub = 10; > cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; > cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; > cfg.ivar = 1; % the 1st row in cfg.design contains the independent variable > cfg.uvar = 2; % the 2nd row in cfg.design contains the subject number > > stat = ft_timelockstatistics(cfg,allsubjFIC{:},allsubjFC{:}) > > % make the plot > cfg = []; > cfg.style = 'blank'; > cfg.layout = 'CTF151_helmet.mat'; > cfg.highlight = 'on'; > cfg.highlightchannel = find(stat.mask); > cfg.comment = 'no'; > figure; ft_topoplotER(cfg, GA_FC) > title('Nonparametric: significant without multiple comparison correction') > > > > > > Best regards > Sanjeev > > > > Sanjeev Nara > Predoctoral Researcher BCBL > www.bcbl.eu > https://sites.google.com/view/sanjeev-nara/ > Tel: +34 943 309 300 (ext 314) > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > _______________________________________________ > 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: 833 bytes Desc: Message signed with OpenPGP URL: From stephen.whitmarsh at gmail.com Thu Apr 12 15:28:03 2018 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 12 Apr 2018 15:28:03 +0200 Subject: [FieldTrip] Neuralynx support on OSX In-Reply-To: References: Message-ID: Hello again, It just needed a second look - on the neurolynx website there is also a Linux/OSX (compiled) library, which seems to work fine. So as far I can tell now, the 'windows only' part of the warning message can be removed :-) Best wishes, Stephen On 11 April 2018 at 14:49, Stephen Whitmarsh wrote: > Dear FieldTrippers, > > I just started with intracranial data for the first time (yeah!), recorded > to .ncs-files with Neuralynx' Cheetah (okay...), while also starting > working on an Apple Mac (hmmm...). > > My first step was to try to load the header of the .ncs files, which gives > me the warning: > > *Warning: the NEURALYNX_V6 toolbox is not installed, see > http://neuralynx.com/research_software/file_converters_and_utilities/ > and > take the* > *version from Neuralynx (windows only) * > > I see that previously there was a V3 which supported Mac, but not anymore. > So I am afraid to ask ... can I really not read Neuralynx .ncs files with > FieldTrip *on OSX*? > > Best, > Stephen > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From roycox.roycox at gmail.com Thu Apr 12 20:54:40 2018 From: roycox.roycox at gmail.com (Roy Cox) Date: Thu, 12 Apr 2018 14:54:40 -0400 Subject: [FieldTrip] excessive channel correlations Message-ID: hello EEG community, We have a rather peculiar problem that we're hoping to get some input on. In reviewing some existing 64-channel recordings, we noticed that some records show near-identical signals across al channels, with median channel-by-channel correlations of >0.99. This suggests some kind of electrical shorting, somewhere in the cap-cable-amplifier-montage-recording-exporting chain. The problem appears to be infrequent (most records have more acceptable R values of 0.6-0.9), but common enough that we'll need to review several hundred records. We haven't been able to identify the cause of the problem yet, and it affects ongoing data collection. Some details: - we use Grass AURA amplifiers and TWin software with the Easycap system - the problem has been observed with different amplifiers, different caps, different pcs, and at different sites - the problem is there regardless of reference montage (e.g., forehead and averaged mastoids) - gel bridging, while theoretically possible, seems unlikely given that literally all EEG channels are (almost) identical We're still investigating but wanted to hear if anyone ever observed anything like this? Were they able to solve it? Thanks, Roy -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.spaak at donders.ru.nl Fri Apr 13 08:45:23 2018 From: e.spaak at donders.ru.nl (Eelke Spaak) Date: Fri, 13 Apr 2018 08:45:23 +0200 Subject: [FieldTrip] excessive channel correlations In-Reply-To: References: Message-ID: Hi Roy, I have no suggestion as to what might be causing this, but one suggestion on how to pragmatically deal with it, or at least maybe get some more insight. > - the problem is there regardless of reference montage (e.g., forehead and > averaged mastoids) Have you tried common average reference? If the signal is there on all channels, subtracting the common average should get rid of it. Cheers, Eelke > - gel bridging, while theoretically possible, seems unlikely given that > literally all EEG channels are (almost) identical > > We're still investigating but wanted to hear if anyone ever observed > anything like this? Were they able to solve it? > > Thanks, > > Roy > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From maximilien.chaumon at gmail.com Fri Apr 13 16:16:35 2018 From: maximilien.chaumon at gmail.com (Maximilien Chaumon) Date: Fri, 13 Apr 2018 14:16:35 +0000 Subject: [FieldTrip] extracting a continuous patch on a mesh Message-ID: Dear all, I'm trying to extract a connected patch of vertices at most say 2 cm away from a given seed. Is there an easy way to do this in FieldTrip? Many thanks, Max -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.smulders at maastrichtuniversity.nl Fri Apr 13 16:45:50 2018 From: f.smulders at maastrichtuniversity.nl (Smulders, F (PSYCHOLOGY)) Date: Fri, 13 Apr 2018 14:45:50 +0000 Subject: [FieldTrip] excessive channel correlations In-Reply-To: References: , Message-ID: I have seen this occasionally, also on Brainvision's BrainAmp. I find it worrying, and would also like a good explanation. I have seen before that open channels on an AD converter just pass a copy of an occupied channel. So if you have a bad connection, that might explain it. Subtracting the channel-average would possibly 'hide' a serious hardware problem, it seems to me that you just might end up with pure noise. kind regards, Fren > On 13 Apr 2018, at 08:56, Eelke Spaak wrote: > > Hi Roy, > > I have no suggestion as to what might be causing this, but one > suggestion on how to pragmatically deal with it, or at least maybe get > some more insight. > >> - the problem is there regardless of reference montage (e.g., forehead and >> averaged mastoids) > > Have you tried common average reference? If the signal is there on all > channels, subtracting the common average should get rid of it. > > Cheers, > Eelke > >> - gel bridging, while theoretically possible, seems unlikely given that >> literally all EEG channels are (almost) identical >> >> We're still investigating but wanted to hear if anyone ever observed >> anything like this? Were they able to solve it? >> >> Thanks, >> >> Roy >> >> _______________________________________________ >> 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 From thomas.bancel at icm-institute.org Wed Apr 18 11:17:01 2018 From: thomas.bancel at icm-institute.org (BANCEL Thomas) Date: Wed, 18 Apr 2018 09:17:01 +0000 Subject: [FieldTrip] Opening .smr file with ft Message-ID: <28FC02000FAE4C418B74665EF5E368BA8A6E02@SRVMAIL-ICM.icm-institute.org> Hi everyone, My name is Thomas Bancel, I am working on