From s.bogels at psy.gla.ac.uk Thu Dec 1 10:34:20 2011 From: s.bogels at psy.gla.ac.uk (=?UTF-8?B?U2FyYSBCw7ZnZWxz?=) Date: Thu, 01 Dec 2011 09:34:20 +0000 Subject: [FieldTrip] second-level statistical inference In-Reply-To: <007e01ccaf95$536c0dc0$fa442940$@maris@psych.ru.nl> References: <744936625.46871.1322211858651.JavaMail.root@sculptor.zimbra.ru.nl> <4ECF8144.4010706@psy.gla.ac.uk> <007e01ccaf95$536c0dc0$fa442940$@maris@psych.ru.nl> Message-ID: <4ED74A1C.40701@psy.gla.ac.uk> Hi Eric, I understand that is another option. However, I do not see how to look at an interaction between two variables in this way. Do you have any advice if I want to do that? Thanks, Sara On 30/11/2011 19:21, Eric Maris wrote: > Hi Sara, > > > I'm replying to your initial question (somewhere below in this email). > > Why don't you calculate per-subject averages in the two within-subject > experimental conditions (using timelockgrandaverage with > keepindividual='yes'), and then do your second-level inference on these > averages? See also the Fieldtrip statistics tutorials. > > Best, > > Eric Maris > > >> -----Original Message----- >> From: Sara Bögels [mailto:s.bogels at psy.gla.ac.uk] >> Sent: vrijdag 25 november 2011 12:52 >> To: fieldtrip at donders.ru.nl >> Subject: Re: [FieldTrip] second-level statistical inference >> >> Hi Arjen, >> >> Thank you very much for your answer. That sounds good, but step 2 does >> not work straightforwardly, since matlab gives the error message that it >> cannot find an avg field (which would not be in the structure created by >> ft_timelockstatistics). Just saying cfg.parameter = 'stat' does not >> work. I tried to get around that by inserting an avg field which is the >> same as the stat field for each participant. Matlab also asked for an >> fsample field, which I inserted from an earlier datafile. Then it >> worked. Is it ok to do this? >> >> I did step 3 as well, using the field individual (which you get by >> keepindividuals = 'yes'). In step 4, I should just use cfg.statistic = >> 'depsamplesT', right (because the variables are within subject)? >> >> Thank you! >> Sara >> >> On 25/11/2011 09:04, Stolk, A. wrote: >>> Hi Sara, >>> >>> If I understand correctly, you want to test intra-subject differences >> (between conditions) at the second level? This would require the following >> steps: >>> 1) subject-level statistics, which you have done already >>> >>> 2) grandaverage all these, with keepindividuals=yes. >>> >>> 3) copy the output of the grandaverage (into a dummy variable), and >> replace the fields containing the subject T-values with zeros (for >> timelock >> data this may be the trial fields?) >>> 4) again timelockstatistics, as in step 1, now with the variables >>> following >> step 3. this should give you the resulting statistics of contrasting >> intra- >> subject differences vs. null at the group level. >>> Hope this helps, >>> >>> Arjen >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ----- "Sara Bögels" schreef: >>> >>>> Van: "Sara Bögels" >>>> Aan: fieldtrip at donders.ru.nl >>>> Verzonden: Donderdag 24 november 2011 15:49:17 >>>> Onderwerp: [FieldTrip] second-level statistical inference >>>> >>>> Hi all, >>>> >>>> I have been trying to do second-level statistical inference (as >>>> described in one of the FAQs) on ERFs, but I am not sure whether I am >>>> >>>> doing everything correctly. >>>> >>>> In the first step I calculate the T-values for the difference between >>>> >>>> two conditions (twice), which are between items, with >>>> ft_timelockstatistics. I put the output of all participants in a cell >>>> >>>> (called 'stat1a' and 'stat1b'). (I tried to use >>>> ft_timelockgrandaverage >>>> to combine the subjects together but it needs a field avg). >>>> >>>> Then I use ft_timelockstatistics again but subject level. I first >>>> want >>>> to look at the difference between the two conditions. This difference >>>> is >>>> reflected in the T-values of the first step so I create a dummy which >>>> is >>>> the same as 'stat1' but I replace all the values in the field 'stat' >>>> per >>>> participant with zeros. Then I call (with appropriate cfg >>>> parameters): >>>> >>>> stat2a = ft_timelockstatistics(cfg,stat1a{:},dummy{:}); >>>> stat2b = ft_timelockstatistics(cfg,stat1b{:},dummy{:}); >>>> >>>> To compare the two differences (stat1a and stat1b) and thereby look at >>>> >>>> an interaction, I call: >>>> >>>> stat2a-b = ft_timelockstatistics(cfg,stat1a{:},stat1b{:}); >>>> >>>> I am uncertain whether the dummy works (or is there a way to compare >>>> the >>>> t-values to zero directly?) and whether the stat1a{:} trick works with >>>> >>>> ft_timelockstatistics. >>>> >>>> Thanks in advance for your answer. >>>> >>>> Sara >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From max-philipp.stenner at med.ovgu.de Thu Dec 1 14:22:52 2011 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 01 Dec 2011 13:22:52 +0000 Subject: [FieldTrip] readCTFds Message-ID: Dear fieldtrip users, as a beginner I am encountering a rather fundamental problem even when trying to read the tutorial data (Subject01.ds): ft_read_data reports readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) and Matlab adds index exceeding matrix dimension errors ft_read_hdr reports nTrials = -1 The same happens with my own CTF data. I would be very grateful for any help on this very basic problem thanks! Best Max From jan.schoffelen at donders.ru.nl Thu Dec 1 14:54:08 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 1 Dec 2011 14:54:08 +0100 Subject: [FieldTrip] readCTFds In-Reply-To: References: Message-ID: <9F142CD3-12CB-4184-AF91-3233D42AE3FA@donders.ru.nl> Dear Max, Before we can think along with you, could you please give some more details? Some basic things such as the fieldtrip version you are using, matlab version and operating system? Thanks, Jan-Mathijs On Dec 1, 2011, at 2:22 PM, Stenner, Max-Philipp wrote: > Dear fieldtrip users, > > > > as a beginner I am encountering a rather fundamental problem even when trying to read the tutorial data (Subject01.ds): > > > > ft_read_data reports > > > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > > > and Matlab adds index exceeding matrix dimension errors > > > > ft_read_hdr reports > > > > nTrials = -1 > > > > The same happens with my own CTF data. > > > > I would be very grateful for any help on this very basic problem > > > > thanks! > > Best > > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Heng-RuMay.Tan at glasgow.ac.uk Thu Dec 1 15:52:52 2011 From: Heng-RuMay.Tan at glasgow.ac.uk (May (Heng-Ru May TAN)) Date: Thu, 01 Dec 2011 14:52:52 +0000 Subject: [FieldTrip] Grad and labels Message-ID: <4ED794C4.5070909@glasgow.ac.uk> Hello I would like to plot the grad.pnt for a few channels but realised that there are fewer labels (271) than grad.pnt rows (276) Presumably some of the channels have more than 1 grad.pnt > D = > > hdr: [1x1 struct] > label: {248x1 cell} > time: {1x9 cell} > trial: {1x9 cell} > fsample: 1.0172e+003 > grad: [1x1 struct] > cfg: [1x1 struct] > > >> D.grad > > ans = > > pnt: [276x3 double] > ori: [276x3 double] > tra: [271x276 double] > label: {271x1 cell} > unit: 'm' > balance: [1x1 struct] But how do the grad labels correspond to the grad.pnt with the numbers don't match? Can someone help? Thanks! May The above was derived using the following: > cfg = []; > > cfg.subjNUM = subjNUM; > cfg.irun=irun; > > cfg.headerfile = 'c,rfDC'; > cfg.datafile = cfg.headerfile; > cfg.trialfun ='trialfun_general'; > cfg.channel={'MEG'}; > cfg.continuous='yes'; > cfg.trialdef.eventtype = '?'; > > cfg=ft_definetrial(cfg); %--->cfg.events > cfg.header = ft_read_header(cfg.headerfile); > % just to be sure > cfg = rmfield(cfg,'trl'); > > > %% specify 'trial' information for 'epoching' > cfg.detrend='yes'; %no other filtering at the moment. > > cfg.trialdef.stimulusSETnum = [iset]; > cfg.trialdef.eventtype = 'PostStimTriggerIdx'; %% > cfg.trialdef.eventinfo = 'PostStimSampleTime'; > cfg.trialdef.eventvalue = [iset].*2 + 128; > > cfg.trialdef.response_time=[1]; % to include RXNtime in the > definetrial procedure... > cfg.trialdef.CorrectWrong = [1]; %only correct ones > > cfg.trialdef.prestim = 2; % duration in secs before '0' > cfg.trialdef.poststim = 2; % duration in secs after '0' > > cfg.trialfun ='trialfun_readEventgetRespInfo'; %%CHANGE 3rd > Column!!! > > cfg=ft_definetrial(cfg); > % cfg.trl ==//// [begsam endsam off runN stimN ] > > D=ft_preprocessing(cfg); From Heng-RuMay.Tan at glasgow.ac.uk Thu Dec 1 16:08:56 2011 From: Heng-RuMay.Tan at glasgow.ac.uk (May (Heng-Ru May TAN)) Date: Thu, 01 Dec 2011 15:08:56 +0000 Subject: [FieldTrip] change in ft_definetrial event output? Message-ID: <4ED79888.4020907@glasgow.ac.uk> Hi again, Another question -- possibly me missing out on all the updates! Was wondering if there has been changes to how events are output in newer versions of FT because previously using fieldtrip-20100419 > cfg = > > subjNUM: 1 > irun: 1 > headerfile: 'c,rfDC' > datafile: 'c,rfDC' > trialfun: 'trialfun_general' > channel: {'MEG'} > continuous: 'yes' > trialdef: [1x1 struct] > trackconfig: 'off' > checkconfig: 'loose' > checksize: 100000 > _ event: [850x1 struct] > _ trl: [] > version: [1x1 struct] > header: [1x1 struct] Now the newer versions only give _event: [849x1 struct]_ Is the 'trial' heading in the previous first row removed by default now? Thanks, May -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Thu Dec 1 16:15:56 2011 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 01 Dec 2011 15:15:56 +0000 Subject: [FieldTrip] readCTFds In-Reply-To: References: Message-ID: Dear all, in addition to my email sent earlier today (see below) here's some information on the OS, fieldtrip and MatLab versions: Windows7 Fieldtrip version 20111130 (20111129 caused the same error) Matlab R2011a Whereas readCTFds reports 'Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file)' a direct call to the dir command of the .meg4 file returns ' bytes: 179071208' for the number of trials ft_read_header('Subject01.ds') returns ' nTrials: -1' Thanks, best Max ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]" im Auftrag von "Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de] Gesendet: Donnerstag, 1. Dezember 2011 14:22 Bis: fieldtrip at donders.ru.nl Betreff: [FieldTrip] readCTFds Dear fieldtrip users, as a beginner I am encountering a rather fundamental problem even when trying to read the tutorial data (Subject01.ds): ft_read_data reports readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) and Matlab adds index exceeding matrix dimension errors ft_read_hdr reports nTrials = -1 The same happens with my own CTF data. I would be very grateful for any help on this very basic problem thanks! Best Max _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From b.reuderink at donders.ru.nl Thu Dec 1 17:58:45 2011 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Thu, 1 Dec 2011 17:58:45 +0100 Subject: [FieldTrip] Error in Java buffer reader and fakebiosemiclient.cc In-Reply-To: References: Message-ID: Dear Jacob, I have created bug 1209 (http://bugzilla.fcdonders.nl/show_bug.cgi?id=1209) for your issue. Could you provide some additional details to reproduce the bug on that page? And, could you (perhaps privately --- bypassing the list) explain how you are planning to use the FieldTrip buffer? We might find a workaround for you problem. Best regards, Boris On Tue, Nov 29, 2011 at 12:13 AM, Jacob Martin wrote: > Ok, seems like it has to do with exceeding the maximum number of > samples.  Not sure what to do here though yet: > > http://code.google.com/p/fieldtrip/source/browse/trunk/realtime/buffer/src/dmarequest.c?r=1218#413 > > On Mon, Nov 28, 2011 at 6:10 PM, Jacob Martin wrote: >> Hi, >> >> After letting the server run for a while (see below size at 512hz), I >> get an "err3": >> >> data: >> size = 176960 x 34 >> dmarequest: err3 >> Exception in thread "main" java.io.IOException: Error returned from >> FieldTrip buffer server. >>        at nl.fcdonders.fieldtrip.BufferClient.readResponse(BufferClient.java:646) >>        at nl.fcdonders.fieldtrip.BufferClient.getEvents(BufferClient.java:386) >>        at testclient.main(testclient.java:71) >> >> >> >> Any ideas? >> >> Thanks, >> Jake >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Fri Dec 2 10:03:40 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 02 Dec 2011 10:03:40 +0100 Subject: [FieldTrip] readCTFds In-Reply-To: References: Message-ID: <4ED8946C.2050209@donders.ru.nl> Hi Max, I usually encounter similar problems when CTF data is not fully saved, i.e. aborted the saving and forgot to click on 'OK' in the next dialog or something else went wrong. Maybe ther went something wrong when downloading the data? Since it says 0 bytes in dir, it could maybe also be that you something more basic wrong. Just to be sure, you could check whether Subject01.ds is a folder and whether it contains all the relevant files, and none of these have size 0. Best, Jörn On 12/1/2011 4:15 PM, Stenner, Max-Philipp wrote: > Dear all, > > in addition to my email sent earlier today (see below) here's some information on the OS, fieldtrip and MatLab versions: > > Windows7 > Fieldtrip version 20111130 (20111129 caused the same error) > Matlab R2011a > > Whereas readCTFds reports > > 'Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file)' > > a direct call to the dir command of the .meg4 file returns > > ' bytes: 179071208' > > for the number of trials ft_read_header('Subject01.ds') returns > > ' nTrials: -1' > > Thanks, > best > Max > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]" im Auftrag von"Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de] > Gesendet: Donnerstag, 1. Dezember 2011 14:22 > Bis: fieldtrip at donders.ru.nl > Betreff: [FieldTrip] readCTFds > > Dear fieldtrip users, > > > > as a beginner I am encountering a rather fundamental problem even when trying to read the tutorial data (Subject01.ds): > > > > ft_read_data reports > > > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > > > and Matlab adds index exceeding matrix dimension errors > > > > ft_read_hdr reports > > > > nTrials = -1 > > > > The same happens with my own CTF data. > > > > I would be very grateful for any help on this very basic problem > > > > thanks! > > Best > > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From sonjasuntrup at uni-muenster.de Fri Dec 2 12:16:20 2011 From: sonjasuntrup at uni-muenster.de (Sonja Suntrup) Date: Fri, 02 Dec 2011 12:16:20 +0100 (CET) Subject: [FieldTrip] source statistics, group level Message-ID: Dear fieldtrip users, I would like to do sourcestatistics on a group level with meg data. I have a pre and post intervention measurement for each of my 21 subjects (within-subjects design). After source reconstruction using an LCMV beamformer and volume normalization I calculated the sourcegrandaverage for the pre and post condition with the parameter cfg.keepindividual = 'yes'. However, when I use the grandaverage results in ft_sourcestatistics in the configuration shown below and plot the result I just get a blank anatomical mri. Do I have to set any additional parameters or do I make a general mistake? Whould you recommend to use a cluster-based permutation test comparable to ft_timelockstatistics and would I have to set the same parameters in ft_sourcestatistics then? cfg=[]; cfg.dim = grandAVGsourcePre.dim; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.parameter = 'avg.pow'; cfg.correctm = 'cluster'; cfg.numrandomization = 100; cfg.alpha = 0.05; cfg.tail = 0; nsubj=length(sourcePre.trial); cfg.design(1,:) = [1:nsubj 1:nsubj]; cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2]; cfg.uvar = 1; cfg.ivar = 2; stat = ft_sourcestatistics(cfg, grandAVGsourcePre, grandAVGsourcePost); Your help is greatly appreciated! Best, Sonja -- Dr. med. Sonja Suntrup Institute for Biomagnetism and Biosignalanalysis University of Muenster Malmedyweg 15 48149 Münster, Germany From max-philipp.stenner at med.ovgu.de Fri Dec 2 12:28:38 2011 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Fri, 02 Dec 2011 11:28:38 +0000 Subject: [FieldTrip] readCTFds In-Reply-To: <4ED8946C.2050209@donders.ru.nl> References: <4ED8946C.2050209@donders.ru.nl> Message-ID: Hi Joern, thank you very much for your reply, the (rather trivial) problem turned out to be indeed that the path wasn't added correctly, best Max ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]" im Auftrag von ""Jörn M. Horschig" [jm.horschig at donders.ru.nl] Gesendet: Freitag, 2. Dezember 2011 10:03 Bis: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] readCTFds Hi Max, I usually encounter similar problems when CTF data is not fully saved, i.e. aborted the saving and forgot to click on 'OK' in the next dialog or something else went wrong. Maybe ther went something wrong when downloading the data? Since it says 0 bytes in dir, it could maybe also be that you something more basic wrong. Just to be sure, you could check whether Subject01.ds is a folder and whether it contains all the relevant files, and none of these have size 0. Best, Jörn On 12/1/2011 4:15 PM, Stenner, Max-Philipp wrote: > Dear all, > > in addition to my email sent earlier today (see below) here's some information on the OS, fieldtrip and MatLab versions: > > Windows7 > Fieldtrip version 20111130 (20111129 caused the same error) > Matlab R2011a > > Whereas readCTFds reports > > 'Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file)' > > a direct call to the dir command of the .meg4 file returns > > ' bytes: 179071208' > > for the number of trials ft_read_header('Subject01.ds') returns > > ' nTrials: -1' > > Thanks, > best > Max > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]" im Auftrag von"Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de] > Gesendet: Donnerstag, 1. Dezember 2011 14:22 > Bis: fieldtrip at donders.ru.nl > Betreff: [FieldTrip] readCTFds > > Dear fieldtrip users, > > > > as a beginner I am encountering a rather fundamental problem even when trying to read the tutorial data (Subject01.ds): > > > > ft_read_data reports > > > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > > > and Matlab adds index exceeding matrix dimension errors > > > > ft_read_hdr reports > > > > nTrials = -1 > > > > The same happens with my own CTF data. > > > > I would be very grateful for any help on this very basic problem > > > > thanks! > > Best > > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Jan.Hirschmann at med.uni-duesseldorf.de Fri Dec 2 18:20:43 2011 From: Jan.Hirschmann at med.uni-duesseldorf.de (Jan.Hirschmann at med.uni-duesseldorf.de) Date: Fri, 2 Dec 2011 18:20:43 +0100 Subject: [FieldTrip] coherence normalization Message-ID: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> Hi community, Regarding this thread on suppressing the reference dipole from 2004, what is the current status? Has anybody found and implemented a recommendable way to project out activity from unwanted dipoles? Thank you for any comments/opinions! Best, Jan Hirschmann On 21 Oct 2004, at 17:23, Tom Holroyd wrote: > When running a coherence volume using a reference dipole, one > naturally expects the coherence will be high around the reference > dipole. > > This effect tends to dominate the images. > > Is there a way to normalize the coherence volume to eliminate > this effect? Perhaps by dividing by the coherence in a "control" > state? Hi Tom, The dominating effect of the refdip is indeed very problematic. I just happened to have discussed this with Joachim Gross, and I have included our email exchange below. Please first read that ... Basically I agree with Joachim, and I don't trust the supdip that is implemented in FieldTrip's sourceanalysis function. Better test and map the significance of the difference in coherence between two conditions using randomization of the trials before the coherence is beamed (that is implemented in sourceanalysis + sourcestatistics). Robert -------------------------------------------------------------------- my question to Joachim was ---------------------------------------------------------------------- Begin forwarded message: > From: Robert Oostenveld > > Date: 1 October 2004 10:26:02 GMT+02:00 > To: Joachim Gross > > Subject: dipole suppression > > Hi Joachim, > > What I always still had to ask you is how you do supression of dipoles > in DICS, especially in the case of coherence imaging. I have thought > of two ways of projecting them out: > > 1) compute supdip leadfield and its projection on the COV/CSD matrix, > then project it out of the COV/CSD matrix (which looses 2 or 3 from > its rank). > > 2) compute supdip leadfield and add it to the leadfield of the dipole > with which is scanned (scandip). Subsequently compute the source > COV/CSD on those 6 leadfield components and select the 3x3 submatrix > that corresponds with the scandip to continue the computations with. > > Both methods don't really gave me very convincing results. A third > approach would be to add the supdip leadfield to the (identity) noise > matrix and project it through the filters. Then nai=pow/noise is > corrected for the presence of the supdip, but that does not result in > a supressed source coherence distribution. What is your idea or > approach for this? > > best regards > Robert > ---------------------------------------------------------------------- and his answer (Joachim, I hope you don't mind me sharing this on the list) ---------------------------------------------------------------------- Begin forwarded message: > From: Joachim Gross > > Date: 14 October 2004 17:20:45 GMT+02:00 > To: "robert.oostenveld at fcdonders.kun.nl " > > > Subject: dipole suppression > > Hi Robert, > > sorry for the delay. > > The dipole suppression is indeed a complex issue. > We first implemented it because it facilitates visualization and the > exact identification of the first > strongest local maxima. > Nevertheless, it is quite dangerous because the map is (locally) > distorted in a non-trivial way. > We are now trying to move away from suppressing the sources. I think > it would be better to identify the > significant local maxima (significance based on > randomization/permutation). > But what we are doing at the moment is your approach 3. > So we add the supdip leadfield to the noise covariance matrix and look > at pow/noise. > > For coherence we are basically doing the same thing. > So we divide the coherence map (or actually the map of cross spectral > densities) by a noise map > that peaks at the locations of the "unwanted" dipoles. > With this procedure we loose absolute coherence values. > This is not so important for us since we get the absolute values from > the coherence and partial coherence spectra > that are computed afterwards. > It works surprisingly well but should be used with care. > > A better approach would be to map partial coherence (with the unwanted > dipoles removed). But we have not implemented > this so far. > > Again, I think it is better to have regions of interest identified by > their significance. > > Joachim ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. Jan Hirschmann MSc. Neuroscience Insititute of Clinical Neuroscience and Medical Psychology Heinrich Heine University Duesseldorf Universitaetsstr. 1 40225 Duesseldorf Tel: 0049 - (0)211 - 81 - 18415 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at kurage.nimh.nih.gov Fri Dec 2 18:52:07 2011 From: tomh at kurage.nimh.nih.gov (Tom Holroyd (NIH/NIMH) [E]) Date: Fri, 02 Dec 2011 12:52:07 -0500 Subject: [FieldTrip] coherence normalization In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> Message-ID: <4ED91047.6050107@kurage.nimh.nih.gov> The solution I have adopted is to always look at coherence contrasts. Make two volumes using the same reference dipole in two different conditions, then subtract the volumes. The self-coherence of the reference will disappear. Mostly. Then use stats, like a U-test. Jan.Hirschmann at med.uni-duesseldorf.de wrote: > Hi community, > > > > Regarding this thread on suppressing the reference dipole from 2004, what is the current status? Has anybody found and implemented a recommendable way to project out activity from unwanted dipoles? Thank you for any comments/opinions! > > > > Best, > > Jan Hirschmann > > > > > > > > On 21 Oct 2004, at 17:23, Tom Holroyd wrote: > > > >>/ When running a coherence volume using a reference dipole, one/ > >>/ naturally expects the coherence will be high around the reference/ > >>/ dipole./ > >>/ / > >>/ This effect tends to dominate the images./ > >>/ / > >>/ Is there a way to normalize the coherence volume to eliminate/ > >>/ this effect? Perhaps by dividing by the coherence in a "control"/ > >>/ state?/ > > > > Hi Tom, > > > > The dominating effect of the refdip is indeed very problematic. I just > > happened to have discussed this with Joachim Gross, and I have included > > our email exchange below. Please first read that ... > > > > Basically I agree with Joachim, and I don't trust the supdip that is > > implemented in FieldTrip's sourceanalysis function. Better test and map > > the significance of the difference in coherence between two conditions > > using randomization of the trials before the coherence is beamed (that > > is implemented in sourceanalysis + sourcestatistics). > > > > Robert > > > > -------------------------------------------------------------------- > > my question to Joachim was > > ---------------------------------------------------------------------- > > > > Begin forwarded message: > > > >>/ From: Robert Oostenveld //>/ > >>/ Date: 1 October 2004 10:26:02 GMT+02:00/ > >>/ To: Joachim Gross //>/ > >>/ Subject: dipole suppression/ > >>/ / > >>/ Hi Joachim,/ > >>/ / > >>/ What I always still had to ask you is how you do supression of dipoles/ > >>/ in DICS, especially in the case of coherence imaging. I have thought/ > >>/ of two ways of projecting them out:/ > >>/ / > >>/ 1) compute supdip leadfield and its projection on the COV/CSD matrix,/ > >>/ then project it out of the COV/CSD matrix (which looses 2 or 3 from/ > >>/ its rank)./ > >>/ / > >>/ 2) compute supdip leadfield and add it to the leadfield of the dipole/ > >>/ with which is scanned (scandip). Subsequently compute the source/ > >>/ COV/CSD on those 6 leadfield components and select the 3x3 submatrix/ > >>/ that corresponds with the scandip to continue the computations with./ > >>/ / > >>/ Both methods don't really gave me very convincing results. A third/ > >>/ approach would be to add the supdip leadfield to the (identity) noise/ > >>/ matrix and project it through the filters. Then nai=pow/noise is/ > >>/ corrected for the presence of the supdip, but that does not result in/ > >>/ a supressed source coherence distribution. What is your idea or/ > >>/ approach for this?/ > >>/ / > >>/ best regards/ > >>/ Robert/ > >>/ / > > > > ---------------------------------------------------------------------- > > and his answer (Joachim, I hope you don't mind me sharing this on the > > list) > > ---------------------------------------------------------------------- > > > > Begin forwarded message: > > > >>/ From: Joachim Gross //>/ > >>/ Date: 14 October 2004 17:20:45 GMT+02:00/ > >>/ To: "//robert.oostenveld at fcdonders.kun.nl //"/ > >>/ //>/ > >>/ Subject: dipole suppression/ > >>/ / > >>/ Hi Robert,/ > >>/ / > >>/ sorry for the delay./ > >>/ / > >>/ The dipole suppression is indeed a complex issue./ > >>/ We first implemented it because it facilitates visualization and the/ > >>/ exact identification of the first/ > >>/ strongest local maxima./ > >>/ Nevertheless, it is quite dangerous because the map is (locally)/ > >>/ distorted in a non-trivial way./ > >>/ We are now trying to move away from suppressing the sources. I think/ > >>/ it would be better to identify the/ > >>/ significant local maxima (significance based on/ > >>/ randomization/permutation)./ > >>/ But what we are doing at the moment is your approach 3./ > >>/ So we add the supdip leadfield to the noise covariance matrix and look/ > >>/ at pow/noise./ > >>/ / > >>/ For coherence we are basically doing the same thing./ > >>/ So we divide the coherence map (or actually the map of cross spectral/ > >>/ densities) by a noise map/ > >>/ that peaks at the locations of the "unwanted" dipoles./ > >>/ With this procedure we loose absolute coherence values./ > >>/ This is not so important for us since we get the absolute values from/ > >>/ the coherence and partial coherence spectra/ > >>/ that are computed afterwards./ > >>/ It works surprisingly well but should be used with care./ > >>/ / > >>/ A better approach would be to map partial coherence (with the unwanted/ > >>/ dipoles removed). But we have not implemented/ > >>/ this so far./ > >>/ / > >>/ Again, I think it is better to have regions of interest identified by/ > >>/ their significance./ > >>/ / > >>/ Joachim/ > > > > > > ---------------------------------------------------------------------- > > Robert Oostenveld, PhD > > Center for Sensory-Motor Interaction (SMI) > > Aalborg University, Denmark > > > > and > > > > F.C. Donders Centre for Cognitive Neuroimaging > > University Nijmegen > > P.O. Box 9101 > > NL-6500 AH Nijmegen > > The Netherlands > > > > Tel: +31 (0)24 3619695 > > Fax: +31 (0)24 3610989 > > ---------------------------------------------------------------------- > > N.B. Starting from 1 September 2004, the University of Nijmegen has > > changed its name to Radboud University Nijmegen. All web- and > > email-addresses ending in ".kun.nl" should therefore be changed into > > ".ru.nl". Please update your address book and links. > > > > > > Jan Hirschmann > > MSc. Neuroscience > > Insititute of Clinical Neuroscience and Medical Psychology > > Heinrich Heine University Duesseldorf > > Universitaetsstr. 1 > 40225 Duesseldorf > > Tel: 0049 - (0)211 - 81 - 18415 > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- "The test of a first-rate intelligence is the ability to hold two opposed ideas in the mind at the same time, and still retain the ability to function." — F. Scott Fitzgerald From jan.schoffelen at donders.ru.nl Fri Dec 2 19:49:33 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 2 Dec 2011 19:49:33 +0100 Subject: [FieldTrip] coherence normalization In-Reply-To: <4ED91047.6050107@kurage.nimh.nih.gov> References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> <4ED91047.6050107@kurage.nimh.nih.gov> Message-ID: <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> Hi Jan, Tom and the rest, I agree with Tom, but would like to strongly emphasize that differences in power across conditions more often than not will affect the coherence landscape in a non-trivial way. This does not only count for power changes in the reference dipole, but also for changes in power for third party dipoles (i.e. any potential other source). Therefore the interpretation of the subtracted coherence volumes should be done with care. BW, JM On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote: > The solution I have adopted is to always look at coherence contrasts. Make two volumes using the same reference dipole in two different conditions, then subtract the volumes. The self-coherence of the reference will disappear. Mostly. Then use stats, like a U-test. > > Jan.Hirschmann at med.uni-duesseldorf.de wrote: >> Hi community, >> Regarding this thread on suppressing the reference dipole from 2004, what is the current status? Has anybody found and implemented a recommendable way to project out activity from unwanted dipoles? Thank you for any comments/opinions! >> Best, >> Jan Hirschmann >> On 21 Oct 2004, at 17:23, Tom Holroyd wrote: >> >>> / When running a coherence volume using a reference dipole, one/ >>> / naturally expects the coherence will be high around the reference/ >>> / dipole./ >>> / / >>> / This effect tends to dominate the images./ >>> / / >>> / Is there a way to normalize the coherence volume to eliminate/ >>> / this effect? Perhaps by dividing by the coherence in a "control"/ >>> / state?/ >> Hi Tom, >> The dominating effect of the refdip is indeed very problematic. I just >> happened to have discussed this with Joachim Gross, and I have included >> our email exchange below. Please first read that ... >> Basically I agree with Joachim, and I don't trust the supdip that is >> implemented in FieldTrip's sourceanalysis function. Better test and map >> the significance of the difference in coherence between two conditions >> using randomization of the trials before the coherence is beamed (that >> is implemented in sourceanalysis + sourcestatistics). >> Robert >> -------------------------------------------------------------------- >> my question to Joachim was >> ---------------------------------------------------------------------- >> Begin forwarded message: >> >>> / From: Robert Oostenveld //>/ >>> / Date: 1 October 2004 10:26:02 GMT+02:00/ >>> / To: Joachim Gross //>/ >>> / Subject: dipole suppression/ >>> / / >>> / Hi Joachim,/ >>> / / >>> / What I always still had to ask you is how you do supression of dipoles/ >>> / in DICS, especially in the case of coherence imaging. I have thought/ >>> / of two ways of projecting them out:/ >>> / / >>> / 1) compute supdip leadfield and its projection on the COV/CSD matrix,/ >>> / then project it out of the COV/CSD matrix (which looses 2 or 3 from/ >>> / its rank)./ >>> / / >>> / 2) compute supdip leadfield and add it to the leadfield of the dipole/ >>> / with which is scanned (scandip). Subsequently compute the source/ >>> / COV/CSD on those 6 leadfield components and select the 3x3 submatrix/ >>> / that corresponds with the scandip to continue the computations with./ >>> / / >>> / Both methods don't really gave me very convincing results. A third/ >>> / approach would be to add the supdip leadfield to the (identity) noise/ >>> / matrix and project it through the filters. Then nai=pow/noise is/ >>> / corrected for the presence of the supdip, but that does not result in/ >>> / a supressed source coherence distribution. What is your idea or/ >>> / approach for this?/ >>> / / >>> / best regards/ >>> / Robert/ >>> / / >> ---------------------------------------------------------------------- >> and his answer (Joachim, I hope you don't mind me sharing this on the >> list) >> ---------------------------------------------------------------------- >> Begin forwarded message: >> >>> / From: Joachim Gross //>/ >>> / Date: 14 October 2004 17:20:45 GMT+02:00/ >>> / To: "//robert.oostenveld at fcdonders.kun.nl //"/ >>> / //>/ >>> / Subject: dipole suppression/ >>> / / >>> / Hi Robert,/ >>> / / >>> / sorry for the delay./ >>> / / >>> / The dipole suppression is indeed a complex issue./ >>> / We first implemented it because it facilitates visualization and the/ >>> / exact identification of the first/ >>> / strongest local maxima./ >>> / Nevertheless, it is quite dangerous because the map is (locally)/ >>> / distorted in a non-trivial way./ >>> / We are now trying to move away from suppressing the sources. I think/ >>> / it would be better to identify the/ >>> / significant local maxima (significance based on/ >>> / randomization/permutation)./ >>> / But what we are doing at the moment is your approach 3./ >>> / So we add the supdip leadfield to the noise covariance matrix and look/ >>> / at pow/noise./ >>> / / >>> / For coherence we are basically doing the same thing./ >>> / So we divide the coherence map (or actually the map of cross spectral/ >>> / densities) by a noise map/ >>> / that peaks at the locations of the "unwanted" dipoles./ >>> / With this procedure we loose absolute coherence values./ >>> / This is not so important for us since we get the absolute values from/ >>> / the coherence and partial coherence spectra/ >>> / that are computed afterwards./ >>> / It works surprisingly well but should be used with care./ >>> / / >>> / A better approach would be to map partial coherence (with the unwanted/ >>> / dipoles removed). But we have not implemented/ >>> / this so far./ >>> / / >>> / Again, I think it is better to have regions of interest identified by/ >>> / their significance./ >>> / / >>> / Joachim/ >> ---------------------------------------------------------------------- >> Robert Oostenveld, PhD >> Center for Sensory-Motor Interaction (SMI) >> Aalborg University, Denmark >> and >> F.C. Donders Centre for Cognitive Neuroimaging >> University Nijmegen >> P.O. Box 9101 >> NL-6500 AH Nijmegen >> The Netherlands >> Tel: +31 (0)24 3619695 >> Fax: +31 (0)24 3610989 >> ---------------------------------------------------------------------- >> N.B. Starting from 1 September 2004, the University of Nijmegen has >> changed its name to Radboud University Nijmegen. All web- and >> email-addresses ending in ".kun.nl" should therefore be changed into >> ".ru.nl". Please update your address book and links. >> Jan Hirschmann >> MSc. Neuroscience >> Insititute of Clinical Neuroscience and Medical Psychology >> Heinrich Heine University Duesseldorf >> Universitaetsstr. 1 >> 40225 Duesseldorf >> Tel: 0049 - (0)211 - 81 - 18415 >> ------------------------------------------------------------------------ >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- > "The test of a first-rate intelligence is the ability to hold two > opposed ideas in the mind at the same time, and still retain the > ability to function." — F. Scott Fitzgerald > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tolgacan1 at yahoo.com Sun Dec 4 15:00:40 2011 From: tolgacan1 at yahoo.com (=?utf-8?B?VG9sZ2Egw5Z6a3VydA==?=) Date: Sun, 4 Dec 2011 06:00:40 -0800 (PST) Subject: [FieldTrip] coherence normalization In-Reply-To: <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> <4ED91047.6050107@kurage.nimh.nih.gov> <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> Message-ID: <1323007240.37048.YahooMailNeo@web111505.mail.gq1.yahoo.com> Regarding the discussion here, I've gotten onto a recent paper (Sekihara et al., 2011) talking about "imaginary coherence" to prevent the seed region effects.  Even though imaginary coherence does not contain total connectivity information, it might at least be used to select the coherent regions that you want to project on your brain image and ignore the rest. Tolga ________________________________ From: jan-mathijs schoffelen To: Email discussion list for the FieldTrip project Sent: Friday, December 2, 2011 8:49 PM Subject: Re: [FieldTrip] coherence normalization Hi Jan, Tom and the rest, I agree with Tom, but would like to strongly emphasize that differences in power across conditions more often than not will affect the coherence landscape in a non-trivial way. This does not only count for power changes in the reference dipole, but also for changes in power for third party dipoles (i.e. any potential other source). Therefore the interpretation of the subtracted  coherence volumes should be done with care. BW, JM On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote: The solution I have adopted is to always look at coherence contrasts. Make two volumes using the same reference dipole in two different conditions, then subtract the volumes. The self-coherence of the reference will disappear. Mostly. Then use stats, like a U-test. > >Jan.Hirschmann at med.uni-duesseldorf.de wrote: > >Hi community, >> >Regarding this thread on suppressing the reference dipole from 2004, what is the current status? Has anybody found and implemented a recommendable way to project out activity from unwanted dipoles? Thank you for any comments/opinions! >> >Best, >> >Jan Hirschmann >> >  On 21 Oct 2004, at 17:23, Tom Holroyd wrote: >> > >> >/ When running a coherence volume using a reference dipole, one/ >>> >/ naturally expects the coherence will be high around the reference/ >>> >/ dipole./ >>> >/ / >>> >/ This effect tends to dominate the images./ >>> >/ / >>> >/ Is there a way to normalize the coherence volume to eliminate/ >>> >/ this effect?  Perhaps by dividing by the coherence in a "control"/ >>> >/ state?/ >>> >Hi Tom, >> >The dominating effect of the refdip is indeed very problematic. I just >> >happened to have discussed this with Joachim Gross, and I have included >> >our email exchange below. Please first read that ... >> >Basically I agree with Joachim, and I don't trust the supdip that is >> >implemented in FieldTrip's sourceanalysis function. Better test and map >> >the significance of the difference in coherence between two conditions >> >using randomization of the trials before the coherence is beamed (that >> >is implemented in sourceanalysis + sourcestatistics). >> >Robert >> >-------------------------------------------------------------------- >> >my question to Joachim was >> >---------------------------------------------------------------------- >> >Begin forwarded message: >> > >> >/ From: Robert Oostenveld //>/ >>> >/ Date: 1 October 2004 10:26:02 GMT+02:00/ >>> >/ To: Joachim Gross //>/ >>> >/ Subject: dipole suppression/ >>> >/ / >>> >/ Hi Joachim,/ >>> >/ / >>> >/ What I always still had to ask you is how you do supression of dipoles/ >>> >/ in DICS, especially in the case of coherence imaging. I have thought/ >>> >/ of two ways of projecting them out:/ >>> >/ / >>> >/ 1) compute supdip leadfield and its projection on the COV/CSD matrix,/ >>> >/ then project it out of the COV/CSD matrix (which looses 2 or 3 from/ >>> >/ its rank)./ >>> >/ / >>> >/ 2) compute supdip leadfield and add it to the leadfield of the dipole/ >>> >/ with which is scanned (scandip). Subsequently compute the source/ >>> >/ COV/CSD on those 6 leadfield components and select the 3x3 submatrix/ >>> >/ that corresponds with the scandip to continue the computations with./ >>> >/ / >>> >/ Both methods don't really gave me very convincing results. A third/ >>> >/ approach would be to add the supdip leadfield to the (identity) noise/ >>> >/ matrix and project it through the filters. Then nai=pow/noise is/ >>> >/ corrected for the presence of the supdip, but that does not result in/ >>> >/ a supressed source coherence distribution. What is your idea or/ >>> >/ approach for this?