epilepsy at ICM and we have recordings from the Spike2 (v 9.02) software (CED, .smr file) that I would like to put into Matlab using Fieldtrip (and not the SONLibrary). When I call the following script: addpath('C:\Users\thomas.bancel\Documents\MATLAB\fieldtrip-20180228\'); ft_defaults smr_filepath = 'C:\Users\thomas.bancel\Documents\Crises annotées Mark\557 GAERS S1 2015_10_19\557 GAERS S1 2015_10_19 _M.smr'; smrx_filepath = 'C:\Users\thomas.bancel\Documents\Crises annotées Mark\557 GAERS S1 2015_10_19\smrx557 GAERS S1 2015_10_19.smrx'; dll_name = 'C:\Users\thomas.bancel\Documents\MATLAB\nsMCDLibrary_3.7b\Matlab\Matlab-Import-Filter\Matlab_Interface\nsMCDLibrary64.dll'; [result] = ns_SetLibrary(dll_name) % give 0 ft_read_data(smr_filepath) I get the following message: Call ns_SetLibrary first! Process interrupted! Error using read_ced_son (line 97) Could not get NeuroShare library info, please use the NS_SETLIBRARY function. Can someone help me ? I work on Matlab R2017b, fieldtrip release 2018/02/28, windows 7 professional, 64 bit. Thank you in advance, Thomas PS: this is my first message in the discussion list, sorry if it lacks info or if it is unclear, I can update if needed. Thomas Bancel ICM - Equipe Charpier thomas.bancel at icm-institute.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From R.Mehraram2 at newcastle.ac.uk Wed Apr 18 11:28:36 2018 From: R.Mehraram2 at newcastle.ac.uk (Ramtin Mehraram (Student)) Date: Wed, 18 Apr 2018 09:28:36 +0000 Subject: [FieldTrip] Not timefrequency data on fieldtrip: cluster-based statistics References: Message-ID: Hi all! I need to run a statistical analysis across four independent groups for some network measure I obtained with the brain connectivity toolbox (degree, clustering coefficient, etc.) from EEG data. I am dealing with the multiple comparison issue. Since I am using a high density cap, nothing survives the Bonferroni correction (and variants), nor the FDR. I am trying to perform a cluster-based (montecarlo) analysis as implemented in Fieldtrip, but the toolbox needs the input to be organized as a time-frequency structure. I tried to rebuild a similar structure (degree values instead of power spectrum values), but it seems that I am being unsuccessful. Indeed: if I run a "cfg.statistic = indepsamplesF" across the groups I get NaNs in the probability output matrix. If I just perform a "cfg.statistic = indepsamplesT" between two random groups, I get a couple of channels or so with p<0.05. In all the cases, any form of fieldtrip plotting (such as ft_clusterplot) shows as output the message "Argument to mbscalar must be scalar". Any idea? Is it actually sensible to proceed in this way or is there any smarter way to work with not time-frequency data on fieldtrip? Many thanks in advance for your help. Ramtin Mehraram PhD Student @ramtinTVT Biomedical Research Building 3rd floor Institute of Neuroscience Newcastle University NE4 5PL, United Kingdom www.lewybodylab.org https://www.newcastlebrc.nihr.ac.uk/research-themes/dementia/ From e.maris at donders.ru.nl Wed Apr 18 13:39:45 2018 From: e.maris at donders.ru.nl (Maris, E.G.G. (Eric)) Date: Wed, 18 Apr 2018 11:39:45 +0000 Subject: [FieldTrip] PhD position at the Donders Institute on competition between internal and external attention states In-Reply-To: References: Message-ID: PhD position at the Donders Institute for Brain, Cognition and Behaviour: Watch out! Competition between internal and external attention states in brain and behavior Supervisors: Eric Maris & Marius Peelen Summary: Attention can be directed externally (to the outside world) or internally (to representations in the mind). While this distinction features prominently in current models of attention, there are surprisingly few empirical studies directly investigating this distinction. This project provides a comprehensive investigation of the external-internal attention distinction, its neurophysiological characteristics, and its relation to behavior. Using advanced analysis of both ongoing and evoked EEG/MEG data we will classify spontaneous brain states as corresponding to external versus internal attention states. We will link these brain states to perceptual performance in naturalistic object recognition tasks, testing the hypothesis that an external attention state leads to better perceptual performance. In addition, we will induce attention states by having participants perform externally and internally directed tasks. Finally, we will test the hypothesis that shifting gaze, even in complete darkness, directs attention externally, leading to better perceptual performance. Results of these studies will: (1) provide empirical evidence for the proposed distinction between external and internal attention, (2) provide a neurophysiological characterization of these attention states, and (3) shed light on the feasibility to improve perceptual performance by biasing attention towards the external state. Contact: e.maris at donders.ru.nl or m.peelen at donders.ru.nl Eric Maris | Donders Institute for Brain, Cognition, and Behaviour & Faculty of Social Sciences | Radboud University | PO Box 9104, 6500 HE Nijmegen | (024) 3612651 | www.ru.nl This message (and any attachments) is intended solely for the addressee(s) and may contain confidential information. If you are not the addressee, do not copy this message (and any attachments), forward or share this message with third parties. You are requested to notify the sender immediately and delete this message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.stoica at uke.de Wed Apr 18 15:32:51 2018 From: m.stoica at uke.de (Mircea Stoica) Date: Wed, 18 Apr 2018 15:32:51 +0200 Subject: [FieldTrip] Social cognition in humans and robots (Hamburg, September 27-28, 2018) Message-ID: Dear all, we are pleased to invite you to the "Social cognition in humans and robots" conference that will take place in Hamburg between the 27th and 28th of September, 2018. Over decades, a range of theories and concepts for explaining how we understand others have been developed. This conference turns the spotlight on the idea that social cognition is grounded in sensorimotor and informational dynamic coupling of agents. According to this view, interaction dynamics is one of the keys to understand the mechanisms of successful social interaction because it provides substantial clues to social understanding and gives rise to high-level capabilities such as joint shared intentionality and joint action. Moreover it suggests that many disturbances of social cognition may be rooted in the impaired capacity for entraining and sustaining sensorimotor and informational coupling. The conference will provide an interdisciplinary podium which overviews trends and recent developments of concepts, methods, basic research and applications of sensorimotor approaches in social cognitive science, neuroscience, and robotic research. A particularly interesting question will be how concepts and methods from social cognitive and neuroscience transfer to human-robot interaction. The meeting will also gauge the societal impact of progress in understanding dynamic coupling processes in human-human and human-robot interactions. The event is organized by the FET Proactive H2020 project "Socializing Sensorimotor Contingencies - soSMCs" (socSMCs.eu) in partner alliance with the European Society for Cognitive Systems - EUCog (eucognition.org). Keynote speakers - Natalie Sebanz (Central European University, Hungary) - Antonia Hamilton (University College London, UK) - Scott Kelso (Florida Atlantic University, USA) - Luciano Fadiga (University of Ferrara and IIT, Italy) - Iain Couzin (University of Konstanz, Germany) - Paul Verschure (Institute for Bioengineering of Catalonia, Spain) Submissions - Conference contributions (talks, posters) - Research articles (to be published in a Frontiers Research Topic) - Venues for the EUCognition meeting in 2019 For all submission types, please send an abstract of no more than 1.000 words to conference2018 at socSMCs.eu and indicate the type of your contribution (poster|talk|article|venue), the title (500 characters max.), all author names and affiliations. Important dates - May 25, 2018: Deadline for submission of abstracts - June 29, 2018: Registration closes - Decemnaber 3, 2018: Submission of research articles Fee The registration fee of 110€ includes coffee, soft drinks and snacks on both days. On September 27th, a social dinner at an extra charge of 20€ will be hosted at the MS Cap San Diego (http://www.capsandiego.de/in- brief.html).Booking of the social dinner is only possible in combination with a conference registration. Register today at https://en.xing-events.com/TEHHWXM More info at https://www.socsmcs.eu/conference2018 Best regards, Mircea Stoica -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Martina Saurin (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING -------------- next part -------------- An HTML attachment was scrubbed... URL: From elam4hcp at gmail.com Wed Apr 18 18:55:25 2018 From: elam4hcp at gmail.com (Jennifer Elam) Date: Wed, 18 Apr 2018 11:55:25 -0500 Subject: [FieldTrip] HCP Course 2018 at Oxford: Final Course Schedule posted -- Register Now! Message-ID: Faculty listings and the full schedule of covered topics are now available for the *2018 HCP Course: "Exploring the Human Connectome" *, to be held *June 25 – 29, 2018* at the Blavatnik School of Government , at the University of Oxford , in Oxford, UK! The 5-day intensive course is a great opportunity to learn directly from HCP investigators and gain practical experience with the Human Connectome Project's approach to multimodal whole brain imaging acquisition, processing, analysis, visualization, and sharing of data and results. For more info and to register visit the HCP Course 2018 website . Don't delay, registration is limited, and the course is filling up fast! Nearby affordable accommodations are available at Worcester College at Oxford by selecting registration with accommodations on the site. If you have any questions, please contact us at: hcpcourse at humanconnectome. org We look forward to seeing you in Oxford! Best, 2018 HCP Course Staff -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam at wustl.edu www.humanconnectome.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.nara at bcbl.eu Thu Apr 19 23:15:13 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Thu, 19 Apr 2018 23:15:13 +0200 (CEST) Subject: [FieldTrip] Brainhack Donostia 2018 In-Reply-To: <2051471137.10611732.1524143917106.JavaMail.zimbra@bcbl.eu> References: <2051471137.10611732.1524143917106.JavaMail.zimbra@bcbl.eu> Message-ID: <1069339273.10622399.1524172513356.JavaMail.zimbra@bcbl.eu> Hello Everyone The Basque Center on Cognition Brain and Language (BCBL) will host the first edition of the BrainhackDonostia2018. The event aims at bringing together students and scientists at all levels of their careers to enjoy science and a couple of Cider glasses together. This year's edition will focus on Neuroimaging techniques, in particular fMRI (functional magnetic resonance) MEG (magnetoencephalography, EEG (electroencephalogaphy) and fNIRS (functional near infrared spectroscopy). Through a combination of lectures and tutorials, participants will be introduced on these techniques, and how they can be used to study the mind and brain. For those that have more experience, and have an interest in three days of project development, there is also the possibility to propose and develop a project related to neuroimaging and/or electrophysiology recruiting participants on site. The event is open to people from different disciplines and backgrounds, with a genuine interest in neuroimaging methods, psychology, neuroscience, and more generally interdisciplinary research. Feel free to explore our website for further information. http://www.bcbl.eu/events/BrainhackDonostia2018/en/ The event will be hosted on May 2nd-4th 2018 in the Basque Center on Cognition Brain and Language in San Sebastian, Spain. The cost is 10€ for Master Students, 15€ for PhD and PostDocs, 40€ for Seniors and "Industrials" + optional 13€ for the T-shirt. Registration to the event is needed and can be done on the website, until the 25th of April. A certificate of attendance will be provided to participants. If you have more questions, we remain at your disposal at the address info.bhg-donostia at bcbl.eu We look forward to see you in May! From s.nara at bcbl.eu Thu Apr 19 23:48:24 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Thu, 19 Apr 2018 23:48:24 +0200 (CEST) Subject: [FieldTrip] Common Baseline for uneven length trials Message-ID: <356285164.10622632.1524174504598.JavaMail.zimbra@bcbl.eu> Hello Researchers I am working on a dataset where i have some trials per subject which are time locked to target1. I computed the time frequency response by specifying first 400 miliseconds as Baseline. Then i redefine the trials to a different triggers by providing the pre calculated offset. The offset introduces the trials (pre trig) with different timings. I mean some trials start with say -2.5 seconds and some starts at say -2.4 (my offsets is varying). i have mainly two questions: 1. How can take a common baseline for both the cases. 