/ >>> >/ / >>> >/ best regards/ >>> >/ Robert/ >>> >/ / >>> >---------------------------------------------------------------------- >> >and his answer (Joachim, I hope you don't mind me sharing this on the >> >list) >> >---------------------------------------------------------------------- >> >Begin forwarded message: >> > >> >/ From: Joachim Gross //>/ >>> >/ Date: 14 October 2004 17:20:45 GMT+02:00/ >>> >/ To: "//robert.oostenveld at fcdonders.kun.nl //"/ >>> >/ //>/ >>> >/ Subject: dipole suppression/ >>> >/ / >>> >/ Hi Robert,/ >>> >/ / >>> >/ sorry for the delay./ >>> >/ / >>> >/ The dipole suppression is indeed a complex issue./ >>> >/ We first implemented it because it facilitates visualization and the/ >>> >/ exact identification of the first/ >>> >/ strongest local maxima./ >>> >/ Nevertheless, it is quite dangerous because the map is (locally)/ >>> >/ distorted in a non-trivial way./ >>> >/ We are now trying to move away from suppressing the sources. I think/ >>> >/ it would be better to identify the/ >>> >/ significant local maxima (significance based on/ >>> >/ randomization/permutation)./ >>> >/ But what we are doing at the moment is your approach 3./ >>> >/ So we add the supdip leadfield to the noise covariance matrix and look/ >>> >/ at pow/noise./ >>> >/ / >>> >/ For coherence we are basically doing the same thing./ >>> >/ So we divide the coherence map (or actually the map of cross spectral/ >>> >/ densities) by a noise map/ >>> >/ that peaks at the locations of the "unwanted" dipoles./ >>> >/ With this procedure we loose absolute coherence values./ >>> >/ This is not so important for us since we get the absolute values from/ >>> >/ the coherence and partial coherence spectra/ >>> >/ that are computed afterwards./ >>> >/ It works surprisingly well but should be used with care./ >>> >/ / >>> >/ A better approach would be to map partial coherence (with the unwanted/ >>> >/ dipoles removed). But we have not implemented/ >>> >/ this so far./ >>> >/ / >>> >/ Again, I think it is better to have regions of interest identified by/ >>> >/ their significance./ >>> >/ / >>> >/ Joachim/ >>> > ---------------------------------------------------------------------- >> >Robert Oostenveld, PhD >> >Center for Sensory-Motor Interaction (SMI) >> >Aalborg University, Denmark >> >and >> >F.C. Donders Centre for Cognitive Neuroimaging >> >University Nijmegen >> >P.O. Box 9101 >> >NL-6500 AH Nijmegen >> >The Netherlands >> >Tel: +31 (0)24 3619695 >> >Fax: +31 (0)24 3610989 >> >---------------------------------------------------------------------- >> >N.B. Starting from 1 September 2004, the University of Nijmegen has >> >changed its name to Radboud University Nijmegen. All web- and >> >email-addresses ending in ".kun.nl" should therefore be changed into >> >".ru.nl". Please update your address book and links. >> > Jan Hirschmann >> >MSc. Neuroscience >> >Insititute of Clinical Neuroscience and Medical Psychology >> >Heinrich Heine University Duesseldorf >> >Universitaetsstr.  1 >> >40225  Duesseldorf >> >Tel: 0049 - (0)211 - 81 - 18415 >> >------------------------------------------------------------------------ >> >_______________________________________________ >> >fieldtrip mailing list >> >fieldtrip at donders.ru.nl >> >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >-- >"The test of a first-rate intelligence is the ability to hold two >opposed ideas in the mind at the same time, and still retain the >ability to function." — F. Scott Fitzgerald >_______________________________________________ >fieldtrip mailing list >fieldtrip at donders.ru.nl >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > Jan-Mathijs Schoffelen, MD PhD  Donders Institute for Brain, Cognition and Behaviour,  Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From nkremers at uni-bonn.de Mon Dec 5 13:58:58 2011 From: nkremers at uni-bonn.de (Nico Alexander Willi Kremers) Date: Mon, 05 Dec 2011 13:58:58 +0100 Subject: [FieldTrip] 2x3 anova in cluster analysis Message-ID: Hi, I followed the discussion about implementing a 2x2 within subjects design into a cluster statistic with much interest. I want to implement a 2x3 repeated measure anova in a cluster analysis using fieldtrip. I think for this type of analysis subracting two conditions from each other and then calculate a ttest is not appropriate. Is there another way of calculating the interaction effect between the two factors and generate clusters for real and permutation data? What specifications must be set and how? Thank you very much for your answer, Nico From tomh at kurage.nimh.nih.gov Mon Dec 5 19:56:02 2011 From: tomh at kurage.nimh.nih.gov (Tom Holroyd (NIH/NIMH) [E]) Date: Mon, 05 Dec 2011 13:56:02 -0500 Subject: [FieldTrip] coherence normalization In-Reply-To: <1323007240.37048.YahooMailNeo@web111505.mail.gq1.yahoo.com> References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> <4ED91047.6050107@kurage.nimh.nih.gov> <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> <1323007240.37048.YahooMailNeo@web111505.mail.gq1.yahoo.com> Message-ID: <4EDD13C2.3000305@kurage.nimh.nih.gov> Yes, Guido Nolte came up with that around the same time (2004). I found this link by google, there might be a better one http://keck.ucsf.edu/~houde/sensorimotor_jc/GNolte04a.pdf Imaginary coherence is insensitive to volume conduction in EEG. I think the interpretation is different for MEG, but you can certainly easily compute it; you might still want to contrast different conditions. Tolga Özkurt wrote: > Regarding the discussion here, I've gotten onto a recent paper (Sekihara > et al., 2011) talking about "imaginary coherence" to prevent the seed > region effects. > > Even though imaginary coherence does not contain total connectivity > information, it might at least be used to select the coherent regions > that you want to project on your brain image and ignore the rest. > > Tolga > > > ------------------------------------------------------------------------ > *From:* jan-mathijs schoffelen > *To:* Email discussion list for the FieldTrip project > > *Sent:* Friday, December 2, 2011 8:49 PM > *Subject:* Re: [FieldTrip] coherence normalization > > Hi Jan, Tom and the rest, > > I agree with Tom, but would like to strongly emphasize that differences > in power across conditions more often than not will affect the coherence > landscape in a non-trivial way. This does not only count for power > changes in the reference dipole, but also for changes in power for third > party dipoles (i.e. any potential other source). Therefore the > interpretation of the subtracted coherence volumes should be done with > care. > > BW, > > JM > > On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote: > >> The solution I have adopted is to always look at coherence contrasts. >> Make two volumes using the same reference dipole in two different >> conditions, then subtract the volumes. The self-coherence of the >> reference will disappear. Mostly. Then use stats, like a U-test. >> >> Jan.Hirschmann at med.uni-duesseldorf.de >> wrote: >>> Hi community, >>> Regarding this thread on suppressing the reference dipole from 2004, >>> what is the current status? Has anybody found and implemented a >>> recommendable way to project out activity from unwanted dipoles? >>> Thank you for any comments/opinions! >>> Best, >>> Jan Hirschmann >>> On 21 Oct 2004, at 17:23, Tom Holroyd wrote: >>> >>>> / When running a coherence volume using a reference dipole, one/ >>>> / naturally expects the coherence will be high around the reference/ >>>> / dipole./ >>>> / / >>>> / This effect tends to dominate the images./ >>>> / / >>>> / Is there a way to normalize the coherence volume to eliminate/ >>>> / this effect? Perhaps by dividing by the coherence in a "control"/ >>>> / state?/ >>> Hi Tom, >>> The dominating effect of the refdip is indeed very problematic. I just >>> happened to have discussed this with Joachim Gross, and I have included >>> our email exchange below. Please first read that ... >>> Basically I agree with Joachim, and I don't trust the supdip that is >>> implemented in FieldTrip's sourceanalysis function. Better test and map >>> the significance of the difference in coherence between two conditions >>> using randomization of the trials before the coherence is beamed (that >>> is implemented in sourceanalysis + sourcestatistics). >>> Robert >>> -------------------------------------------------------------------- >>> my question to Joachim was >>> ---------------------------------------------------------------------- >>> Begin forwarded message: >>> >>>> / From: Robert Oostenveld >>> >>>> //>/ >>>> / Date: 1 October 2004 10:26:02 GMT+02:00/ >>>> / To: Joachim Gross >>> >>>> //>/ >>>> / Subject: dipole suppression/ >>>> / / >>>> / Hi Joachim,/ >>>> / / >>>> / What I always still had to ask you is how you do supression of >>>> dipoles/ >>>> / in DICS, especially in the case of coherence imaging. I have thought/ >>>> / of two ways of projecting them out:/ >>>> / / >>>> / 1) compute supdip leadfield and its projection on the COV/CSD matrix,/ >>>> / then project it out of the COV/CSD matrix (which looses 2 or 3 from/ >>>> / its rank)./ >>>> / / >>>> / 2) compute supdip leadfield and add it to the leadfield of the dipole/ >>>> / with which is scanned (scandip). Subsequently compute the source/ >>>> / COV/CSD on those 6 leadfield components and select the 3x3 submatrix/ >>>> / that corresponds with the scandip to continue the computations with./ >>>> / / >>>> / Both methods don't really gave me very convincing results. A third/ >>>> / approach would be to add the supdip leadfield to the (identity) noise/ >>>> / matrix and project it through the filters. Then nai=pow/noise is/ >>>> / corrected for the presence of the supdip, but that does not result in/ >>>> / a supressed source coherence distribution. What is your idea or/ >>>> / approach for this?/ >>>> / / >>>> / best regards/ >>>> / Robert/ >>>> / / >>> ---------------------------------------------------------------------- >>> and his answer (Joachim, I hope you don't mind me sharing this on the >>> list) >>> ---------------------------------------------------------------------- >>> Begin forwarded message: >>> >>>> / From: Joachim Gross >>> >>>> //>/ >>>> / Date: 14 October 2004 17:20:45 GMT+02:00/ >>>> / To: "//robert.oostenveld at fcdonders.kun.nl >>>> >>>> //"/ >>>> / >>>> //>/ >>>> / Subject: dipole suppression/ >>>> / / >>>> / Hi Robert,/ >>>> / / >>>> / sorry for the delay./ >>>> / / >>>> / The dipole suppression is indeed a complex issue./ >>>> / We first implemented it because it facilitates visualization and the/ >>>> / exact identification of the first/ >>>> / strongest local maxima./ >>>> / Nevertheless, it is quite dangerous because the map is (locally)/ >>>> / distorted in a non-trivial way./ >>>> / We are now trying to move away from suppressing the sources. I think/ >>>> / it would be better to identify the/ >>>> / significant local maxima (significance based on/ >>>> / randomization/permutation)./ >>>> / But what we are doing at the moment is your approach 3./ >>>> / So we add the supdip leadfield to the noise covariance matrix and >>>> look/ >>>> / at pow/noise./ >>>> / / >>>> / For coherence we are basically doing the same thing./ >>>> / So we divide the coherence map (or actually the map of cross spectral/ >>>> / densities) by a noise map/ >>>> / that peaks at the locations of the "unwanted" dipoles./ >>>> / With this procedure we loose absolute coherence values./ >>>> / This is not so important for us since we get the absolute values from/ >>>> / the coherence and partial coherence spectra/ >>>> / that are computed afterwards./ >>>> / It works surprisingly well but should be used with care./ >>>> / / >>>> / A better approach would be to map partial coherence (with the >>>> unwanted/ >>>> / dipoles removed). But we have not implemented/ >>>> / this so far./ >>>> / / >>>> / Again, I think it is better to have regions of interest identified by/ >>>> / their significance./ >>>> / / >>>> / Joachim/ >>> ---------------------------------------------------------------------- >>> Robert Oostenveld, PhD >>> Center for Sensory-Motor Interaction (SMI) >>> Aalborg University, Denmark >>> and >>> F.C. Donders Centre for Cognitive Neuroimaging >>> University Nijmegen >>> P.O. Box 9101 >>> NL-6500 AH Nijmegen >>> The Netherlands >>> Tel: +31 (0)24 3619695 >>> Fax: +31 (0)24 3610989 >>> ---------------------------------------------------------------------- >>> N.B. Starting from 1 September 2004, the University of Nijmegen has >>> changed its name to Radboud University Nijmegen. All web- and >>> email-addresses ending in ".kun.nl" should therefore be changed into >>> ".ru.nl". Please update your address book and links. >>> Jan Hirschmann >>> MSc. Neuroscience >>> Insititute of Clinical Neuroscience and Medical Psychology >>> Heinrich Heine University Duesseldorf >>> Universitaetsstr. 1 >>> 40225 Duesseldorf >>> Tel: 0049 - (0)211 - 81 - 18415 >>> ------------------------------------------------------------------------ >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> "The test of a first-rate intelligence is the ability to hold two >> opposed ideas in the mind at the same time, and still retain the >> ability to function." — F. Scott Fitzgerald >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > ------------------------------------------------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- "The test of a first-rate intelligence is the ability to hold two opposed ideas in the mind at the same time, and still retain the ability to function." — F. Scott Fitzgerald From dualitystan at gmail.com Mon Dec 5 20:17:04 2011 From: dualitystan at gmail.com (Stanley Klein) Date: Mon, 5 Dec 2011 11:17:04 -0800 Subject: [FieldTrip] 2x3 anova in cluster analysis In-Reply-To: References: Message-ID: Nico, Your question gives me the chance to ask something I've been curious about. It seems to me that one of the nifty things about permutation cluster analysis is that it allows you to do anything that seems reasonable as long you decide on the process ahead of time and don't do any future tweaking other than fixing coding errors. I'm curious whether the Fieldtrip code make it easy to insert new statistics modules. I presume your actual question had to do with whether Fieldtrip already has the possibility of doing that 2x3 ANOVA. I suspect it doesn't have that capability. However, it would be nice if the permutation cluster analysis could be made sufficiently modular that one could make use of all the complicated clustering and permuting and all, but enable the user to substitute their own statistical method. I haven't actually watched my students doing the nitty-gritty use of Fieldtrip's version of the permutation test (other than knowing that is is very nice and well documented) so I don't know how easy it is to stick in one's own favorite statistic, but I'm hoping it is easy. Stan On Mon, Dec 5, 2011 at 4:58 AM, Nico Alexander Willi Kremers < nkremers at uni-bonn.de> wrote: > > Hi, > > I followed the discussion about implementing a 2x2 within subjects design > into a cluster statistic with much interest. I want to implement a 2x3 > repeated measure anova in a cluster analysis using fieldtrip. I think for > this type of analysis subracting two conditions from each other and then > calculate a ttest is not appropriate. Is there another way of calculating > the interaction effect between the two factors and generate clusters for > real and permutation data? What specifications must be set and how? > > Thank you very much for your answer, > > Nico > ______________________________**_________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Dec 5 21:01:39 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 5 Dec 2011 21:01:39 +0100 Subject: [FieldTrip] 2x3 anova in cluster analysis In-Reply-To: References: Message-ID: <6A25053C-2EB2-437A-A96F-2C1047DC862F@donders.ru.nl> Hi Stan et al, Actually FieldTrip allows in a very straightforward way to plug-in one's favourite statistic. The idea is the following: when specifying cfg.statistic you need to specify a string that under the hood points to a function, e.g. 'indepsamplesT' eventually causes a function to be called, answering to the aptly chosen name: 'statfun_indepsamplesT' which is doing the legwork. As long as the statfun_younameit has properly defined input and output arguments, you can let it do whatever you want. FieldTrip contains a bunch of 'statfuns' in the statfun directory but there's no reason not to implement any yourself (and ideally contribute them to the repository). Another discussion altogether is the question whether the test statistic of interest is an appropriate one that allows for statistical inference using the permutation framework. Over the past years there have been various threads on this mailing list regarding the possibility to test for interactions using a permutation test. You can look this up in the archive. Strictly speaking this is statistically not possible this way. The permutation-framework tests the null-hypothesis of exchangeability of data across allocated conditions, whereas when one wants to test for an interaction effect tests one tests for a particular linear (parametric) model of the dependent variables explaining variance in the dependent variable. Inferring that exchangeability across conditions is unlikely (i.e. obtaining a small p-value through permutation) does not necessarily lead to the conclusion that there is an actual interaction effect. Though opinions among the statisticians about this seem to vary, there may be a way out: one could either use bootstrapping to obtain confidence intervals for the interaction F under the null-hypothesis. The recipe for this would be to do a cell-specific demeaning of the data to impose the null-hypothesis of no interaction, and then through bootstrap resampling obtain a reference distribution of the interaction F. Alternatively, although I haven't thought this one through for any case other than a 2x2 anova, one could reduce the interaction effect to a two-condition contrast where observations belonging to the 'main diagonal' of the 2x2 conditions design are labeled as condition 1, and the observations belonging to the other diagonal are labeled as condition 2. One could then proceed with using a T-statistic as a descriptive statistic across these two 'conditions' on which inference can be done. Cheers and a happy Sinterklaas to you all, Jan-Mathijs On Dec 5, 2011, at 8:17 PM, Stanley Klein wrote: > Nico, > > Your question gives me the chance to ask something I've been curious about. It seems to me that one of the nifty things about permutation cluster analysis is that it allows you to do anything that seems reasonable as long you decide on the process ahead of time and don't do any future tweaking other than fixing coding errors. I'm curious whether the Fieldtrip code make it easy to insert new statistics modules. > > I presume your actual question had to do with whether Fieldtrip already has the possibility of doing that 2x3 ANOVA. I suspect it doesn't have that capability. However, it would be nice if the permutation cluster analysis could be made sufficiently modular that one could make use of all the complicated clustering and permuting and all, but enable the user to substitute their own statistical method. I haven't actually watched my students doing the nitty-gritty use of Fieldtrip's version of the permutation test (other than knowing that is is very nice and well documented) so I don't know how easy it is to stick in one's own favorite statistic, but I'm hoping it is easy. > > Stan > > > On Mon, Dec 5, 2011 at 4:58 AM, Nico Alexander Willi Kremers wrote: > > Hi, > > I followed the discussion about implementing a 2x2 within subjects design into a cluster statistic with much interest. I want to implement a 2x3 repeated measure anova in a cluster analysis using fieldtrip. I think for this type of analysis subracting two conditions from each other and then calculate a ttest is not appropriate. Is there another way of calculating the interaction effect between the two factors and generate clusters for real and permutation data? What specifications must be set and how? > > Thank you very much for your answer, > > Nico > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Dec 5 21:13:30 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 5 Dec 2011 21:13:30 +0100 Subject: [FieldTrip] coherence normalization In-Reply-To: <4EDD13C2.3000305@kurage.nimh.nih.gov> References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> <4ED91047.6050107@kurage.nimh.nih.gov> <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> <1323007240.37048.YahooMailNeo@web111505.mail.gq1.yahoo.com> <4EDD13C2.3000305@kurage.nimh.nih.gov> Message-ID: Hi all, I would not venture to interpret a conditional difference in the imaginary part of the coherency. When this quantity changes, it could either be due to a change in the phase or to a change of the magnitude of the coherency (or of any combination of the two). BW, JM On Dec 5, 2011, at 7:56 PM, Tom Holroyd (NIH/NIMH) [E] wrote: > Yes, Guido Nolte came up with that around the same time (2004). > > I found this link by google, there might be a better one > > http://keck.ucsf.edu/~houde/sensorimotor_jc/GNolte04a.pdf > > Imaginary coherence is insensitive to volume conduction in EEG. > > I think the interpretation is different for MEG, but you can certainly easily compute it; you might still want to contrast different conditions. > > Tolga Özkurt wrote: >> Regarding the discussion here, I've gotten onto a recent paper (Sekihara et al., 2011) talking about "imaginary coherence" to prevent the seed region effects. Even though imaginary coherence does not contain total connectivity information, it might at least be used to select the coherent regions that you want to project on your brain image and ignore the rest. >> Tolga >> ------------------------------------------------------------------------ >> *From:* jan-mathijs schoffelen >> *To:* Email discussion list for the FieldTrip project >> *Sent:* Friday, December 2, 2011 8:49 PM >> *Subject:* Re: [FieldTrip] coherence normalization >> Hi Jan, Tom and the rest, >> I agree with Tom, but would like to strongly emphasize that differences in power across conditions more often than not will affect the coherence landscape in a non-trivial way. This does not only count for power changes in the reference dipole, but also for changes in power for third party dipoles (i.e. any potential other source). Therefore the interpretation of the subtracted coherence volumes should be done with care. >> BW, >> JM >> On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote: >>> The solution I have adopted is to always look at coherence contrasts. Make two volumes using the same reference dipole in two different conditions, then subtract the volumes. The self-coherence of the reference will disappear. Mostly. Then use stats, like a U-test. >>> >>> Jan.Hirschmann at med.uni-duesseldorf.de wrote: >>>> Hi community, >>>> Regarding this thread on suppressing the reference dipole from 2004, what is the current status? Has anybody found and implemented a recommendable way to project out activity from unwanted dipoles? Thank you for any comments/opinions! >>>> Best, >>>> Jan Hirschmann >>>> On 21 Oct 2004, at 17:23, Tom Holroyd wrote: >>>> >>>>> / When running a coherence volume using a reference dipole, one/ >>>>> / naturally expects the coherence will be high around the reference/ >>>>> / dipole./ >>>>> / / >>>>> / This effect tends to dominate the images./ >>>>> / / >>>>> / Is there a way to normalize the coherence volume to eliminate/ >>>>> / this effect? Perhaps by dividing by the coherence in a "control"/ >>>>> / state?/ >>>> Hi Tom, >>>> The dominating effect of the refdip is indeed very problematic. I just >>>> happened to have discussed this with Joachim Gross, and I have included >>>> our email exchange below. Please first read that ... >>>> Basically I agree with Joachim, and I don't trust the supdip that is >>>> implemented in FieldTrip's sourceanalysis function. Better test and map >>>> the significance of the difference in coherence between two conditions >>>> using randomization of the trials before the coherence is beamed (that >>>> is implemented in sourceanalysis + sourcestatistics). >>>> Robert >>>> -------------------------------------------------------------------- >>>> my question to Joachim was >>>> ---------------------------------------------------------------------- >>>> Begin forwarded message: >>>> >>>>> / From: Robert Oostenveld //>/ >>>>> / Date: 1 October 2004 10:26:02 GMT+02:00/ >>>>> / To: Joachim Gross //>/ >>>>> / Subject: dipole suppression/ >>>>> / / >>>>> / Hi Joachim,/ >>>>> / / >>>>> / What I always still had to ask you is how you do supression of dipoles/ >>>>> / in DICS, especially in the case of coherence imaging. I have thought/ >>>>> / of two ways of projecting them out:/ >>>>> / / >>>>> / 1) compute supdip leadfield and its projection on the COV/CSD matrix,/ >>>>> / then project it out of the COV/CSD matrix (which looses 2 or 3 from/ >>>>> / its rank)./ >>>>> / / >>>>> / 2) compute supdip leadfield and add it to the leadfield of the dipole/ >>>>> / with which is scanned (scandip). Subsequently compute the source/ >>>>> / COV/CSD on those 6 leadfield components and select the 3x3 submatrix/ >>>>> / that corresponds with the scandip to continue the computations with./ >>>>> / / >>>>> / Both methods don't really gave me very convincing results. A third/ >>>>> / approach would be to add the supdip leadfield to the (identity) noise/ >>>>> / matrix and project it through the filters. Then nai=pow/noise is/ >>>>> / corrected for the presence of the supdip, but that does not result in/ >>>>> / a supressed source coherence distribution. What is your idea or/ >>>>> / approach for this?/ >>>>> / / >>>>> / best regards/ >>>>> / Robert/ >>>>> / / >>>> ---------------------------------------------------------------------- >>>> and his answer (Joachim, I hope you don't mind me sharing this on the >>>> list) >>>> ---------------------------------------------------------------------- >>>> Begin forwarded message: >>>> >>>>> / From: Joachim Gross //>/ >>>>> / Date: 14 October 2004 17:20:45 GMT+02:00/ >>>>> / To: "//robert.oostenveld at fcdonders.kun.nl //"/ >>>>> / //>/ >>>>> / Subject: dipole suppression/ >>>>> / / >>>>> / Hi Robert,/ >>>>> / / >>>>> / sorry for the delay./ >>>>> / / >>>>> / The dipole suppression is indeed a complex issue./ >>>>> / We first implemented it because it facilitates visualization and the/ >>>>> / exact identification of the first/ >>>>> / strongest local maxima./ >>>>> / Nevertheless, it is quite dangerous because the map is (locally)/ >>>>> / distorted in a non-trivial way./ >>>>> / We are now trying to move away from suppressing the sources. I think/ >>>>> / it would be better to identify the/ >>>>> / significant local maxima (significance based on/ >>>>> / randomization/permutation)./ >>>>> / But what we are doing at the moment is your approach 3./ >>>>> / So we add the supdip leadfield to the noise covariance matrix and look/ >>>>> / at pow/noise./ >>>>> / / >>>>> / For coherence we are basically doing the same thing./ >>>>> / So we divide the coherence map (or actually the map of cross spectral/ >>>>> / densities) by a noise map/ >>>>> / that peaks at the locations of the "unwanted" dipoles./ >>>>> / With this procedure we loose absolute coherence values./ >>>>> / This is not so important for us since we get the absolute values from/ >>>>> / the coherence and partial coherence spectra/ >>>>> / that are computed afterwards./ >>>>> / It works surprisingly well but should be used with care./ >>>>> / / >>>>> / A better approach would be to map partial coherence (with the unwanted/ >>>>> / dipoles removed). But we have not implemented/ >>>>> / this so far./ >>>>> / / >>>>> / Again, I think it is better to have regions of interest identified by/ >>>>> / their significance./ >>>>> / / >>>>> / Joachim/ >>>> ---------------------------------------------------------------------- >>>> Robert Oostenveld, PhD >>>> Center for Sensory-Motor Interaction (SMI) >>>> Aalborg University, Denmark >>>> and >>>> F.C. Donders Centre for Cognitive Neuroimaging >>>> University Nijmegen >>>> P.O. Box 9101 >>>> NL-6500 AH Nijmegen >>>> The Netherlands >>>> Tel: +31 (0)24 3619695 >>>> Fax: +31 (0)24 3610989 >>>> ---------------------------------------------------------------------- >>>> N.B. Starting from 1 September 2004, the University of Nijmegen has >>>> changed its name to Radboud University Nijmegen. All web- and >>>> email-addresses ending in ".kun.nl" should therefore be changed into >>>> ".ru.nl". Please update your address book and links. >>>> Jan Hirschmann >>>> MSc. Neuroscience >>>> Insititute of Clinical Neuroscience and Medical Psychology >>>> Heinrich Heine University Duesseldorf >>>> Universitaetsstr. 1 >>>> 40225 Duesseldorf >>>> Tel: 0049 - (0)211 - 81 - 18415 >>>> ------------------------------------------------------------------------ >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> -- >>> "The test of a first-rate intelligence is the ability to hold two >>> opposed ideas in the mind at the same time, and still retain the >>> ability to function." — F. Scott Fitzgerald >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> ------------------------------------------------------------------------ >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- > "The test of a first-rate intelligence is the ability to hold two > opposed ideas in the mind at the same time, and still retain the > ability to function." — F. Scott Fitzgerald > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at kurage.nimh.nih.gov Mon Dec 5 21:38:55 2011 From: tomh at kurage.nimh.nih.gov (Tom Holroyd (NIH/NIMH) [E]) Date: Mon, 05 Dec 2011 15:38:55 -0500 Subject: [FieldTrip] coherence normalization In-Reply-To: References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> <4ED91047.6050107@kurage.nimh.nih.gov> <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> <1323007240.37048.YahooMailNeo@web111505.mail.gq1.yahoo.com> <4EDD13C2.3000305@kurage.nimh.nih.gov> Message-ID: <4EDD2BDF.6090506@kurage.nimh.nih.gov> Yes. Nolte mentions that although one often computes coherency relative to a baseline, one must be careful because of this and random flips of pi making hash of it if you just blindly subtract. Same thing for any relative phase calculation. Also, I was misunderstanding things below; the interpretation is the same for MEG as it is for EEG, any source affects multiple sensors simultaneously. It is this spatial correlation that allows us to see it as a source after all, and what makes the imaginary part positive. If there were no spatial correlations there would be no imaginary part in the coherence. heh, yes, it took me that long to understand this paper ... :-) jan-mathijs schoffelen wrote: > Hi all, > > I would not venture to interpret a conditional difference in the > imaginary part of the coherency. When this quantity changes, it could > either be due to a change in the phase or to a change of the magnitude > of the coherency (or of any combination of the two). > > BW, > > JM > > > On Dec 5, 2011, at 7:56 PM, Tom Holroyd (NIH/NIMH) [E] wrote: > >> Yes, Guido Nolte came up with that around the same time (2004). >> >> I found this link by google, there might be a better one >> >> http://keck.ucsf.edu/~houde/sensorimotor_jc/GNolte04a.pdf >> >> Imaginary coherence is insensitive to volume conduction in EEG. >> >> I think the interpretation is different for MEG, but you can certainly >> easily compute it; you might still want to contrast different conditions. >> >> Tolga Özkurt wrote: >>> Regarding the discussion here, I've gotten onto a recent paper >>> (Sekihara et al., 2011) talking about "imaginary coherence" to >>> prevent the seed region effects. Even though imaginary coherence does >>> not contain total connectivity information, it might at least be used >>> to select the coherent regions that you want to project on your brain >>> image and ignore the rest. >>> Tolga >>> ------------------------------------------------------------------------ >>> *From:* jan-mathijs schoffelen >>> *To:* Email discussion list for the FieldTrip project >>> >>> *Sent:* Friday, December 2, 2011 8:49 PM >>> *Subject:* Re: [FieldTrip] coherence normalization >>> Hi Jan, Tom and the rest, >>> I agree with Tom, but would like to strongly emphasize that >>> differences in power across conditions more often than not will >>> affect the coherence landscape in a non-trivial way. This does not >>> only count for power changes in the reference dipole, but also for >>> changes in power for third party dipoles (i.e. any potential other >>> source). Therefore the interpretation of the subtracted coherence >>> volumes should be done with care. >>> BW, >>> JM >>> On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote: >>>> The solution I have adopted is to always look at coherence >>>> contrasts. Make two volumes using the same reference dipole in two >>>> different conditions, then subtract the volumes. The self-coherence >>>> of the reference will disappear. Mostly. Then use stats, like a U-test. >>>> >>>> Jan.Hirschmann at med.uni-duesseldorf.de >>>> wrote: >>>>> Hi community, >>>>> Regarding this thread on suppressing the reference dipole from >>>>> 2004, what is the current status? Has anybody found and implemented >>>>> a recommendable way to project out activity from unwanted dipoles? >>>>> Thank you for any comments/opinions! >>>>> Best, >>>>> Jan Hirschmann >>>>> On 21 Oct 2004, at 17:23, Tom Holroyd wrote: >>>>> >>>>>> / When running a coherence volume using a reference dipole, one/ >>>>>> / naturally expects the coherence will be high around the reference/ >>>>>> / dipole./ >>>>>> / / >>>>>> / This effect tends to dominate the images./ >>>>>> / / >>>>>> / Is there a way to normalize the coherence volume to eliminate/ >>>>>> / this effect? Perhaps by dividing by the coherence in a "control"/ >>>>>> / state?/ >>>>> Hi Tom, >>>>> The dominating effect of the refdip is indeed very problematic. I just >>>>> happened to have discussed this with Joachim Gross, and I have included >>>>> our email exchange below. Please first read that ... >>>>> Basically I agree with Joachim, and I don't trust the supdip that is >>>>> implemented in FieldTrip's sourceanalysis function. Better test and map >>>>> the significance of the difference in coherence between two conditions >>>>> using randomization of the trials before the coherence is beamed (that >>>>> is implemented in sourceanalysis + sourcestatistics). >>>>> Robert >>>>> -------------------------------------------------------------------- >>>>> my question to Joachim was >>>>> ---------------------------------------------------------------------- >>>>> Begin forwarded message: >>>>> >>>>>> / From: Robert Oostenveld >>>>> >>>>>> //>/ >>>>>> / Date: 1 October 2004 10:26:02 GMT+02:00/ >>>>>> / To: Joachim Gross >>>>> >>>>>> //>/ >>>>>> / Subject: dipole suppression/ >>>>>> / / >>>>>> / Hi Joachim,/ >>>>>> / / >>>>>> / What I always still had to ask you is how you do supression of >>>>>> dipoles/ >>>>>> / in DICS, especially in the case of coherence imaging. I have >>>>>> thought/ >>>>>> / of two ways of projecting them out:/ >>>>>> / / >>>>>> / 1) compute supdip leadfield and its projection on the COV/CSD >>>>>> matrix,/ >>>>>> / then project it out of the COV/CSD matrix (which looses 2 or 3 from/ >>>>>> / its rank)./ >>>>>> / / >>>>>> / 2) compute supdip leadfield and add it to the leadfield of the >>>>>> dipole/ >>>>>> / with which is scanned (scandip). Subsequently compute the source/ >>>>>> / COV/CSD on those 6 leadfield components and select the 3x3 >>>>>> submatrix/ >>>>>> / that corresponds with the scandip to continue the computations >>>>>> with./ >>>>>> / / >>>>>> / Both methods don't really gave me very convincing results. A third/ >>>>>> / approach would be to add the supdip leadfield to the (identity) >>>>>> noise/ >>>>>> / matrix and project it through the filters. Then nai=pow/noise is/ >>>>>> / corrected for the presence of the supdip, but that does not >>>>>> result in/ >>>>>> / a supressed source coherence distribution. What is your idea or/ >>>>>> / approach for this?/ >>>>>> / / >>>>>> / best regards/ >>>>>> / Robert/ >>>>>> / / >>>>> ---------------------------------------------------------------------- >>>>> and his answer (Joachim, I hope you don't mind me sharing this on the >>>>> list) >>>>> ---------------------------------------------------------------------- >>>>> Begin forwarded message: >>>>> >>>>>> / From: Joachim Gross >>>>> >>>>>> //>/ >>>>>> / Date: 14 October 2004 17:20:45 GMT+02:00/ >>>>>> / To: "//robert.oostenveld at fcdonders.kun.nl >>>>>> >>>>>> //"/ >>>>>> / >>>>> >>>>>> //>/ >>>>>> / Subject: dipole suppression/ >>>>>> / / >>>>>> / Hi Robert,/ >>>>>> / / >>>>>> / sorry for the delay./ >>>>>> / / >>>>>> / The dipole suppression is indeed a complex issue./ >>>>>> / We first implemented it because it facilitates visualization and >>>>>> the/ >>>>>> / exact identification of the first/ >>>>>> / strongest local maxima./ >>>>>> / Nevertheless, it is quite dangerous because the map is (locally)/ >>>>>> / distorted in a non-trivial way./ >>>>>> / We are now trying to move away from suppressing the sources. I >>>>>> think/ >>>>>> / it would be better to identify the/ >>>>>> / significant local maxima (significance based on/ >>>>>> / randomization/permutation)./ >>>>>> / But what we are doing at the moment is your approach 3./ >>>>>> / So we add the supdip leadfield to the noise covariance matrix >>>>>> and look/ >>>>>> / at pow/noise./ >>>>>> / / >>>>>> / For coherence we are basically doing the same thing./ >>>>>> / So we divide the coherence map (or actually the map of cross >>>>>> spectral/ >>>>>> / densities) by a noise map/ >>>>>> / that peaks at the locations of the "unwanted" dipoles./ >>>>>> / With this procedure we loose absolute coherence values./ >>>>>> / This is not so important for us since we get the absolute values >>>>>> from/ >>>>>> / the coherence and partial coherence spectra/ >>>>>> / that are computed afterwards./ >>>>>> / It works surprisingly well but should be used with care./ >>>>>> / / >>>>>> / A better approach would be to map partial coherence (with the >>>>>> unwanted/ >>>>>> / dipoles removed). But we have not implemented/ >>>>>> / this so far./ >>>>>> / / >>>>>> / Again, I think it is better to have regions of interest >>>>>> identified by/ >>>>>> / their significance./ >>>>>> / / >>>>>> / Joachim/ >>>>> ---------------------------------------------------------------------- >>>>> Robert Oostenveld, PhD >>>>> Center for Sensory-Motor Interaction (SMI) >>>>> Aalborg University, Denmark >>>>> and >>>>> F.C. Donders Centre for Cognitive Neuroimaging >>>>> University Nijmegen >>>>> P.O. Box 9101 >>>>> NL-6500 AH Nijmegen >>>>> The Netherlands >>>>> Tel: +31 (0)24 3619695 >>>>> Fax: +31 (0)24 3610989 >>>>> ---------------------------------------------------------------------- >>>>> N.B. Starting from 1 September 2004, the University of Nijmegen has >>>>> changed its name to Radboud University Nijmegen. All web- and >>>>> email-addresses ending in ".kun.nl" should therefore be changed into >>>>> ".ru.nl". Please update your address book and links. >>>>> Jan Hirschmann >>>>> MSc. Neuroscience >>>>> Insititute of Clinical Neuroscience and Medical Psychology >>>>> Heinrich Heine University Duesseldorf >>>>> Universitaetsstr. 