2. is it possible to specify the samples in fieldtrip Baseline option. Thanks Best regards Sanjeev Sanjeev Nara Predoctoral Researcher BCBL www.bcbl.eu https://sites.google.com/view/sanjeev-nara/ Tel: +34 943 309 300 (ext 314) Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From zoran at nyu.edu Fri Apr 20 16:59:02 2018 From: zoran at nyu.edu (Zoran Josipovic) Date: Fri, 20 Apr 2018 10:59:02 -0400 Subject: [FieldTrip] fieldtrip Digest, Vol 89, Issue 9 In-Reply-To: References: Message-ID: Hello fieldtrip community, Does anyone know if the fieldtrip can run Matlab firpm filter, and if so, what is the correct script to do it? Here is the Matlab page for this filter: https://www.mathworks.com/help/signal/ref/firpm.html Thanks! Zoran On Fri, Apr 20, 2018 at 6:00 AM, 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. Brainhack Donostia 2018 (Sanjeev Nara) > 2. Common Baseline for uneven length trials (Sanjeev Nara) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 19 Apr 2018 23:15:13 +0200 (CEST) > From: Sanjeev Nara > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Brainhack Donostia 2018 > Message-ID: > <1069339273.10622399.1524172513356.JavaMail.zimbra at bcbl.eu> > Content-Type: text/plain; charset=utf-8 > > > Hello Everyone > > The Basque Center on Cognition Brain and Language (BCBL) will host the > first edition of the BrainhackDonostia2018. The event aims at bringing > together students and scientists at all levels of their careers to enjoy > science and a couple of Cider glasses together. > > This year's edition will focus on Neuroimaging techniques, in particular > fMRI (functional magnetic resonance) MEG (magnetoencephalography, EEG > (electroencephalogaphy) and fNIRS (functional near infrared spectroscopy). > Through a combination of lectures and tutorials, participants will be > introduced on these techniques, and how they can be used to study the mind > and brain. > For those that have more experience, and have an interest in three days of > project development, there is also the possibility to propose and develop a > project related to neuroimaging and/or electrophysiology recruiting > participants on site. > > The event is open to people from different disciplines and backgrounds, > with a genuine interest in neuroimaging methods, psychology, neuroscience, > and more generally interdisciplinary research. Feel free to explore our > website for further information. > http://www.bcbl.eu/events/BrainhackDonostia2018/en/ > > The event will be hosted on May 2nd-4th 2018 in the Basque Center on > Cognition Brain and Language in San Sebastian, Spain. The cost is 10? for > Master Students, 15? for PhD and PostDocs, 40? for Seniors and > "Industrials" + optional 13? for the T-shirt. Registration to the event is > needed and can be done on the website, until the 25th of April. A > certificate of attendance will be provided to participants. > > If you have more questions, we remain at your disposal at the address > info.bhg-donostia at bcbl.eu > > We look forward to see you in May! > > > > > ------------------------------ > > Message: 2 > Date: Thu, 19 Apr 2018 23:48:24 +0200 (CEST) > From: Sanjeev Nara > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Common Baseline for uneven length trials > Message-ID: <356285164.10622632.1524174504598.JavaMail.zimbra at bcbl.eu> > Content-Type: text/plain; charset=utf-8 > > Hello Researchers > > I am working on a dataset where i have some trials per subject which are > time locked to target1. I computed the time frequency response by > specifying first 400 miliseconds as Baseline. Then i redefine the trials to > a different triggers by providing the pre calculated offset. The offset > introduces the trials (pre trig) with different timings. I mean some trials > start with say -2.5 seconds and some starts at say -2.4 (my offsets is > varying). i have mainly two questions: > > 1. How can take a common baseline for both the cases. > 2. is it possible to specify the samples in fieldtrip Baseline option. > > Thanks > > > Best regards > Sanjeev > > > > Sanjeev Nara > Predoctoral Researcher BCBL > www.bcbl.eu > https://sites.google.com/view/sanjeev-nara/ > Tel: +34 943 309 300 (ext 314) > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 89, Issue 9 > **************************************** > -- Zoran Josipovic, PhD Adjunct Assistant Professor Psychology Dept. Research Associate NYULMC New York University -------------- next part -------------- An HTML attachment was scrubbed... URL: From virginie.van.wassenhove at gmail.com Sat Apr 21 23:45:25 2018 From: virginie.van.wassenhove at gmail.com (Virginie van Wassenhove) Date: Sat, 21 Apr 2018 23:45:25 +0200 Subject: [FieldTrip] Fwd: [last call for a position in the Cognition & Brain Dynamics lab, NeuroSpin - Closing date: April 22nd 2018] In-Reply-To: References: Message-ID: Dear all, this is a last reminder for a previously advertised job opening in my lab, description available here: https://brainthemind.files.wordpress.com/2018/02/2018_vvw_ jobdescription_cea1.pdf **Deadline is tomorrow April 22nd at midnight (UTC-12)** Best wishes, Virginie -- Virginie van Wassenhove *https://brainthemind.com/ * -------------- next part -------------- An HTML attachment was scrubbed... URL: From luca.turella at unitn.it Sun Apr 22 21:41:14 2018 From: luca.turella at unitn.it (Luca Turella) Date: Sun, 22 Apr 2018 21:41:14 +0200 Subject: [FieldTrip] Call for 11 fully-funded PhD positions NOW OPEN @ CIMeC, UNITrento. Italy Message-ID: Dear all, We are pleased to announce the opening of a call for *11 fellowships* for our international PhD Program in Cognitive and Brain Sciences (CIMeC), commencing November 2018 at the University of Trento, Italy. As you will see from the links below, the PhD call is open to several fields of cognitive neuroscience research. Interested candidates should feel free to contact the PIs that might have topics of interest to them. - *Admissions*: http://www.unitn.it/drcimec/admission - PhD research areas outline: http://www.unitn.it/drcimec/research-topics - PhD Application *summary*: http://www.unitn.it/drcimec/node/118 - PhD *Application *link: https://webapps.unitn.it/Apply/en/MyUnitn/Home/669/dott/cbs34 - PhD Application *Deadline*:* Thursday May 31, 2018, at 4pm (Italian time)* - *CIMeC*: http://www.unitn.it/cimec This year’s research topics proposed by the Doctoral Program Committee for 5 UNITN grants are visible here: http://www.unitn.it/drcimec/research-topics, while the 6 topic-specific grants’ details can be found here: http://www.unitn.it/drcimec/topic-specific-grants *The CIMeC, it’s doctoral program and UNITN in numbers:* - 2018 UNITrento ranks among top Italian Universities in THE - Times Higher Education - *4-yr program* (Nov. 1, 2018- Oct. 31, 2022). - Why a 4-yr program - Courses are given in English - 11 positions, 100% funded - Salary: starting at approximately €1.200/mo., net - Winners receive a €4887 tax-free research/mobility budget - Why choose UNITRENTO Please feel free to browse the FAQ pages on our website for further information, or contact the Director of the Programme, Prof. Francesco Pavani phd.cimec at unitn.it. -- Luca Turella, PhD Assistant Professor CIMeC - Center for Mind/Brain Sciences University of Trento Mattarello (TN), Via Delle Regole 101 Tel.