1 >>>>> 40225 Duesseldorf >>>>> Tel: 0049 - (0)211 - 81 - 18415 >>>>> ------------------------------------------------------------------------ >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> -- >>>> "The test of a first-rate intelligence is the ability to hold two >>>> opposed ideas in the mind at the same time, and still retain the >>>> ability to function." — F. Scott Fitzgerald >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition >>> and Behaviour, Centre for Cognitive Neuroimaging, >>> Radboud University Nijmegen, The Netherlands >>> Max Planck Institute for Psycholinguistics, >>> Nijmegen, The Netherlands >>> J.Schoffelen at donders.ru.nl >>> Telephone: +31-24-3614793 >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> ------------------------------------------------------------------------ >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> "The test of a first-rate intelligence is the ability to hold two >> opposed ideas in the mind at the same time, and still retain the >> ability to function." — F. Scott Fitzgerald >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > ------------------------------------------------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- "The test of a first-rate intelligence is the ability to hold two opposed ideas in the mind at the same time, and still retain the ability to function." — F. Scott Fitzgerald From jan.schoffelen at donders.ru.nl Mon Dec 5 22:03:06 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 5 Dec 2011 22:03:06 +0100 Subject: [FieldTrip] source statistics, group level In-Reply-To: References: Message-ID: <2A18BE4D-384F-4EE3-8D57-F11C642A089B@donders.ru.nl> Hi Sonja I think you are almost there. What I am not sure about is the name of the field in the grandaverage structure which contains the concatenated individual subject data. Isn't this field called '.trial'? In that case you should specify cfg.parameter to be 'trial'. If this is not the cause of the problem, did you check the individual subject volumes? Do these contain colored data? What do you exactly mean by getting a blank mri? Does the stat.stat field contain only zeros, nans or something else? Best, Jan-Mathijs On Dec 2, 2011, at 12:16 PM, Sonja Suntrup wrote: > Dear fieldtrip users, > I would like to do sourcestatistics on a group level with meg data. I have a > pre and post intervention measurement for each of my 21 subjects > (within-subjects design). After source reconstruction using an LCMV beamformer > and volume normalization I calculated the sourcegrandaverage for the pre and > post condition with the parameter cfg.keepindividual = 'yes'. > However, when I use the grandaverage results in ft_sourcestatistics in the > configuration shown below and plot the result I just get a blank anatomical > mri. Do I have to set any additional parameters or do I make a general > mistake? Whould you recommend to use a cluster-based permutation test > comparable to ft_timelockstatistics and would I have to set the same > parameters in ft_sourcestatistics then? > > cfg=[]; > cfg.dim = grandAVGsourcePre.dim; > cfg.method = 'montecarlo'; > cfg.statistic = 'depsamplesT'; > cfg.parameter = 'avg.pow'; > cfg.correctm = 'cluster'; > cfg.numrandomization = 100; > cfg.alpha = 0.05; > cfg.tail = 0; > > nsubj=length(sourcePre.trial); > cfg.design(1,:) = [1:nsubj 1:nsubj]; > cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2]; > cfg.uvar = 1; > cfg.ivar = 2; > stat = ft_sourcestatistics(cfg, grandAVGsourcePre, grandAVGsourcePost); > > Your help is greatly appreciated! > Best, > Sonja > > > -- > Dr. med. Sonja Suntrup > Institute for Biomagnetism and Biosignalanalysis > University of Muenster > Malmedyweg 15 > 48149 Münster, Germany > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From dderiso at ucsd.edu Tue Dec 6 02:45:45 2011 From: dderiso at ucsd.edu (Dave Deriso) Date: Mon, 5 Dec 2011 17:45:45 -0800 Subject: [FieldTrip] Problem plotting independent components Message-ID: Dear Fieldtrip Users, I am trying to implement the tutorial on using ICA to extract eyeblink artifacts ( http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). Everything works, except that the labels from the IC data do not match the labels from the layout file, causing an error in the topoplotIC function. Your help in solving this is most appreciated. Layout labels (I am using a Neuromag 306 MEG): 'MEG0113' 'MEG0112' 'MEG0111' 'MEG0122' 'MEG0123' IC labels: 'runica001' 'runica002' 'runica003' 'runica004' 'runica005' Matlab Output: ft_topoplotIC(cfg, comp); creating layout from data.grad creating layout for neuromag306alt system Error using ft_topoplotTFR (line 659) labels in data and labels in layout do not match Error in ft_topoplotIC (line 122) ft_topoplotTFR(cfg, varargin{:}); Cheers, Dave Deriso -- UCSD Institute for Neural Computation UCSD Department of Neurosurgery -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Dec 6 07:46:17 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 6 Dec 2011 07:46:17 +0100 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: Message-ID: <195A02BE-0BCE-4A9A-B25B-15657D7DDC53@donders.ru.nl> Hi Dave, Could you try and report back what happens when you specify cfg.layout = 'NM306.lay', prior to calling ft_topoplotTFR? Cheers, JM On Dec 6, 2011, at 2:45 AM, Dave Deriso wrote: > Dear Fieldtrip Users, > > I am trying to implement the tutorial on using ICA to extract eyeblink artifacts (http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). Everything works, except that the labels from the IC data do not match the labels from the layout file, causing an error in the topoplotIC function. Your help in solving this is most appreciated. > > > Layout labels (I am using a Neuromag 306 MEG): > 'MEG0113' > 'MEG0112' > 'MEG0111' > 'MEG0122' > 'MEG0123' > > IC labels: > 'runica001' > 'runica002' > 'runica003' > 'runica004' > 'runica005' > > Matlab Output: > ft_topoplotIC(cfg, comp); > creating layout from data.grad > creating layout for neuromag306alt system > Error using ft_topoplotTFR (line 659) > labels in data and labels in layout do not match > Error in ft_topoplotIC (line 122) > ft_topoplotTFR(cfg, varargin{:}); > > > > Cheers, > Dave Deriso > > -- > UCSD Institute for Neural Computation > UCSD Department of Neurosurgery > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue Dec 6 12:55:31 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 06 Dec 2011 12:55:31 +0100 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: Message-ID: <4EDE02B3.1010103@donders.ru.nl> Dear Dave, the labels do not match indeed, because ICs do not correspond to single channel (obviously). I am not exactly sure how ft_topoplotIC is built, but you could try using ft_databrowser instead, with cfg.viewmode = 'component' Hope that at least circumvents your problem. Best, Jörn On 12/6/2011 2:45 AM, Dave Deriso wrote: > Dear Fieldtrip Users, > > I am trying to implement the tutorial on using ICA to extract eyeblink > artifacts > (http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). > Everything works, except that the labels from the IC data do not match > the labels from the layout file, causing an error in the topoplotIC > function. Your help in solving this is most appreciated. > > > Layout labels (I am using a Neuromag 306 MEG): > 'MEG0113' > 'MEG0112' > 'MEG0111' > 'MEG0122' > 'MEG0123' > > IC labels: > 'runica001' > 'runica002' > 'runica003' > 'runica004' > 'runica005' > > Matlab Output: > ft_topoplotIC(cfg, comp); > creating layout from data.grad > creating layout for neuromag306alt system > Error using ft_topoplotTFR (line 659) > labels in data and labels in layout do not match > Error in ft_topoplotIC (line 122) > ft_topoplotTFR(cfg, varargin{:}); > > > > Cheers, > Dave Deriso > > -- > UCSD Institute for Neural Computation > UCSD Department of Neurosurgery > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From h.rossiter at ucl.ac.uk Tue Dec 6 14:18:28 2011 From: h.rossiter at ucl.ac.uk (Rossiter, Holly) Date: Tue, 6 Dec 2011 13:18:28 +0000 Subject: [FieldTrip] DICS beamformer images Message-ID: Hi all, I am using DICS to assess coherence and viewing the beamformer images through SPM. What I want to know is what is the value given in the image and how is it calculated? I thought it was a coherence value but it is not bounded between 0 and 1. Also what do you think is the best way to threshold the images in order to get rid of low value peaks? Thanks, Holly -------------- next part -------------- An HTML attachment was scrubbed... URL: From dderiso at ucsd.edu Tue Dec 6 20:17:03 2011 From: dderiso at ucsd.edu (Dave Deriso) Date: Tue, 6 Dec 2011 11:17:03 -0800 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: <4EDE02B3.1010103@donders.ru.nl> References: <4EDE02B3.1010103@donders.ru.nl> Message-ID: Dear JM and Jörn, Thank you so much for your helpful suggestions. Matlab could not find/open layout file: *NM306.lay* with both *ft_topoplotTFR* and* ft_topoplotIC*. I have also tried each of the following layouts without success: cfg.layout =3D data.grad; cfg.layout =3D 'neuromag306all.lay'; cfg.layout =3D 'neuromag306cmb.lay'; cfg.layout =3D 'neuromag306mag.lay'; cfg.layout =3D 'neuromag306planar.lay'; (and no layout cfg, as prescribed by the bottom of http://fieldtrip.fcdonders.nl/reference/ft_topoplotic) As Jörn mentioned, the IC and sensor labels are different and, therefore, doing a string comparison will return an error. The question is then, how can I project the ICs back into sensor space and plot them topographically using the pre-existing sensor layouts? If this accomplished by the *ft_topoplotIC* function, shouldn't it expect the IC labels to be different from the layout labels? Thanks again for all of your help! Cheers, Dave Deriso -- UCSD Institute for Neural Computation UCSD Department of Neurosurgery On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" < jm.horschig at donders.ru.nl> wrote: > Dear Dave, > > the labels do not match indeed, because ICs do not correspond to single > channel (obviously). I am not exactly sure how ft_topoplotIC is built, but > you could try using ft_databrowser instead, with cfg.viewmode = 'component' > Hope that at least circumvents your problem. > > Best, > Jörn > > > On 12/6/2011 2:45 AM, Dave Deriso wrote: > > Dear Fieldtrip Users, > > I am trying to implement the tutorial on using ICA to extract eyeblink > artifacts ( > http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). > Everything works, except that the labels from the IC data do not match the > labels from the layout file, causing an error in the topoplotIC > function. Your help in solving this is most appreciated. > > > Layout labels (I am using a Neuromag 306 MEG): > 'MEG0113' > 'MEG0112' > 'MEG0111' > 'MEG0122' > 'MEG0123' > > IC labels: > 'runica001' > 'runica002' > 'runica003' > 'runica004' > 'runica005' > > Matlab Output: > ft_topoplotIC(cfg, comp); > creating layout from data.grad > creating layout for neuromag306alt system > Error using ft_topoplotTFR (line 659) > labels in data and labels in layout do not match > Error in ft_topoplotIC (line 122) > ft_topoplotTFR(cfg, varargin{:}); > > > > Cheers, > Dave Deriso > > -- > UCSD Institute for Neural Computation > UCSD Department of Neurosurgery > > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dderiso at ucsd.edu Wed Dec 7 02:07:55 2011 From: dderiso at ucsd.edu (Dave Deriso) Date: Tue, 6 Dec 2011 17:07:55 -0800 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: <4EDE02B3.1010103@donders.ru.nl> Message-ID: I should also note that when I tried the *ft_databrowser* function it was unable to plot the component topographies because there weren't enough grid points. Have you encountered this before? Thanks again for all of your great help!! My code: cfg = []; cfg.viewmode = 'component' ft_databrowser(cfg, comp); Output: creating layout from cfg.grad creating layout for neuromag306alt system the input is component data with 306 components and 306 original channels detected 0 visual artifacts redrawing with viewmode component fetching data... done fetching artifacts... done preprocessing data... done plotting artifacts... plotting events... plotting data... Warning: Imaginary parts of complex X and/or Y arguments ignored > In ft_plot_vector at 191 In ft_databrowser>redraw_cb at 1309 In ft_databrowser at 508 Warning: Imaginary parts of complex X and/or Y arguments ignored > In ft_plot_vector at 191 In ft_databrowser>redraw_cb at 1309 In ft_databrowser at 508 ****** these errors repeat about 10 times, then: plotting component topographies... Error using griddata (line 79) Not enough unique sample points specified. Error in ft_plot_topo (line 153) [Xi,Yi,Zi] = griddata(chanX', chanY, dat, xi', yi, interpmethod); % interpolate the topographic data Error in ft_databrowser>redraw_cb (line 1377) ft_plot_topo(chanx, chany, chanz, 'mask', laychan.mask, 'interplim', 'mask', 'outline', laychan.outline, 'tag', 'topography', ... Error in ft_databrowser (line 508) redraw_cb(h); Cheers, Dave On Tue, Dec 6, 2011 at 11:17 AM, Dave Deriso wrote: > Dear JM and Jörn, > > Thank you so much for your helpful suggestions. Matlab could not find/open > layout file: *NM306.lay* with both *ft_topoplotTFR* and* ft_topoplotIC*. > I have also tried each of the following layouts without success: > > cfg.layout =3D data.grad; > cfg.layout =3D 'neuromag306all.lay'; > cfg.layout =3D 'neuromag306cmb.lay'; > cfg.layout =3D 'neuromag306mag.lay'; > cfg.layout =3D 'neuromag306planar.lay'; > (and no layout cfg, as prescribed by the bottom of > http://fieldtrip.fcdonders.nl/reference/ft_topoplotic) > > > As Jörn mentioned, the IC and sensor labels are different and, > therefore, doing a string comparison will return an error. The question is > then, how can I project the ICs back into sensor space and plot them > topographically using the pre-existing sensor layouts? If this accomplished > by the *ft_topoplotIC* function, shouldn't it expect the IC labels to be > different from the layout labels? > > Thanks again for all of your help! > > Cheers, > Dave Deriso > > -- > UCSD Institute for Neural Computation > UCSD Department of Neurosurgery > > > > > On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" < > jm.horschig at donders.ru.nl> wrote: > >> Dear Dave, >> >> the labels do not match indeed, because ICs do not correspond to single >> channel (obviously). I am not exactly sure how ft_topoplotIC is built, but >> you could try using ft_databrowser instead, with cfg.viewmode = 'component' >> Hope that at least circumvents your problem. >> >> Best, >> Jörn >> >> >> On 12/6/2011 2:45 AM, Dave Deriso wrote: >> >> Dear Fieldtrip Users, >> >> I am trying to implement the tutorial on using ICA to extract eyeblink >> artifacts ( >> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). >> Everything works, except that the labels from the IC data do not match the >> labels from the layout file, causing an error in the topoplotIC >> function. Your help in solving this is most appreciated. >> >> >> Layout labels (I am using a Neuromag 306 MEG): >> 'MEG0113' >> 'MEG0112' >> 'MEG0111' >> 'MEG0122' >> 'MEG0123' >> >> IC labels: >> 'runica001' >> 'runica002' >> 'runica003' >> 'runica004' >> 'runica005' >> >> Matlab Output: >> ft_topoplotIC(cfg, comp); >> creating layout from data.grad >> creating layout for neuromag306alt system >> Error using ft_topoplotTFR (line 659) >> labels in data and labels in layout do not match >> Error in ft_topoplotIC (line 122) >> ft_topoplotTFR(cfg, varargin{:}); >> >> >> >> Cheers, >> Dave Deriso >> >> -- >> UCSD Institute for Neural Computation >> UCSD Department of Neurosurgery >> >> >> >> _______________________________________________ >> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Jörn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jarang.hahm at gmail.com Wed Dec 7 03:34:49 2011 From: jarang.hahm at gmail.com (Jarang Hahm) Date: Wed, 7 Dec 2011 11:34:49 +0900 Subject: [FieldTrip] Question about the identification of sensor type & proper timing of gradiometer selection Message-ID: Dear fieldtrip user. I'm newcomer on an MEG analysis and the fieldtrip. I have MEG data (.fif file) measured by Neuromag 306 channel system. Recently I got two problems on 1) identification of sensor type and 2) proper time to separate gradiometer in data processing. 1) First one is about identification of sensor type when using fieldtrip toolbox (20111204 version) After trial definition and preprocessing, I got some warnings in series when doing time-frequency analysis: Warning: could be Yokogawa system > In fileio\private\ft_senstype at 271 In ft_chantype at 71 In ft_chantype at 477 In ft_datatype_sens at 124 In ft_datatype_raw at 95 In ft_checkdata at 175 In ft_freqanalysis at 188 Warning: could be Yokogawa system > In fileio\private\ft_senstype at 271 In ft_chantype at 166 In ft_chantype at 477 In ft_datatype_sens at 124 In ft_datatype_raw at 95 In ft_checkdata at 175 In ft_freqanalysis at 188 (...There were also the other 12 warnings, which were simillar to above except for the specific line in ft_chantype.) As warning indicated, I've been ft_senstype at the line 271 and found that it couldn't recognize the data as a Neuromag 306 system although the sensor label of my data was matched with that of Neuromag 306. I wonder whether those warnings might affect overall analysis procedure or not and wish to fix this problem. 2) The second question is about a proper time for gradiometer selection. My analysis of interest is only gradiometer channels, not magnetometer one, so that the magnetometer can be removed at some time. In data processing, when is the proper time to separate the gradiometer channel from magnetometer? My data will be processed like this way: Trial definition -> preprocessing -> ICA for EOG rejection -> artifact rejection -> time-frequency analysis at sensor level & source analysis. Should I keep apart gradiometer channel from magnetometer after artifact rejection? or before ICA analysis? Need your help. Sincerely, Jarang Hahm -------------- next part -------------- An HTML attachment was scrubbed... URL: From miellet at psy.gla.ac.uk Wed Dec 7 07:52:28 2011 From: miellet at psy.gla.ac.uk (miellet at psy.gla.ac.uk) Date: Wed, 07 Dec 2011 06:52:28 +0000 Subject: [FieldTrip] second-level stats with TFR In-Reply-To: <4ECE596D.90504@psy.gla.ac.uk> References: <4ECE596D.90504@psy.gla.ac.uk> Message-ID: <20111207065228.27673d9bz74irz8s@horde.psy.gla.ac.uk> Hello, I've got problems doing second-level stats with TFR because of the data structure. I previously did it with ERF and didn't experience any difficulty. I'm just comparing 2 conditions so the design is very simple. The dimord for ERF was rpt_chan_time so I had access to the different trials. For ERF, I computed individual t-values between my conditions and across trials; then averaged the result across participants and compared the grand-average to zero. Do you think this strategy makes sense? For TFR, the dimord is chan_freq_time (with cfg.keeptrials='yes', before or after ft_freqbaseline). Obviously I don't want to compute the individual t-values across channels, freq bands or time points but across trials. Do you have any idea where I could find this information please? (I look in previous.....previous but couldn't find anything useful. I also specify keeptrials at each step of the process) Thank you very much for your help, Sebastien ---------------------------------------------- Dr. Sébastien Miellet, Lecturer Department of Psychology University of Fribourg Faucigny 2 1700 Fribourg Switzerland tel: +41 26 300 7666 ---------------------------------------------- Quoting Sara Bögels : > Hi all, > > I have been trying to do second-level statistical inference (as > described in one of the FAQs) on ERFs, but I am not sure whether I > am doing everything correctly. > > In the first step I calculate the T-values for the difference > between two conditions (twice), which are between items, with > ft_timelockstatistics. I put the output of all participants in a > cell (called 'stat1a' and 'stat1b'). (I tried to use > ft_timelockgrandaverage to combine the subjects together but it > needs a field avg). > > Then I use ft_timelockstatistics again but subject level. I first > want to look at the difference between the two conditions. This > difference is reflected in the T-values of the first step so I > create a dummy which is the same as 'stat1' but I replace all the > values in the field 'stat' per participant with zeros. Then I call > (with appropriate cfg parameters): > > stat2a = ft_timelockstatistics(cfg,stat1a{:},dummy{:}); > stat2b = ft_timelockstatistics(cfg,stat1b{:},dummy{:}); > > To compare the two differences (stat1a and stat1b) and thereby look > at an interaction, I call: > > stat2a-b = ft_timelockstatistics(cfg,stat1a{:},stat1b{:}); > > I am uncertain whether the dummy works (or is there a way to compare > the t-values to zero directly?) and whether the stat1a{:} trick > works with ft_timelockstatistics. > > Thanks in advance for your answer. > > Sara > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > ---------------------------------------------------------------- This message was sent using the Web mail system for The University of Glasgow School of Psychology ------------------------------------------------------------------ From jm.horschig at donders.ru.nl Wed Dec 7 08:33:08 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 07 Dec 2011 08:33:08 +0100 Subject: [FieldTrip] Critical bug in ft_freqstatistic fixed Message-ID: <4EDF16B4.4030605@donders.ru.nl> Dear 'trippers, last week we fixed a *critical bug in freqstatistic *which might have caused wrong clustering on channel-level. You might have been affected by this *if your channel labels were not ordered alphabetically by default *(e.g. BTI system, EEG systems, etc.). In essence, the bug caused channelclusters which did not make sense (e.g. frontal channels and occipital channels in one cluster). You might have noticed already whether you were affected by critically looking at the plots. *This bug was introduced in May 2011*, so if you made a cluster-based permutation test on channel-level between May and now, *please make the effort to rerun *to be sure that your clusters are not due to this bug! Thanks to Gregor Volberg who reported this bug and Tobias Staudigl for also looking into this one and providing a fix. Our sincere apologies for this. On behalf of the FieldTrip team, Jörn -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Dec 7 08:52:21 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 7 Dec 2011 08:52:21 +0100 Subject: [FieldTrip] second-level stats with TFR In-Reply-To: <20111207065228.27673d9bz74irz8s@horde.psy.gla.ac.uk> References: <4ECE596D.90504@psy.gla.ac.uk> <20111207065228.27673d9bz74irz8s@horde.psy.gla.ac.uk> Message-ID: Cher Seb, In order to be able to compute a single subject T-statistic on the TFR you indeed need to specify cfg.keeptrials = 'yes', prior to calling ft_freqanalysis. Are you absolutely sure that you did this? If so, we need to look into this. Could you create yourself an account on our bugzilla file-server (bugzilla.fcdonders.nl) and file this as a bug. Just copy and paste your e-mail message and also upload some script+data facilitating the reproduction of the problem? Cheers, Jan-Mathijs On Dec 7, 2011, at 7:52 AM, miellet at psy.gla.ac.uk wrote: > Hello, > I've got problems doing second-level stats with TFR because of the data structure. > I previously did it with ERF and didn't experience any difficulty. I'm just comparing 2 conditions so the design is very simple. The dimord for ERF was rpt_chan_time so I had access to the different trials. > For ERF, I computed individual t-values between my conditions and across trials; then averaged the result across participants and compared the grand-average to zero. Do you think this strategy makes sense? > For TFR, the dimord is chan_freq_time (with cfg.keeptrials='yes', before or after ft_freqbaseline). Obviously I don't want to compute the individual t-values across channels, freq bands or time points but across trials. > Do you have any idea where I could find this information please? (I look in previous.....previous but couldn't find anything useful. I also specify keeptrials at each step of the process) > Thank you very much for your help, > Sebastien > > ---------------------------------------------- > Dr. Sébastien Miellet, Lecturer > > Department of Psychology > University of Fribourg > Faucigny 2 > 1700 Fribourg > Switzerland > > tel: +41 26 300 7666 > ---------------------------------------------- > > > > Quoting Sara Bögels : > >> Hi all, >> >> I have been trying to do second-level statistical inference (as described in one of the FAQs) on ERFs, but I am not sure whether I am doing everything correctly. >> >> In the first step I calculate the T-values for the difference between two conditions (twice), which are between items, with ft_timelockstatistics. I put the output of all participants in a cell (called 'stat1a' and 'stat1b'). (I tried to use ft_timelockgrandaverage to combine the subjects together but it needs a field avg). >> >> Then I use ft_timelockstatistics again but subject level. I first want to look at the difference between the two conditions. This difference is reflected in the T-values of the first step so I create a dummy which is the same as 'stat1' but I replace all the values in the field 'stat' per participant with zeros. Then I call (with appropriate cfg parameters): >> >> stat2a = ft_timelockstatistics(cfg,stat1a{:},dummy{:}); >> stat2b = ft_timelockstatistics(cfg,stat1b{:},dummy{:}); >> >> To compare the two differences (stat1a and stat1b) and thereby look at an interaction, I call: >> >> stat2a-b = ft_timelockstatistics(cfg,stat1a{:},stat1b{:}); >> >> I am uncertain whether the dummy works (or is there a way to compare the t-values to zero directly?) and whether the stat1a{:} trick works with ft_timelockstatistics. >> >> Thanks in advance for your answer. >> >> Sara >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > ---------------------------------------------------------------- > This message was sent using the Web mail system for > The University of Glasgow School of Psychology > ------------------------------------------------------------------ > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed Dec 7 10:42:12 2011 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 7 Dec 2011 10:42:12 +0100 Subject: [FieldTrip] Interactive Plotting in ft_rejectvisual Message-ID: <1C5AEC7D-4B54-428E-BE54-B408171837FC@gmail.com> Hi, Not really a bug report, so I put this on the discussion List. I noticed that when plotting single trials in the ft_rejectivusal function, the figure popping up is not interactive which makes a closer inspection of the trials somewhat harder. Maybe this is intentional, but I can't see a reason for it. However, simply adding "cfg_mp.interactive='yes';" at line 510 of "reject visual_summary" fixes this. Best, Julian Dipl. Psych. Julian Keil OBOB-Lab University of Konstanz Department of Psychology P.O. Box D25 78457 Konstanz Germany Tel: ++49 - (0)7531 - 88 42 50 Fax: ++49 - (0)7531 - 88 28 91 Email: julian.keil at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at donders.ru.nl Wed Dec 7 12:59:48 2011 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Wed, 7 Dec 2011 12:59:48 +0100 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: <4EDE02B3.1010103@donders.ru.nl> Message-ID: Hi Dave, Perhaps this error is due to the complex data that ft_databrowser cannot plot? If you re-calculate the components and get out real-only values, do you still get this error? Best, Johanna On 7 December 2011 02:07, Dave Deriso wrote: > I should also note that when I tried the *ft_databrowser* function it was > unable to plot the component topographies because there weren't enough grid > points. Have you encountered this before? Thanks again for all of your > great help!! > > My code: > > cfg = []; > cfg.viewmode = 'component' > ft_databrowser(cfg, comp); > > > Output: > > creating layout from cfg.grad > creating layout for neuromag306alt system > the input is component data with 306 components and 306 original channels > detected 0 visual artifacts > redrawing with viewmode component > fetching data... done > fetching artifacts... done > preprocessing data... done > plotting artifacts... > plotting events... > plotting data... > > Warning: Imaginary parts of complex X and/or Y arguments ignored > > In ft_plot_vector at 191 > In ft_databrowser>redraw_cb at 1309 > In ft_databrowser at 508 > Warning: Imaginary parts of complex X and/or Y arguments ignored > > In ft_plot_vector at 191 > In ft_databrowser>redraw_cb at 1309 > In ft_databrowser at 508 > ****** these errors repeat about > 10 times, then: > plotting component topographies... > Error using griddata (line 79) > Not enough unique sample points specified. > > Error in ft_plot_topo (line 153) > [Xi,Yi,Zi] = griddata(chanX', chanY, dat, xi', yi, interpmethod); % > interpolate the topographic data > > Error in ft_databrowser>redraw_cb (line 1377) > ft_plot_topo(chanx, chany, chanz, 'mask', laychan.mask, 'interplim', > 'mask', 'outline', laychan.outline, 'tag', 'topography', > ... > > Error in ft_databrowser (line 508) > redraw_cb(h); > > > > > > Cheers, > Dave > > > On Tue, Dec 6, 2011 at 11:17 AM, Dave Deriso wrote: > >> Dear JM and Jörn, >> >> Thank you so much for your helpful suggestions. Matlab could not >> find/open layout file: *NM306.lay* with both *ft_topoplotTFR* and* >> ft_topoplotIC*. I have also tried each of the following layouts without >> success: >> >> cfg.layout =3D data.grad; >> cfg.layout =3D 'neuromag306all.lay'; >> cfg.layout =3D 'neuromag306cmb.lay'; >> cfg.layout =3D 'neuromag306mag.lay'; >> cfg.layout =3D 'neuromag306planar.lay'; >> (and no layout cfg, as prescribed by the bottom of >> http://fieldtrip.fcdonders.nl/reference/ft_topoplotic) >> >> >> As Jörn mentioned, the IC and sensor labels are different and, >> therefore, doing a string comparison will return an error. The question is >> then, how can I project the ICs back into sensor space and plot them >> topographically using the pre-existing sensor layouts? If this accomplished >> by the *ft_topoplotIC* function, shouldn't it expect the IC labels to be >> different from the layout labels? >> >> Thanks again for all of your help! >> >> Cheers, >> Dave Deriso >> >> -- >> UCSD Institute for Neural Computation >> UCSD Department of Neurosurgery >> >> >> >> >> On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" < >> jm.horschig at donders.ru.nl> wrote: >> >>> Dear Dave, >>> >>> the labels do not match indeed, because ICs do not correspond to single >>> channel (obviously). I am not exactly sure how ft_topoplotIC is built, but >>> you could try using ft_databrowser instead, with cfg.viewmode = 'component' >>> Hope that at least circumvents your problem. >>> >>> Best, >>> Jörn >>> >>> >>> On 12/6/2011 2:45 AM, Dave Deriso wrote: >>> >>> Dear Fieldtrip Users, >>> >>> I am trying to implement the tutorial on using ICA to extract eyeblink >>> artifacts ( >>> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). >>> Everything works, except that the labels from the IC data do not match the >>> labels from the layout file, causing an error in the topoplotIC >>> function. Your help in solving this is most appreciated. >>> >>> >>> Layout labels (I am using a Neuromag 306 MEG): >>> 'MEG0113' >>> 'MEG0112' >>> 'MEG0111' >>> 'MEG0122' >>> 'MEG0123' >>> >>> IC labels: >>> 'runica001' >>> 'runica002' >>> 'runica003' >>> 'runica004' >>> 'runica005' >>> >>> Matlab Output: >>> ft_topoplotIC(cfg, comp); >>> creating layout from data.grad >>> creating layout for neuromag306alt system >>> Error using ft_topoplotTFR (line 659) >>> labels in data and labels in layout do not match >>> Error in ft_topoplotIC (line 122) >>> ft_topoplotTFR(cfg, varargin{:}); >>> >>> >>> >>> Cheers, >>> Dave Deriso >>> >>> -- >>> UCSD Institute for Neural Computation >>> UCSD Department of Neurosurgery >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> -- >>> Jörn M. Horschig >>> PhD Student >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognitive Neuroimaging >>> Radboud University Nijmegen >>> Neuronal Oscillations Group >>> >>> P.O. Box 9101 >>> NL-6500 HB Nijmegen >>> The Netherlands >>> >>> Contact: >>> E-Mail: jm.horschig at donders.ru.nl >>> Tel: +31-(0)24-36-68493 >>> Web: http://www.ru.nl/donders >>> >>> Visiting address: >>> Trigon, room 2.30 >>> Kapittelweg 29 >>> NL-6525 EN Nijmegen >>> The Netherlands >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed Dec 7 22:51:48 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 7 Dec 2011 22:51:48 +0100 Subject: [FieldTrip] how to avoid displaying function info In-Reply-To: References: Message-ID: <5A6D62F9-DD15-4683-B212-72517DB4AE3D@donders.ru.nl> Dear Marco This is now possible, see http://bugzilla.fcdonders.nl/show_bug.cgi?id=1191 and especially the last comment for details. Note that in case the callinfo is printed, the memory estimate only returns something useful on Linux and OS X. On Windows the memory useage cannot be estimated yet. best regards, Robert PS the main reason for printing the callinfo is to educate users about the memory and time requirements, so that users can more easily get reasonable lower-bound estimates for the resources required when doing distributed computing on a torque/sge linux cluster. On 25 Nov 2011, at 12:27, Marco Buiatti wrote: > Dear FTrippers, > > an aesthetic question: When I plot several topoplots, I would like to > avoid displaying information about the duration and RAM used by the > plotting functions, as: > the call to "ft_topoplotTFR" took 0 seconds and an estimated 0 MB > the call to "ft_prepare_layout" took 0 seconds and an estimated 0 MB > > Is there a simple way to do this? > > Thanks, > > Marco > > > -- > Marco Buiatti, PhD > > CEA/DSV/I2BM / NeuroSpin > INSERM U992 - Cognitive Neuroimaging Unit > Bât 145 - Point Courrier 156 > Gif sur Yvette F-91191 FRANCE > Ph: +33(0)169.08.65.21 > Fax: +33(0)169.08.79.73 > E-mail: marco.buiatti at gmail.com > http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti > > *********************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From dderiso at ucsd.edu Wed Dec 7 23:34:48 2011 From: dderiso at ucsd.edu (Dave Deriso) Date: Wed, 7 Dec 2011 14:34:48 -0800 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: <4EDE02B3.1010103@donders.ru.nl> Message-ID: Hi Johanna, Thanks for taking a look. I could not find a method inside * ft_componentanalysis* that extracts real values (although using real() could also accomplish this), however the warning seems to indicate that the complex values are ignored. Do you think this is still an issue? The error with *ft_databrowser* indicates a lack of "unique sample points" from some kind of grid, which is perhaps a bigger problem. Any thoughts? Thanks again! Cheers, Dave On Wed, Dec 7, 2011 at 3:59 AM, Johanna Zumer wrote: > Hi Dave, > Perhaps this error is due to the complex data that ft_databrowser cannot > plot? If you re-calculate the components and get out real-only values, do > you still get this error? > > Best, > Johanna > > > On 7 December 2011 02:07, Dave Deriso wrote: > >> I should also note that when I tried the *ft_databrowser* function it >> was unable to plot the component topographies because there weren't enough >> grid points. Have you encountered this before? Thanks again for all of your >> great help!! >> >> My code: >> >> cfg = []; >> cfg.viewmode = 'component' >> ft_databrowser(cfg, comp); >> >> >> Output: >> >> creating layout from cfg.grad >> creating layout for neuromag306alt system >> the input is component data with 306 components and 306 original channels >> detected 0 visual artifacts >> redrawing with viewmode component >> fetching data... done >> fetching artifacts... done >> preprocessing data... done >> plotting artifacts... >> plotting events... >> plotting data... >> >> Warning: Imaginary parts of complex X and/or Y arguments ignored >> > In ft_plot_vector at 191 >> In ft_databrowser>redraw_cb at 1309 >> In ft_databrowser at 508 >> Warning: Imaginary parts of complex X and/or Y arguments ignored >> > In ft_plot_vector at 191 >> In ft_databrowser>redraw_cb at 1309 >> In ft_databrowser at 508 >> ****** these errors repeat >> about 10 times, then: >> plotting component topographies... >> Error using griddata (line 79) >> Not enough unique sample points specified. >> >> Error in ft_plot_topo (line 153) >> [Xi,Yi,Zi] = griddata(chanX', chanY, dat, xi', yi, interpmethod); % >> interpolate the topographic data >> >> Error in ft_databrowser>redraw_cb (line 1377) >> ft_plot_topo(chanx, chany, chanz, 'mask', laychan.mask, >> 'interplim', 'mask', 'outline', laychan.outline, 'tag', 'topography', >> ... >> >> Error in ft_databrowser (line 508) >> redraw_cb(h); >> >> >> >> >> >> Cheers, >> Dave >> >> >> On Tue, Dec 6, 2011 at 11:17 AM, Dave Deriso wrote: >> >>> Dear JM and Jörn, >>> >>> Thank you so much for your helpful suggestions. Matlab could not >>> find/open layout file: *NM306.lay* with both *ft_topoplotTFR* and* >>> ft_topoplotIC*. I have also tried each of the following layouts >>> without success: >>> >>> cfg.layout =3D data.grad; >>> cfg.layout =3D 'neuromag306all.lay'; >>> cfg.layout =3D 'neuromag306cmb.lay'; >>> cfg.layout =3D 'neuromag306mag.lay'; >>> cfg.layout =3D 'neuromag306planar.lay'; >>> (and no layout cfg, as prescribed by the bottom of >>> http://fieldtrip.fcdonders.nl/reference/ft_topoplotic) >>> >>> >>> As Jörn mentioned, the IC and sensor labels are different and, >>> therefore, doing a string comparison will return an error. The question is >>> then, how can I project the ICs back into sensor space and plot them >>> topographically using the pre-existing sensor layouts? If this accomplished >>> by the *ft_topoplotIC* function, shouldn't it expect the IC labels to >>> be different from the layout labels? >>> >>> Thanks again for all of your help! >>> >>> Cheers, >>> Dave Deriso >>> >>> -- >>> UCSD Institute for Neural Computation >>> UCSD Department of Neurosurgery >>> >>> >>> >>> >>> On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" < >>> jm.horschig at donders.ru.nl> wrote: >>> >>>> Dear Dave, >>>> >>>> the labels do not match indeed, because ICs do not correspond to single >>>> channel (obviously). I am not exactly sure how ft_topoplotIC is built, but >>>> you could try using ft_databrowser instead, with cfg.viewmode = 'component' >>>> Hope that at least circumvents your problem. >>>> >>>> Best, >>>> Jörn >>>> >>>> >>>> On 12/6/2011 2:45 AM, Dave Deriso wrote: >>>> >>>> Dear Fieldtrip Users, >>>> >>>> I am trying to implement the tutorial on using ICA to extract >>>> eyeblink artifacts ( >>>> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). >>>> Everything works, except that the labels from the IC data do not match the >>>> labels from the layout file, causing an error in the topoplotIC >>>> function. Your help in solving this is most appreciated. >>>> >>>> >>>> Layout labels (I am using a Neuromag 306 MEG): >>>> 'MEG0113' >>>> 'MEG0112' >>>> 'MEG0111' >>>> 'MEG0122' >>>> 'MEG0123' >>>> >>>> IC labels: >>>> 'runica001' >>>> 'runica002' >>>> 'runica003' >>>> 'runica004' >>>> 'runica005' >>>> >>>> Matlab Output: >>>> ft_topoplotIC(cfg, comp); >>>> creating layout from data.grad >>>> creating layout for neuromag306alt system >>>> Error using ft_topoplotTFR (line 659) >>>> labels in data and labels in layout do not match >>>> Error in ft_topoplotIC (line 122) >>>> ft_topoplotTFR(cfg, varargin{:}); >>>> >>>> >>>> >>>> Cheers, >>>> Dave Deriso >>>> >>>> -- >>>> UCSD Institute for Neural Computation >>>> UCSD Department of Neurosurgery >>>> >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> >>>> -- >>>> Jörn M. Horschig >>>> PhD Student >>>> Donders Institute for Brain, Cognition and Behaviour >>>> Centre for Cognitive Neuroimaging >>>> Radboud University Nijmegen >>>> Neuronal Oscillations Group >>>> >>>> P.O. Box 9101 >>>> NL-6500 HB Nijmegen >>>> The Netherlands >>>> >>>> Contact: >>>> E-Mail: jm.horschig at donders.ru.nl >>>> Tel: +31-(0)24-36-68493 >>>> Web: http://www.ru.nl/donders >>>> >>>> Visiting address: >>>> Trigon, room 2.30 >>>> Kapittelweg 29 >>>> NL-6525 EN Nijmegen >>>> The Netherlands >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Dec 8 07:58:13 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 8 Dec 2011 07:58:13 +0100 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: <4EDE02B3.1010103@donders.ru.nl> Message-ID: Dear Dave, The output of an ICA should actually not contain complex numbers. It can happen though, and this is indicative of a problem. You should probably have a look at this FAQ: http://fieldtrip.fcdonders.nl/faq/why_does_my_ica_output_contain_complex_numbers Best, Eelke 2011/12/7 Dave Deriso : > Hi Johanna, > > Thanks for taking a look. I could not find a method inside > ft_componentanalysis that extracts real values (although using real() could > also accomplish this), however the warning seems to indicate that the > complex values are ignored. Do you think this is still an issue? The error > with ft_databrowser indicates a lack of "unique sample points" from some > kind of grid, which is perhaps a bigger problem. Any thoughts? Thanks again! > > Cheers, > Dave > > On Wed, Dec 7, 2011 at 3:59 AM, Johanna Zumer > wrote: >> >> Hi Dave, >> Perhaps this error is due to the complex data that ft_databrowser cannot >> plot?  