+39 0461-28 3098 http://www.unitn.it/cimec Legal Disclaimer This electronic message contains information that is confidential. The information is intended for the use of the addressee only. If you are not the addressee we would appreciate your notification in this respect. Please note that any disclosure, copy, distribution or use of the contents of this message is prohibited and may be unlawful. Avvertenza legale Questo messaggio Email contiene informazioni confidenziali riservate ai soli destinatari. Qualora veniate in possesso di tali informazioni senza essere definito come destinatario vi reghiamo di leggere le seguenti note. Ogni apertura, copia, distribuzione del contenuto del messaggio e dei suoi allegati è proibito e potrebbe violare le presenti leggi. -------------- next part -------------- An HTML attachment was scrubbed... URL: From maximilien.chaumon at gmail.com Mon Apr 23 14:15:19 2018 From: maximilien.chaumon at gmail.com (Maximilien Chaumon) Date: Mon, 23 Apr 2018 12:15:19 +0000 Subject: [FieldTrip] extracting a continuous patch on a mesh In-Reply-To: References: Message-ID: Hi all, So I coded something that could perhaps be useful to others. It grows a patch around a seed up to a certain distance. See below function [list] = mesh_patch(mesh,seed,dmax) % [list] = mesh_patch(mesh,seed,d) % % return the list of connected vertices that are at most d mesh.unit away % from seed. % % Maximilien Chaumon 2018 % measure distance to seed seedpos = mesh.pos(seed,:); distances = sqrt(sum(bsxfun(@minus,mesh.pos,seedpos).^2,2)); % crawl starting from seed list = crawl(mesh.tri,distances,dmax,seed); function final = crawl(tri,d,dmax,vert) % bookkeeping: the list of vertices persistent listi st = dbstack; level = sum(strcmp({st.name},'crawl')); if level == 1 listi = []; end % listi(end+1) = vert; % append this vertex to the list conn = tri(any(tri==vert,2),:);% connected vertices conn = unique(conn); conn(d(conn) > dmax) = []; % remove those that are too far. conn(ismember(conn,listi)) = [];%keep only vertices that have not been crawled yet for i = 1:numel(conn) crawl(tri,d,dmax,conn(i));% move to next end % bookkeeping: return the list at last if level == 1 final = listi; % return list if it's last call end Le ven. 13 avr. 2018 à 16:16, Maximilien Chaumon < maximilien.chaumon at gmail.com> a écrit : > Dear all, > > I'm trying to extract a connected patch of vertices at most say 2 cm away > from a given seed. > Is there an easy way to do this in FieldTrip? > > Many thanks, > Max > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ph442 at cam.ac.uk Mon Apr 23 14:48:06 2018 From: ph442 at cam.ac.uk (parham hashemzadeh) Date: Mon, 23 Apr 2018 13:48:06 +0100 Subject: [FieldTrip] extracting a continuous patch on a mesh In-Reply-To: References: Message-ID: Hi All Is there a Matlab implementation of openMEEG lying around somewhere? I was wondering, if openMEEG has a pure Matlab or python implementation. Pure form. Many of us (INCLUDING ME) are using code, without really digging deep into the details. I would be grateful, if it can be shared. Many thanks best regards parham On 2018-04-23 13:15, Maximilien Chaumon wrote: > Hi all, > > So I coded something that could perhaps be useful to others. It grows > a patch around a seed up to a certain distance. See below > > function [list] = mesh_patch(mesh,seed,dmax) > > % [list] = mesh_patch(mesh,seed,d) > % > % return the list of connected vertices that are at most d mesh.unit > away > % from seed. > % > % Maximilien Chaumon 2018 > > % measure distance to seed > seedpos = mesh.pos(seed,:); > distances = sqrt(sum(bsxfun(@minus,mesh.pos,seedpos).^2,2)); > > % crawl starting from seed > list = crawl(mesh.tri,distances,dmax,seed); > > function final = crawl(tri,d,dmax,vert) > > % bookkeeping: the list of vertices > persistent listi > st = dbstack; > level = sum(strcmp({st.name [1]},'crawl')); > if level == 1 > listi = []; > end > % > > listi(end+1) = vert; % append this vertex to the list > > conn = tri(any(tri==vert,2),:);% connected vertices > conn = unique(conn); > conn(d(conn) > dmax) = []; % remove those that are too far. > conn(ismember(conn,listi)) = [];%keep only vertices that have not been > crawled yet > for i = 1:numel(conn) > crawl(tri,d,dmax,conn(i));% move to next > end > > % bookkeeping: return the list at last > if level == 1 > final = listi; % return list if it's last call > end > > Le ven. 13 avr. 2018 à 16:16, Maximilien Chaumon > a écrit : > >> Dear all, >> >> I'm trying to extract a connected patch of vertices at most say 2 cm >> away from a given seed. >> Is there an easy way to do this in FieldTrip? >> >> Many thanks, >> Max > > > Links: > ------ > [1] http://st.name > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- best regards Parham Hashemzadeh Research Associate Department of Applied Mathematics and Theoretical Physics University of Cambridge, UK. email: hashemzadeh at damtp.cam.ac.uk From Joshua.Bear at childrenscolorado.org Wed Apr 25 19:07:13 2018 From: Joshua.Bear at childrenscolorado.org (Bear, Joshua) Date: Wed, 25 Apr 2018 17:07:13 +0000 Subject: [FieldTrip] ft_sourceinterpolate question Message-ID: <2E9B4D36-9330-49D1-8F3D-2EEAFA4E40B2@contoso.com> Dear FieldTrip Users: I am trying to apply the Network Analysis tutorial to my own data, and I have hit a stumbling block with the atlas and parcellation steps. Briefly, I am using a mesh exported from Brainstorm with 15002 vertices, so at the end of all steps through ft_connectivityanalysis I have a connectivity structure with pos = 15002. The atlas has pos = 8004. I tried to use ft_sourceinterpolate to make my connectivity structure match the atlas, but it is only seems to be interpolating the first dimension of the source data as shown below. My question: How can I make ft_sourceinterpolate apply to both dimensions of my cohspctrm parameter rather than only the first dimension? RESULTS from ft_connectivityanalysis: source_conn = struct with fields: inside: [15002×1 logical] pos: [15002×3 double] tri: [29989×3 double] cohspctrm: [15002×15002 double] dimord: 'pos_pos_freq' freq: 9.9340 cfg: [1×1 struct] INTERPOLATION commands: cfg = []; cfg.parameter = 'cohspctrm'; cfg.interpmethod = 'nearest'; source_conn_interp = ft_sourceinterpolate(cfg, source_conn, atlas); RESULTS from ft_sourceinterpolate: source_conn_interp = struct with fields: freq: 9.9340 pos: [8004×3 double] tri: [16000×3 double] unit: 'mm' inside: [8004×1 logical] cohspctrm: [8004×15002 double] cfg: [1×1 struct] Notice that the cohspctrm is interpolated from a [15002×15002 double] to a [8004×15002 double]. This then translates to the parcellation step where only the first dimension can be parcellated using the atlas. I’m sure I am missing something obvious and appreciate your thoughts and patience, Josh -- Joshua Bear, MD, MA Neuroscience Institute, Children’s Hospital Colorado ------------------------------------------------------------------------------ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ------------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.nara at bcbl.eu Wed Apr 25 21:52:39 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Wed, 25 Apr 2018 21:52:39 +0200 (CEST) Subject: [FieldTrip] Mismatch between cluster activation and * marks Message-ID: <158854153.10803185.1524685959460.JavaMail.zimbra@bcbl.eu> Hi Fieldtrip Experts Apologies for a long mail. I have a experiment where i have 20 subjects which have performed 2 different tasks. I want to implement a cluster based permutation test for compare the Time frequency analysis in two different conditions. I a following this tutorial for computing the stats http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_freq . I have computed the stats using ft_freqstatistics by providing input a 4 D matrix which has size (20 subjects * 102 channels * 70 frequency bins * 190 time points ). The analysis give me positive and negative clusters. I want to plot first positive and negative cluster in terms of channels which are significant during a specifies frequency range (say 12 - 30 ) in a specified time range. After that i use ft_descriptive on difference of powerspectrum in both conditions. I am plotting the cluster within a specified time and frequency duration computed from first positive and negative cluster. The problem is i am getting topoplots which have a difference in the colour activation and the ' * ' marks. I have attached few plots to show what is the issue. The image img1_correct and img2_correct shows the match between activations and ' * ' marks whereas the img1_incorrect and img2_incorrect shows the mismatch. I shall be thankful if you could please help me debugging the issue. Best regards Sanjeev Sanjeev Nara Predoctoral Researcher BCBL www.bcbl.eu https://sites.google.com/view/sanjeev-nara/ Tel: +34 943 309 300 (ext 314) Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer -------------- next part -------------- A non-text attachment was scrubbed... Name: img1_correct.png Type: image/png Size: 48736 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: img1_incorrect.png Type: image/png Size: 52018 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: img2_incorrect.png Type: image/png Size: 48615 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: img2_correct.png Type: image/png Size: 49975 bytes Desc: not available URL: From seymourr at aston.ac.uk Thu Apr 26 01:48:31 2018 From: seymourr at aston.ac.uk (Seymour, Robert (Research Student)) Date: Wed, 25 Apr 2018 23:48:31 +0000 Subject: [FieldTrip] ft_sourceinterpolate question Message-ID: Hi Josh, It seems like you are using the HCP Glasser atlas ('A multi-modal parcellation of human cerebral cortex')? The atlas presented as part of the network analysis tutorial is designed for a cortical mesh with 8004 vertices, rather than the 15002 you are using. I don’t believe ft_sourceinterpolate can currently cope with the surface-based transformation upwards from 8000—> 15000 vertices. To use the HCP atlas you will need to downsample the original 32k atlas in fs_LR space to 15000 space and transform to whichever standard-brain template you are using. This is non-trivial and requires some functions from the HCP project (e.g. wb_command which can be found here: https://www.humanconnectome.org/software/workbench-command). If your mesh is created using Freesurfer you can use this script here: https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh If the mesh is not constructed using Freesurfer it will be tricker & I would recommend contacting the HCP mailing list. Good luck! Robert Seymour (Aston Brain Centre & Department of Cognitive Science, Macquarie University). -------------- next part -------------- An HTML attachment was scrubbed... URL: From Joshua.Bear at childrenscolorado.org Thu Apr 26 04:14:09 2018 From: Joshua.Bear at childrenscolorado.org (Bear, Joshua) Date: Thu, 26 Apr 2018 02:14:09 +0000 Subject: [FieldTrip] ft_sourceinterpolate question In-Reply-To: References: Message-ID: Hi Robert, Thank you so much for the response! My ultimate intention is actually to use the parcellation scheme proposed by Gordon et al. (Cerebral Cortex, Volume 26, Issue 1, 1 January 2016, Pages 288–303, https://doi.org/10.1093/cercor/bhu239) though at this time I was using the atlas provided in the tutorial. The problem I ran into is that I am trying to interpolate my brain’s mesh DOWN from 15002 to 8004 (to match the atlas), not up. As you pointed out, I have had some problems with other high resolution meshes, but in this case ft_sourceinterpolate seemed to work — it just only worked for one of the two dimensions of my connectivity data. That is, it went from a [15002×15002 double] to a [8004×15002 double]. Of course it’s possible the interpolation for that first dimension was incorrect, but what confused me was that it did not interpolate the second dimension. (As I write this, I’m wondering if I should simply try transposing the matrix and running the interpolation again!). I will try, as you suggest, downsampling the mesh externally and trying again. I’m not able to match the 8004 vertices perfectly, but perhaps if I drop it slightly below this number it will be able to interpolate up correctly. Any other thoughts or suggestions are greatly appreciated as well. Best, Josh From: on behalf of "Seymour, Robert (Research Student)" Reply-To: FieldTrip discussion list Date: Wednesday, April 25, 2018 at 5:48 PM To: "fieldtrip at science.ru.nl" Subject: Re: [FieldTrip] ft_sourceinterpolate question Hi Josh, It seems like you are using the HCP Glasser atlas ('A multi-modal parcellation of human cerebral cortex')? The atlas presented as part of the network analysis tutorial is designed for a cortical mesh with 8004 vertices, rather than the 15002 you are using. I don’t believe ft_sourceinterpolate can currently cope with the surface-based transformation upwards from 8000—> 15000 vertices. To use the HCP atlas you will need to downsample the original 32k atlas in fs_LR space to 15000 space and transform to whichever standard-brain template you are using. This is non-trivial and requires some functions from the HCP project (e.g. wb_command which can be found here: https://www.humanconnectome.org/software/workbench-command). If your mesh is created using Freesurfer you can use this script here: https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh If the mesh is not constructed using Freesurfer it will be tricker & I would recommend contacting the HCP mailing list. Good luck! Robert Seymour (Aston Brain Centre & Department of Cognitive Science, Macquarie University). ------------------------------------------------------------------------------ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ------------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From Joshua.Bear at childrenscolorado.org Thu Apr 26 08:01:28 2018 From: Joshua.Bear at childrenscolorado.org (Bear, Joshua) Date: Thu, 26 Apr 2018 06:01:28 +0000 Subject: [FieldTrip] ft_sourceinterpolate question In-Reply-To: References: Message-ID: <271913CA-10AE-4E5B-8424-429132D272A7@childrenscolorado.org> Hi all, It occurs to me that using ft_sourceinterpolate to decrease, rather than increase, the dimensions is not intuitive, and I found that it was actually fairly easy to get the Gorden et al. atlas loaded in as they provide an MNI-registered form of the atlas. So I repeated my steps using the selected atlas and with a smaller headmodel and leadfield resulting in a source file that had to be interpolated in the more anticipated direction. The problem persists, however. I now have connectivity results with the following pertinent values: dim: [18 15 15] pos: [4050×3 double] cohspctrm: [4050×4050 double] dimord: 'pos_pos_freq' My atlas