If you re-calculate the components and get out real-only values, do >> you still get this error? >> >> Best, >> Johanna >> >> >> On 7 December 2011 02:07, Dave Deriso wrote: >>> >>> I should also note that when I tried the ft_databrowser function it was >>> unable to plot the component topographies because there weren't enough grid >>> points. Have you encountered this before? Thanks again for all of your great >>> help!! >>> >>> My code: >>> >>> cfg = []; >>> cfg.viewmode = 'component' >>> ft_databrowser(cfg, comp); >>> >>> >>> Output: >>> >>> creating layout from cfg.grad >>> creating layout for neuromag306alt system >>> the input is component data with 306 components and 306 original channels >>> detected   0 visual artifacts >>> redrawing with viewmode component >>> fetching data... done >>> fetching artifacts... done >>> preprocessing data... done >>> plotting artifacts... >>> plotting events... >>> plotting data... >>> >>> Warning: Imaginary parts of complex X and/or Y arguments ignored >>> > In ft_plot_vector at 191 >>>   In ft_databrowser>redraw_cb at 1309 >>>   In ft_databrowser at 508 >>> Warning: Imaginary parts of complex X and/or Y arguments ignored >>> > In ft_plot_vector at 191 >>>   In ft_databrowser>redraw_cb at 1309 >>>   In ft_databrowser at 508 >>>                                           ****** these errors repeat >>> about 10 times, then: >>> plotting component topographies... >>> Error using griddata (line 79) >>> Not enough unique sample points specified. >>> >>> Error in ft_plot_topo (line 153) >>> [Xi,Yi,Zi] = griddata(chanX', chanY, dat, xi', yi, interpmethod); % >>> interpolate the topographic data >>> >>> Error in ft_databrowser>redraw_cb (line 1377) >>>       ft_plot_topo(chanx, chany, chanz, 'mask', laychan.mask, >>> 'interplim', 'mask', 'outline', laychan.outline, 'tag', 'topography', >>>       ... >>> >>> Error in ft_databrowser (line 508) >>> redraw_cb(h); >>> >>> >>> >>> >>> >>> Cheers, >>> Dave >>> >>> >>> On Tue, Dec 6, 2011 at 11:17 AM, Dave Deriso wrote: >>>> >>>> Dear JM and Jörn, >>>> >>>> Thank you so much for your helpful suggestions. Matlab could not >>>> find/open layout file: NM306.lay with both ft_topoplotTFR and ft_topoplotIC. >>>> I have also tried each of the following layouts without success: >>>> >>>> cfg.layout    =3D data.grad; >>>> cfg.layout    =3D 'neuromag306all.lay'; >>>> cfg.layout    =3D 'neuromag306cmb.lay'; >>>> cfg.layout    =3D 'neuromag306mag.lay'; >>>> cfg.layout    =3D 'neuromag306planar.lay'; >>>> (and no layout cfg, as prescribed by the bottom >>>> of http://fieldtrip.fcdonders.nl/reference/ft_topoplotic) >>>> >>>> >>>> As Jörn mentioned, the IC and sensor labels are different and, >>>> therefore, doing a string comparison will return an error. The question is >>>> then, how can I project the ICs back into sensor space and plot them >>>> topographically using the pre-existing sensor layouts? If this accomplished >>>> by the ft_topoplotIC function, shouldn't it expect the IC labels to be >>>> different from the layout labels? >>>> >>>> Thanks again for all of your help! >>>> >>>> Cheers, >>>> Dave Deriso >>>> >>>> -- >>>> UCSD Institute for Neural Computation >>>> UCSD Department of Neurosurgery >>>> >>>> >>>> >>>> >>>> On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" >>>> wrote: >>>>> >>>>> Dear Dave, >>>>> >>>>> the labels do not match indeed, because ICs do not correspond to single >>>>> channel (obviously). I am not exactly sure how ft_topoplotIC is built, but >>>>> you could try using ft_databrowser instead, with cfg.viewmode = 'component' >>>>> Hope that at least circumvents your problem. >>>>> >>>>> Best, >>>>> Jörn >>>>> >>>>> >>>>> On 12/6/2011 2:45 AM, Dave Deriso wrote: >>>>> >>>>> Dear Fieldtrip Users, >>>>> >>>>> I am trying to implement the tutorial on using ICA to extract eyeblink >>>>> artifacts >>>>> (http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). >>>>> Everything works, except that the labels from the IC data do not match the >>>>> labels from the layout file, causing an error in the topoplotIC >>>>> function. Your help in solving this is most appreciated. >>>>> >>>>> >>>>> Layout labels (I am using a Neuromag 306 MEG): >>>>> 'MEG0113' >>>>> 'MEG0112' >>>>> 'MEG0111' >>>>> 'MEG0122' >>>>> 'MEG0123' >>>>> >>>>> IC labels: >>>>> 'runica001' >>>>> 'runica002' >>>>> 'runica003' >>>>> 'runica004' >>>>> 'runica005' >>>>> >>>>> Matlab Output: >>>>> ft_topoplotIC(cfg, comp); >>>>> creating layout from data.grad >>>>> creating layout for neuromag306alt system >>>>> Error using ft_topoplotTFR (line 659) >>>>> labels in data and labels in layout do not match >>>>> Error in ft_topoplotIC (line 122) >>>>> ft_topoplotTFR(cfg, varargin{:}); >>>>> >>>>> >>>>> >>>>> Cheers, >>>>> Dave Deriso >>>>> >>>>> -- >>>>> UCSD Institute for Neural Computation >>>>> UCSD Department of Neurosurgery >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>> >>>>> >>>>> >>>>> -- >>>>> Jörn M. Horschig >>>>> PhD Student >>>>> Donders Institute for Brain, Cognition and Behaviour >>>>> Centre for Cognitive Neuroimaging >>>>> Radboud University Nijmegen >>>>> Neuronal Oscillations Group >>>>> >>>>> P.O. Box 9101 >>>>> NL-6500 HB Nijmegen >>>>> The Netherlands >>>>> >>>>> Contact: >>>>> E-Mail: jm.horschig at donders.ru.nl >>>>> Tel: +31-(0)24-36-68493 >>>>> Web: http://www.ru.nl/donders >>>>> >>>>> Visiting address: >>>>> Trigon, room 2.30 >>>>> Kapittelweg 29 >>>>> NL-6525 EN Nijmegen >>>>> The Netherlands >>>>> >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From ole.jensen at donders.ru.nl Thu Dec 8 10:14:44 2011 From: ole.jensen at donders.ru.nl (Ole Jensen) Date: Thu, 08 Dec 2011 10:14:44 +0100 Subject: [FieldTrip] PhD position at the Donders Institute, Nijmegen Message-ID: <4EE08004.9020903@donders.ru.nl> Dear colleagues, If you know of potential PhD candidates please forward them the job listing below. All the best, Ole Jensen -- Ole Jensen http://www.neuosc.com ------- PhD position on 'Bridging the Gap between Neuronal Activity and Neuroimaging' (1,0 fte) *Donders Institute, Centre for Cognitive Neuroimaging* *Maximum salary: EUR 2,612 gross/month* *Vacancy number: 30.08.11* *Closing date: 1 January 2012* *Responsibilities* The Neuronal Oscillation group and the MR Techniques in Brain Function group at the Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, have funding available for a PhD position, aimed at quantitative evaluation of neuroimaging signal characteristics resulting from activity of neurons in the working human brain. The human brain is composed of multiple regions that are flexibly engaged and disengaged depending on the cognitive task performed. Each of these regions comprises large numbers of neurons that interact non-linearly. A fundamental question in cognitive neuroscience is how the connections and interactions of the neurons shape the functional architecture of the working brain. At the Donders Institute this question is addressed experimentally by measuring cognitive signals by means of magneto-encephalography (MEG), electro-encephalography (EEG) and functional magnetic resonance imaging (fMRI). You will work on this project from a complementary perspective, using computer simulation to investigate which plausible networks of neurons can explain measured signals. You will use and extend numerical software developed at the institute and elsewhere. Your results will improve the interpretation of measured cognitive signals. You will focus on positive and negative spatial and temporal correlations between various signals obtained in cognitive experiments. *Work environment* The Donders Institute for Brain, Cognition and Behaviour consists of the Centre for Cognition, the Centre for Cognitive Neuroimaging and the Centre for Neuroscience. The mission of the Centre for Cognitive Neuroimaging is to conduct cutting-edge fundamental research in cognitive neuroscience. Much of the rapid progress in this field is being driven by the development of complex neuroimaging techniques for measuring activity in the human working brain - an area in which the Centre plays a leading role. The research themes cover central cognitive functions such as perception, action, control, decision making, attention, memory, language, learning and plasticity. The Centre also aims to establish how the different brain areas coordinate their activity with very high temporal precision to enable human and animal cognition. This internationally renowned centre currently employs more than 100 PhD students and post-doctoral researchers of more than 20 different nationalities, offering a stimulating and multidisciplinary research environment. The centre is equipped with three MRI scanners (7T, 3T, 1.5T), a 275-channel MEG system, an EEG-TMS laboratory, several (MR-compatible) EEG systems, and high-performance computational facilities. English is the lingua franca at the centre. You will work within a joint project of the Neuronal Oscillations group and the MR Methods for Cognitive Neuroscience group at the Centre for Cognitive Neuroimaging, and the Neuroinformatics department at the Centre for Neuroscience. *What we expect from you* You should have a Master's degree (or equivalent). Applicants with a background in neuroscience should be willing to acquire the mathematical and numerical skills required to simulate complex systems. Applicants with a background in mathematics, physics or computer science should be willing to develop in-depth knowledge of cognitive neuroscience and physiology. You are enthusiastic to understand the dynamic properties of the human brain and to probe the interaction between different regions, all on the basis of what is known of the physiology of the brain. Furthermore, you are prepared to take courses and workshops offered at the Donders Graduate School for Cognitive Neuroscience to bring your knowledge of cognitive neuroscience up to the standard required. You should be willing to work in a multidisciplinary environment in which the results and methods from various disciplines, ranging from natural to behavioural sciences, are integrated. And you are eager to work with us at the cutting edge of science, where your personal commitment and skills are both essential and appreciated. Proficiency in oral and written English is essential. You are expected to work in a team, sharing technical know-how and ideas. *What we have to offer* We offer you: - employment: 1,0 fte; - a maximum gross monthly salary of EUR 2,612 based on a 38-hour working week; - in addition to the salary: an 8% holiday allowance and an 8.3% end-of-year bonus; - The starting salary is EUR2,042 per month and will increase to EUR2,612 per month in the fourth year; - duration of the contract: 4 years. Are you interested in our excellent employment conditions ? *Other Information* This vacancy was advertised earlier this year in July/August. If you applied for this position at the time and were rejected, please do not apply again. *Would you like to know more?* Further information on: DCCN Prof. dr. Jan van der Eerden, project leader Telephone:+31 24 3614602 E-mail: j.vandereerden at donders.ru.nl Dr. Ole Jensen, PI Neuronal Oscillation group Telephone:+31 24 3610884 E-mail: ole.jensen at donders.ru.nl * * *Applications* Are you interested? Please submit an application letter, a CV, and the names of two persons who can provide references. Please explain your interest in neuroscience and the above mentioned scientific approaches in your application letter. It is Radboud University Nijmegen's policy to only accept applications by e-mail. Please send your application, /stating vacancy number 30.08.11/, to vacatures at dpo.ru.nl , for the attention of Prof. dr. Jan van der Eerden, before 1 January 2012. For more information on the application procedure:+ 31 24 3611173 -- Ole Jensen http://www.neuosc.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.leszczynski.m at googlemail.com Thu Dec 8 17:33:45 2011 From: m.leszczynski.m at googlemail.com (Marcin Leszczynski) Date: Thu, 8 Dec 2011 17:33:45 +0100 Subject: [FieldTrip] 2x3 anova in cluster analysis In-Reply-To: References: Message-ID: Hi Jan-Mathijs and Fieldtrippers, I have a follow up question refering to statistical inference about monotonic trends in the permutation framework. I have four conditions A, B, C, D and I would like to test whether there is a monotonic change in the ERP/TF among the conditions (i.e. A > 2011/12/5 jan-mathijs schoffelen > >> Hi Stan et al, >> >> Actually FieldTrip allows in a very straightforward way to plug-in one's >> favourite statistic. The idea is the following: when specifying >> cfg.statistic you need to specify a string that under the hood points to a >> function, e.g. 'indepsamplesT' eventually causes a function to be called, >> answering to the aptly chosen name: 'statfun_indepsamplesT' which is doing >> the legwork. As long as the statfun_younameit has properly defined input >> and output arguments, you can let it do whatever you want. FieldTrip >> contains a bunch of 'statfuns' in the statfun directory but there's no >> reason not to implement any yourself (and ideally contribute them to the >> repository). >> Another discussion altogether is the question whether the test statistic >> of interest is an appropriate one that allows for statistical inference >> using the permutation framework. Over the past years there have been >> various threads on this mailing list regarding the possibility to test for >> interactions using a permutation test. You can look this up in the archive. >> Strictly speaking this is statistically not possible this way. The >> permutation-framework tests the null-hypothesis of exchangeability of data >> across allocated conditions, whereas when one wants to test for an >> interaction effect tests one tests for a particular linear (parametric) >> model of the dependent variables explaining variance in the dependent >> variable. Inferring that exchangeability across conditions is unlikely >> (i.e. obtaining a small p-value through permutation) does not necessarily >> lead to the conclusion that there is an actual interaction effect. Though >> opinions among the statisticians about this seem to vary, there may be a >> way out: one could either use bootstrapping to obtain confidence intervals >> for the interaction F under the null-hypothesis. The recipe for this would >> be to do a cell-specific demeaning of the data to impose the >> null-hypothesis of no interaction, and then through bootstrap resampling >> obtain a reference distribution of the interaction F. Alternatively, >> although I haven't thought this one through for any case other than a 2x2 >> anova, one could reduce the interaction effect to a two-condition contrast >> where observations belonging to the 'main diagonal' of the 2x2 conditions >> design are labeled as condition 1, and the observations belonging to the >> other diagonal are labeled as condition 2. One could then proceed with >> using a T-statistic as a descriptive statistic across these two >> 'conditions' on which inference can be done. >> >> Cheers and a happy Sinterklaas to you all, >> >> Jan-Mathijs >> >> >> On Dec 5, 2011, at 8:17 PM, Stanley Klein wrote: >> >> Nico, >> >> Your question gives me the chance to ask something I've been curious >> about. It seems to me that one of the nifty things about permutation >> cluster analysis is that it allows you to do anything that seems reasonable >> as long you decide on the process ahead of time and don't do any future >> tweaking other than fixing coding errors. I'm curious whether the Fieldtrip >> code make it easy to insert new statistics modules. >> >> I presume your actual question had to do with whether Fieldtrip already >> has the possibility of doing that 2x3 ANOVA. I suspect it doesn't have >> that capability. However, it would be nice if the permutation cluster >> analysis could be made sufficiently modular that one could make use of all >> the complicated clustering and permuting and all, but enable the user to >> substitute their own statistical method. I haven't actually watched my >> students doing the nitty-gritty use of Fieldtrip's version of the >> permutation test (other than knowing that is is very nice and well >> documented) so I don't know how easy it is to stick in one's own favorite >> statistic, but I'm hoping it is easy. >> >> Stan >> >> On Mon, Dec 5, 2011 at 4:58 AM, Nico Alexander Willi Kremers < >> nkremers at uni-bonn.de> wrote: >> >>> >>> Hi, >>> >>> I followed the discussion about implementing a 2x2 within subjects >>> design into a cluster statistic with much interest. I want to implement a >>> 2x3 repeated measure anova in a cluster analysis using fieldtrip. I think >>> for this type of analysis subracting two conditions from each other and >>> then calculate a ttest is not appropriate. Is there another way of >>> calculating the interaction effect between the two factors and generate >>> clusters for real and permutation data? What specifications must be set and >>> how? >>> >>> Thank you very much for your answer, >>> >>> Nico >>> ______________________________**_________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.m.groppe at gmail.com Fri Dec 9 20:18:21 2011 From: david.m.groppe at gmail.com (David Groppe) Date: Fri, 9 Dec 2011 14:18:21 -0500 Subject: [FieldTrip] 2x3 anova in cluster analysis In-Reply-To: References: Message-ID: Hi Marcin, You could use a permutation test based on a rank correlation statistic (e.g., Kendall's tau or Spearman's rho) to test for such a monotonic relationship. I do not know if FieldTrip currently implements this or not though. cheers, -D On Thu, Dec 8, 2011 at 11:33 AM, Marcin Leszczynski wrote: > Hi Jan-Mathijs and Fieldtrippers, > > I have a follow up question refering to statistical inference about > monotonic trends in the permutation framework. > > I have four conditions A, B, C, D and I would like to test whether there is > a monotonic change in the ERP/TF among the conditions (i.e. A possibly also A < B <= C < D). I guess one way would be to run multiple t > tests. However it seems a bit unconvenient as one needs to correct for > multiple comparisons. Furtheremore, the second case (A < B <= C < D) might > not be well captured. > > I found a thread from 31 Aug 2011 ("[FieldTrip] depsamplesregrT help" by > Jonas Obleser) suggesting that depsamplesregrT will be the way to go. > However, your reply to Nico somehow destroyed my confidence. If I got the > reply correctly this is not that easy as I would be testing a particular > linear model which is a bit of a problem. Thus, the question: > > How would you suggest testing for such a monotonic effect in the permutation > framework? > > Best, > Marcin > >> >> >> 2011/12/5 jan-mathijs schoffelen >>> >>> Hi Stan et al, >>> >>> Actually FieldTrip allows in a very straightforward way to plug-in one's >>> favourite statistic. The idea is the following: when specifying >>> cfg.statistic you need to specify a string that under the hood points to a >>> function, e.g. 'indepsamplesT' eventually causes a function to be called, >>> answering to the aptly chosen name: 'statfun_indepsamplesT' which is doing >>> the legwork. As long as the statfun_younameit has properly defined input and >>> output arguments, you can let it do whatever you want. FieldTrip contains a >>> bunch of 'statfuns' in the statfun directory but there's no reason not to >>> implement any yourself (and ideally contribute them to the repository). >>> Another discussion altogether is the question whether the test statistic >>> of interest is an appropriate one that allows for statistical inference >>> using the permutation framework. Over the past years there have been various >>> threads on this mailing list regarding the possibility to test for >>> interactions using a permutation test. You can look this up in the archive. >>> Strictly speaking this is statistically not possible this way. The >>> permutation-framework tests the null-hypothesis of exchangeability of data >>> across allocated conditions, whereas when one wants to test for an >>> interaction effect tests one tests for a particular linear (parametric) >>> model of the dependent variables explaining variance in the dependent >>> variable. Inferring that exchangeability across conditions is unlikely (i.e. >>> obtaining a small p-value through permutation) does not necessarily lead to >>> the conclusion that there is an actual interaction effect. Though opinions >>> among the statisticians about this seem to vary, there may be a way out: one >>> could either use bootstrapping to obtain confidence intervals for the >>> interaction F under the null-hypothesis. The recipe for this would be to do >>> a cell-specific demeaning of the data to impose the null-hypothesis of no >>> interaction, and then through bootstrap resampling obtain a reference >>> distribution of the interaction F. Alternatively, although I haven't thought >>> this one through for any case other than a 2x2 anova, one could reduce the >>> interaction effect to a two-condition contrast where observations belonging >>> to the 'main diagonal' of the 2x2 conditions design are labeled as condition >>> 1, and the observations belonging to the other diagonal are labeled as >>> condition 2. One could then proceed with using a T-statistic as a >>> descriptive statistic across these two 'conditions' on which inference can >>> be done. >>> >>> Cheers and a happy Sinterklaas to you all, >>> >>> Jan-Mathijs >>> >>> >>> On Dec 5, 2011, at 8:17 PM, Stanley Klein wrote: >>> >>> Nico, >>> >>> Your question gives me the chance to ask something I've been curious >>> about. It seems to me that one of the nifty things about permutation cluster >>> analysis is that it allows you to do anything that seems reasonable as long >>> you decide on the process ahead of time and don't do any future tweaking >>> other than fixing coding errors. I'm curious whether the Fieldtrip code make >>> it easy to insert new statistics modules. >>> >>> I presume your actual question had to do with whether Fieldtrip already >>> has the possibility of doing that 2x3 ANOVA.  I suspect it doesn't have that >>> capability. However, it would be nice if the permutation cluster analysis >>> could be made sufficiently modular that one could make use of all the >>> complicated clustering and permuting and all, but enable the user to >>> substitute their own statistical method.  I haven't actually watched my >>> students doing the nitty-gritty use of Fieldtrip's version of the >>> permutation test (other than knowing that is is very nice and well >>> documented) so I don't know how easy it is to stick in one's own favorite >>> statistic, but I'm hoping it is easy. >>> >>> Stan >>> >>> On Mon, Dec 5, 2011 at 4:58 AM, Nico Alexander Willi Kremers >>> wrote: >>>> >>>> >>>> Hi, >>>> >>>> I followed the discussion about implementing a 2x2 within subjects >>>> design into a cluster statistic with much interest. I want to implement a >>>> 2x3 repeated measure anova in a cluster analysis using fieldtrip. I think >>>> for this type of analysis subracting two conditions from each other and then >>>> calculate a ttest is not appropriate. Is there another way of calculating >>>> the interaction effect between the two factors and generate clusters for >>>> real and permutation data? What specifications must be set and how? >>>> >>>> Thank you very much for your answer, >>>> >>>> Nico >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> Jan-Mathijs Schoffelen, MD PhD >>> >>> Donders Institute for Brain, Cognition and Behaviour, >>> Centre for Cognitive Neuroimaging, >>> Radboud University Nijmegen, The Netherlands >>> >>> Max Planck Institute for Psycholinguistics, >>> Nijmegen, The Netherlands >>> >>> J.Schoffelen at donders.ru.nl >>> Telephone: +31-24-3614793 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- David Groppe, Ph.D. Postdoctoral Researcher North Shore LIJ Health System New Hyde Park, New York http://www.cogsci.ucsd.edu/~dgroppe/ From eva.patai at psy.ox.ac.uk Sun Dec 11 20:28:51 2011 From: eva.patai at psy.ox.ac.uk (Zita Eva Patai) Date: Sun, 11 Dec 2011 19:28:51 +0000 Subject: [FieldTrip] clusterstat on multiple frequencies Message-ID: Dear FT-ers, I have tried to run a permutation test on time-frequency data, and would have like to see a statistical evealuation over a set of frequencies (ex: 4-8Hz) It seems that the test itself runs, but it crashes when i try to plot the data, saying that 'stat' must not contain multiple frequencies. I was wondering if there was a way to evaluate the difference between two conditions over a set range of frequencies? Thank you! zita -- Zita Patai DPhil Candidate, Experimental Psychology University of Oxford bcl.psy.ox.ac.uk/people/zita-eva-patai/ eva.patai at psy.ox.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From inieuwenhuis at berkeley.edu Sun Dec 11 21:06:11 2011 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Sun, 11 Dec 2011 12:06:11 -0800 Subject: [FieldTrip] rereference to repaired channel Message-ID: <4EE50D33.8030500@berkeley.edu> Hi all, I've measured EEG data with Cz as the reference. I now want to rereference to linked mastoids. However, in one participant one of the mastoid electrodes is really noisy. Is it valid to throw out the noisy channel, then fix it (with ft_channelrepair), and then rereference to this fixed mastoid channel? In other words, is channelrepair a linear operation? Or would I be mixing (a little) Cz into all channels now...? Any other options? Or another way of asking: do I get the same result if I first rereference and then fix bad channels, compared to first fixing bad channels and then rereference? In the participant with the bad mastoid chan, I don't have a choice, I have to first fix the channel first, or I'd be mixing noise into all channels. But, in other participants, where I also have bad channels (but not the mastoid ones), does the order matter, which order is better? I'd think first rereference, then fix... Correct? Thanks!! Ingrid -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 From jan.schoffelen at donders.ru.nl Mon Dec 12 08:59:38 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 12 Dec 2011 08:59:38 +0100 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: References: Message-ID: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> Hi Zita, Could you provide some more information please? What plotting function are you using? What does the stat-structure look like etc.? With sufficient additional information we can try and reproduce the problem, and if it's a bug fix it. If it's not a bug, we may give you some hints to fool the system... BW, Jan-Mathijs On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: > Dear FT-ers, > > I have tried to run a permutation test on time-frequency data, and would have like to see a statistical evealuation over a set of frequencies (ex: 4-8Hz) > > It seems that the test itself runs, but it crashes when i try to plot the data, saying that 'stat' must not contain multiple frequencies. > > I was wondering if there was a way to evaluate the difference between two conditions over a set range of frequencies? > > Thank you! > zita > > > -- > > Zita Patai > DPhil Candidate, Experimental Psychology > University of Oxford > bcl.psy.ox.ac.uk/people/zita-eva-patai/ > eva.patai at psy.ox.ac.uk > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From boracbci at gmail.com Mon Dec 12 09:18:17 2011 From: boracbci at gmail.com (Bora Cebeci) Date: Mon, 12 Dec 2011 10:18:17 +0200 Subject: [FieldTrip] Brainvision recorder RDA Message-ID: Hi, I want to use the Fieldtrip functions for real-time data processing. I'm testing the delay. Neither rda2ft.exe nor ft_realtime_brainampproxy.m is working properly. If you don't get an event, ft_realtime_brainampproxy.m can be usable. I found three messages about Brain Vision Recorder in the mail list. I have similar problems as mentioned in those messages. 1) I think that using rda2ft.exe is faster than ft_realtime_brainampproxy.m, so finding a solution for rda2ft.exe problem will be enough. I have the same error message as *Casper van Heck. Casper *said: " >* When running rda2ft.exe (with the parameters localhost and 51244) it does seem to connect; it shows the list of channels (all channels), their resolution, and their names, and some other assorted stuff. However, it then says: *>* "Unrecognized packet type (10000), has size 24 - exiting"* " My parameters : " rda2ft.exe localhost 51234" and I tried it in a different PC: " rda2ft.exe 10.1.54.160 51234" I got the same error message. 2) Secondly, I tried to use ft_realtime_brainampproxy.m, but I cannot use it efficiently. When an event occurs, buffering freezes and there is no error message. I have a bad solution for this problem. I'm stopping the program by "Ctrl+C" then I start it again. Meanwhile I measured 179ms delay (average of 45 trials), it is really big ?? 3) Even the above problem is solved, the events cannot read. Khalid mentioned before about this problem. I couldn't find the reading code for events in the ft_realtime_brainampproxy.m file. Here is the related part of the code: % convert the RDA message into data and/or events dat = []; event = []; if msg.nType==2 && msg.nPoints>0 % FIXME should I apply the calibration here? dat = msg.nData(chanindx,:); end if msg.nType==4 && msg.nPoints>0 % FIXME should I apply the calibration here? dat = msg.fData(chanindx,:); end if (msg.nType==2 || msg.nType==4) && msg.nMarkers>0 % FIXME convert the message to events end The variable 'event' doesn't get any value here. So by using ft_read_event function , you get an empty vector. Thanks -- Bora Cebeci -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Mon Dec 12 10:40:49 2011 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Mon, 12 Dec 2011 10:40:49 +0100 Subject: [FieldTrip] Brainvision recorder RDA In-Reply-To: References: Message-ID: Dear Bora Cebeci, Thank your for reporting this issue. There are indeed other reports that reading the RDA protocol is not working properly: http://bugzilla.fcdonders.nl/show_bug.cgi?id=1172 http://bugzilla.fcdonders.nl/show_bug.cgi?id=1164 The packet that causes rda2ft.exe to crash is not documented in the RDA protocol, and we are in contact with BrainProducts in order to resolve this issue. The problem you mention in (3) is unforgivable, and I would like to ask you to report this as a separate bug on http:/bugzilla.fcdonders.nl (just copy and past the email). You can then also subscribe to the other two bugs, which allows you to track our progress on fixing this issue. Best regards, Boris Reuderink On Mon, Dec 12, 2011 at 9:18 AM, Bora Cebeci wrote: > Hi, > > I want to use the Fieldtrip functions for real-time data processing. I'm > testing the delay. Neither rda2ft.exe nor ft_realtime_brainampproxy.m is > working properly. If you don't get an event, ft_realtime_brainampproxy.m can > be usable. > I found three messages about Brain Vision Recorder in the mail list. I have > similar problems as mentioned in those messages. > > 1) I think that using rda2ft.exe is faster than ft_realtime_brainampproxy.m, > so finding a solution for rda2ft.exe problem will be enough. I have the same > error message as Casper van Heck. > Casper  said: > " > >> When running rda2ft.exe (with the parameters localhost and 51244) it does >> seem to connect; it shows the list of channels (all channels), their >> resolution, and their names, and some other assorted stuff. However, it then >> says: > > >> "Unrecognized packet type (10000), has size 24 - exiting" > > " > My parameters : " rda2ft.exe localhost 51234" > and I tried it in a different PC: " rda2ft.exe 10.1.54.160 51234" > I got the same error message. > > > 2) Secondly, I tried to use ft_realtime_brainampproxy.m, but I cannot use it > efficiently. When an event occurs, buffering freezes and there is no error > message. > > I have a bad solution for this problem. I'm stopping the program by "Ctrl+C" > then I start it again. > Meanwhile I measured 179ms delay (average of 45 trials), it is really big ?? > > > 3) Even the above problem is solved, the events cannot read. Khalid > mentioned before about this problem. I couldn't find the reading code for > events in the ft_realtime_brainampproxy.m file. Here is the related part of > the code: > >  % convert the RDA message into data and/or events >   dat   = []; >   event = []; > >   if msg.nType==2 && msg.nPoints>0 >     % FIXME should I apply the calibration here? >     dat = msg.nData(chanindx,:); >   end > >   if msg.nType==4 && msg.nPoints>0 >     % FIXME should I apply the calibration here? >     dat = msg.fData(chanindx,:); >   end > >   if (msg.nType==2 || msg.nType==4) && msg.nMarkers>0 >     % FIXME convert the message to events >   end > > The variable 'event' doesn't get any value here. So by using ft_read_event > function , you get an empty vector. > > Thanks > > > -- > Bora Cebeci > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From eva.patai at psy.ox.ac.uk Mon Dec 12 12:22:57 2011 From: eva.patai at psy.ox.ac.uk (Zita Eva Patai) Date: Mon, 12 Dec 2011 11:22:57 +0000 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> Message-ID: Dear Jan-Mathijs, Sorry I was so vague, i thought maybe it was a common problem... OK, so i was running a clusterstat with the following input ( main point, i want to look at the difference between conditions over a set of frequencies) *** load blk1_tf_avg load blk3_tf_avg cfg = []; cfg.latency = [1.0 1.5 ]; cfg.frequency = [4 8]; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 1000; cfg.feedback = 'yes'; cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg); subj = 15; design = zeros(2,2*subj); for i = 1:subj design(1,i) = i; end for i = 1:subj design(1,subj+i) = i; end design(2,1:subj) = 1; design(2,subj+1:2*subj) = 2; cfg.design = design; cfg.uvar = 1; cfg.ivar = 2; [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg); save stat_tf_theta_1000_1500_bkey3vsbkey1 stat *** The error comes during the plotting phase when it says that i should not have multiple frequencies, as the data should be averaged across frequencies. And it does save my file (stat_theta....) but and i can see the pos/neg clusters in the data structure...but i can't plot with : cfg = []; cfg.highlightsymbolseries = ['*','*','.','.','.']; cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay'; cfg.contournum = 0; cfg.markersymbol = '.'; cfg.alpha = 0.05; cfg.zparam = 'stat'; ft_clusterplot(cfg,stat); I have also tried plotting with the script from the tutorial pos_cluster_pvals = [stat.posclusters(:).prob]; pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha); pos = ismember(stat.posclusterslabelmat, pos_signif_clust); neg_cluster_pvals = [stat.negclusters(:).prob]; neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha); neg = ismember(stat.negclusterslabelmat, neg_signif_clust); for k = 1:20; etc. but this makes the plot really weird looking...and i am not sure how i can only plot the data from the frequencies i would like to display (in this case 4-8Hz). I know how to make the subtraction image (between my two conditions), but not how to specify the frequency range that i want displayed... If this is too complicated, is there a way to average over a set of frequencies in the data, and then just input files into the permutation test that are already collapsed across the frequency range i am interested in? Thank you! z On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Zita, > > Could you provide some more information please? What plotting function are > you using? What does the stat-structure look like etc.? With sufficient > additional information we can try and reproduce the problem, and if it's a > bug fix it. If it's not a bug, we may give you some hints to fool the > system... > > BW, > > Jan-Mathijs > > On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: > > Dear FT-ers, > > I have tried to run a permutation test on time-frequency data, and would > have like to see a statistical evealuation over a set of frequencies (ex: > 4-8Hz) > > It seems that the test itself runs, but it crashes when i try to plot the > data, saying that 'stat' must not contain multiple frequencies. > > I was wondering if there was a way to evaluate the difference between two > conditions over a set range of frequencies? > > Thank you! > zita > > > -- > > Zita Patai > DPhil Candidate, Experimental Psychology > University of Oxford > bcl.psy.ox.ac.uk/people/zita-eva-patai/ > eva.patai at psy.ox.ac.uk > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Zita Patai DPhil Candidate, Experimental Psychology University of Oxford bcl.psy.ox.ac.uk/people/zita-eva-patai/ eva.patai at psy.ox.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From dporada at uos.de Mon Dec 12 16:16:01 2011 From: dporada at uos.de (Porada Danja) Date: Mon, 12 Dec 2011 16:16:01 +0100 Subject: [FieldTrip] Automatic artifact rejection Message-ID: <5BCBAF3A-26D5-4B64-BC0C-DD8284D6551D@uos.de> Hi, I want to use automatic artifact detection to clean my MEG-data. Does it make sense to clean the data visually first, remove very odd trials (like very huge slow waveforms which were caused by a passing car) and then apply the ft_artifact_zvalue function? I went step by step through the ft_artifact_zvalue function using the same parameters as proposed in the "automatic artifact rejection" tutorial for jump artifacts. It seems to me that the function doesn't use the parameter "absdiff" which is specified in cfg.artfctdef.zvalue.absdiff = 'yes'. Is this right? I am using the fieldtrip-20111115-version. Best, Danja From jm.horschig at donders.ru.nl Mon Dec 12 16:18:34 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 12 Dec 2011 16:18:34 +0100 Subject: [FieldTrip] rereference to repaired channel In-Reply-To: <4EE50D33.8030500@berkeley.edu> References: <4EE50D33.8030500@berkeley.edu> Message-ID: <4EE61B4A.4050208@donders.ru.nl> Hi Ingrid, ft_channelrepair is simply taking the average of the neighbouring channels. So, you would need to specify your neighbours and based on this, and it just gets the average of the neighbours of your mastoid. However, imho, you cannot really define neighbours for a mastoid channel. There is a method to interpolate not using nearest neighbours but spherical splines, however this is not (yet) part of FieldTrip, see also here: http://bugzilla.fcdonders.nl/show_bug.cgi?id=634 But, I am not sure if this would help in this case either. If you really want to use linked mastoid as a reference, I would probably reject that subject due to bad signal quality. I don't know if anyone on the list has a better idea (or more experience). Second, if you first rereference, all noise from this one channel will leak into all other channels, as you said. As long as your mastoid is not a bad channel, there should be no difference whether you first rereference or then interpolate bad channels or the other way around (assuming that I got no mathematical blackout right now). Should be easy to verify, e.g. if you have channels A, B, and C (all neighbours) and want to reference to R, then your referenced channels would be A-R, B-R and C-R. If B is a bad channel, and you interpolate first, you get B=(A+C)/2 (i.e. just the average of the neighbouring sensors). If you then rereference you will obtain (A+C)/2 - R, which is the same as (A+C) /2 - (R+R)/2 = (A-R + C-R) /2. If you first rereference and then interpolate you obtain B-R = (A-R + C-R) /2 immediately (because A-R and C-R are the only neighbours of B-R). Hope it helps! Best, Jörn On 12/11/2011 9:06 PM, Ingrid Nieuwenhuis wrote: > Hi all, > > I've measured EEG data with Cz as the reference. I now want to > rereference to linked mastoids. However, in one participant one of the > mastoid electrodes is really noisy. Is it valid to throw out the noisy > channel, then fix it (with ft_channelrepair), and then rereference to > this fixed mastoid channel? In other words, is channelrepair a linear > operation? Or would I be mixing (a little) Cz into all channels > now...? Any other options? > > Or another way of asking: do I get the same result if I first > rereference and then fix bad channels, compared to first fixing bad > channels and then rereference? In the participant with the bad mastoid > chan, I don't have a choice, I have to first fix the channel first, or > I'd be mixing noise into all channels. But, in other participants, > where I also have bad channels (but not the mastoid ones), does the > order matter, which order is better? I'd think first rereference, then > fix... Correct? > > Thanks!! > Ingrid > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From inieuwenhuis at berkeley.edu Mon Dec 12 18:00:06 2011 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Mon, 12 Dec 2011 09:00:06 -0800 Subject: [FieldTrip] rereference to repaired channel In-Reply-To: <4EE61B4A.4050208@donders.ru.nl> References: <4EE50D33.8030500@berkeley.edu> <4EE61B4A.4050208@donders.ru.nl> Message-ID: <4EE63316.40104@berkeley.edu> Hi Jorn, Thanks a lot! And fortunately, the mastoid has plenty neighbours ('E95' 'E96' 'E99' 'E101' 'E107' 'E108'), since I'm using high density EEG (128 EGI). The spherical spline method sounds pretty cool as well. Would be cool to implement one day indeed! Cheers, Ingrid On 12/12/2011 7:18 AM, "Jörn M. Horschig" wrote: > Hi Ingrid, > > ft_channelrepair is simply taking the average of the neighbouring > channels. So, you would need to specify your neighbours and based on > this, and it just gets the average of the neighbours of your mastoid. > However, imho, you cannot really define neighbours for a mastoid > channel. There is a method to interpolate not using nearest neighbours > but spherical splines, however this is not (yet) part of FieldTrip, > see also here: > http://bugzilla.fcdonders.nl/show_bug.cgi?id=634 > But, I am not sure if this would help in this case either. If you > really want to use linked mastoid as a reference, I would probably > reject that subject due to bad signal quality. I don't know if anyone > on the list has a better idea (or more experience). > > Second, if you first rereference, all noise from this one channel will > leak into all other channels, as you said. As long as your mastoid is > not a bad channel, there should be no difference whether you first > rereference or then interpolate bad channels or the other way around > (assuming that I got no mathematical blackout right now). > Should be easy to verify, e.g. if you have channels A, B, and C (all > neighbours) and want to reference to R, then your referenced channels > would be A-R, B-R and C-R. > If B is a bad channel, and you interpolate first, you get B=(A+C)/2 > (i.e. just the average of the neighbouring sensors). If you then > rereference you will obtain (A+C)/2 - R, which is the same as (A+C) /2 > - (R+R)/2 = (A-R + C-R) /2. > If you first rereference and then interpolate you obtain B-R = (A-R + > C-R) /2 immediately (because A-R and C-R are the only neighbours of B-R). > > Hope it helps! Best, > Jörn > > On 12/11/2011 9:06 PM, Ingrid Nieuwenhuis wrote: >> Hi all, >> >> I've measured EEG data with Cz as the reference. I now want to >> rereference to linked mastoids. However, in one participant one of >> the mastoid electrodes is really noisy. Is it valid to throw out the >> noisy channel, then fix it (with ft_channelrepair), and then >> rereference to this fixed mastoid channel? In other words, is >> channelrepair a linear operation? Or would I be mixing (a little) Cz >> into all channels now...? Any other options? >> >> Or another way of asking: do I get the same result if I first >> rereference and then fix bad channels, compared to first fixing bad >> channels and then rereference? In the participant with the bad >> mastoid chan, I don't have a choice, I have to first fix the channel >> first, or I'd be mixing noise into all channels. But, in other >> participants, where I also have bad channels (but not the mastoid >> ones), does the order matter, which order is better? I'd think first >> rereference, then fix... Correct? >> >> Thanks!! >> Ingrid >> > > -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 From jan.schoffelen at donders.ru.nl Tue Dec 13 09:27:45 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 13 Dec 2011 09:27:45 +0100 Subject: [FieldTrip] PhD studentship available in cortical networks of aging at CCNi Glasgow References: <218D83BF-2F53-4471-881B-0AF4CE682E97@glasgow.ac.uk> Message-ID: <875C1820-4679-49F6-8952-85ABF6C24EC9@donders.ru.nl> Dear all, Please see below a PhD-position available at Glasgow university. Cheers, JM A 4-year PhD studentship is available to work with Philippe Schyns & Guillaume Rousselet in the Institute of Neuroscience and Psychology. Understanding age-related changes in the processing of emotion information Deadline: Friday 27th January 2012 Stipend: £13,848 per annum The start date is October 2012 and applicants will normally be expected to reside (or have residency) within the UK or EU. The financial package will include a four year stipend, approved University fees, Research Training Support Grant and a Conference Allowance. Information about the training and how to apply is available here: http://www.gla.ac.uk/colleges/mvls/graduateschool/informationforprospectivestudents/phdandmresscholarships/phdprogrammes/ Contact us directly for inquiries about the project: Philippe Schyns Guillaume Rousselet Abstract: It is estimated that, by 2060, one quarter of the British population will be over 65, many of whom will still be working. Over a lifetime, the brain ages as dramatically as the body, manifesting itself in the decline of the basic and essential task of interpreting social signals. Research has established that ageing adults show specific differences in the emotional interpretation of facial expressions, particularly anger. These perceptual differences could have drastic impacts on everyday social interactions and decision-making. Failure to accurately interpret social signals may lead to vulnerabilities in critical social interactions such as identifying deception and predicting the behavioural intentions of others. With the development of new methods in computational neuroscience, it has become possible to further understand why the ageing brain fails in what are deceptively simple information processing tasks—i.e. interpreting the emotions of others. We will study how oscillatory networks in the ageing brain extract and further process visual information to recognize facial expressions of emotion at different intensities. Our framework will combine a unique platform that precisely controls the photo-realistic biological motion of faces with other developments in applications of information theoretic mathematics to analyses of brain signals. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Dec 13 17:06:53 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 13 Dec 2011 17:06:53 +0100 Subject: [FieldTrip] DICS beamformer images In-Reply-To: References: Message-ID: <3A18CB06-2B78-41C6-8F9C-BC21C0147BEF@donders.ru.nl> Hi Holly, DICS can also be used to compute univariate power in a given frequency band. This yields not a bounded quantity. Depending on your analysis settings you will observe a depth bias which is not physiologically relevant. Best way to deal with this is to compute the beamformer maps using an experimental contrast. Best Jan-Mathijs On Dec 6, 2011, at 2:18 PM, Rossiter, Holly wrote: > Hi all, > > I am using DICS to assess coherence and viewing the beamformer images through SPM. What I want to know is what is the value given in the image and how is it calculated? I thought it was a coherence value but it is not bounded between 0 and 1. > > Also what do you think is the best way to threshold the images in order to get rid of low value peaks? > > Thanks, > > Holly > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Dec 13 17:10:22 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 13 Dec 2011 17:10:22 +0100 Subject: [FieldTrip] Interactive Plotting in ft_rejectvisual In-Reply-To: <1C5AEC7D-4B54-428E-BE54-B408171837FC@gmail.com> References: <1C5AEC7D-4B54-428E-BE54-B408171837FC@gmail.com> Message-ID: <31D7B637-547A-4C66-ADE1-351F59CAD83B@donders.ru.nl> Dear Julian, Thanks for reporting this. We will look into the issue. If you want to stay informed about this you can consider creating yourself a bugzilla account on www.bugzilla.fcdonders.nl. People who have an account can add themselves in the CC for a particular bug/feature request. The issue you sketched has been filed by me as bug 1230. Best wishes, Jan-Mathijs On Dec 7, 2011, at 10:42 AM, Julian Keil wrote: > Hi, > > Not really a bug report, so I put this on the discussion List. > I noticed that when plotting single trials in the ft_rejectivusal function, the figure popping up is not interactive which makes a closer inspection of the trials somewhat harder. > Maybe this is intentional, but I can't see a reason for it. > However, simply adding "cfg_mp.interactive='yes';" at line 510 of "reject visual_summary" fixes this. > > Best, > > Julian > > > Dipl. Psych. Julian Keil > > OBOB-Lab > University of Konstanz > Department of Psychology > P.O. Box D25 > 78457 Konstanz > Germany > > Tel: ++49 - (0)7531 - 88 42 50 > Fax: ++49 - (0)7531 - 88 28 91 > Email: julian.keil at uni-konstanz.de > Homepage: http://www.uni-konstanz.de/obob > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Dec 13 17:22:42 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 13 Dec 2011 17:22:42 +0100 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> Message-ID: <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> Hi Zita, OK. I now understand the point. ft_clusterplot throws an error because it does not know how to collapse across frequencies. If the clusters have spectral extent (as well as spatial extent) it's a non-trivial question what are the channels to be plotted, because different channels can contribute different time and frequency points to the significant cluster. The time points are dealt with because ft_clusterplot shows the cluster evolving over time; the frequencies are not dealt with. FieldTrip does not make the choice of which channels to highlight for you (should all frequencies be significant for a given time point, or only one, or just a few?) and thus throws an error. However, if you have a priori reasons to expect your effect to occur in a particular frequency range (as you seem to do, because of your specification of the cfg before calling ft_freqstatistics), you can also specify cfg.avgoverfreq to 'yes', yielding a single observation per channel (and by construction the clustering only occurs over channels), making the plotting trivial. I hope this helps. BW, JM On Dec 12, 2011, at 12:22 PM, Zita Eva Patai wrote: > Dear Jan-Mathijs, > > Sorry I was so vague, i thought maybe it was a common problem... > > OK, so i was running a clusterstat with the following input ( main point, i want to look at the difference between conditions over a set of frequencies) > *** > load blk1_tf_avg > load blk3_tf_avg > > cfg = []; > cfg.latency = [1.0 1.5 ]; > cfg.frequency = [4 8]; > cfg.method = 'montecarlo'; > cfg.statistic = 'depsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 1000; > cfg.feedback = 'yes'; > cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg); > subj = 15; > design = zeros(2,2*subj); > for i = 1:subj > design(1,i) = i; > end > for i = 1:subj > design(1,subj+i) = i; > end > design(2,1:subj) = 1; > design(2,subj+1:2*subj) = 2; > > > cfg.design = design; > cfg.uvar = 1; > cfg.ivar = 2; > > [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg); > > save stat_tf_theta_1000_1500_bkey3vsbkey1 stat > > > *** > > The error comes during the plotting phase when it says that i should not have multiple frequencies, as the data should be averaged across frequencies. And it does save my file (stat_theta....) but and i can see the pos/neg clusters in the data structure...but i can't plot with : > > cfg = []; > cfg.highlightsymbolseries = ['*','*','.','.','.']; > cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay'; > cfg.contournum = 0; > cfg.markersymbol = '.'; > cfg.alpha = 0.05; > cfg.zparam = 'stat'; > ft_clusterplot(cfg,stat); > > > I have also tried plotting with the script from the tutorial > > pos_cluster_pvals = [stat.posclusters(:).prob]; > pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha); > pos = ismember(stat.posclusterslabelmat, pos_signif_clust); > > neg_cluster_pvals = [stat.negclusters(:).prob]; > neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha); > neg = ismember(stat.negclusterslabelmat, neg_signif_clust); > > for k = 1:20; > > etc. > but this makes the plot really weird looking...and i am not sure how i can only plot the data from the frequencies i would like to display (in this case 4-8Hz). I know how to make the subtraction image (between my two conditions), but not how to specify the frequency range that i want displayed... > > If this is too complicated, is there a way to average over a set of frequencies in the data, and then just input files into the permutation test that are already collapsed across the frequency range i am interested in? > > > Thank you! > z > > > On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen wrote: > Hi Zita, > > Could you provide some more information please? What plotting function are you using? What does the stat-structure look like etc.? With sufficient additional information we can try and reproduce the problem, and if it's a bug fix it. If it's not a bug, we may give you some hints to fool the system... > > BW, > > Jan-Mathijs > > On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: > >> Dear FT-ers, >> >> I have tried to run a permutation test on time-frequency data, and would have like to see a statistical evealuation over a set of frequencies (ex: 4-8Hz) >> >> It seems that the test itself runs, but it crashes when i try to plot the data, saying that 'stat' must not contain multiple frequencies. >> >> I was wondering if there was a way to evaluate the difference between two conditions over a set range of frequencies? >> >> Thank you! >> zita >> >> >> -- >> >> Zita Patai >> DPhil Candidate, Experimental Psychology >> University of Oxford >> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >> eva.patai at psy.ox.ac.uk >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > > Zita Patai > DPhil Candidate, Experimental Psychology > University of Oxford > bcl.psy.ox.ac.uk/people/zita-eva-patai/ > eva.patai at psy.ox.ac.uk > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From eva.patai at psy.ox.ac.uk Tue Dec 13 18:10:58 2011 From: eva.patai at psy.ox.ac.uk (Zita Eva Patai) Date: Tue, 13 Dec 2011 17:10:58 +0000 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> Message-ID: Dear Jan-Mathijs, Thank you for that, it makes a lot more sense. I figured the data was too complex for display, so I will average over frequencies as you suggested, as I am interested in an effect that would encompass that range anyway... Thank you again and happy holidays! z On Tue, Dec 13, 2011 at 4:22 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Zita, > > OK. I now understand the point. ft_clusterplot throws an error because it > does not know how to collapse across frequencies. If the clusters have > spectral extent (as well as spatial extent) it's a non-trivial question > what are the channels to be plotted, because different channels can > contribute different time and frequency points to the significant cluster. > The time points are dealt with because ft_clusterplot shows the cluster > evolving over time; the frequencies are not dealt with. FieldTrip does not > make the choice of which channels to highlight for you (should all > frequencies be significant for a given time point, or only one, or just a > few?) and thus throws an error. However, if you have a priori reasons to > expect your effect to occur in a particular frequency range (as you seem to > do, because of your specification of the cfg before calling > ft_freqstatistics), you can also specify cfg.avgoverfreq to 'yes', yielding > a single observation per channel (and by construction the clustering only > occurs over channels), making the plotting trivial. > > I hope this helps. > > BW, > > JM > > > > On Dec 12, 2011, at 12:22 PM, Zita Eva Patai wrote: > > Dear Jan-Mathijs, > > Sorry I was so vague, i thought maybe it was a common problem... > > OK, so i was running a clusterstat with the following input ( main point, > i want to look at the difference between conditions over a set of > frequencies) > *** > load blk1_tf_avg > load blk3_tf_avg > > cfg = []; > cfg.latency = [1.0 1.5 ]; > cfg.frequency = [4 8]; > cfg.method = 'montecarlo'; > cfg.statistic = 'depsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 1000; > cfg.feedback = 'yes'; > cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg); > subj = 15; > design = zeros(2,2*subj); > for i = 1:subj > design(1,i) = i; > end > for i = 1:subj > design(1,subj+i) = i; > end > design(2,1:subj) = 1; > design(2,subj+1:2*subj) = 2; > > > cfg.design = design; > cfg.uvar = 1; > cfg.ivar = 2; > > > [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg); > > > save stat_tf_theta_1000_1500_bkey3vsbkey1 stat > > > *** > > The error comes during the plotting phase when it says that i should not > have multiple frequencies, as the data should be averaged across > frequencies. And it does save my file (stat_theta....) but and i can see > the pos/neg clusters in the data structure...but i can't plot with : > > cfg = []; > cfg.highlightsymbolseries = ['*','*','.','.','.']; > cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay'; > cfg.contournum = 0; > cfg.markersymbol = '.'; > cfg.alpha = 0.05; > cfg.zparam = 'stat'; > ft_clusterplot(cfg,stat); > > > > I have also tried plotting with the script from the tutorial > > > pos_cluster_pvals = [stat.posclusters(:).prob]; > pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha); > pos = ismember(stat.posclusterslabelmat, pos_signif_clust); > > > neg_cluster_pvals = [stat.negclusters(:).prob]; > neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha); > neg = ismember(stat.negclusterslabelmat, neg_signif_clust); > > for k = 1:20; > > etc. > but this makes the plot really weird looking...and i am not sure how i can > only plot the data from the frequencies i would like to display (in this > case 4-8Hz). I know how to make the subtraction image (between my two > conditions), but not how to specify the frequency range that i want > displayed... > > If this is too complicated, is there a way to average over a set of > frequencies in the data, and then just input files into the permutation > test that are already collapsed across the frequency range i am interested > in? > > > Thank you! > z > > > On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Zita, >> >> Could you provide some more information please? What plotting function >> are you using? What does the stat-structure look like etc.? With sufficient >> additional information we can try and reproduce the problem, and if it's a >> bug fix it. If it's not a bug, we may give you some hints to fool the >> system... >> >> BW, >> >> Jan-Mathijs >> >> On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: >> >> Dear FT-ers, >> >> I have tried to run a permutation test on time-frequency data, and would >> have like to see a statistical evealuation over a set of frequencies (ex: >> 4-8Hz) >> >> It seems that the test itself runs, but it crashes when i try to plot the >> data, saying that 'stat' must not contain multiple frequencies. >> >> I was wondering if there was a way to evaluate the difference between two >> conditions over a set range of frequencies? >> >> Thank you! >> zita >> >> >> -- >> >> Zita Patai >> DPhil Candidate, Experimental Psychology >> University of Oxford >> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >> eva.patai at psy.ox.ac.uk >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > > Zita Patai > DPhil Candidate, Experimental Psychology > University of Oxford > bcl.psy.ox.ac.uk/people/zita-eva-patai/ > eva.patai at psy.ox.ac.uk > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Zita Patai DPhil Candidate, Experimental Psychology University of Oxford bcl.psy.ox.ac.uk/people/zita-eva-patai/ eva.patai at psy.ox.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Tue Dec 13 18:47:40 2011 From: matt.mollison at gmail.com (Matt Mollison) Date: Tue, 13 Dec 2011 10:47:40 -0700 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> Message-ID: Hi Zita, I have not used this method much, but it actually is possible to plot clusters without averaging over the frequency dimension using ft_multiplotTFR (where cfg.avgoverchan = 'no'; cfg.avgovertime = 'no'; cfg.avgoverfreq='no'; in your statistical test—so you'll get space, time, and frequency information). You can also highlight the significant portions of time and frequency space, using cfg.mask='yes', cfg.maskparameter='mask', and set a cfg.maskalpha. Do keep in mind that there are important reasons for averaging over frequency, as Dr. Maris described in this post (specifically, to increase power): < http://mailman.science.ru.nl/pipermail/fieldtrip/2010-November/003312.html>. Cheers, Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Tue, Dec 13, 2011 at 10:10 AM, Zita Eva Patai wrote: > Dear Jan-Mathijs, > > Thank you for that, it makes a lot more sense. I figured the data was too > complex for display, so I will average over frequencies as you suggested, > as I am interested in an effect that would encompass that range anyway... > > Thank you again and happy holidays! > z > > On Tue, Dec 13, 2011 at 4:22 PM, jan-mathijs schoffelen < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Zita, >> >> OK. I now understand the point. ft_clusterplot throws an error because it >> does not know how to collapse across frequencies. If the clusters have >> spectral extent (as well as spatial extent) it's a non-trivial question >> what are the channels to be plotted, because different channels can >> contribute different time and frequency points to the significant cluster. >> The time points are dealt with because ft_clusterplot shows the cluster >> evolving over time; the frequencies are not dealt with. FieldTrip does not >> make the choice of which channels to highlight for you (should all >> frequencies be significant for a given time point, or only one, or just a >> few?) and thus throws an error. However, if you have a priori reasons to >> expect your effect to occur in a particular frequency range (as you seem to >> do, because of your specification of the cfg before calling >> ft_freqstatistics), you can also specify cfg.avgoverfreq to 'yes', yielding >> a single observation per channel (and by construction the clustering only >> occurs over channels), making the plotting trivial. >> >> I hope this helps. >> >> BW, >> >> JM >> >> >> >> On Dec 12, 2011, at 12:22 PM, Zita Eva Patai wrote: >> >> Dear Jan-Mathijs, >> >> Sorry I was so vague, i thought maybe it was a common problem... >> >> OK, so i was running a clusterstat with the following input ( main point, >> i want to look at the difference between conditions over a set of >> frequencies) >> *** >> load blk1_tf_avg >> load blk3_tf_avg >> >> cfg = []; >> cfg.latency = [1.0 1.5 ]; >> cfg.frequency = [4 8]; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'depsamplesT'; >> cfg.correctm = 'cluster'; >> cfg.clusteralpha = 0.05; >> cfg.clusterstatistic = 'maxsum'; >> cfg.minnbchan = 2; >> cfg.tail = 0; >> cfg.clustertail = 0; >> cfg.alpha = 0.025; >> cfg.numrandomization = 1000; >> cfg.feedback = 'yes'; >> cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg); >> subj = 15; >> design = zeros(2,2*subj); >> for i = 1:subj >> design(1,i) = i; >> end >> for i = 1:subj >> design(1,subj+i) = i; >> end >> design(2,1:subj) = 1; >> design(2,subj+1:2*subj) = 2; >> >> >> cfg.design = design; >> cfg.uvar = 1; >> cfg.ivar = 2; >> >> >> [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg); >> >> >> save stat_tf_theta_1000_1500_bkey3vsbkey1 stat >> >> >> *** >> >> The error comes during the plotting phase when it says that i should not >> have multiple frequencies, as the data should be averaged across >> frequencies. And it does save my file (stat_theta....) but and i can see >> the pos/neg clusters in the data structure...but i can't plot with : >> >> cfg = []; >> cfg.highlightsymbolseries = ['*','*','.','.','.']; >> cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay'; >> cfg.contournum = 0; >> cfg.markersymbol = '.'; >> cfg.alpha = 0.05; >> cfg.zparam = 'stat'; >> ft_clusterplot(cfg,stat); >> >> >> >> I have also tried plotting with the script from the tutorial >> >> >> pos_cluster_pvals = [stat.posclusters(:).prob]; >> pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha); >> pos = ismember(stat.posclusterslabelmat, pos_signif_clust); >> >> >> neg_cluster_pvals = [stat.negclusters(:).prob]; >> neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha); >> neg = ismember(stat.negclusterslabelmat, neg_signif_clust); >> >> for k = 1:20; >> >> etc. >> but this makes the plot really weird looking...and i am not sure how i >> can only plot the data from the frequencies i would like to display (in >> this case 4-8Hz). I know how to make the subtraction image (between my two >> conditions), but not how to specify the frequency range that i want >> displayed... >> >> If this is too complicated, is there a way to average over a set of >> frequencies in the data, and then just input files into the permutation >> test that are already collapsed across the frequency range i am interested >> in? >> >> >> Thank you! >> z >> >> >> On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen < >> jan.schoffelen at donders.ru.nl> wrote: >> >>> Hi Zita, >>> >>> Could you provide some more information please? What plotting function >>> are you using? What does the stat-structure look like etc.? With sufficient >>> additional information we can try and reproduce the problem, and if it's a >>> bug fix it. If it's not a bug, we may give you some hints to fool the >>> system... >>> >>> BW, >>> >>> Jan-Mathijs >>> >>> On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: >>> >>> Dear FT-ers, >>> >>> I have tried to run a permutation test on time-frequency data, and would >>> have like to see a statistical evealuation over a set of frequencies (ex: >>> 4-8Hz) >>> >>> It seems that the test itself runs, but it crashes when i try to plot >>> the data, saying that 'stat' must not contain multiple frequencies. >>> >>> I was wondering if there was a way to evaluate the difference between >>> two conditions over a set range of frequencies? >>> >>> Thank you! >>> zita >>> >>> >>> -- >>> >>> Zita Patai >>> DPhil Candidate, Experimental Psychology >>> University of Oxford >>> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >>> eva.patai at psy.ox.ac.uk >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> Jan-Mathijs Schoffelen, MD PhD >>> >>> Donders Institute for Brain, Cognition and Behaviour, >>> Centre for Cognitive Neuroimaging, >>> Radboud University Nijmegen, The Netherlands >>> >>> Max Planck Institute for Psycholinguistics, >>> Nijmegen, The Netherlands >>> >>> J.Schoffelen at donders.ru.nl >>> Telephone: +31-24-3614793 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> >> Zita Patai >> DPhil Candidate, Experimental Psychology >> University of Oxford >> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >> eva.patai at psy.ox.ac.uk >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > > Zita Patai > DPhil Candidate, Experimental Psychology > University of Oxford > bcl.psy.ox.ac.uk/people/zita-eva-patai/ > eva.patai at psy.ox.ac.uk > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eva.patai at psy.ox.ac.uk Tue Dec 13 19:18:36 2011 From: eva.patai at psy.ox.ac.uk (Zita Eva Patai) Date: Tue, 13 Dec 2011 18:18:36 +0000 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> Message-ID: Thank you Matt, that further makes my situation more clear to me! On Tue, Dec 13, 2011 at 5:47 PM, Matt Mollison wrote: > Hi Zita, > > I have not used this method much, but it actually is possible to plot > clusters without averaging over the frequency dimension > using ft_multiplotTFR (where cfg.avgoverchan = 'no'; cfg.avgovertime = > 'no'; cfg.avgoverfreq='no'; in your statistical test—so you'll get space, > time, and frequency information). You can also highlight the significant > portions of time and frequency space, using cfg.mask='yes', > cfg.maskparameter='mask', and set a cfg.maskalpha. Do keep in mind that > there are important reasons for averaging over frequency, as Dr. Maris > described in this post (specifically, to increase power): < > http://mailman.science.ru.nl/pipermail/fieldtrip/2010-November/003312.html > >. > > Cheers, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > > On Tue, Dec 13, 2011 at 10:10 AM, Zita Eva Patai wrote: > >> Dear Jan-Mathijs, >> >> Thank you for that, it makes a lot more sense. I figured the data was too >> complex for display, so I will average over frequencies as you suggested, >> as I am interested in an effect that would encompass that range anyway... >> >> Thank you again and happy holidays! >> z >> >> On Tue, Dec 13, 2011 at 4:22 PM, jan-mathijs schoffelen < >> jan.schoffelen at donders.ru.nl> wrote: >> >>> Hi Zita, >>> >>> OK. I now understand the point. ft_clusterplot throws an error because >>> it does not know how to collapse across frequencies. If the clusters have >>> spectral extent (as well as spatial extent) it's a non-trivial question >>> what are the channels to be plotted, because different channels can >>> contribute different time and frequency points to the significant cluster. >>> The time points are dealt with because ft_clusterplot shows the cluster >>> evolving over time; the frequencies are not dealt with. FieldTrip does not >>> make the choice of which channels to highlight for you (should all >>> frequencies be significant for a given time point, or only one, or just a >>> few?) and thus throws an error. However, if you have a priori reasons to >>> expect your effect to occur in a particular frequency range (as you seem to >>> do, because of your specification of the cfg before calling >>> ft_freqstatistics), you can also specify cfg.avgoverfreq to 'yes', yielding >>> a single observation per channel (and by construction the clustering only >>> occurs over channels), making the plotting trivial. >>> >>> I hope this helps. >>> >>> BW, >>> >>> JM >>> >>> >>> >>> On Dec 12, 2011, at 12:22 PM, Zita Eva Patai wrote: >>> >>> Dear Jan-Mathijs, >>> >>> Sorry I was so vague, i thought maybe it was a common problem... >>> >>> OK, so i was running a clusterstat with the following input ( main >>> point, i want to look at the difference between conditions over a set of >>> frequencies) >>> *** >>> load blk1_tf_avg >>> load blk3_tf_avg >>> >>> cfg = []; >>> cfg.latency = [1.0 1.5 ]; >>> cfg.frequency = [4 8]; >>> cfg.method = 'montecarlo'; >>> cfg.statistic = 'depsamplesT'; >>> cfg.correctm = 'cluster'; >>> cfg.clusteralpha = 0.05; >>> cfg.clusterstatistic = 'maxsum'; >>> cfg.minnbchan = 2; >>> cfg.tail = 0; >>> cfg.clustertail = 0; >>> cfg.alpha = 0.025; >>> cfg.numrandomization = 1000; >>> cfg.feedback = 'yes'; >>> cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg); >>> subj = 15; >>> design = zeros(2,2*subj); >>> for i = 1:subj >>> design(1,i) = i; >>> end >>> for i = 1:subj >>> design(1,subj+i) = i; >>> end >>> design(2,1:subj) = 1; >>> design(2,subj+1:2*subj) = 2; >>> >>> >>> cfg.design = design; >>> cfg.uvar = 1; >>> cfg.ivar = 2; >>> >>> >>> [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg); >>> >>> >>> save stat_tf_theta_1000_1500_bkey3vsbkey1 stat >>> >>> >>> *** >>> >>> The error comes during the plotting phase when it says that i should not >>> have multiple frequencies, as the data should be averaged across >>> frequencies. And it does save my file (stat_theta....) but and i can see >>> the pos/neg clusters in the data structure...but i can't plot with : >>> >>> cfg = []; >>> cfg.highlightsymbolseries = ['*','*','.','.','.']; >>> cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay'; >>> cfg.contournum = 0; >>> cfg.markersymbol = '.'; >>> cfg.alpha = 0.05; >>> cfg.zparam = 'stat'; >>> ft_clusterplot(cfg,stat); >>> >>> >>> >>> I have also tried plotting with the script from the tutorial >>> >>> >>> pos_cluster_pvals = [stat.posclusters(:).prob]; >>> pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha); >>> pos = ismember(stat.posclusterslabelmat, pos_signif_clust); >>> >>> >>> neg_cluster_pvals = [stat.negclusters(:).prob]; >>> neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha); >>> neg = ismember(stat.negclusterslabelmat, neg_signif_clust); >>> >>> for k = 1:20; >>> >>> etc. >>> but this makes the plot really weird looking...and i am not sure how i >>> can only plot the data from the frequencies i would like to display (in >>> this case 4-8Hz). I know how to make the subtraction image (between my two >>> conditions), but not how to specify the frequency range that i want >>> displayed... >>> >>> If this is too complicated, is there a way to average over a set of >>> frequencies in the data, and then just input files into the permutation >>> test that are already collapsed across the frequency range i am interested >>> in? >>> >>> >>> Thank you! >>> z >>> >>> >>> On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen < >>> jan.schoffelen at donders.ru.nl> wrote: >>> >>>> Hi Zita, >>>> >>>> Could you provide some more information please? What plotting function >>>> are you using? What does the stat-structure look like etc.? With sufficient >>>> additional information we can try and reproduce the problem, and if it's a >>>> bug fix it. If it's not a bug, we may give you some hints to fool the >>>> system... >>>> >>>> BW, >>>> >>>> Jan-Mathijs >>>> >>>> On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: >>>> >>>> Dear FT-ers, >>>> >>>> I have tried to run a permutation test on time-frequency data, and >>>> would have like to see a statistical evealuation over a set of frequencies >>>> (ex: 4-8Hz) >>>> >>>> It seems that the test itself runs, but it crashes when i try to plot >>>> the data, saying that 'stat' must not contain multiple frequencies. >>>> >>>> I was wondering if there was a way to evaluate the difference between >>>> two conditions over a set range of frequencies? >>>> >>>> Thank you! >>>> zita >>>> >>>> >>>> -- >>>> >>>> Zita Patai >>>> DPhil Candidate, Experimental Psychology >>>> University of Oxford >>>> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >>>> eva.patai at psy.ox.ac.uk >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> Jan-Mathijs Schoffelen, MD PhD >>>> >>>> Donders Institute for Brain, Cognition and Behaviour, >>>> Centre for Cognitive Neuroimaging, >>>> Radboud University Nijmegen, The Netherlands >>>> >>>> Max Planck Institute for Psycholinguistics, >>>> Nijmegen, The Netherlands >>>> >>>> J.Schoffelen at donders.ru.nl >>>> Telephone: +31-24-3614793 >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> >>> Zita Patai >>> DPhil Candidate, Experimental Psychology >>> University of Oxford >>> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >>> eva.patai at psy.ox.ac.uk >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> Jan-Mathijs Schoffelen, MD PhD >>> >>> Donders Institute for Brain, Cognition and Behaviour, >>> Centre for Cognitive Neuroimaging, >>> Radboud University Nijmegen, The Netherlands >>> >>> Max Planck Institute for Psycholinguistics, >>> Nijmegen, The Netherlands >>> >>> J.Schoffelen at donders.ru.nl >>> Telephone: +31-24-3614793 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> >> Zita Patai >> DPhil Candidate, Experimental Psychology >> University of Oxford >> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >> eva.patai at psy.ox.ac.uk >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Zita Patai DPhil Candidate, Experimental Psychology University of Oxford bcl.psy.ox.ac.uk/people/zita-eva-patai/ eva.patai at psy.ox.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From Gregor.Volberg at psychologie.uni-regensburg.de Wed Dec 14 10:32:17 2011 From: Gregor.Volberg at psychologie.uni-regensburg.de (Gregor Volberg) Date: Wed, 14 Dec 2011 10:32:17 +0100 Subject: [FieldTrip] read_eeglab, header file? In-Reply-To: References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> Message-ID: <4EE87B31020000570000BF1A@gwsmtp1.uni-regensburg.de> Dear Fieldtrip developers, I encountered an error warning when reading in an eeglab *.set - file for preprocessing (version fieldtrip-20111206), where the call to ft_preprocessing says ??? Undefined function or variable "hdr". Error in ==> read_eeglabdata at 52 if isempty(hdr) Shouldn't code lines 52 to 54 read if isempty(header) header = read_eeglabheader(filename); end instead of if isempty(hdr) hdr = read_eeglabheader(filename); end Not really a problem, just to bring it to your attention... Best regards, Gregor -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.hesselmann at gmail.com Wed Dec 14 18:53:46 2011 From: g.hesselmann at gmail.com (Guido Hesselmann) Date: Wed, 14 Dec 2011 18:53:46 +0100 Subject: [FieldTrip] Time-frequency analysis: based on single trials or on average? Message-ID: Hi all, I am new to fieldtrip and have a very simple question. I have EEG data and would like to run a time-frequency analysis (e.g., using a Hanning taper with fixed window length). If I have 100 trials, how is this analysis performed? On a trial-by-trial basis, or based on the average? Can I choose between these options in fieldtrip? Thanks a lot! Guido Hesselmann Visual Perception Lab Department of Psychiatry & Psychotherapy Charité Berlin -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Wed Dec 14 19:03:49 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Wed, 14 Dec 2011 19:03:49 +0100 Subject: [FieldTrip] Time-frequency analysis: based on single trials or on average? In-Reply-To: References: Message-ID: Hi Guido, The FieldTrip method that performs time-frequency analyses is called ft_freqanalysis. By default, ft_freqanalysis gives you power averaged over trials as output. You can easily override this default behaviour by specifying cfg.keeptrials='yes', you will then get a power estimate for each individual trial. You might want to take a look at the following tutorial, which covers the basics of how to do time-frequency analysis in FieldTrip: http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis The reference documentation for ft_freqanalysis also might be of use: http://fieldtrip.fcdonders.nl/reference/ft_freqanalysis (which is the same information you get when you type 'help ft_freqanalysis' or 'doc ft_freqanalysis' at the matlab prompt). Hope this was of help. Best, Eelke 2011/12/14 Guido Hesselmann : > Hi all, > > I am new to fieldtrip and have a very simple question. I have EEG data and > would like to run a > time-frequency analysis (e.g., using a Hanning taper with fixed window > length). If I have 100 trials, > how is this analysis performed? On a trial-by-trial basis, or based on the > average? Can I choose > between these options in fieldtrip? > > Thanks a lot! > > Guido Hesselmann > Visual Perception Lab > Department of Psychiatry & Psychotherapy > Charité Berlin > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From lihqih at gmail.com Wed Dec 14 19:04:37 2011 From: lihqih at gmail.com (qi li) Date: Wed, 14 Dec 2011 13:04:37 -0500 Subject: [FieldTrip] remove trials after ft_preprocessing Message-ID: I am new to fieldtrip. After I processed the data, I got triggered_trials = hdr: [1x1 struct] label: {273x1 cell} time: {1x20 cell} trial: {1x20 cell} fsample: 600 sampleinfo: [20x2 double] grad: [1x1 struct] cfg: [1x1 struct] Now I want to remove a few trials with trial no 1 3 5 8. What command do I need to remove the trials and keep the structure of triggered_trials unchanged? Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From ucbtmba at ucl.ac.uk Wed Dec 14 19:08:48 2011 From: ucbtmba at ucl.ac.uk (Markus Bauer) Date: Wed, 14 Dec 2011 18:08:48 +0000 Subject: [FieldTrip] Time-frequency analysis: based on single trials or on average? In-Reply-To: References: Message-ID: <4EE8E630.2050600@ucl.ac.uk> An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Wed Dec 14 19:15:06 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Wed, 14 Dec 2011 19:15:06 +0100 Subject: [FieldTrip] remove trials after ft_preprocessing In-Reply-To: References: Message-ID: Dear Qi Li, There are several ways to achieve this. Both ft_selectdata and ft_preprocessing allow you to select a subset of trials without altering anything else in the data. Both of these functions require a vector as input that contains the indices of the trials to be *retained*, so you need to create this yourself. For instance: trialsToKeep = 1:20; % initialize vector with all trial indices trialsToKeep([1 3 5 8]) = []; % remove the trials that should go After this you can call either: data = ft_selectdata(data, 'rpt', trialsToKeep); Or: cfg = []; cfg.trials = trialsToKeep; data = ft_preprocessing(cfg, data); Best, Eelke 2011/12/14 qi li : > I am new to fieldtrip. After I processed the data, I got > triggered_trials = > >            hdr: [1x1 struct] >          label: {273x1 cell} >           time: {1x20 cell} >          trial: {1x20 cell} >        fsample: 600 >     sampleinfo: [20x2 double] >           grad: [1x1 struct] >            cfg: [1x1 struct] > Now I want to remove a few trials with trial no 1 3 5 8. What command do I > need to remove the trials and keep the structure of triggered_trials > unchanged? Thanks! > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Thu Dec 15 10:15:56 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 15 Dec 2011 10:15:56 +0100 Subject: [FieldTrip] read_eeglab, header file? In-Reply-To: <4EE87B31020000570000BF1A@gwsmtp1.uni-regensburg.de> References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> <4EE87B31020000570000BF1A@gwsmtp1.uni-regensburg.de> Message-ID: <4EE9BACC.7040809@donders.ru.nl> Hi Gregor, thanks for reporting this. It looks indeed like it should be like that, so I changed it to what you suggested (otherwise, if-clause does not make any sense at all). Best, Jörn On 12/14/2011 10:32 AM, Gregor Volberg wrote: > > Dear Fieldtrip developers, > > > I encountered an error warning when reading in an eeglab *.set - file > for preprocessing (version fieldtrip-20111206), where the call to > ft_preprocessing says > > > ??? Undefined function or variable "hdr". > > Error in ==> read_eeglabdata at 52 > > if isempty(hdr) > > > > Shouldn't code lines 52 to 54 read > > > if isempty(header) > > header = read_eeglabheader(filename); > > end > > > instead of > > > if isempty(hdr) > > hdr = read_eeglabheader(filename); > > end > > > > Not really a problem, just to bring it to your attention... > > > Best regards, > > Gregor > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Thu Dec 15 21:00:59 2011 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Thu, 15 Dec 2011 14:00:59 -0600 Subject: [FieldTrip] Topographic scaling of ERP data Message-ID: Hello, Our lab is interested in performing the topographic scaling method described in the following paper to compare ERP topographies: Jing, H., Pivik, R., & Dykman, R. (2006). A new scaling method for topographic comparisons of event-related potentials. *Journal of Neuroscience Methods 151*. Are there any FieldTrip functions available that implement this method? Thank you,, Steve Politzer-Ahles -- Stephen Politzer-Ahles University of Kansas Linguistics Department http://www.linguistics.ku.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From chenzuyue at live.cn Fri Dec 16 13:14:22 2011 From: chenzuyue at live.cn (chenzuyue) Date: Fri, 16 Dec 2011 12:14:22 +0000 Subject: [FieldTrip] Problems time-frequency analysis of Local Field Potential Message-ID: Hi, everyone, I am a new user of FieldTrip. In my study, I want to computes the difference of time-frequency representations of event-related LFP in two conditions. The data in the first condition is a 4 X 1100 X 103 matrix (Nchan X Nsamples X Ntrials). The data in the second condition is a 4 X 1100 X 107 matrix. The data reformatted are as follows: dataset1.label (4 X 1 cell ); dataset1.fsample 1000; dataset1.trial (1 X 103 cell ); dataset1.time (1X 103 cell); % time is from -100ms to 999ms. dataset2.label (4 X 1 cell ); dataset2.fsample 1000; dataset2.trial (1 X 107 cell ); dataset2.time (1X 107 cell ); % time is from -100ms to 999ms. The frequency interested is 0-100Hz. The method to calculate TFRs is the multitaper method. The configuration is as below: cfg = []; cfg.output = 'pow'; cfg.method = 'mtmconvol'; cfg.foi = 1:2:100; cfg.t_ftimwin = 5./cfg.foi; cfg.tapsmofrq = 0.4 *cfg.foi; cfg.toi = -0.1:0.05:1; cfg.pad = 'maxperlen'; TFRmult1 = ft_freqanalysis(cfg, dataset1); But after running, I can not get the right results. When I use ft_singleplotTFR to plot graph, there is only blue color. I wonder whether the process and configuration is right. The method is from one paper of E Maris and R Oostenvels published on the Journal of Neuroscience Methods.164(2007), 177-190; Figure 3. http://www.ncbi.nlm.nih.gov/pubmed/17517438 Any help is much appreciated. Yours Sincerely, Zuyue -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Fri Dec 16 13:44:51 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Fri, 16 Dec 2011 13:44:51 +0100 Subject: [FieldTrip] Problems time-frequency analysis of Local Field Potential In-Reply-To: References: Message-ID: Dear Zuyue, When you invoke ft_singleplotTFR, do you specify a means of baseline correction and/or explicit z-limits (i.e., limits of the color axis)? When looking at raw power (i.e., not contrasted), it is advisable to use a baseline correction in order to see something. Also, specifying z-limits of a different order of magnitude than your data will of course lead to all blue plots. You should take a look at the time-frequency analysis tutorial, particularly the part about visualization: http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis#visualization If you still don't see anything after you use baseline correction (or plot a contrast instead) and have proper z-limits, there might be something else wrong. Best, Eelke 2011/12/16 chenzuyue : > Hi, everyone, > > I am a new user of FieldTrip. In my study, I want to computes the difference > of time-frequency representations of event-related LFP in two conditions. > > The data in the first condition is a 4 X 1100 X 103 matrix (Nchan X Nsamples > X Ntrials). The data in the second condition is a 4 X 1100 X 107 matrix. The > data reformatted are as follows: > > dataset1.label (4 X 1 cell ); > > dataset1.fsample 1000; > > dataset1.trial (1 X 103 cell ); > > dataset1.time (1X 103 cell); % time is from -100ms to 999ms. > > > dataset2.label (4 X 1 cell ); > > dataset2.fsample 1000; > > dataset2.trial (1 X 107 cell ); > > dataset2.time (1X 107 cell ); % time is from -100ms to 999ms. > > > The frequency interested is 0-100Hz. The method to calculate TFRs is the > multitaper method. The configuration is as below: > > cfg = []; > cfg.output = 'pow'; > cfg.method = 'mtmconvol'; > cfg.foi = 1:2:100; > cfg.t_ftimwin = 5./cfg.foi; > cfg.tapsmofrq = 0.4 *cfg.foi; > cfg.toi = -0.1:0.05:1; > cfg.pad = 'maxperlen'; > TFRmult1 = ft_freqanalysis(cfg, dataset1); > > But after running, I can not get the right results. When I use > ft_singleplotTFR to plot graph, there is only blue color. I wonder whether > the process and configuration is right. > > The method is from one paper of E Maris and R Oostenvels published on the > Journal of Neuroscience Methods.164(2007), 177-190; Figure 3. > http://www.ncbi.nlm.nih.gov/pubmed/17517438 > > Any help is much appreciated. > > Yours Sincerely, > > Zuyue > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Fri Dec 16 14:02:36 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 16 Dec 2011 14:02:36 +0100 Subject: [FieldTrip] Problems time-frequency analysis of Local Field Potential In-Reply-To: References: Message-ID: <46831F4B-7707-496E-B55C-DDE4E4E5BB15@donders.ru.nl> Dear Zuyue, I agree with Eelke. One thing you need to check is whether the time axis (in data.time{}) is in seconds or milliseconds. In the cfg to ft_freqanalysis you specify it in seconds. FieldTrip does not care about the exact units, so you need to ensure that the units in the time-axis correspond. BW, Jan-Mathijs On Dec 16, 2011, at 1:44 PM, Eelke Spaak wrote: > Dear Zuyue, > > When you invoke ft_singleplotTFR, do you specify a means of baseline > correction and/or explicit z-limits (i.e., limits of the color axis)? > When looking at raw power (i.e., not contrasted), it is advisable to > use a baseline correction in order to see something. Also, specifying > z-limits of a different order of magnitude than your data will of > course lead to all blue plots. > > You should take a look at the time-frequency analysis tutorial, > particularly the part about visualization: > http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis#visualization > > If you still don't see anything after you use baseline correction (or > plot a contrast instead) and have proper z-limits, there might be > something else wrong. > > Best, > Eelke > > 2011/12/16 chenzuyue : >> Hi, everyone, >> >> I am a new user of FieldTrip. In my study, I want to computes the difference >> of time-frequency representations of event-related LFP in two conditions. >> >> The data in the first condition is a 4 X 1100 X 103 matrix (Nchan X Nsamples >> X Ntrials). The data in the second condition is a 4 X 1100 X 107 matrix. The >> data reformatted are as follows: >> >> dataset1.label (4 X 1 cell ); >> >> dataset1.fsample 1000; >> >> dataset1.trial (1 X 103 cell ); >> >> dataset1.time (1X 103 cell); % time is from -100ms to 999ms. >> >> >> dataset2.label (4 X 1 cell ); >> >> dataset2.fsample 1000; >> >> dataset2.trial (1 X 107 cell ); >> >> dataset2.time (1X 107 cell ); % time is from -100ms to 999ms. >> >> >> The frequency interested is 0-100Hz. The method to calculate TFRs is the >> multitaper method. The configuration is as below: >> >> cfg = []; >> cfg.output = 'pow'; >> cfg.method = 'mtmconvol'; >> cfg.foi = 1:2:100; >> cfg.t_ftimwin = 5./cfg.foi; >> cfg.tapsmofrq = 0.4 *cfg.foi; >> cfg.toi = -0.1:0.05:1; >> cfg.pad = 'maxperlen'; >> TFRmult1 = ft_freqanalysis(cfg, dataset1); >> >> But after running, I can not get the right results. When I use >> ft_singleplotTFR to plot graph, there is only blue color. I wonder whether >> the process and configuration is right. >> >> The method is from one paper of E Maris and R Oostenvels published on the >> Journal of Neuroscience Methods.164(2007), 177-190; Figure 3. >> http://www.ncbi.nlm.nih.gov/pubmed/17517438 >> >> Any help is much appreciated. >> >> Yours Sincerely, >> >> Zuyue >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Mon Dec 19 10:03:51 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Mon, 19 Dec 2011 11:03:51 +0200 Subject: [FieldTrip] Address of biosemi device Message-ID: Hello, I'd tried to use the biosemi2ft function for realtime acquiring. But the following message appears: "Could not connect to buffer server at localhost: 1972". Should I change the Hostname and the Port, if yes what should they be? Best, -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Dec 19 11:04:47 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 19 Dec 2011 11:04:47 +0100 Subject: [FieldTrip] Topographic scaling of ERP data In-Reply-To: References: Message-ID: Dear Stephen, I am not aware of any FieldTrip function that achieves this scaling. Looking at the method, it seems that it should be able to implement this is not too many lines of matlab code. Maybe someone else on the list has some code lying around. Best wishes, Jan-Mathijs On Dec 15, 2011, at 9:00 PM, Stephen Politzer-Ahles wrote: > Hello, > > Our lab is interested in performing the topographic scaling method described in the following paper to compare ERP topographies: > > Jing, H., Pivik, R., & Dykman, R. (2006). A new scaling method for topographic comparisons of event-related potentials. Journal of Neuroscience Methods 151. > > Are there any FieldTrip functions available that implement this method? > > Thank you,, > Steve Politzer-Ahles > > -- > Stephen Politzer-Ahles > University of Kansas > Linguistics Department > http://www.linguistics.ku.edu/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Tue Dec 20 02:54:53 2011 From: lihqih at gmail.com (qi li) Date: Mon, 19 Dec 2011 20:54:53 -0500 Subject: [FieldTrip] operation order difference Message-ID: Hi, I have a CTF axial data. Is the result of timelock first then do the ft_megplanar same as ft_megplanar first then timelock? I think both method should get the same result. Qi -------------- next part -------------- An HTML attachment was scrubbed... URL: From adam at adamcsnyder.com Tue Dec 20 04:54:39 2011 From: adam at adamcsnyder.com (Adam C. Snyder) Date: Mon, 19 Dec 2011 22:54:39 -0500 Subject: [FieldTrip] Problem detecting triggers with real time synchronous analysis Message-ID: <29E38593-B980-47D1-9E86-E197EF62994E@adamcsnyder.com> Hello, I'm trying to perform a real time synchronous analysis in response to a particular trigger, but it isn't working. Here are some brief details of the setup: we're using BioSemi ActiveTwo, a December 2011 version of FieldTrip and MATLAB 2010b. I've managed to get the biosemi2ft executable running, and if I send a trigger through the BioSemi system, the details are noted in the command window. However, within the ft_realtime_synchronous function, the trigger events are not being found. The built-in status updates (e.g., "CMS_IN_RANGE", etc.), in contrast, are picked up by the ft_read_event call within ft_realtime_synchronous function, which adds to my confusion. My configurations are something like these: cfg.dataset = 'buffer://localhost:1972'; cfg.bcifun = @hello_world; cfg.blocksize = 1; cfg.trigger = [4 2]; cfg.jumptoeof = 'yes'; cfg.bufferdata = 'last'; %maybe the name of this option was different -- I'm typing from memory I hope someone can kindly help me to figure this out, and thank you in advance for whatever help you can provide. In Science, Adam C. Snyder Postdoctoral Fellow Cognitive Neurophysiology Lab Albert Einstein College of Medicine Bronx, NY From eelke.spaak at donders.ru.nl Tue Dec 20 10:56:13 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 20 Dec 2011 10:56:13 +0100 Subject: [FieldTrip] operation order difference In-Reply-To: References: Message-ID: Hi Qi, I think so too. Have you tried it? Best, Eelke 2011/12/20 qi li : > Hi, > > I have a CTF axial data. Is the result of timelock first then do the > ft_megplanar same as ft_megplanar first then timelock? > > I think both method should get the same result. > > Qi > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From lihqih at gmail.com Tue Dec 20 17:39:19 2011 From: lihqih at gmail.com (qi li) Date: Tue, 20 Dec 2011 11:39:19 -0500 Subject: [FieldTrip] operation order difference In-Reply-To: References: Message-ID: Hi Eelke, Thanks for your reply. I tried a particular sample and the difference between these two methods are small. However, timelock first is faster whereas ft_megplanar first makes much more sense. Qi On Tue, Dec 20, 2011 at 4:56 AM, Eelke Spaak wrote: > Hi Qi, > > I think so too. Have you tried it? > > Best, > Eelke > > 2011/12/20 qi li : > > Hi, > > > > I have a CTF axial data. Is the result of timelock first then do the > > ft_megplanar same as ft_megplanar first then timelock? > > > > I think both method should get the same result. > > > > Qi > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Wed Dec 21 11:56:26 2011 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Wed, 21 Dec 2011 11:56:26 +0100 Subject: [FieldTrip] Address of biosemi device In-Reply-To: References: Message-ID: Dear Hamza, I think this message appears when you specify a specific buffer server to connect to. The biosemi2ft.exe can be run in two modes, 1) it starts an baked-in buffer server (default), or 2) it can can use a buffer server that is run in a separate process. The default mode is probably a good choice. You can select the default mode *by not specifying a server of port*. Best regards, Boris On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) wrote: > Hello, > > I'd tried to use the biosemi2ft function for realtime acquiring. But the > following message appears: > > "Could not connect to buffer server at localhost: 1972". > > Should I change the Hostname and the Port, if yes what should they be? > > Best, > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From hamzaf at sabanciuniv.edu Wed Dec 21 15:36:21 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Wed, 21 Dec 2011 16:36:21 +0200 Subject: [FieldTrip] Address of biosemi device In-Reply-To: References: Message-ID: Thank you Boris. Well, I tried the default mode (just by specifying the configuration file and the gdf file in the cmd). But this message appeared. Could you or anyone just tell me exactly what should I do or modify. Thanks a lot On Wed, Dec 21, 2011 at 12:56 PM, Boris Reuderink wrote: > Dear Hamza, > > I think this message appears when you specify a specific buffer server > to connect to. The biosemi2ft.exe can be run in two modes, 1) it > starts an baked-in buffer server (default), or 2) it can can use a > buffer server that is run in a separate process. > > The default mode is probably a good choice. You can select the default > mode *by not specifying a server of port*. > > Best regards, > > Boris > > On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) > wrote: > > Hello, > > > > I'd tried to use the biosemi2ft function for realtime acquiring. But the > > following message appears: > > > > "Could not connect to buffer server at localhost: 1972". > > > > Should I change the Hostname and the Port, if yes what should they be? > > > > Best, > > > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Wed Dec 21 16:48:02 2011 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Wed, 21 Dec 2011 16:48:02 +0100 Subject: [FieldTrip] Address of biosemi device In-Reply-To: References: Message-ID: Could you perhaps send me the exact command you executed? Tomorrow I'll have access to a windows machine --- maybe I can find out what went wrong. Best regards, Boris 2011/12/21 Hamza Fawzi Altakroury (Student) : > Thank you Boris. > > Well, I tried the default mode (just by specifying the configuration file > and the gdf file in the cmd). But this message appeared. > Could you or anyone just tell me exactly what should I do or modify. > > Thanks a lot > > > On Wed, Dec 21, 2011 at 12:56 PM, Boris Reuderink > wrote: >> >> Dear Hamza, >> >> I think this message appears when you specify a specific buffer server >> to connect to. The biosemi2ft.exe can be run in two modes, 1) it >> starts an baked-in buffer server (default), or 2) it can can use a >> buffer server that is run in a separate process. >> >> The default mode is probably a good choice. You can select the default >> mode *by not specifying a server of port*. >> >> Best regards, >> >> Boris >> >> On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) >> wrote: >> > Hello, >> > >> > I'd tried to use the biosemi2ft function for realtime acquiring. But the >> > following message appears: >> > >> > "Could not connect to buffer server at localhost: 1972". >> > >> > Should I change the Hostname and the Port, if yes what should they be? >> > >> > Best, >> > >> > >> > -- >> > Hamza Fawzi Altakroury >> > Graduate student - MA >> > Faculty of Engineering and Natural Sciences >> > Sabancı University >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From johemart at gmail.com Wed Dec 21 16:50:42 2011 From: johemart at gmail.com (=?ISO-8859-1?Q?Johann_Heinz_Mart=EDnez_Huartos?=) Date: Wed, 21 Dec 2011 16:50:42 +0100 Subject: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? Message-ID: Hello dear fieldtripers Currently im using ft_topoplotER() function in order to visualize a cluster of channels in the head. But i cant fill the marker im using to highlight those channels. I know that the commend to chage this opction in matlab is markerfacecolor = 'k'. if i want to fill it up with black color, but this option does not makes anything happend and the markers are not filled. So, anyone knows how to fill the marker in ft_topoplotER() funtion? Thanks -- Atentamente: Johann Martínez. M.Sc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Wed Dec 21 17:50:03 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Wed, 21 Dec 2011 18:50:03 +0200 Subject: [FieldTrip] Address of biosemi device In-Reply-To: References: Message-ID: The directory: fieldtrip-20111211\realtime\acquisition\biosemi The command: biosemi2ft config.txt ex.gdf Output : could not connect to buffer server at localhost:1972. Thank a lot On Wed, Dec 21, 2011 at 5:48 PM, Boris Reuderink wrote: > Could you perhaps send me the exact command you executed? Tomorrow > I'll have access to a windows machine --- maybe I can find out what > went wrong. > > Best regards, > > Boris > > 2011/12/21 Hamza Fawzi Altakroury (Student) : > > Thank you Boris. > > > > Well, I tried the default mode (just by specifying the configuration file > > and the gdf file in the cmd). But this message appeared. > > Could you or anyone just tell me exactly what should I do or modify. > > > > Thanks a lot > > > > > > On Wed, Dec 21, 2011 at 12:56 PM, Boris Reuderink > > wrote: > >> > >> Dear Hamza, > >> > >> I think this message appears when you specify a specific buffer server > >> to connect to. The biosemi2ft.exe can be run in two modes, 1) it > >> starts an baked-in buffer server (default), or 2) it can can use a > >> buffer server that is run in a separate process. > >> > >> The default mode is probably a good choice. You can select the default > >> mode *by not specifying a server of port*. > >> > >> Best regards, > >> > >> Boris > >> > >> On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) > >> wrote: > >> > Hello, > >> > > >> > I'd tried to use the biosemi2ft function for realtime acquiring. But > the > >> > following message appears: > >> > > >> > "Could not connect to buffer server at localhost: 1972". > >> > > >> > Should I change the Hostname and the Port, if yes what should they be? > >> > > >> > Best, > >> > > >> > > >> > -- > >> > Hamza Fawzi Altakroury > >> > Graduate student - MA > >> > Faculty of Engineering and Natural Sciences > >> > Sabancı University > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > fieldtrip at donders.ru.nl > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Wed Dec 21 19:19:24 2011 From: lihqih at gmail.com (qi li) Date: Wed, 21 Dec 2011 13:19:24 -0500 Subject: [FieldTrip] how to plot the selected trials in the same plot Message-ID: Hi, I am trying to plot a single plot for a particular sensor with multiple trials by ft_singleplotER. Even I set the cfg.trials='all', it only gives one curve. If I want to use ft_multiplotER for the various sensors and multiple trials, what should I do? The multiplotER dosen't show the axes ticks and labels, how to fix it? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed Dec 21 20:58:10 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 21 Dec 2011 20:58:10 +0100 Subject: [FieldTrip] Address of biosemi device In-Reply-To: References: Message-ID: <28B62884-7633-4554-A460-31E1BF711582@donders.ru.nl> Dear Hamza According to the documentation on http://fieldtrip.fcdonders.nl/development/realtime/biosemi the full command line is biosemi2ft and "The first argument must be the name of a configuration file (see below). The second argument determines the base name of a GDF file that data is written to. The .gdf will be added automatically, as well as session counters (see below) and additional file name parts _1, _2 and so on for splitting the data over multiple files (to avoid 2 GB limits). The optional third and fourth argument are the hostname and port of the FieldTrip buffer. Defaults are localhost and 1972. Replacinghostname by a minus (-) tells the software to spawn its own buffer server on the given port." If you did not start buffer.exe prior to biosemi2ft.exe, you don't have a buffer server running and the error message makes sense because the buffer cannot be found. If you specify "-" as 3rd argument then biosemi2ft.exe will spawn its own buffer server in a separate thread and will connect to that. See http://fieldtrip.fcdonders.nl/development/realtime/biosemi and http://fieldtrip.fcdonders.nl/development/realtime/buffer. Note that you should name the output file "ex", not "ex.gdf". best Robert On 21 Dec 2011, at 17:50, Hamza Fawzi Altakroury (Student) wrote: > The directory: fieldtrip-20111211\realtime\acquisition\biosemi > > The command: biosemi2ft config.txt ex.gdf > > Output : could not connect to buffer server at localhost:1972. > > Thank a lot > > > > On Wed, Dec 21, 2011 at 5:48 PM, Boris Reuderink wrote: > Could you perhaps send me the exact command you executed? Tomorrow > I'll have access to a windows machine --- maybe I can find out what > went wrong. > > Best regards, > > Boris > > 2011/12/21 Hamza Fawzi Altakroury (Student) : > > Thank you Boris. > > > > Well, I tried the default mode (just by specifying the configuration file > > and the gdf file in the cmd). But this message appeared. > > Could you or anyone just tell me exactly what should I do or modify. > > > > Thanks a lot > > > > > > On Wed, Dec 21, 2011 at 12:56 PM, Boris Reuderink > > wrote: > >> > >> Dear Hamza, > >> > >> I think this message appears when you specify a specific buffer server > >> to connect to. The biosemi2ft.exe can be run in two modes, 1) it > >> starts an baked-in buffer server (default), or 2) it can can use a > >> buffer server that is run in a separate process. > >> > >> The default mode is probably a good choice. You can select the default > >> mode *by not specifying a server of port*. > >> > >> Best regards, > >> > >> Boris > >> > >> On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) > >> wrote: > >> > Hello, > >> > > >> > I'd tried to use the biosemi2ft function for realtime acquiring. But the > >> > following message appears: > >> > > >> > "Could not connect to buffer server at localhost: 1972". > >> > > >> > Should I change the Hostname and the Port, if yes what should they be? > >> > > >> > Best, > >> > > >> > > >> > -- > >> > Hamza Fawzi Altakroury > >> > Graduate student - MA > >> > Faculty of Engineering and Natural Sciences > >> > Sabancı University > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > fieldtrip at donders.ru.nl > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From s.bogels at psy.gla.ac.uk Thu Dec 22 10:26:57 2011 From: s.bogels at psy.gla.ac.uk (Sara =?iso-8859-1?b?QvZnZWxz?=) Date: Thu, 22 Dec 2011 09:26:57 +0000 Subject: [FieldTrip] problems with ft_multiplotTFR Message-ID: <20111222092657.846462fkkxbzywgx@horde.psy.gla.ac.uk> Hi all, I have performed a cluster-based permutation test on time-frequency data and I am trying to plot the significant clusters. Since I used multiple frequencies I cannot use ft_clusterplot but I should use ft_multiplotTFR if I understand correctly. I also did not average over time and I used all channels. The analysis resulted in 1 significant positive cluster and 1 significant negative cluster. I have tried ft_multiplotTFR with the following settings (plus a correct cfg.layout): cfg = []: cfg.maskparameter = 'mask'; cfg.parameter = 'stat'; cfg.maskalpha = 0.025; figure, ft_multiplotTFR(cfg,stats) This gives me plots on the head for all channels but they are all black. If I outcomment cfg.maskparameter I do get nicely coloured plots (of the teststatistic I assume) but of course without the significant cluster(s). Any help is appreciated. Thank you, Sara ---------------------------------------------------------------- This message was sent using the Web mail system for The University of Glasgow School of Psychology ------------------------------------------------------------------ From r.vandermeij at donders.ru.nl Thu Dec 22 10:37:43 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Thu, 22 Dec 2011 10:37:43 +0100 Subject: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? In-Reply-To: References: Message-ID: <4EF2FA67.8010108@donders.ru.nl> Hi Johann, If you update to the newest fieldtrip version, you can use the option cfg.highlightsymbol or cfg.markersymbol to pick a marker that is filled, like '.'. Best, Roemer On 21-12-11 16:50, Johann Heinz Martínez Huartos wrote: > Hello dear fieldtripers > > Currently im using ft_topoplotER() function in order to visualize a > cluster of channels in the head. But i cant fill the marker im using > to highlight those channels. I know that the commend to chage this > opction in matlab is markerfacecolor = 'k'. > if i want to fill it up with black color, but this option does not > makes anything happend and the markers are not filled. So, anyone > knows how to fill the marker in ft_topoplotER() funtion? > > Thanks > > -- > Atentamente: > Johann Martínez. M.Sc. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Thu Dec 22 14:36:31 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 22 Dec 2011 15:36:31 +0200 Subject: [FieldTrip] Address of biosemi device In-Reply-To: <28B62884-7633-4554-A460-31E1BF711582@donders.ru.nl> References: <28B62884-7633-4554-A460-31E1BF711582@donders.ru.nl> Message-ID: Dear Mr Robert Thanks a lot for your help. It works. Best On Wed, Dec 21, 2011 at 9:58 PM, Robert Oostenveld < r.oostenveld at donders.ru.nl> wrote: > Dear Hamza > > According to the documentation on > http://fieldtrip.fcdonders.nl/development/realtime/biosemi the full > command line is > biosemi2ft > and "The first argument must be the name of a configuration file (see > below). The second argument determines the base name of a GDF file that > data is written to. The .gdf will be added automatically, as well as > session counters (see below) and additional file name parts _1, _2 and so > on for splitting the data over multiple files (to avoid 2 GB limits). The > optional third and fourth argument are the hostname and port of the > FieldTrip buffer. Defaults are localhost and 1972. Replacinghostname by a > minus (-) tells the software to spawn its own buffer server on the given > port." > > If you did not start buffer.exe prior to biosemi2ft.exe, you don't have a > buffer server running and the error message makes sense because the buffer > cannot be found. > > If you specify "-" as 3rd argument then biosemi2ft.exe will spawn its own > buffer server in a separate thread and will connect to that. See > http://fieldtrip.fcdonders.nl/development/realtime/biosemi and > http://fieldtrip.fcdonders.nl/development/realtime/buffer. Note that you > should name the output file "ex", not "ex.gdf". > > best > Robert > > > On 21 Dec 2011, at 17:50, Hamza Fawzi Altakroury (Student) wrote: > > > The directory: fieldtrip-20111211\realtime\acquisition\biosemi > > > > The command: biosemi2ft config.txt ex.gdf > > > > Output : could not connect to buffer server at localhost:1972. > > > > Thank a lot > > > > > > > > On Wed, Dec 21, 2011 at 5:48 PM, Boris Reuderink < > b.reuderink at donders.ru.nl> wrote: > > Could you perhaps send me the exact command you executed? Tomorrow > > I'll have access to a windows machine --- maybe I can find out what > > went wrong. > > > > Best regards, > > > > Boris > > > > 2011/12/21 Hamza Fawzi Altakroury (Student) : > > > Thank you Boris. > > > > > > Well, I tried the default mode (just by specifying the configuration > file > > > and the gdf file in the cmd). But this message appeared. > > > Could you or anyone just tell me exactly what should I do or modify. > > > > > > Thanks a lot > > > > > > > > > On Wed, Dec 21, 2011 at 12:56 PM, Boris Reuderink > > > wrote: > > >> > > >> Dear Hamza, > > >> > > >> I think this message appears when you specify a specific buffer server > > >> to connect to. The biosemi2ft.exe can be run in two modes, 1) it > > >> starts an baked-in buffer server (default), or 2) it can can use a > > >> buffer server that is run in a separate process. > > >> > > >> The default mode is probably a good choice. You can select the default > > >> mode *by not specifying a server of port*. > > >> > > >> Best regards, > > >> > > >> Boris > > >> > > >> On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) > > >> wrote: > > >> > Hello, > > >> > > > >> > I'd tried to use the biosemi2ft function for realtime acquiring. > But the > > >> > following message appears: > > >> > > > >> > "Could not connect to buffer server at localhost: 1972". > > >> > > > >> > Should I change the Hostname and the Port, if yes what should they > be? > > >> > > > >> > Best, > > >> > > > >> > > > >> > -- > > >> > Hamza Fawzi Altakroury > > >> > Graduate student - MA > > >> > Faculty of Engineering and Natural Sciences > > >> > Sabancı University > > >> > > > >> > _______________________________________________ > > >> > fieldtrip mailing list > > >> > fieldtrip at donders.ru.nl > > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > >> > > >> _______________________________________________ > > >> fieldtrip mailing list > > >> fieldtrip at donders.ru.nl > > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > -- > > > Hamza Fawzi Altakroury > > > Graduate student - MA > > > Faculty of Engineering and Natural Sciences > > > Sabancı University > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Thu Dec 22 19:47:56 2011 From: lihqih at gmail.com (qi li) Date: Thu, 22 Dec 2011 13:47:56 -0500 Subject: [FieldTrip] artifact removal Message-ID: Hi, I am following the automatic_artifact_rejection tutorial but the interactive graphic window doesn't show. I am using fieldtrip 1014 version. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sat Dec 24 20:37:27 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sat, 24 Dec 2011 21:37:27 +0200 Subject: [FieldTrip] offset2time function Message-ID: Hello I tried to run the "ft_realtime_synchronous" function but, the following error appeared. ??? Undefined function or method 'offset2time' for input arguments of type 'double'. How can I get the offset2time function. Note: I read the "resampledata/offset2time" email and updated the folder but I same problem appeared. Best -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sun Dec 25 18:48:24 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sun, 25 Dec 2011 19:48:24 +0200 Subject: [FieldTrip] Reading online-data from a file Message-ID: Hello, I am using biosemi2ft for saving data into a gdf file online. I want to process the data as the acquiring is taking place. The "ft_read_event" function give me an easy way to get the triggers values. But as I think it reads the file each time from the beginning. Unfortunately the sread function which keep track of the file, does not extract the triggers' values. Any suggestions. -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sun Dec 25 20:46:33 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sun, 25 Dec 2011 21:46:33 +0200 Subject: [FieldTrip] Trigger values in data matrix Message-ID: Hello, I can't get the real trigger values if use sopen function (or ft_read_data), even after adding the min value -1.7281e+009 to get a positive values. Note: I plotted the triggers and their proportion is right but I can't get their exact values, what should I do. Best, -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From johemart at gmail.com Wed Dec 28 14:39:14 2011 From: johemart at gmail.com (=?ISO-8859-1?Q?Johann_Heinz_Mart=EDnez_Huartos?=) Date: Wed, 28 Dec 2011 14:39:14 +0100 Subject: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? In-Reply-To: <4EF2FA67.8010108@donders.ru.nl> References: <4EF2FA67.8010108@donders.ru.nl> Message-ID: Hi Roemer. Thnkx 4 ur answer. But Im using the fieldtrip version October 2011 and in this version cfg.highlightsymbol already appear just for ft_topoplotER() and cfg.markersymbol just appear for ft.singleplot() nor in ft_topoplotER(). In fact, I looking for a way to fill whichever marker i want to use for. (i.e. ^ > < o) not neccesarilly with '.' Do you know how to do that? thnx again for ur answer or comments. Johann On 22 December 2011 10:37, Roemer van der Meij wrote: > Hi Johann, > > If you update to the newest fieldtrip version, you can use the option > cfg.highlightsymbol or cfg.markersymbol to pick a marker that is filled, > like '.'. > > Best, > Roemer > > > > On 21-12-11 16:50, Johann Heinz Martínez Huartos wrote: > > Hello dear fieldtripers > > Currently im using ft_topoplotER() function in order to visualize a > cluster of channels in the head. But i cant fill the marker im using to > highlight those channels. I know that the commend to chage this opction in > matlab is markerfacecolor = 'k'. > if i want to fill it up with black color, but this option does not makes > anything happend and the markers are not filled. So, anyone knows how to > fill the marker in ft_topoplotER() funtion? > > Thanks > > -- > Atentamente: > Johann Martínez. M.Sc. > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Atentamente: Johann Martínez. M.Sc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Wed Dec 28 16:43:19 2011 From: lihqih at gmail.com (qi li) Date: Wed, 28 Dec 2011 10:43:19 -0500 Subject: [FieldTrip] combine sessions Message-ID: Hi, I have 3 identical sessions. Each of them has 40 trials. Is there any command to combine the 3 sessions into one 120 trials? Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at mac.com Wed Dec 28 16:48:39 2011 From: nathanweisz at mac.com (Nathan Weisz) Date: Wed, 28 Dec 2011 16:48:39 +0100 Subject: [FieldTrip] combine sessions In-Reply-To: References: Message-ID: hi, ft_appenddata.m is likely what you need. best, nathan On 28.12.2011, at 16:43, qi li wrote: > Hi, > > I have 3 identical sessions. Each of them has 40 trials. Is there any command to combine the 3 sessions into one 120 trials? > > Thanks! > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From adam at adamcsnyder.com Thu Dec 29 13:33:21 2011 From: adam at adamcsnyder.com (Adam C. Snyder) Date: Thu, 29 Dec 2011 07:33:21 -0500 Subject: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? In-Reply-To: References: Message-ID: <4EFC5E11.8090404@adamcsnyder.com> What about just using a command such as the following: set(findobj(gca,'type','hggroup'),'markerfacecolor','k'); -Adam C. Snyder P.s., on another note, I asked for some help some time ago with a problem I was having using triggers from BioSemi to instigate online analysis using ft_realtime_synchronous. Does anyone have any thoughts about that? I can restate the problem, if needed. Your help would be greatly appreciated. On 29-Dec-2011 06:00, fieldtrip-request at donders.ru.nl wrote: > Send fieldtrip mailing list submissions to > fieldtrip at donders.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at donders.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at donders.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: How to fill the markers in FT_TOPOPLOTER?? > (Johann Heinz Mart?nez Huartos) > 2. combine sessions (qi li) > 3. Re: combine sessions (Nathan Weisz) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 28 Dec 2011 14:39:14 +0100 > From: Johann Heinz Mart?nez Huartos > To: r.vandermeij at donders.ru.nl, Email discussion list for the > FieldTrip project > Subject: Re: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Roemer. > > Thnkx 4 ur answer. But Im using the fieldtrip version October 2011 and in > this version cfg.highlightsymbol already appear just for ft_topoplotER() > and cfg.markersymbol just appear for ft.singleplot() nor in > ft_topoplotER(). > In fact, I looking for a way to fill whichever marker i want to use for. > (i.e. ^> < o) not neccesarilly with '.' > > Do you know how to do that? > > thnx again for ur answer or comments. > > Johann > > > On 22 December 2011 10:37, Roemer van der Meij > wrote: > >> Hi Johann, >> >> If you update to the newest fieldtrip version, you can use the option >> cfg.highlightsymbol or cfg.markersymbol to pick a marker that is filled, >> like '.'. >> >> Best, >> Roemer >> >> >> >> On 21-12-11 16:50, Johann Heinz Mart?nez Huartos wrote: >> >> Hello dear fieldtripers >> >> Currently im using ft_topoplotER() function in order to visualize a >> cluster of channels in the head. But i cant fill the marker im using to >> highlight those channels. I know that the commend to chage this opction in >> matlab is markerfacecolor = 'k'. >> if i want to fill it up with black color, but this option does not makes >> anything happend and the markers are not filled. So, anyone knows how to >> fill the marker in ft_topoplotER() funtion? >> >> Thanks >> >> -- >> Atentamente: >> Johann Mart?nez. M.Sc. >> >> >> _______________________________________________ >> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> Roemer van der Meij M.Sc. >> PhD student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> P.O. Box 9104 >> 6500 HE Nijmegen >> The Netherlands >> Tel: +31(0)24 3655932 >> E-mail: r.vandermeij at donders.ru.nl >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > From johemart at gmail.com Thu Dec 29 16:44:03 2011 From: johemart at gmail.com (=?ISO-8859-1?Q?Johann_Heinz_Mart=EDnez_Huartos?=) Date: Thu, 29 Dec 2011 16:44:03 +0100 Subject: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? In-Reply-To: <4EFC5E11.8090404@adamcsnyder.com> References: <4EFC5E11.8090404@adamcsnyder.com> Message-ID: thnkx Adam. I,ll try to use that command. good luck with your question! Johann. On 29 December 2011 13:33, Adam C. Snyder wrote: > What about just using a command such as the following: > > set(findobj(gca,'type','**hggroup'),'markerfacecolor','**k'); > > -Adam C. Snyder > > P.s., on another note, I asked for some help some time ago with a problem > I was having using triggers from BioSemi to instigate online analysis using > ft_realtime_synchronous. Does anyone have any thoughts about that? I can > restate the problem, if needed. Your help would be greatly appreciated. > > On 29-Dec-2011 06:00, fieldtrip-request at donders.ru.**nlwrote: > >> Send fieldtrip mailing list submissions to >> fieldtrip at donders.ru.nl >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >> or, via email, send a message with subject or body 'help' to >> fieldtrip-request at donders.ru.**nl >> >> You can reach the person managing the list at >> fieldtrip-owner at donders.ru.nl >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of fieldtrip digest..." >> >> >> Today's Topics: >> >> 1. Re: How to fill the markers in FT_TOPOPLOTER?? >> (Johann Heinz Mart?nez Huartos) >> 2. combine sessions (qi li) >> 3. Re: combine sessions (Nathan Weisz) >> >> >> ------------------------------**------------------------------** >> ---------- >> >> Message: 1 >> Date: Wed, 28 Dec 2011 14:39:14 +0100 >> From: Johann Heinz Mart?nez Huartos >> To: r.vandermeij at donders.ru.nl, Email discussion list for the >> FieldTrip project >> Subject: Re: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? >> Message-ID: >> > gmail.com <75UhLSw at mail.gmail.com>> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Hi Roemer. >> >> Thnkx 4 ur answer. But Im using the fieldtrip version October 2011 and in >> this version cfg.highlightsymbol already appear just for ft_topoplotER() >> and cfg.markersymbol just appear for ft.singleplot() nor in >> ft_topoplotER(). >> In fact, I looking for a way to fill whichever marker i want to use for. >> (i.e. ^> < o) not neccesarilly with '.' >> >> Do you know how to do that? >> >> thnx again for ur answer or comments. >> >> Johann >> >> >> On 22 December 2011 10:37, Roemer van der Meij >> **wrote: >> >> Hi Johann, >>> >>> If you update to the newest fieldtrip version, you can use the option >>> cfg.highlightsymbol or cfg.markersymbol to pick a marker that is filled, >>> like '.'. >>> >>> Best, >>> Roemer >>> >>> >>> >>> On 21-12-11 16:50, Johann Heinz Mart?nez Huartos wrote: >>> >>> Hello dear fieldtripers >>> >>> Currently im using ft_topoplotER() function in order to visualize a >>> cluster of channels in the head. But i cant fill the marker im using to >>> highlight those channels. I know that the commend to chage this opction >>> in >>> matlab is markerfacecolor = 'k'. >>> if i want to fill it up with black color, but this option does not makes >>> anything happend and the markers are not filled. So, anyone knows how to >>> fill the marker in ft_topoplotER() funtion? >>> >>> Thanks >>> >>> -- >>> Atentamente: >>> Johann Mart?nez. M.Sc. >>> >>> >>> ______________________________**_________________ >>> fieldtrip mailing listfieldtrip at donders.ru.**nlhttp:// >>> mailman.science.ru.**nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> -- >>> Roemer van der Meij M.Sc. >>> PhD student >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognition >>> P.O. Box 9104 >>> 6500 HE Nijmegen >>> The Netherlands >>> Tel: +31(0)24 3655932 >>> E-mail: r.vandermeij at donders.ru.nl >>> >>> ______________________________**_________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >>> >>> >> >> > ______________________________**_________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip > -- Atentamente: Johann Martínez. M.Sc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eva.patai at psy.ox.ac.uk Thu Dec 29 23:22:16 2011 From: eva.patai at psy.ox.ac.uk (Zita Eva Patai) Date: Thu, 29 Dec 2011 22:22:16 +0000 Subject: [FieldTrip] clusterplot not plotting for gradiometeres Message-ID: Dear All (happy holidays) when plotting significant clusters of tf/erf output of permutation test, i can plot sig. clusters for magnetometers but not gradiometers please see attached image...there are indications that there should be highlights...yet not visible...i am using exact same script, everything, difference is the layout file i use (neuromag306mag vs neuromag306cmb) thank you! z -- Zita Patai DPhil Candidate, Experimental Psychology University of Oxford bcl.psy.ox.ac.uk/people/zita-eva-patai/ eva.patai at psy.ox.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: wherearethehighlights Type: application/octet-stream Size: 30527 bytes Desc: not available URL: From marco.rotonda at gmail.com Fri Dec 30 13:07:15 2011 From: marco.rotonda at gmail.com (Marco Rotonda) Date: Fri, 30 Dec 2011 13:07:15 +0100 Subject: [FieldTrip] Strange path problem? Message-ID: Hi fieldtrippers, yesterday I moved to a win7 64bit version, installed latest matlab (2011b) and updated fieldtrip to the latest version (fieldtrip-20111223). After setting up all I tried to run a script I used until yesterday and I get a strange error: Invalid MEX-file 'C:\Program Files\fieldtrip\fileio\private\read_16bit.mexw64': The specified module could not be found. fileio is in the path, so I thought it was about the x86 program and I moved fieldtrip there, but same result: Invalid MEX-file 'C:\Program Files (x86)\fieldtrip\fileio\private\read_16bit.mexw64': The specified module could not be found. I think I miss a stupid thing. Sorry to disturb you, Marco From bibi.raquel at gmail.com Fri Dec 30 15:18:12 2011 From: bibi.raquel at gmail.com (Raquel Bibi) Date: Fri, 30 Dec 2011 09:18:12 -0500 Subject: [FieldTrip] Strange path problem? In-Reply-To: References: Message-ID: Hi, Marco. As a first test I would run "mbuild -setup" at the Matlab command line and select a C/C++ compiler. If this doesn't fix problem see: http://fieldtrip.fcdonders.nl/faq/how_can_i_compile_the_mex_files_on_64_bit_windows. This should fix the problems your having. Best, Raquel On Fri, Dec 30, 2011 at 7:07 AM, Marco Rotonda wrote: > Hi fieldtrippers, > yesterday I moved to a win7 64bit version, installed latest matlab > (2011b) and updated fieldtrip to the latest version > (fieldtrip-20111223). > After setting up all I tried to run a script I used until yesterday > and I get a strange error: > > Invalid MEX-file 'C:\Program > Files\fieldtrip\fileio\private\read_16bit.mexw64': The > specified module could not be found. > > fileio is in the path, so I thought it was about the x86 program and I > moved fieldtrip there, but same result: > > Invalid MEX-file 'C:\Program Files > (x86)\fieldtrip\fileio\private\read_16bit.mexw64': The > specified module could not be found. > > I think I miss a stupid thing. > > Sorry to disturb you, > > Marco > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Fri Dec 30 17:04:35 2011 From: lihqih at gmail.com (qi li) Date: Fri, 30 Dec 2011 11:04:35 -0500 Subject: [FieldTrip] question of planar gradient decomposition Message-ID: Hi, We have a axial ctf 1st order gradiometer. So it measures the axial gradient of the the magnetic field-(dB/dr). If I do the planar gradient transformation by 'sincos ,distance,' your codes looks like computing d^2B/d(theta) and d^2B/d(phi) where theta and phi are azimuth angle and polar angle respectively. It is well known in a spherical coordinate, there is no way to derive the tangential components from axial component, so what is the purpose of your linear transformation? Compared to neuromag which does pick up the planar gradient, is there any advantage for you to do so? Thanks a lot! Happy new year! Qi * * -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.rotonda at gmail.com Fri Dec 30 17:20:34 2011 From: marco.rotonda at gmail.com (Marco Rotonda) Date: Fri, 30 Dec 2011 17:20:34 +0100 Subject: [FieldTrip] Strange path problem? In-Reply-To: References: Message-ID: Thanks, I know it was a quite simple problem... sorry to disturb not reading the faq :( 2011/12/30 Raquel Bibi : > Hi, Marco. > > As a first test I would run "mbuild -setup" at the Matlab command line and > select a C/C++ compiler.  If this doesn't fix problem see: > > http://fieldtrip.fcdonders.nl/faq/how_can_i_compile_the_mex_files_on_64_bit_windows. >  This should fix the problems your having. > > Best, > > Raquel > > On Fri, Dec 30, 2011 at 7:07 AM, Marco Rotonda > wrote: >> >> Hi fieldtrippers, >> yesterday I moved to a win7 64bit version, installed latest matlab >> (2011b) and updated fieldtrip to the latest version >> (fieldtrip-20111223). >> After setting up all I tried to run a script I used until yesterday >> and I get a strange error: >> >> Invalid MEX-file 'C:\Program >> Files\fieldtrip\fileio\private\read_16bit.mexw64': The >> specified module could not be found. >> >> fileio is in the path, so I thought it was about the x86 program and I >> moved fieldtrip there, but same result: >> >> Invalid MEX-file 'C:\Program Files >> (x86)\fieldtrip\fileio\private\read_16bit.mexw64': The >> specified module could not be found. >> >> I think I miss a stupid thing. >> >> Sorry to disturb you, >> >> Marco >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Christos.Papadelis at childrens.harvard.edu Sat Dec 31 18:31:18 2011 From: Christos.Papadelis at childrens.harvard.edu (Papadelis, Christos) Date: Sat, 31 Dec 2011 17:31:18 +0000 Subject: [FieldTrip] Special issue in Advances on Human-Computer Interaction In-Reply-To: <876E0E5B34DB6A4DBD0E65B9091B4350027E0A@CHEXMBX2A.CHBOSTON.ORG> References: <876E0E5B34DB6A4DBD0E65B9091B4350027CAD@CHEXMBX2A.CHBOSTON.ORG>, <876E0E5B34DB6A4DBD0E65B9091B4350027E0A@CHEXMBX2A.CHBOSTON.ORG> Message-ID: <876E0E5B34DB6A4DBD0E65B9091B4350027E95@CHEXMBX2A.CHBOSTON.ORG> Dear Collegues, We would like to draw your attention to the following special issue in Advances on Human-Computer Interaction journal, entitled "Using Brain Waves to Control Computers and Machines" (http://www.hindawi.com/journals/ahci/si/ubw/). We invite authors to submit original research and review articles that explore all aspects of Brain Computer Interfaces (BCIs). My best wishes for Happy New Year. On behalf of all the Editors Christos Papadelis, PhD Instructor in Neurology, Harvard Medical School MEG Lab Manager, Children's Hospital Boston 9 Hope Avenue, Waltham, MA 02453, USA christos.papadelis at childrens.harvard.edu Phone: +1-781-216-1128 Fax: +1-781-216-1172 From s.bogels at psy.gla.ac.uk Thu Dec 1 10:34:20 2011 From: s.bogels at psy.gla.ac.uk (=?UTF-8?B?U2FyYSBCw7ZnZWxz?=) Date: Thu, 01 Dec 2011 09:34:20 +0000 Subject: [FieldTrip] second-level statistical inference In-Reply-To: <007e01ccaf95$536c0dc0$fa442940$@maris@psych.ru.nl> References: <744936625.46871.1322211858651.JavaMail.root@sculptor.zimbra.ru.nl> <4ECF8144.4010706@psy.gla.ac.uk> <007e01ccaf95$536c0dc0$fa442940$@maris@psych.ru.nl> Message-ID: <4ED74A1C.40701@psy.gla.ac.uk> Hi Eric, I understand that is another option. However, I do not see how to look at an interaction between two variables in this way. Do you have any advice if I want to do that? Thanks, Sara On 30/11/2011 19:21, Eric Maris wrote: > Hi Sara, > > > I'm replying to your initial question (somewhere below in this email). > > Why don't you calculate per-subject averages in the two within-subject > experimental conditions (using timelockgrandaverage with > keepindividual='yes'), and then do your second-level inference on these > averages? See also the Fieldtrip statistics tutorials. > > Best, > > Eric Maris > > >> -----Original Message----- >> From: Sara Bögels [mailto:s.bogels at psy.gla.ac.uk] >> Sent: vrijdag 25 november 2011 12:52 >> To: fieldtrip at donders.ru.nl >> Subject: Re: [FieldTrip] second-level statistical inference >> >> Hi Arjen, >> >> Thank you very much for your answer. That sounds good, but step 2 does >> not work straightforwardly, since matlab gives the error message that it >> cannot find an avg field (which would not be in the structure created by >> ft_timelockstatistics). Just saying cfg.parameter = 'stat' does not >> work. I tried to get around that by inserting an avg field which is the >> same as the stat field for each participant. Matlab also asked for an >> fsample field, which I inserted from an earlier datafile. Then it >> worked. Is it ok to do this? >> >> I did step 3 as well, using the field individual (which you get by >> keepindividuals = 'yes'). In step 4, I should just use cfg.statistic = >> 'depsamplesT', right (because the variables are within subject)? >> >> Thank you! >> Sara >> >> On 25/11/2011 09:04, Stolk, A. wrote: >>> Hi Sara, >>> >>> If I understand correctly, you want to test intra-subject differences >> (between conditions) at the second level? This would require the following >> steps: >>> 1) subject-level statistics, which you have done already >>> >>> 2) grandaverage all these, with keepindividuals=yes. >>> >>> 3) copy the output of the grandaverage (into a dummy variable), and >> replace the fields containing the subject T-values with zeros (for >> timelock >> data this may be the trial fields?) >>> 4) again timelockstatistics, as in step 1, now with the variables >>> following >> step 3. this should give you the resulting statistics of contrasting >> intra- >> subject differences vs. null at the group level. >>> Hope this helps, >>> >>> Arjen >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ----- "Sara Bögels" schreef: >>> >>>> Van: "Sara Bögels" >>>> Aan: fieldtrip at donders.ru.nl >>>> Verzonden: Donderdag 24 november 2011 15:49:17 >>>> Onderwerp: [FieldTrip] second-level statistical inference >>>> >>>> Hi all, >>>> >>>> I have been trying to do second-level statistical inference (as >>>> described in one of the FAQs) on ERFs, but I am not sure whether I am >>>> >>>> doing everything correctly. >>>> >>>> In the first step I calculate the T-values for the difference between >>>> >>>> two conditions (twice), which are between items, with >>>> ft_timelockstatistics. I put the output of all participants in a cell >>>> >>>> (called 'stat1a' and 'stat1b'). (I tried to use >>>> ft_timelockgrandaverage >>>> to combine the subjects together but it needs a field avg). >>>> >>>> Then I use ft_timelockstatistics again but subject level. I first >>>> want >>>> to look at the difference between the two conditions. This difference >>>> is >>>> reflected in the T-values of the first step so I create a dummy which >>>> is >>>> the same as 'stat1' but I replace all the values in the field 'stat' >>>> per >>>> participant with zeros. Then I call (with appropriate cfg >>>> parameters): >>>> >>>> stat2a = ft_timelockstatistics(cfg,stat1a{:},dummy{:}); >>>> stat2b = ft_timelockstatistics(cfg,stat1b{:},dummy{:}); >>>> >>>> To compare the two differences (stat1a and stat1b) and thereby look at >>>> >>>> an interaction, I call: >>>> >>>> stat2a-b = ft_timelockstatistics(cfg,stat1a{:},stat1b{:}); >>>> >>>> I am uncertain whether the dummy works (or is there a way to compare >>>> the >>>> t-values to zero directly?) and whether the stat1a{:} trick works with >>>> >>>> ft_timelockstatistics. >>>> >>>> Thanks in advance for your answer. >>>> >>>> Sara >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From max-philipp.stenner at med.ovgu.de Thu Dec 1 14:22:52 2011 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 01 Dec 2011 13:22:52 +0000 Subject: [FieldTrip] readCTFds Message-ID: Dear fieldtrip users, as a beginner I am encountering a rather fundamental problem even when trying to read the tutorial data (Subject01.ds): ft_read_data reports readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) and Matlab adds index exceeding matrix dimension errors ft_read_hdr reports nTrials = -1 The same happens with my own CTF data. I would be very grateful for any help on this very basic problem thanks! Best Max From jan.schoffelen at donders.ru.nl Thu Dec 1 14:54:08 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 1 Dec 2011 14:54:08 +0100 Subject: [FieldTrip] readCTFds In-Reply-To: References: Message-ID: <9F142CD3-12CB-4184-AF91-3233D42AE3FA@donders.ru.nl> Dear Max, Before we can think along with you, could you please give some more details? Some basic things such as the fieldtrip version you are using, matlab version and operating system? Thanks, Jan-Mathijs On Dec 1, 2011, at 2:22 PM, Stenner, Max-Philipp wrote: > Dear fieldtrip users, > > > > as a beginner I am encountering a rather fundamental problem even when trying to read the tutorial data (Subject01.ds): > > > > ft_read_data reports > > > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > > > and Matlab adds index exceeding matrix dimension errors > > > > ft_read_hdr reports > > > > nTrials = -1 > > > > The same happens with my own CTF data. > > > > I would be very grateful for any help on this very basic problem > > > > thanks! > > Best > > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Heng-RuMay.Tan at glasgow.ac.uk Thu Dec 1 15:52:52 2011 From: Heng-RuMay.Tan at glasgow.ac.uk (May (Heng-Ru May TAN)) Date: Thu, 01 Dec 2011 14:52:52 +0000 Subject: [FieldTrip] Grad and labels Message-ID: <4ED794C4.5070909@glasgow.ac.uk> Hello I would like to plot the grad.pnt for a few channels but realised that there are fewer labels (271) than grad.pnt rows (276) Presumably some of the channels have more than 1 grad.pnt > D = > > hdr: [1x1 struct] > label: {248x1 cell} > time: {1x9 cell} > trial: {1x9 cell} > fsample: 1.0172e+003 > grad: [1x1 struct] > cfg: [1x1 struct] > > >> D.grad > > ans = > > pnt: [276x3 double] > ori: [276x3 double] > tra: [271x276 double] > label: {271x1 cell} > unit: 'm' > balance: [1x1 struct] But how do the grad labels correspond to the grad.pnt with the numbers don't match? Can someone help? Thanks! May The above was derived using the following: > cfg = []; > > cfg.subjNUM = subjNUM; > cfg.irun=irun; > > cfg.headerfile = 'c,rfDC'; > cfg.datafile = cfg.headerfile; > cfg.trialfun ='trialfun_general'; > cfg.channel={'MEG'}; > cfg.continuous='yes'; > cfg.trialdef.eventtype = '?'; > > cfg=ft_definetrial(cfg); %--->cfg.events > cfg.header = ft_read_header(cfg.headerfile); > % just to be sure > cfg = rmfield(cfg,'trl'); > > > %% specify 'trial' information for 'epoching' > cfg.detrend='yes'; %no other filtering at the moment. > > cfg.trialdef.stimulusSETnum = [iset]; > cfg.trialdef.eventtype = 'PostStimTriggerIdx'; %% > cfg.trialdef.eventinfo = 'PostStimSampleTime'; > cfg.trialdef.eventvalue = [iset].*2 + 128; > > cfg.trialdef.response_time=[1]; % to include RXNtime in the > definetrial procedure... > cfg.trialdef.CorrectWrong = [1]; %only correct ones > > cfg.trialdef.prestim = 2; % duration in secs before '0' > cfg.trialdef.poststim = 2; % duration in secs after '0' > > cfg.trialfun ='trialfun_readEventgetRespInfo'; %%CHANGE 3rd > Column!!! > > cfg=ft_definetrial(cfg); > % cfg.trl ==//// [begsam endsam off runN stimN ] > > D=ft_preprocessing(cfg); From Heng-RuMay.Tan at glasgow.ac.uk Thu Dec 1 16:08:56 2011 From: Heng-RuMay.Tan at glasgow.ac.uk (May (Heng-Ru May TAN)) Date: Thu, 01 Dec 2011 15:08:56 +0000 Subject: [FieldTrip] change in ft_definetrial event output? Message-ID: <4ED79888.4020907@glasgow.ac.uk> Hi again, Another question -- possibly me missing out on all the updates! Was wondering if there has been changes to how events are output in newer versions of FT because previously using fieldtrip-20100419 > cfg = > > subjNUM: 1 > irun: 1 > headerfile: 'c,rfDC' > datafile: 'c,rfDC' > trialfun: 'trialfun_general' > channel: {'MEG'} > continuous: 'yes' > trialdef: [1x1 struct] > trackconfig: 'off' > checkconfig: 'loose' > checksize: 100000 > _ event: [850x1 struct] > _ trl: [] > version: [1x1 struct] > header: [1x1 struct] Now the newer versions only give _event: [849x1 struct]_ Is the 'trial' heading in the previous first row removed by default now? Thanks, May -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Thu Dec 1 16:15:56 2011 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 01 Dec 2011 15:15:56 +0000 Subject: [FieldTrip] readCTFds In-Reply-To: References: Message-ID: Dear all, in addition to my email sent earlier today (see below) here's some information on the OS, fieldtrip and MatLab versions: Windows7 Fieldtrip version 20111130 (20111129 caused the same error) Matlab R2011a Whereas readCTFds reports 'Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file)' a direct call to the dir command of the .meg4 file returns ' bytes: 179071208' for the number of trials ft_read_header('Subject01.ds') returns ' nTrials: -1' Thanks, best Max ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]" im Auftrag von "Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de] Gesendet: Donnerstag, 1. Dezember 2011 14:22 Bis: fieldtrip at donders.ru.nl Betreff: [FieldTrip] readCTFds Dear fieldtrip users, as a beginner I am encountering a rather fundamental problem even when trying to read the tutorial data (Subject01.ds): ft_read_data reports readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) and Matlab adds index exceeding matrix dimension errors ft_read_hdr reports nTrials = -1 The same happens with my own CTF data. I would be very grateful for any help on this very basic problem thanks! Best Max _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From b.reuderink at donders.ru.nl Thu Dec 1 17:58:45 2011 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Thu, 1 Dec 2011 17:58:45 +0100 Subject: [FieldTrip] Error in Java buffer reader and fakebiosemiclient.cc In-Reply-To: References: Message-ID: Dear Jacob, I have created bug 1209 (http://bugzilla.fcdonders.nl/show_bug.cgi?id=1209) for your issue. Could you provide some additional details to reproduce the bug on that page? And, could you (perhaps privately --- bypassing the list) explain how you are planning to use the FieldTrip buffer? We might find a workaround for you problem. Best regards, Boris On Tue, Nov 29, 2011 at 12:13 AM, Jacob Martin wrote: > Ok, seems like it has to do with exceeding the maximum number of > samples.  Not sure what to do here though yet: > > http://code.google.com/p/fieldtrip/source/browse/trunk/realtime/buffer/src/dmarequest.c?r=1218#413 > > On Mon, Nov 28, 2011 at 6:10 PM, Jacob Martin wrote: >> Hi, >> >> After letting the server run for a while (see below size at 512hz), I >> get an "err3": >> >> data: >> size = 176960 x 34 >> dmarequest: err3 >> Exception in thread "main" java.io.IOException: Error returned from >> FieldTrip buffer server. >>        at nl.fcdonders.fieldtrip.BufferClient.readResponse(BufferClient.java:646) >>        at nl.fcdonders.fieldtrip.BufferClient.getEvents(BufferClient.java:386) >>        at testclient.main(testclient.java:71) >> >> >> >> Any ideas? >> >> Thanks, >> Jake >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Fri Dec 2 10:03:40 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 02 Dec 2011 10:03:40 +0100 Subject: [FieldTrip] readCTFds In-Reply-To: References: Message-ID: <4ED8946C.2050209@donders.ru.nl> Hi Max, I usually encounter similar problems when CTF data is not fully saved, i.e. aborted the saving and forgot to click on 'OK' in the next dialog or something else went wrong. Maybe ther went something wrong when downloading the data? Since it says 0 bytes in dir, it could maybe also be that you something more basic wrong. Just to be sure, you could check whether Subject01.ds is a folder and whether it contains all the relevant files, and none of these have size 0. Best, Jörn On 12/1/2011 4:15 PM, Stenner, Max-Philipp wrote: > Dear all, > > in addition to my email sent earlier today (see below) here's some information on the OS, fieldtrip and MatLab versions: > > Windows7 > Fieldtrip version 20111130 (20111129 caused the same error) > Matlab R2011a > > Whereas readCTFds reports > > 'Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file)' > > a direct call to the dir command of the .meg4 file returns > > ' bytes: 179071208' > > for the number of trials ft_read_header('Subject01.ds') returns > > ' nTrials: -1' > > Thanks, > best > Max > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]" im Auftrag von"Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de] > Gesendet: Donnerstag, 1. Dezember 2011 14:22 > Bis: fieldtrip at donders.ru.nl > Betreff: [FieldTrip] readCTFds > > Dear fieldtrip users, > > > > as a beginner I am encountering a rather fundamental problem even when trying to read the tutorial data (Subject01.ds): > > > > ft_read_data reports > > > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > > > and Matlab adds index exceeding matrix dimension errors > > > > ft_read_hdr reports > > > > nTrials = -1 > > > > The same happens with my own CTF data. > > > > I would be very grateful for any help on this very basic problem > > > > thanks! > > Best > > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From sonjasuntrup at uni-muenster.de Fri Dec 2 12:16:20 2011 From: sonjasuntrup at uni-muenster.de (Sonja Suntrup) Date: Fri, 02 Dec 2011 12:16:20 +0100 (CET) Subject: [FieldTrip] source statistics, group level Message-ID: Dear fieldtrip users, I would like to do sourcestatistics on a group level with meg data. I have a pre and post intervention measurement for each of my 21 subjects (within-subjects design). After source reconstruction using an LCMV beamformer and volume normalization I calculated the sourcegrandaverage for the pre and post condition with the parameter cfg.keepindividual = 'yes'. However, when I use the grandaverage results in ft_sourcestatistics in the configuration shown below and plot the result I just get a blank anatomical mri. Do I have to set any additional parameters or do I make a general mistake? Whould you recommend to use a cluster-based permutation test comparable to ft_timelockstatistics and would I have to set the same parameters in ft_sourcestatistics then? cfg=[]; cfg.dim = grandAVGsourcePre.dim; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.parameter = 'avg.pow'; cfg.correctm = 'cluster'; cfg.numrandomization = 100; cfg.alpha = 0.05; cfg.tail = 0; nsubj=length(sourcePre.trial); cfg.design(1,:) = [1:nsubj 1:nsubj]; cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2]; cfg.uvar = 1; cfg.ivar = 2; stat = ft_sourcestatistics(cfg, grandAVGsourcePre, grandAVGsourcePost); Your help is greatly appreciated! Best, Sonja -- Dr. med. Sonja Suntrup Institute for Biomagnetism and Biosignalanalysis University of Muenster Malmedyweg 15 48149 Münster, Germany From max-philipp.stenner at med.ovgu.de Fri Dec 2 12:28:38 2011 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Fri, 02 Dec 2011 11:28:38 +0000 Subject: [FieldTrip] readCTFds In-Reply-To: <4ED8946C.2050209@donders.ru.nl> References: <4ED8946C.2050209@donders.ru.nl> Message-ID: Hi Joern, thank you very much for your reply, the (rather trivial) problem turned out to be indeed that the path wasn't added correctly, best Max ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]" im Auftrag von ""Jörn M. Horschig" [jm.horschig at donders.ru.nl] Gesendet: Freitag, 2. Dezember 2011 10:03 Bis: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] readCTFds Hi Max, I usually encounter similar problems when CTF data is not fully saved, i.e. aborted the saving and forgot to click on 'OK' in the next dialog or something else went wrong. Maybe ther went something wrong when downloading the data? Since it says 0 bytes in dir, it could maybe also be that you something more basic wrong. Just to be sure, you could check whether Subject01.ds is a folder and whether it contains all the relevant files, and none of these have size 0. Best, Jörn On 12/1/2011 4:15 PM, Stenner, Max-Philipp wrote: > Dear all, > > in addition to my email sent earlier today (see below) here's some information on the OS, fieldtrip and MatLab versions: > > Windows7 > Fieldtrip version 20111130 (20111129 caused the same error) > Matlab R2011a > > Whereas readCTFds reports > > 'Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file)' > > a direct call to the dir command of the .meg4 file returns > > ' bytes: 179071208' > > for the number of trials ft_read_header('Subject01.ds') returns > > ' nTrials: -1' > > Thanks, > best > Max > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]" im Auftrag von"Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de] > Gesendet: Donnerstag, 1. Dezember 2011 14:22 > Bis: fieldtrip at donders.ru.nl > Betreff: [FieldTrip] readCTFds > > Dear fieldtrip users, > > > > as a beginner I am encountering a rather fundamental problem even when trying to read the tutorial data (Subject01.ds): > > > > ft_read_data reports > > > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > > > and Matlab adds index exceeding matrix dimension errors > > > > ft_read_hdr reports > > > > nTrials = -1 > > > > The same happens with my own CTF data. > > > > I would be very grateful for any help on this very basic problem > > > > thanks! > > Best > > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Jan.Hirschmann at med.uni-duesseldorf.de Fri Dec 2 18:20:43 2011 From: Jan.Hirschmann at med.uni-duesseldorf.de (Jan.Hirschmann at med.uni-duesseldorf.de) Date: Fri, 2 Dec 2011 18:20:43 +0100 Subject: [FieldTrip] coherence normalization Message-ID: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> Hi community, Regarding this thread on suppressing the reference dipole from 2004, what is the current status? Has anybody found and implemented a recommendable way to project out activity from unwanted dipoles? Thank you for any comments/opinions! Best, Jan Hirschmann On 21 Oct 2004, at 17:23, Tom Holroyd wrote: > When running a coherence volume using a reference dipole, one > naturally expects the coherence will be high around the reference > dipole. > > This effect tends to dominate the images. > > Is there a way to normalize the coherence volume to eliminate > this effect? Perhaps by dividing by the coherence in a "control" > state? Hi Tom, The dominating effect of the refdip is indeed very problematic. I just happened to have discussed this with Joachim Gross, and I have included our email exchange below. Please first read that ... Basically I agree with Joachim, and I don't trust the supdip that is implemented in FieldTrip's sourceanalysis function. Better test and map the significance of the difference in coherence between two conditions using randomization of the trials before the coherence is beamed (that is implemented in sourceanalysis + sourcestatistics). Robert -------------------------------------------------------------------- my question to Joachim was ---------------------------------------------------------------------- Begin forwarded message: > From: Robert Oostenveld > > Date: 1 October 2004 10:26:02 GMT+02:00 > To: Joachim Gross > > Subject: dipole suppression > > Hi Joachim, > > What I always still had to ask you is how you do supression of dipoles > in DICS, especially in the case of coherence imaging. I have thought > of two ways of projecting them out: > > 1) compute supdip leadfield and its projection on the COV/CSD matrix, > then project it out of the COV/CSD matrix (which looses 2 or 3 from > its rank). > > 2) compute supdip leadfield and add it to the leadfield of the dipole > with which is scanned (scandip). Subsequently compute the source > COV/CSD on those 6 leadfield components and select the 3x3 submatrix > that corresponds with the scandip to continue the computations with. > > Both methods don't really gave me very convincing results. A third > approach would be to add the supdip leadfield to the (identity) noise > matrix and project it through the filters. Then nai=pow/noise is > corrected for the presence of the supdip, but that does not result in > a supressed source coherence distribution. What is your idea or > approach for this? > > best regards > Robert > ---------------------------------------------------------------------- and his answer (Joachim, I hope you don't mind me sharing this on the list) ---------------------------------------------------------------------- Begin forwarded message: > From: Joachim Gross > > Date: 14 October 2004 17:20:45 GMT+02:00 > To: "robert.oostenveld at fcdonders.kun.nl " > > > Subject: dipole suppression > > Hi Robert, > > sorry for the delay. > > The dipole suppression is indeed a complex issue. > We first implemented it because it facilitates visualization and the > exact identification of the first > strongest local maxima. > Nevertheless, it is quite dangerous because the map is (locally) > distorted in a non-trivial way. > We are now trying to move away from suppressing the sources. I think > it would be better to identify the > significant local maxima (significance based on > randomization/permutation). > But what we are doing at the moment is your approach 3. > So we add the supdip leadfield to the noise covariance matrix and look > at pow/noise. > > For coherence we are basically doing the same thing. > So we divide the coherence map (or actually the map of cross spectral > densities) by a noise map > that peaks at the locations of the "unwanted" dipoles. > With this procedure we loose absolute coherence values. > This is not so important for us since we get the absolute values from > the coherence and partial coherence spectra > that are computed afterwards. > It works surprisingly well but should be used with care. > > A better approach would be to map partial coherence (with the unwanted > dipoles removed). But we have not implemented > this so far. > > Again, I think it is better to have regions of interest identified by > their significance. > > Joachim ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. Jan Hirschmann MSc. Neuroscience Insititute of Clinical Neuroscience and Medical Psychology Heinrich Heine University Duesseldorf Universitaetsstr. 1 40225 Duesseldorf Tel: 0049 - (0)211 - 81 - 18415 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at kurage.nimh.nih.gov Fri Dec 2 18:52:07 2011 From: tomh at kurage.nimh.nih.gov (Tom Holroyd (NIH/NIMH) [E]) Date: Fri, 02 Dec 2011 12:52:07 -0500 Subject: [FieldTrip] coherence normalization In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> Message-ID: <4ED91047.6050107@kurage.nimh.nih.gov> The solution I have adopted is to always look at coherence contrasts. Make two volumes using the same reference dipole in two different conditions, then subtract the volumes. The self-coherence of the reference will disappear. Mostly. Then use stats, like a U-test. Jan.Hirschmann at med.uni-duesseldorf.de wrote: > Hi community, > > > > Regarding this thread on suppressing the reference dipole from 2004, what is the current status? Has anybody found and implemented a recommendable way to project out activity from unwanted dipoles? Thank you for any comments/opinions! > > > > Best, > > Jan Hirschmann > > > > > > > > On 21 Oct 2004, at 17:23, Tom Holroyd wrote: > > > >>/ When running a coherence volume using a reference dipole, one/ > >>/ naturally expects the coherence will be high around the reference/ > >>/ dipole./ > >>/ / > >>/ This effect tends to dominate the images./ > >>/ / > >>/ Is there a way to normalize the coherence volume to eliminate/ > >>/ this effect? Perhaps by dividing by the coherence in a "control"/ > >>/ state?/ > > > > Hi Tom, > > > > The dominating effect of the refdip is indeed very problematic. I just > > happened to have discussed this with Joachim Gross, and I have included > > our email exchange below. Please first read that ... > > > > Basically I agree with Joachim, and I don't trust the supdip that is > > implemented in FieldTrip's sourceanalysis function. Better test and map > > the significance of the difference in coherence between two conditions > > using randomization of the trials before the coherence is beamed (that > > is implemented in sourceanalysis + sourcestatistics). > > > > Robert > > > > -------------------------------------------------------------------- > > my question to Joachim was > > ---------------------------------------------------------------------- > > > > Begin forwarded message: > > > >>/ From: Robert Oostenveld //>/ > >>/ Date: 1 October 2004 10:26:02 GMT+02:00/ > >>/ To: Joachim Gross //>/ > >>/ Subject: dipole suppression/ > >>/ / > >>/ Hi Joachim,/ > >>/ / > >>/ What I always still had to ask you is how you do supression of dipoles/ > >>/ in DICS, especially in the case of coherence imaging. I have thought/ > >>/ of two ways of projecting them out:/ > >>/ / > >>/ 1) compute supdip leadfield and its projection on the COV/CSD matrix,/ > >>/ then project it out of the COV/CSD matrix (which looses 2 or 3 from/ > >>/ its rank)./ > >>/ / > >>/ 2) compute supdip leadfield and add it to the leadfield of the dipole/ > >>/ with which is scanned (scandip). Subsequently compute the source/ > >>/ COV/CSD on those 6 leadfield components and select the 3x3 submatrix/ > >>/ that corresponds with the scandip to continue the computations with./ > >>/ / > >>/ Both methods don't really gave me very convincing results. A third/ > >>/ approach would be to add the supdip leadfield to the (identity) noise/ > >>/ matrix and project it through the filters. Then nai=pow/noise is/ > >>/ corrected for the presence of the supdip, but that does not result in/ > >>/ a supressed source coherence distribution. What is your idea or/ > >>/ approach for this?/ > >>/ / > >>/ best regards/ > >>/ Robert/ > >>/ / > > > > ---------------------------------------------------------------------- > > and his answer (Joachim, I hope you don't mind me sharing this on the > > list) > > ---------------------------------------------------------------------- > > > > Begin forwarded message: > > > >>/ From: Joachim Gross //>/ > >>/ Date: 14 October 2004 17:20:45 GMT+02:00/ > >>/ To: "//robert.oostenveld at fcdonders.kun.nl //"/ > >>/ //>/ > >>/ Subject: dipole suppression/ > >>/ / > >>/ Hi Robert,/ > >>/ / > >>/ sorry for the delay./ > >>/ / > >>/ The dipole suppression is indeed a complex issue./ > >>/ We first implemented it because it facilitates visualization and the/ > >>/ exact identification of the first/ > >>/ strongest local maxima./ > >>/ Nevertheless, it is quite dangerous because the map is (locally)/ > >>/ distorted in a non-trivial way./ > >>/ We are now trying to move away from suppressing the sources. I think/ > >>/ it would be better to identify the/ > >>/ significant local maxima (significance based on/ > >>/ randomization/permutation)./ > >>/ But what we are doing at the moment is your approach 3./ > >>/ So we add the supdip leadfield to the noise covariance matrix and look/ > >>/ at pow/noise./ > >>/ / > >>/ For coherence we are basically doing the same thing./ > >>/ So we divide the coherence map (or actually the map of cross spectral/ > >>/ densities) by a noise map/ > >>/ that peaks at the locations of the "unwanted" dipoles./ > >>/ With this procedure we loose absolute coherence values./ > >>/ This is not so important for us since we get the absolute values from/ > >>/ the coherence and partial coherence spectra/ > >>/ that are computed afterwards./ > >>/ It works surprisingly well but should be used with care./ > >>/ / > >>/ A better approach would be to map partial coherence (with the unwanted/ > >>/ dipoles removed). But we have not implemented/ > >>/ this so far./ > >>/ / > >>/ Again, I think it is better to have regions of interest identified by/ > >>/ their significance./ > >>/ / > >>/ Joachim/ > > > > > > ---------------------------------------------------------------------- > > Robert Oostenveld, PhD > > Center for Sensory-Motor Interaction (SMI) > > Aalborg University, Denmark > > > > and > > > > F.C. Donders Centre for Cognitive Neuroimaging > > University Nijmegen > > P.O. Box 9101 > > NL-6500 AH Nijmegen > > The Netherlands > > > > Tel: +31 (0)24 3619695 > > Fax: +31 (0)24 3610989 > > ---------------------------------------------------------------------- > > N.B. Starting from 1 September 2004, the University of Nijmegen has > > changed its name to Radboud University Nijmegen. All web- and > > email-addresses ending in ".kun.nl" should therefore be changed into > > ".ru.nl". Please update your address book and links. > > > > > > Jan Hirschmann > > MSc. Neuroscience > > Insititute of Clinical Neuroscience and Medical Psychology > > Heinrich Heine University Duesseldorf > > Universitaetsstr. 1 > 40225 Duesseldorf > > Tel: 0049 - (0)211 - 81 - 18415 > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- "The test of a first-rate intelligence is the ability to hold two opposed ideas in the mind at the same time, and still retain the ability to function." — F. Scott Fitzgerald From jan.schoffelen at donders.ru.nl Fri Dec 2 19:49:33 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 2 Dec 2011 19:49:33 +0100 Subject: [FieldTrip] coherence normalization In-Reply-To: <4ED91047.6050107@kurage.nimh.nih.gov> References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> <4ED91047.6050107@kurage.nimh.nih.gov> Message-ID: <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> Hi Jan, Tom and the rest, I agree with Tom, but would like to strongly emphasize that differences in power across conditions more often than not will affect the coherence landscape in a non-trivial way. This does not only count for power changes in the reference dipole, but also for changes in power for third party dipoles (i.e. any potential other source). Therefore the interpretation of the subtracted coherence volumes should be done with care. BW, JM On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote: > The solution I have adopted is to always look at coherence contrasts. Make two volumes using the same reference dipole in two different conditions, then subtract the volumes. The self-coherence of the reference will disappear. Mostly. Then use stats, like a U-test. > > Jan.Hirschmann at med.uni-duesseldorf.de wrote: >> Hi community, >> Regarding this thread on suppressing the reference dipole from 2004, what is the current status? Has anybody found and implemented a recommendable way to project out activity from unwanted dipoles? Thank you for any comments/opinions! >> Best, >> Jan Hirschmann >> On 21 Oct 2004, at 17:23, Tom Holroyd wrote: >> >>> / When running a coherence volume using a reference dipole, one/ >>> / naturally expects the coherence will be high around the reference/ >>> / dipole./ >>> / / >>> / This effect tends to dominate the images./ >>> / / >>> / Is there a way to normalize the coherence volume to eliminate/ >>> / this effect? Perhaps by dividing by the coherence in a "control"/ >>> / state?/ >> Hi Tom, >> The dominating effect of the refdip is indeed very problematic. I just >> happened to have discussed this with Joachim Gross, and I have included >> our email exchange below. Please first read that ... >> Basically I agree with Joachim, and I don't trust the supdip that is >> implemented in FieldTrip's sourceanalysis function. Better test and map >> the significance of the difference in coherence between two conditions >> using randomization of the trials before the coherence is beamed (that >> is implemented in sourceanalysis + sourcestatistics). >> Robert >> -------------------------------------------------------------------- >> my question to Joachim was >> ---------------------------------------------------------------------- >> Begin forwarded message: >> >>> / From: Robert Oostenveld //>/ >>> / Date: 1 October 2004 10:26:02 GMT+02:00/ >>> / To: Joachim Gross //>/ >>> / Subject: dipole suppression/ >>> / / >>> / Hi Joachim,/ >>> / / >>> / What I always still had to ask you is how you do supression of dipoles/ >>> / in DICS, especially in the case of coherence imaging. I have thought/ >>> / of two ways of projecting them out:/ >>> / / >>> / 1) compute supdip leadfield and its projection on the COV/CSD matrix,/ >>> / then project it out of the COV/CSD matrix (which looses 2 or 3 from/ >>> / its rank)./ >>> / / >>> / 2) compute supdip leadfield and add it to the leadfield of the dipole/ >>> / with which is scanned (scandip). Subsequently compute the source/ >>> / COV/CSD on those 6 leadfield components and select the 3x3 submatrix/ >>> / that corresponds with the scandip to continue the computations with./ >>> / / >>> / Both methods don't really gave me very convincing results. A third/ >>> / approach would be to add the supdip leadfield to the (identity) noise/ >>> / matrix and project it through the filters. Then nai=pow/noise is/ >>> / corrected for the presence of the supdip, but that does not result in/ >>> / a supressed source coherence distribution. What is your idea or/ >>> / approach for this?