has the following pertinent values: dim: [61 73 61] transform: [4×4 double] brick0: [61×73×61 uint16] brick0label: {1×333 cell} The results of interpolating my connectivity source to the atlas lead to the same peculiar asymmetry in the cohspctrm results: dim: [61 73 61] transform: [4×4 double] inside: [61×73×61 logical] cohspctrm: [271633×4050 double] pos: [271633×3 double] And as the whole point is to then use ft_sourceparcellate, I found that this carries over the asymmetrical results of the interpolation with the following source values after parcellation: freq: 9.9340 label: {1×333 cell} cohspctrm: [333×4050 double] brainordinate: [1×1 struct] cfg: [1×1 struct] As you can see, the first dimension of the cohspctrm results increased from 4050 to 271633 with interpolation and then decreased to 333, the number of parcels in my chosen atlas, exactly as I would have expected. The second dimension, however, did not budge from its initial 4050. The interpolation step is necessary to ensure the source matches the atlas (FT throws an error otherwise). Could this be a bug in ft_sourceinterpolate and ft_sourceparcellate, or is there some crucial step such as converting everything into another format that I am missing? Thanks again and sorry for the serial messages, Josh From: on behalf of Joshua Bear Reply-To: FieldTrip discussion list Date: Wednesday, April 25, 2018 at 8:14 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] ft_sourceinterpolate question Hi Robert, Thank you so much for the response! My ultimate intention is actually to use the parcellation scheme proposed by Gordon et al. (Cerebral Cortex, Volume 26, Issue 1, 1 January 2016, Pages 288–303, https://doi.org/10.1093/cercor/bhu239) though at this time I was using the atlas provided in the tutorial. The problem I ran into is that I am trying to interpolate my brain’s mesh DOWN from 15002 to 8004 (to match the atlas), not up. As you pointed out, I have had some problems with other high resolution meshes, but in this case ft_sourceinterpolate seemed to work — it just only worked for one of the two dimensions of my connectivity data. That is, it went from a [15002×15002 double] to a [8004×15002 double]. Of course it’s possible the interpolation for that first dimension was incorrect, but what confused me was that it did not interpolate the second dimension. (As I write this, I’m wondering if I should simply try transposing the matrix and running the interpolation again!). I will try, as you suggest, downsampling the mesh externally and trying again. I’m not able to match the 8004 vertices perfectly, but perhaps if I drop it slightly below this number it will be able to interpolate up correctly. Any other thoughts or suggestions are greatly appreciated as well. Best, Josh From: on behalf of "Seymour, Robert (Research Student)" Reply-To: FieldTrip discussion list Date: Wednesday, April 25, 2018 at 5:48 PM To: "fieldtrip at science.ru.nl" Subject: Re: [FieldTrip] ft_sourceinterpolate question Hi Josh, It seems like you are using the HCP Glasser atlas ('A multi-modal parcellation of human cerebral cortex')? The atlas presented as part of the network analysis tutorial is designed for a cortical mesh with 8004 vertices, rather than the 15002 you are using. I don’t believe ft_sourceinterpolate can currently cope with the surface-based transformation upwards from 8000—> 15000 vertices. To use the HCP atlas you will need to downsample the original 32k atlas in fs_LR space to 15000 space and transform to whichever standard-brain template you are using. This is non-trivial and requires some functions from the HCP project (e.g. wb_command which can be found here: https://www.humanconnectome.org/software/workbench-command). If your mesh is created using Freesurfer you can use this script here: https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh If the mesh is not constructed using Freesurfer it will be tricker & I would recommend contacting the HCP mailing list. Good luck! Robert Seymour (Aston Brain Centre & Department of Cognitive Science, Macquarie University). ________________________________ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ________________________________ ------------------------------------------------------------------------------ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ------------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Apr 26 09:35:39 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 26 Apr 2018 07:35:39 +0000 Subject: [FieldTrip] ft_sourceinterpolate question In-Reply-To: <271913CA-10AE-4E5B-8424-429132D272A7@childrenscolorado.org> References: <271913CA-10AE-4E5B-8424-429132D272A7@childrenscolorado.org> Message-ID: <420D1830-F271-4955-9D48-B9F3E68F809E@donders.ru.nl> The most sensible approach to take here would be to interpolate the atlas onto the low-resolution grid that was used for the sourcereconstruction+connectivity analysis, and then parcellate. Be aware that the functional data should be defined in the same coordinate system as the anatomical data. For the interpolation set the parameter to ‘brick0’, and the interpolation method to ‘nearest’. Good luck, Jan-Mathijs On 26 Apr 2018, at 08:01, Bear, Joshua > wrote: Hi all, It occurs to me that using ft_sourceinterpolate to decrease, rather than increase, the dimensions is not intuitive, and I found that it was actually fairly easy to get the Gorden et al. atlas loaded in as they provide an MNI-registered form of the atlas. So I repeated my steps using the selected atlas and with a smaller headmodel and leadfield resulting in a source file that had to be interpolated in the more anticipated direction. The problem persists, however. I now have connectivity results with the following pertinent values: dim: [18 15 15] pos: [4050×3 double] cohspctrm: [4050×4050 double] dimord: 'pos_pos_freq' My atlas has the following pertinent values: dim: [61 73 61] transform: [4×4 double] brick0: [61×73×61 uint16] brick0label: {1×333 cell} The results of interpolating my connectivity source to the atlas lead to the same peculiar asymmetry in the cohspctrm results: dim: [61 73 61] transform: [4×4 double] inside: [61×73×61 logical] cohspctrm: [271633×4050 double] pos: [271633×3 double] And as the whole point is to then use ft_sourceparcellate, I found that this carries over the asymmetrical results of the interpolation with the following source values after parcellation: freq: 9.9340 label: {1×333 cell} cohspctrm: [333×4050 double] brainordinate: [1×1 struct] cfg: [1×1 struct] As you can see, the first dimension of the cohspctrm results increased from 4050 to 271633 with interpolation and then decreased to 333, the number of parcels in my chosen atlas, exactly as I would have expected. The second dimension, however, did not budge from its initial 4050. The interpolation step is necessary to ensure the source matches the atlas (FT throws an error otherwise). Could this be a bug in ft_sourceinterpolate and ft_sourceparcellate, or is there some crucial step such as converting everything into another format that I am