/ >>> / / >>> / best regards/ >>> / Robert/ >>> / / >> ---------------------------------------------------------------------- >> and his answer (Joachim, I hope you don't mind me sharing this on the >> list) >> ---------------------------------------------------------------------- >> Begin forwarded message: >> >>> / From: Joachim Gross //>/ >>> / Date: 14 October 2004 17:20:45 GMT+02:00/ >>> / To: "//robert.oostenveld at fcdonders.kun.nl //"/ >>> / //>/ >>> / Subject: dipole suppression/ >>> / / >>> / Hi Robert,/ >>> / / >>> / sorry for the delay./ >>> / / >>> / The dipole suppression is indeed a complex issue./ >>> / We first implemented it because it facilitates visualization and the/ >>> / exact identification of the first/ >>> / strongest local maxima./ >>> / Nevertheless, it is quite dangerous because the map is (locally)/ >>> / distorted in a non-trivial way./ >>> / We are now trying to move away from suppressing the sources. I think/ >>> / it would be better to identify the/ >>> / significant local maxima (significance based on/ >>> / randomization/permutation)./ >>> / But what we are doing at the moment is your approach 3./ >>> / So we add the supdip leadfield to the noise covariance matrix and look/ >>> / at pow/noise./ >>> / / >>> / For coherence we are basically doing the same thing./ >>> / So we divide the coherence map (or actually the map of cross spectral/ >>> / densities) by a noise map/ >>> / that peaks at the locations of the "unwanted" dipoles./ >>> / With this procedure we loose absolute coherence values./ >>> / This is not so important for us since we get the absolute values from/ >>> / the coherence and partial coherence spectra/ >>> / that are computed afterwards./ >>> / It works surprisingly well but should be used with care./ >>> / / >>> / A better approach would be to map partial coherence (with the unwanted/ >>> / dipoles removed). But we have not implemented/ >>> / this so far./ >>> / / >>> / Again, I think it is better to have regions of interest identified by/ >>> / their significance./ >>> / / >>> / Joachim/ >> ---------------------------------------------------------------------- >> Robert Oostenveld, PhD >> Center for Sensory-Motor Interaction (SMI) >> Aalborg University, Denmark >> and >> F.C. Donders Centre for Cognitive Neuroimaging >> University Nijmegen >> P.O. Box 9101 >> NL-6500 AH Nijmegen >> The Netherlands >> Tel: +31 (0)24 3619695 >> Fax: +31 (0)24 3610989 >> ---------------------------------------------------------------------- >> N.B. Starting from 1 September 2004, the University of Nijmegen has >> changed its name to Radboud University Nijmegen. All web- and >> email-addresses ending in ".kun.nl" should therefore be changed into >> ".ru.nl". Please update your address book and links. >> Jan Hirschmann >> MSc. Neuroscience >> Insititute of Clinical Neuroscience and Medical Psychology >> Heinrich Heine University Duesseldorf >> Universitaetsstr. 1 >> 40225 Duesseldorf >> Tel: 0049 - (0)211 - 81 - 18415 >> ------------------------------------------------------------------------ >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- > "The test of a first-rate intelligence is the ability to hold two > opposed ideas in the mind at the same time, and still retain the > ability to function." — F. Scott Fitzgerald > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tolgacan1 at yahoo.com Sun Dec 4 15:00:40 2011 From: tolgacan1 at yahoo.com (=?utf-8?B?VG9sZ2Egw5Z6a3VydA==?=) Date: Sun, 4 Dec 2011 06:00:40 -0800 (PST) Subject: [FieldTrip] coherence normalization In-Reply-To: <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> <4ED91047.6050107@kurage.nimh.nih.gov> <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> Message-ID: <1323007240.37048.YahooMailNeo@web111505.mail.gq1.yahoo.com> Regarding the discussion here, I've gotten onto a recent paper (Sekihara et al., 2011) talking about "imaginary coherence" to prevent the seed region effects.  Even though imaginary coherence does not contain total connectivity information, it might at least be used to select the coherent regions that you want to project on your brain image and ignore the rest. Tolga ________________________________ From: jan-mathijs schoffelen To: Email discussion list for the FieldTrip project Sent: Friday, December 2, 2011 8:49 PM Subject: Re: [FieldTrip] coherence normalization Hi Jan, Tom and the rest, I agree with Tom, but would like to strongly emphasize that differences in power across conditions more often than not will affect the coherence landscape in a non-trivial way. This does not only count for power changes in the reference dipole, but also for changes in power for third party dipoles (i.e. any potential other source). Therefore the interpretation of the subtracted  coherence volumes should be done with care. BW, JM On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote: The solution I have adopted is to always look at coherence contrasts. Make two volumes using the same reference dipole in two different conditions, then subtract the volumes. The self-coherence of the reference will disappear. Mostly. Then use stats, like a U-test. > >Jan.Hirschmann at med.uni-duesseldorf.de wrote: > >Hi community, >> >Regarding this thread on suppressing the reference dipole from 2004, what is the current status? Has anybody found and implemented a recommendable way to project out activity from unwanted dipoles? Thank you for any comments/opinions! >> >Best, >> >Jan Hirschmann >> >  On 21 Oct 2004, at 17:23, Tom Holroyd wrote: >> > >> >/ When running a coherence volume using a reference dipole, one/ >>> >/ naturally expects the coherence will be high around the reference/ >>> >/ dipole./ >>> >/ / >>> >/ This effect tends to dominate the images./ >>> >/ / >>> >/ Is there a way to normalize the coherence volume to eliminate/ >>> >/ this effect?  Perhaps by dividing by the coherence in a "control"/ >>> >/ state?/ >>> >Hi Tom, >> >The dominating effect of the refdip is indeed very problematic. I just >> >happened to have discussed this with Joachim Gross, and I have included >> >our email exchange below. Please first read that ... >> >Basically I agree with Joachim, and I don't trust the supdip that is >> >implemented in FieldTrip's sourceanalysis function. Better test and map >> >the significance of the difference in coherence between two conditions >> >using randomization of the trials before the coherence is beamed (that >> >is implemented in sourceanalysis + sourcestatistics). >> >Robert >> >-------------------------------------------------------------------- >> >my question to Joachim was >> >---------------------------------------------------------------------- >> >Begin forwarded message: >> > >> >/ From: Robert Oostenveld //>/ >>> >/ Date: 1 October 2004 10:26:02 GMT+02:00/ >>> >/ To: Joachim Gross //>/ >>> >/ Subject: dipole suppression/ >>> >/ / >>> >/ Hi Joachim,/ >>> >/ / >>> >/ What I always still had to ask you is how you do supression of dipoles/ >>> >/ in DICS, especially in the case of coherence imaging. I have thought/ >>> >/ of two ways of projecting them out:/ >>> >/ / >>> >/ 1) compute supdip leadfield and its projection on the COV/CSD matrix,/ >>> >/ then project it out of the COV/CSD matrix (which looses 2 or 3 from/ >>> >/ its rank)./ >>> >/ / >>> >/ 2) compute supdip leadfield and add it to the leadfield of the dipole/ >>> >/ with which is scanned (scandip). Subsequently compute the source/ >>> >/ COV/CSD on those 6 leadfield components and select the 3x3 submatrix/ >>> >/ that corresponds with the scandip to continue the computations with./ >>> >/ / >>> >/ Both methods don't really gave me very convincing results. A third/ >>> >/ approach would be to add the supdip leadfield to the (identity) noise/ >>> >/ matrix and project it through the filters. Then nai=pow/noise is/ >>> >/ corrected for the presence of the supdip, but that does not result in/ >>> >/ a supressed source coherence distribution. What is your idea or/ >>> >/ approach for this?/ >>> >/ / >>> >/ best regards/ >>> >/ Robert/ >>> >/ / >>> >---------------------------------------------------------------------- >> >and his answer (Joachim, I hope you don't mind me sharing this on the >> >list) >> >---------------------------------------------------------------------- >> >Begin forwarded message: >> > >> >/ From: Joachim Gross //>/ >>> >/ Date: 14 October 2004 17:20:45 GMT+02:00/ >>> >/ To: "//robert.oostenveld at fcdonders.kun.nl //"/ >>> >/ //>/ >>> >/ Subject: dipole suppression/ >>> >/ / >>> >/ Hi Robert,/ >>> >/ / >>> >/ sorry for the delay./ >>> >/ / >>> >/ The dipole suppression is indeed a complex issue./ >>> >/ We first implemented it because it facilitates visualization and the/ >>> >/ exact identification of the first/ >>> >/ strongest local maxima./ >>> >/ Nevertheless, it is quite dangerous because the map is (locally)/ >>> >/ distorted in a non-trivial way./ >>> >/ We are now trying to move away from suppressing the sources. I think/ >>> >/ it would be better to identify the/ >>> >/ significant local maxima (significance based on/ >>> >/ randomization/permutation)./ >>> >/ But what we are doing at the moment is your approach 3./ >>> >/ So we add the supdip leadfield to the noise covariance matrix and look/ >>> >/ at pow/noise./ >>> >/ / >>> >/ For coherence we are basically doing the same thing./ >>> >/ So we divide the coherence map (or actually the map of cross spectral/ >>> >/ densities) by a noise map/ >>> >/ that peaks at the locations of the "unwanted" dipoles./ >>> >/ With this procedure we loose absolute coherence values./ >>> >/ This is not so important for us since we get the absolute values from/ >>> >/ the coherence and partial coherence spectra/ >>> >/ that are computed afterwards./ >>> >/ It works surprisingly well but should be used with care./ >>> >/ / >>> >/ A better approach would be to map partial coherence (with the unwanted/ >>> >/ dipoles removed). But we have not implemented/ >>> >/ this so far./ >>> >/ / >>> >/ Again, I think it is better to have regions of interest identified by/ >>> >/ their significance./ >>> >/ / >>> >/ Joachim/ >>> > ---------------------------------------------------------------------- >> >Robert Oostenveld, PhD >> >Center for Sensory-Motor Interaction (SMI) >> >Aalborg University, Denmark >> >and >> >F.C. Donders Centre for Cognitive Neuroimaging >> >University Nijmegen >> >P.O. Box 9101 >> >NL-6500 AH Nijmegen >> >The Netherlands >> >Tel: +31 (0)24 3619695 >> >Fax: +31 (0)24 3610989 >> >---------------------------------------------------------------------- >> >N.B. Starting from 1 September 2004, the University of Nijmegen has >> >changed its name to Radboud University Nijmegen. All web- and >> >email-addresses ending in ".kun.nl" should therefore be changed into >> >".ru.nl". Please update your address book and links. >> > Jan Hirschmann >> >MSc. Neuroscience >> >Insititute of Clinical Neuroscience and Medical Psychology >> >Heinrich Heine University Duesseldorf >> >Universitaetsstr.  1 >> >40225  Duesseldorf >> >Tel: 0049 - (0)211 - 81 - 18415 >> >------------------------------------------------------------------------ >> >_______________________________________________ >> >fieldtrip mailing list >> >fieldtrip at donders.ru.nl >> >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >-- >"The test of a first-rate intelligence is the ability to hold two >opposed ideas in the mind at the same time, and still retain the >ability to function." — F. Scott Fitzgerald >_______________________________________________ >fieldtrip mailing list >fieldtrip at donders.ru.nl >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > Jan-Mathijs Schoffelen, MD PhD  Donders Institute for Brain, Cognition and Behaviour,  Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From nkremers at uni-bonn.de Mon Dec 5 13:58:58 2011 From: nkremers at uni-bonn.de (Nico Alexander Willi Kremers) Date: Mon, 05 Dec 2011 13:58:58 +0100 Subject: [FieldTrip] 2x3 anova in cluster analysis Message-ID: Hi, I followed the discussion about implementing a 2x2 within subjects design into a cluster statistic with much interest. I want to implement a 2x3 repeated measure anova in a cluster analysis using fieldtrip. I think for this type of analysis subracting two conditions from each other and then calculate a ttest is not appropriate. Is there another way of calculating the interaction effect between the two factors and generate clusters for real and permutation data? What specifications must be set and how? Thank you very much for your answer, Nico From tomh at kurage.nimh.nih.gov Mon Dec 5 19:56:02 2011 From: tomh at kurage.nimh.nih.gov (Tom Holroyd (NIH/NIMH) [E]) Date: Mon, 05 Dec 2011 13:56:02 -0500 Subject: [FieldTrip] coherence normalization In-Reply-To: <1323007240.37048.YahooMailNeo@web111505.mail.gq1.yahoo.com> References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> <4ED91047.6050107@kurage.nimh.nih.gov> <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> <1323007240.37048.YahooMailNeo@web111505.mail.gq1.yahoo.com> Message-ID: <4EDD13C2.3000305@kurage.nimh.nih.gov> Yes, Guido Nolte came up with that around the same time (2004). I found this link by google, there might be a better one http://keck.ucsf.edu/~houde/sensorimotor_jc/GNolte04a.pdf Imaginary coherence is insensitive to volume conduction in EEG. I think the interpretation is different for MEG, but you can certainly easily compute it; you might still want to contrast different conditions. Tolga Özkurt wrote: > Regarding the discussion here, I've gotten onto a recent paper (Sekihara > et al., 2011) talking about "imaginary coherence" to prevent the seed > region effects. > > Even though imaginary coherence does not contain total connectivity > information, it might at least be used to select the coherent regions > that you want to project on your brain image and ignore the rest. > > Tolga > > > ------------------------------------------------------------------------ > *From:* jan-mathijs schoffelen > *To:* Email discussion list for the FieldTrip project > > *Sent:* Friday, December 2, 2011 8:49 PM > *Subject:* Re: [FieldTrip] coherence normalization > > Hi Jan, Tom and the rest, > > I agree with Tom, but would like to strongly emphasize that differences > in power across conditions more often than not will affect the coherence > landscape in a non-trivial way. This does not only count for power > changes in the reference dipole, but also for changes in power for third > party dipoles (i.e. any potential other source). Therefore the > interpretation of the subtracted coherence volumes should be done with > care. > > BW, > > JM > > On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote: > >> The solution I have adopted is to always look at coherence contrasts. >> Make two volumes using the same reference dipole in two different >> conditions, then subtract the volumes. The self-coherence of the >> reference will disappear. Mostly. Then use stats, like a U-test. >> >> Jan.Hirschmann at med.uni-duesseldorf.de >> wrote: >>> Hi community, >>> Regarding this thread on suppressing the reference dipole from 2004, >>> what is the current status? Has anybody found and implemented a >>> recommendable way to project out activity from unwanted dipoles? >>> Thank you for any comments/opinions! >>> Best, >>> Jan Hirschmann >>> On 21 Oct 2004, at 17:23, Tom Holroyd wrote: >>> >>>> / When running a coherence volume using a reference dipole, one/ >>>> / naturally expects the coherence will be high around the reference/ >>>> / dipole./ >>>> / / >>>> / This effect tends to dominate the images./ >>>> / / >>>> / Is there a way to normalize the coherence volume to eliminate/ >>>> / this effect? Perhaps by dividing by the coherence in a "control"/ >>>> / state?/ >>> Hi Tom, >>> The dominating effect of the refdip is indeed very problematic. I just >>> happened to have discussed this with Joachim Gross, and I have included >>> our email exchange below. Please first read that ... >>> Basically I agree with Joachim, and I don't trust the supdip that is >>> implemented in FieldTrip's sourceanalysis function. Better test and map >>> the significance of the difference in coherence between two conditions >>> using randomization of the trials before the coherence is beamed (that >>> is implemented in sourceanalysis + sourcestatistics). >>> Robert >>> -------------------------------------------------------------------- >>> my question to Joachim was >>> ---------------------------------------------------------------------- >>> Begin forwarded message: >>> >>>> / From: Robert Oostenveld >>> >>>> //>/ >>>> / Date: 1 October 2004 10:26:02 GMT+02:00/ >>>> / To: Joachim Gross >>> >>>> //>/ >>>> / Subject: dipole suppression/ >>>> / / >>>> / Hi Joachim,/ >>>> / / >>>> / What I always still had to ask you is how you do supression of >>>> dipoles/ >>>> / in DICS, especially in the case of coherence imaging. I have thought/ >>>> / of two ways of projecting them out:/ >>>> / / >>>> / 1) compute supdip leadfield and its projection on the COV/CSD matrix,/ >>>> / then project it out of the COV/CSD matrix (which looses 2 or 3 from/ >>>> / its rank)./ >>>> / / >>>> / 2) compute supdip leadfield and add it to the leadfield of the dipole/ >>>> / with which is scanned (scandip). Subsequently compute the source/ >>>> / COV/CSD on those 6 leadfield components and select the 3x3 submatrix/ >>>> / that corresponds with the scandip to continue the computations with./ >>>> / / >>>> / Both methods don't really gave me very convincing results. A third/ >>>> / approach would be to add the supdip leadfield to the (identity) noise/ >>>> / matrix and project it through the filters. Then nai=pow/noise is/ >>>> / corrected for the presence of the supdip, but that does not result in/ >>>> / a supressed source coherence distribution. What is your idea or/ >>>> / approach for this?/ >>>> / / >>>> / best regards/ >>>> / Robert/ >>>> / / >>> ---------------------------------------------------------------------- >>> and his answer (Joachim, I hope you don't mind me sharing this on the >>> list) >>> ---------------------------------------------------------------------- >>> Begin forwarded message: >>> >>>> / From: Joachim Gross >>> >>>> //>/ >>>> / Date: 14 October 2004 17:20:45 GMT+02:00/ >>>> / To: "//robert.oostenveld at fcdonders.kun.nl >>>> >>>> //"/ >>>> / >>>> //>/ >>>> / Subject: dipole suppression/ >>>> / / >>>> / Hi Robert,/ >>>> / / >>>> / sorry for the delay./ >>>> / / >>>> / The dipole suppression is indeed a complex issue./ >>>> / We first implemented it because it facilitates visualization and the/ >>>> / exact identification of the first/ >>>> / strongest local maxima./ >>>> / Nevertheless, it is quite dangerous because the map is (locally)/ >>>> / distorted in a non-trivial way./ >>>> / We are now trying to move away from suppressing the sources. I think/ >>>> / it would be better to identify the/ >>>> / significant local maxima (significance based on/ >>>> / randomization/permutation)./ >>>> / But what we are doing at the moment is your approach 3./ >>>> / So we add the supdip leadfield to the noise covariance matrix and >>>> look/ >>>> / at pow/noise./ >>>> / / >>>> / For coherence we are basically doing the same thing./ >>>> / So we divide the coherence map (or actually the map of cross spectral/ >>>> / densities) by a noise map/ >>>> / that peaks at the locations of the "unwanted" dipoles./ >>>> / With this procedure we loose absolute coherence values./ >>>> / This is not so important for us since we get the absolute values from/ >>>> / the coherence and partial coherence spectra/ >>>> / that are computed afterwards./ >>>> / It works surprisingly well but should be used with care./ >>>> / / >>>> / A better approach would be to map partial coherence (with the >>>> unwanted/ >>>> / dipoles removed). But we have not implemented/ >>>> / this so far./ >>>> / / >>>> / Again, I think it is better to have regions of interest identified by/ >>>> / their significance./ >>>> / / >>>> / Joachim/ >>> ---------------------------------------------------------------------- >>> Robert Oostenveld, PhD >>> Center for Sensory-Motor Interaction (SMI) >>> Aalborg University, Denmark >>> and >>> F.C. Donders Centre for Cognitive Neuroimaging >>> University Nijmegen >>> P.O. Box 9101 >>> NL-6500 AH Nijmegen >>> The Netherlands >>> Tel: +31 (0)24 3619695 >>> Fax: +31 (0)24 3610989 >>> ---------------------------------------------------------------------- >>> N.B. Starting from 1 September 2004, the University of Nijmegen has >>> changed its name to Radboud University Nijmegen. All web- and >>> email-addresses ending in ".kun.nl" should therefore be changed into >>> ".ru.nl". Please update your address book and links. >>> Jan Hirschmann >>> MSc. Neuroscience >>> Insititute of Clinical Neuroscience and Medical Psychology >>> Heinrich Heine University Duesseldorf >>> Universitaetsstr. 1 >>> 40225 Duesseldorf >>> Tel: 0049 - (0)211 - 81 - 18415 >>> ------------------------------------------------------------------------ >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> "The test of a first-rate intelligence is the ability to hold two >> opposed ideas in the mind at the same time, and still retain the >> ability to function." — F. Scott Fitzgerald >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > ------------------------------------------------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- "The test of a first-rate intelligence is the ability to hold two opposed ideas in the mind at the same time, and still retain the ability to function." — F. Scott Fitzgerald From dualitystan at gmail.com Mon Dec 5 20:17:04 2011 From: dualitystan at gmail.com (Stanley Klein) Date: Mon, 5 Dec 2011 11:17:04 -0800 Subject: [FieldTrip] 2x3 anova in cluster analysis In-Reply-To: References: Message-ID: Nico, Your question gives me the chance to ask something I've been curious about. It seems to me that one of the nifty things about permutation cluster analysis is that it allows you to do anything that seems reasonable as long you decide on the process ahead of time and don't do any future tweaking other than fixing coding errors. I'm curious whether the Fieldtrip code make it easy to insert new statistics modules. I presume your actual question had to do with whether Fieldtrip already has the possibility of doing that 2x3 ANOVA. I suspect it doesn't have that capability. However, it would be nice if the permutation cluster analysis could be made sufficiently modular that one could make use of all the complicated clustering and permuting and all, but enable the user to substitute their own statistical method. I haven't actually watched my students doing the nitty-gritty use of Fieldtrip's version of the permutation test (other than knowing that is is very nice and well documented) so I don't know how easy it is to stick in one's own favorite statistic, but I'm hoping it is easy. Stan On Mon, Dec 5, 2011 at 4:58 AM, Nico Alexander Willi Kremers < nkremers at uni-bonn.de> wrote: > > Hi, > > I followed the discussion about implementing a 2x2 within subjects design > into a cluster statistic with much interest. I want to implement a 2x3 > repeated measure anova in a cluster analysis using fieldtrip. I think for > this type of analysis subracting two conditions from each other and then > calculate a ttest is not appropriate. Is there another way of calculating > the interaction effect between the two factors and generate clusters for > real and permutation data? What specifications must be set and how? > > Thank you very much for your answer, > > Nico > ______________________________**_________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Dec 5 21:01:39 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 5 Dec 2011 21:01:39 +0100 Subject: [FieldTrip] 2x3 anova in cluster analysis In-Reply-To: References: Message-ID: <6A25053C-2EB2-437A-A96F-2C1047DC862F@donders.ru.nl> Hi Stan et al, Actually FieldTrip allows in a very straightforward way to plug-in one's favourite statistic. The idea is the following: when specifying cfg.statistic you need to specify a string that under the hood points to a function, e.g. 'indepsamplesT' eventually causes a function to be called, answering to the aptly chosen name: 'statfun_indepsamplesT' which is doing the legwork. As long as the statfun_younameit has properly defined input and output arguments, you can let it do whatever you want. FieldTrip contains a bunch of 'statfuns' in the statfun directory but there's no reason not to implement any yourself (and ideally contribute them to the repository). Another discussion altogether is the question whether the test statistic of interest is an appropriate one that allows for statistical inference using the permutation framework. Over the past years there have been various threads on this mailing list regarding the possibility to test for interactions using a permutation test. You can look this up in the archive. Strictly speaking this is statistically not possible this way. The permutation-framework tests the null-hypothesis of exchangeability of data across allocated conditions, whereas when one wants to test for an interaction effect tests one tests for a particular linear (parametric) model of the dependent variables explaining variance in the dependent variable. Inferring that exchangeability across conditions is unlikely (i.e. obtaining a small p-value through permutation) does not necessarily lead to the conclusion that there is an actual interaction effect. Though opinions among the statisticians about this seem to vary, there may be a way out: one could either use bootstrapping to obtain confidence intervals for the interaction F under the null-hypothesis. The recipe for this would be to do a cell-specific demeaning of the data to impose the null-hypothesis of no interaction, and then through bootstrap resampling obtain a reference distribution of the interaction F. Alternatively, although I haven't thought this one through for any case other than a 2x2 anova, one could reduce the interaction effect to a two-condition contrast where observations belonging to the 'main diagonal' of the 2x2 conditions design are labeled as condition 1, and the observations belonging to the other diagonal are labeled as condition 2. One could then proceed with using a T-statistic as a descriptive statistic across these two 'conditions' on which inference can be done. Cheers and a happy Sinterklaas to you all, Jan-Mathijs On Dec 5, 2011, at 8:17 PM, Stanley Klein wrote: > Nico, > > Your question gives me the chance to ask something I've been curious about. It seems to me that one of the nifty things about permutation cluster analysis is that it allows you to do anything that seems reasonable as long you decide on the process ahead of time and don't do any future tweaking other than fixing coding errors. I'm curious whether the Fieldtrip code make it easy to insert new statistics modules. > > I presume your actual question had to do with whether Fieldtrip already has the possibility of doing that 2x3 ANOVA. I suspect it doesn't have that capability. However, it would be nice if the permutation cluster analysis could be made sufficiently modular that one could make use of all the complicated clustering and permuting and all, but enable the user to substitute their own statistical method. I haven't actually watched my students doing the nitty-gritty use of Fieldtrip's version of the permutation test (other than knowing that is is very nice and well documented) so I don't know how easy it is to stick in one's own favorite statistic, but I'm hoping it is easy. > > Stan > > > On Mon, Dec 5, 2011 at 4:58 AM, Nico Alexander Willi Kremers wrote: > > Hi, > > I followed the discussion about implementing a 2x2 within subjects design into a cluster statistic with much interest. I want to implement a 2x3 repeated measure anova in a cluster analysis using fieldtrip. I think for this type of analysis subracting two conditions from each other and then calculate a ttest is not appropriate. Is there another way of calculating the interaction effect between the two factors and generate clusters for real and permutation data? What specifications must be set and how? > > Thank you very much for your answer, > > Nico > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Dec 5 21:13:30 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 5 Dec 2011 21:13:30 +0100 Subject: [FieldTrip] coherence normalization In-Reply-To: <4EDD13C2.3000305@kurage.nimh.nih.gov> References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> <4ED91047.6050107@kurage.nimh.nih.gov> <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> <1323007240.37048.YahooMailNeo@web111505.mail.gq1.yahoo.com> <4EDD13C2.3000305@kurage.nimh.nih.gov> Message-ID: Hi all, I would not venture to interpret a conditional difference in the imaginary part of the coherency. When this quantity changes, it could either be due to a change in the phase or to a change of the magnitude of the coherency (or of any combination of the two). BW, JM On Dec 5, 2011, at 7:56 PM, Tom Holroyd (NIH/NIMH) [E] wrote: > Yes, Guido Nolte came up with that around the same time (2004). > > I found this link by google, there might be a better one > > http://keck.ucsf.edu/~houde/sensorimotor_jc/GNolte04a.pdf > > Imaginary coherence is insensitive to volume conduction in EEG. > > I think the interpretation is different for MEG, but you can certainly easily compute it; you might still want to contrast different conditions. > > Tolga Özkurt wrote: >> Regarding the discussion here, I've gotten onto a recent paper (Sekihara et al., 2011) talking about "imaginary coherence" to prevent the seed region effects. Even though imaginary coherence does not contain total connectivity information, it might at least be used to select the coherent regions that you want to project on your brain image and ignore the rest. >> Tolga >> ------------------------------------------------------------------------ >> *From:* jan-mathijs schoffelen >> *To:* Email discussion list for the FieldTrip project >> *Sent:* Friday, December 2, 2011 8:49 PM >> *Subject:* Re: [FieldTrip] coherence normalization >> Hi Jan, Tom and the rest, >> I agree with Tom, but would like to strongly emphasize that differences in power across conditions more often than not will affect the coherence landscape in a non-trivial way. This does not only count for power changes in the reference dipole, but also for changes in power for third party dipoles (i.e. any potential other source). Therefore the interpretation of the subtracted coherence volumes should be done with care. >> BW, >> JM >> On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote: >>> The solution I have adopted is to always look at coherence contrasts. Make two volumes using the same reference dipole in two different conditions, then subtract the volumes. The self-coherence of the reference will disappear. Mostly. Then use stats, like a U-test. >>> >>> Jan.Hirschmann at med.uni-duesseldorf.de wrote: >>>> Hi community, >>>> Regarding this thread on suppressing the reference dipole from 2004, what is the current status? Has anybody found and implemented a recommendable way to project out activity from unwanted dipoles? Thank you for any comments/opinions! >>>> Best, >>>> Jan Hirschmann >>>> On 21 Oct 2004, at 17:23, Tom Holroyd wrote: >>>> >>>>> / When running a coherence volume using a reference dipole, one/ >>>>> / naturally expects the coherence will be high around the reference/ >>>>> / dipole./ >>>>> / / >>>>> / This effect tends to dominate the images./ >>>>> / / >>>>> / Is there a way to normalize the coherence volume to eliminate/ >>>>> / this effect? Perhaps by dividing by the coherence in a "control"/ >>>>> / state?/ >>>> Hi Tom, >>>> The dominating effect of the refdip is indeed very problematic. I just >>>> happened to have discussed this with Joachim Gross, and I have included >>>> our email exchange below. Please first read that ... >>>> Basically I agree with Joachim, and I don't trust the supdip that is >>>> implemented in FieldTrip's sourceanalysis function. Better test and map >>>> the significance of the difference in coherence between two conditions >>>> using randomization of the trials before the coherence is beamed (that >>>> is implemented in sourceanalysis + sourcestatistics). >>>> Robert >>>> -------------------------------------------------------------------- >>>> my question to Joachim was >>>> ---------------------------------------------------------------------- >>>> Begin forwarded message: >>>> >>>>> / From: Robert Oostenveld //>/ >>>>> / Date: 1 October 2004 10:26:02 GMT+02:00/ >>>>> / To: Joachim Gross //>/ >>>>> / Subject: dipole suppression/ >>>>> / / >>>>> / Hi Joachim,/ >>>>> / / >>>>> / What I always still had to ask you is how you do supression of dipoles/ >>>>> / in DICS, especially in the case of coherence imaging. I have thought/ >>>>> / of two ways of projecting them out:/ >>>>> / / >>>>> / 1) compute supdip leadfield and its projection on the COV/CSD matrix,/ >>>>> / then project it out of the COV/CSD matrix (which looses 2 or 3 from/ >>>>> / its rank)./ >>>>> / / >>>>> / 2) compute supdip leadfield and add it to the leadfield of the dipole/ >>>>> / with which is scanned (scandip). Subsequently compute the source/ >>>>> / COV/CSD on those 6 leadfield components and select the 3x3 submatrix/ >>>>> / that corresponds with the scandip to continue the computations with./ >>>>> / / >>>>> / Both methods don't really gave me very convincing results. A third/ >>>>> / approach would be to add the supdip leadfield to the (identity) noise/ >>>>> / matrix and project it through the filters. Then nai=pow/noise is/ >>>>> / corrected for the presence of the supdip, but that does not result in/ >>>>> / a supressed source coherence distribution. What is your idea or/ >>>>> / approach for this?/ >>>>> / / >>>>> / best regards/ >>>>> / Robert/ >>>>> / / >>>> ---------------------------------------------------------------------- >>>> and his answer (Joachim, I hope you don't mind me sharing this on the >>>> list) >>>> ---------------------------------------------------------------------- >>>> Begin forwarded message: >>>> >>>>> / From: Joachim Gross //>/ >>>>> / Date: 14 October 2004 17:20:45 GMT+02:00/ >>>>> / To: "//robert.oostenveld at fcdonders.kun.nl //"/ >>>>> / //>/ >>>>> / Subject: dipole suppression/ >>>>> / / >>>>> / Hi Robert,/ >>>>> / / >>>>> / sorry for the delay./ >>>>> / / >>>>> / The dipole suppression is indeed a complex issue./ >>>>> / We first implemented it because it facilitates visualization and the/ >>>>> / exact identification of the first/ >>>>> / strongest local maxima./ >>>>> / Nevertheless, it is quite dangerous because the map is (locally)/ >>>>> / distorted in a non-trivial way./ >>>>> / We are now trying to move away from suppressing the sources. I think/ >>>>> / it would be better to identify the/ >>>>> / significant local maxima (significance based on/ >>>>> / randomization/permutation)./ >>>>> / But what we are doing at the moment is your approach 3./ >>>>> / So we add the supdip leadfield to the noise covariance matrix and look/ >>>>> / at pow/noise./ >>>>> / / >>>>> / For coherence we are basically doing the same thing./ >>>>> / So we divide the coherence map (or actually the map of cross spectral/ >>>>> / densities) by a noise map/ >>>>> / that peaks at the locations of the "unwanted" dipoles./ >>>>> / With this procedure we loose absolute coherence values./ >>>>> / This is not so important for us since we get the absolute values from/ >>>>> / the coherence and partial coherence spectra/ >>>>> / that are computed afterwards./ >>>>> / It works surprisingly well but should be used with care./ >>>>> / / >>>>> / A better approach would be to map partial coherence (with the unwanted/ >>>>> / dipoles removed). But we have not implemented/ >>>>> / this so far./ >>>>> / / >>>>> / Again, I think it is better to have regions of interest identified by/ >>>>> / their significance./ >>>>> / / >>>>> / Joachim/ >>>> ---------------------------------------------------------------------- >>>> Robert Oostenveld, PhD >>>> Center for Sensory-Motor Interaction (SMI) >>>> Aalborg University, Denmark >>>> and >>>> F.C. Donders Centre for Cognitive Neuroimaging >>>> University Nijmegen >>>> P.O. Box 9101 >>>> NL-6500 AH Nijmegen >>>> The Netherlands >>>> Tel: +31 (0)24 3619695 >>>> Fax: +31 (0)24 3610989 >>>> ---------------------------------------------------------------------- >>>> N.B. Starting from 1 September 2004, the University of Nijmegen has >>>> changed its name to Radboud University Nijmegen. All web- and >>>> email-addresses ending in ".kun.nl" should therefore be changed into >>>> ".ru.nl". Please update your address book and links. >>>> Jan Hirschmann >>>> MSc. Neuroscience >>>> Insititute of Clinical Neuroscience and Medical Psychology >>>> Heinrich Heine University Duesseldorf >>>> Universitaetsstr. 1 >>>> 40225 Duesseldorf >>>> Tel: 0049 - (0)211 - 81 - 18415 >>>> ------------------------------------------------------------------------ >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> -- >>> "The test of a first-rate intelligence is the ability to hold two >>> opposed ideas in the mind at the same time, and still retain the >>> ability to function." — F. Scott Fitzgerald >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> ------------------------------------------------------------------------ >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- > "The test of a first-rate intelligence is the ability to hold two > opposed ideas in the mind at the same time, and still retain the > ability to function." — F. Scott Fitzgerald > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at kurage.nimh.nih.gov Mon Dec 5 21:38:55 2011 From: tomh at kurage.nimh.nih.gov (Tom Holroyd (NIH/NIMH) [E]) Date: Mon, 05 Dec 2011 15:38:55 -0500 Subject: [FieldTrip] coherence normalization In-Reply-To: References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> <4ED91047.6050107@kurage.nimh.nih.gov> <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> <1323007240.37048.YahooMailNeo@web111505.mail.gq1.yahoo.com> <4EDD13C2.3000305@kurage.nimh.nih.gov> Message-ID: <4EDD2BDF.6090506@kurage.nimh.nih.gov> Yes. Nolte mentions that although one often computes coherency relative to a baseline, one must be careful because of this and random flips of pi making hash of it if you just blindly subtract. Same thing for any relative phase calculation. Also, I was misunderstanding things below; the interpretation is the same for MEG as it is for EEG, any source affects multiple sensors simultaneously. It is this spatial correlation that allows us to see it as a source after all, and what makes the imaginary part positive. If there were no spatial correlations there would be no imaginary part in the coherence. heh, yes, it took me that long to understand this paper ... :-) jan-mathijs schoffelen wrote: > Hi all, > > I would not venture to interpret a conditional difference in the > imaginary part of the coherency. When this quantity changes, it could > either be due to a change in the phase or to a change of the magnitude > of the coherency (or of any combination of the two). > > BW, > > JM > > > On Dec 5, 2011, at 7:56 PM, Tom Holroyd (NIH/NIMH) [E] wrote: > >> Yes, Guido Nolte came up with that around the same time (2004). >> >> I found this link by google, there might be a better one >> >> http://keck.ucsf.edu/~houde/sensorimotor_jc/GNolte04a.pdf >> >> Imaginary coherence is insensitive to volume conduction in EEG. >> >> I think the interpretation is different for MEG, but you can certainly >> easily compute it; you might still want to contrast different conditions. >> >> Tolga Özkurt wrote: >>> Regarding the discussion here, I've gotten onto a recent paper >>> (Sekihara et al., 2011) talking about "imaginary coherence" to >>> prevent the seed region effects. Even though imaginary coherence does >>> not contain total connectivity information, it might at least be used >>> to select the coherent regions that you want to project on your brain >>> image and ignore the rest. >>> Tolga >>> ------------------------------------------------------------------------ >>> *From:* jan-mathijs schoffelen >>> *To:* Email discussion list for the FieldTrip project >>> >>> *Sent:* Friday, December 2, 2011 8:49 PM >>> *Subject:* Re: [FieldTrip] coherence normalization >>> Hi Jan, Tom and the rest, >>> I agree with Tom, but would like to strongly emphasize that >>> differences in power across conditions more often than not will >>> affect the coherence landscape in a non-trivial way. This does not >>> only count for power changes in the reference dipole, but also for >>> changes in power for third party dipoles (i.e. any potential other >>> source). Therefore the interpretation of the subtracted coherence >>> volumes should be done with care. >>> BW, >>> JM >>> On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote: >>>> The solution I have adopted is to always look at coherence >>>> contrasts. Make two volumes using the same reference dipole in two >>>> different conditions, then subtract the volumes. The self-coherence >>>> of the reference will disappear. Mostly. Then use stats, like a U-test. >>>> >>>> Jan.Hirschmann at med.uni-duesseldorf.de >>>> wrote: >>>>> Hi community, >>>>> Regarding this thread on suppressing the reference dipole from >>>>> 2004, what is the current status? Has anybody found and implemented >>>>> a recommendable way to project out activity from unwanted dipoles? >>>>> Thank you for any comments/opinions! >>>>> Best, >>>>> Jan Hirschmann >>>>> On 21 Oct 2004, at 17:23, Tom Holroyd wrote: >>>>> >>>>>> / When running a coherence volume using a reference dipole, one/ >>>>>> / naturally expects the coherence will be high around the reference/ >>>>>> / dipole./ >>>>>> / / >>>>>> / This effect tends to dominate the images./ >>>>>> / / >>>>>> / Is there a way to normalize the coherence volume to eliminate/ >>>>>> / this effect? Perhaps by dividing by the coherence in a "control"