missing? Thanks again and sorry for the serial messages, Josh From: > on behalf of Joshua Bear > Reply-To: FieldTrip discussion list > Date: Wednesday, April 25, 2018 at 8:14 PM To: FieldTrip discussion list > Subject: Re: [FieldTrip] ft_sourceinterpolate question Hi Robert, Thank you so much for the response! My ultimate intention is actually to use the parcellation scheme proposed by Gordon et al. (Cerebral Cortex, Volume 26, Issue 1, 1 January 2016, Pages 288–303, https://doi.org/10.1093/cercor/bhu239) though at this time I was using the atlas provided in the tutorial. The problem I ran into is that I am trying to interpolate my brain’s mesh DOWN from 15002 to 8004 (to match the atlas), not up. As you pointed out, I have had some problems with other high resolution meshes, but in this case ft_sourceinterpolate seemed to work — it just only worked for one of the two dimensions of my connectivity data. That is, it went from a [15002×15002 double] to a [8004×15002 double]. Of course it’s possible the interpolation for that first dimension was incorrect, but what confused me was that it did not interpolate the second dimension. (As I write this, I’m wondering if I should simply try transposing the matrix and running the interpolation again!). I will try, as you suggest, downsampling the mesh externally and trying again. I’m not able to match the 8004 vertices perfectly, but perhaps if I drop it slightly below this number it will be able to interpolate up correctly. Any other thoughts or suggestions are greatly appreciated as well. Best, Josh From: > on behalf of "Seymour, Robert (Research Student)" > Reply-To: FieldTrip discussion list > Date: Wednesday, April 25, 2018 at 5:48 PM To: "fieldtrip at science.ru.nl" > Subject: Re: [FieldTrip] ft_sourceinterpolate question Hi Josh, It seems like you are using the HCP Glasser atlas ('A multi-modal parcellation of human cerebral cortex')? The atlas presented as part of the network analysis tutorial is designed for a cortical mesh with 8004 vertices, rather than the 15002 you are using. I don’t believe ft_sourceinterpolate can currently cope with the surface-based transformation upwards from 8000—> 15000 vertices. To use the HCP atlas you will need to downsample the original 32k atlas in fs_LR space to 15000 space and transform to whichever standard-brain template you are using. This is non-trivial and requires some functions from the HCP project (e.g. wb_command which can be found here: https://www.humanconnectome.org/software/workbench-command). If your mesh is created using Freesurfer you can use this script here: https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh If the mesh is not constructed using Freesurfer it will be tricker & I would recommend contacting the HCP mailing list. Good luck! Robert Seymour (Aston Brain Centre & Department of Cognitive Science, Macquarie University). ________________________________ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ________________________________ ________________________________ CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not an intended recipient, or the person responsible for delivering this message to an intended recipient, you are hereby notified that reading, copying, using or distributing this message is prohibited. If you are not an intended recipient, please contact the sender by reply email and destroy all copies of the original message from your computer system. ________________________________ _______________________________________________ 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 yoniilevy at gmail.com Thu Apr 26 15:39:42 2018 From: yoniilevy at gmail.com (Yoni Levy) Date: Thu, 26 Apr 2018 16:39:42 +0300 Subject: [FieldTrip] Appending acquisition files Message-ID: Hi there, what is the way to append two acquisition files from the same experiment (say, in case I needed to stop recording and restart it during the experiment) ? >From my understanding, ft_appenddata doesnt work on acquisition files. p.s. I am using 4D system with files named "c,rfhp0.1Hz" Thank you, Yoni -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Apr 26 16:23:57 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 26 Apr 2018 14:23:57 +0000 Subject: [FieldTrip] Appending acquisition files In-Reply-To: References: Message-ID: Hi Yoni, In FieldTrip this is impossible. You may need to check the command line tools that come with the system. Jan-Mathijs On 26 Apr 2018, at 15:39, Yoni Levy > wrote: Hi there, what is the way to append two acquisition files from the same experiment (say, in case I needed to stop recording and restart it during the experiment) ? >From my understanding, ft_appenddata doesnt work on acquisition files. p.s. I am using 4D system with files named "c,rfhp0.1Hz" Thank you, Yoni _______________________________________________ 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 johnnguyen.education at gmail.com Fri Apr 27 05:13:16 2018 From: johnnguyen.education at gmail.com (John Nguyen) Date: Thu, 26 Apr 2018 23:13:16 -0400 Subject: [FieldTrip] ft_freqanalysis fourier rpttap to rpt conversion? Message-ID: Hi, I noticed that it's not an option to remove the tapers if the output is "fourier". Is this because the resulting output won't be a true Fourier if the tapers are removed, and is forced as a preventive measure? I was looking to reduce my fourier size by removing the tapers but not the trials, is there a danger to this? Thank you! John Nguyen -------------- next part -------------- An HTML attachment was scrubbed... URL: From dr.ritwik257 at gmail.com Mon Apr 30 03:00:10 2018 From: dr.ritwik257 at gmail.com (Ritwik Das) Date: Sun, 29 Apr 2018 21:00:10 -0400 Subject: [FieldTrip] Introduction and query regarding EEG file Message-ID: Dear all I am Ritwik Das, a faculty at St. George's University, Grenada, W.I. I am presently working with Dr. Thomas Thesen, from NYU, on the EEG analysis of children. The problem I am currently having is the format in which I am getting my EEG recordings. I have data in NEDF format and text documents. I want to ask two questions, 1. Is it possible to convert NEDF file format to EDF format? 2. Is it possible for Fieldtrip to use EEG data in formats other than EDF? Thank you so much for the help. Regards Ritwik Dr Ritwik Das, MBBS Department of Pathology St. George's University Grenada, W.I. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bernhard.spitzer at bccn-berlin.de Mon Apr 30 15:53:09 2018 From: bernhard.spitzer at bccn-berlin.de (Bernhard Spitzer) Date: Mon, 30 Apr 2018 15:53:09 +0200 Subject: [FieldTrip] Postdoc position in cognitive neuroscience at MPIB Berlin Message-ID: <096b6df3-0425-9012-45c5-f10e49160f56@bccn-berlin.de> We are looking for a postdoctoral researcher to work with us on the neural mechanisms of memory and decision making. For details, please see https://www.mpib-berlin.mpg.de/sites/default/files/download/jobs/16-2018_stellenanzeige_arc-ie.pdf or contact me if you have any questions: spitzer at mpib-berlin.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: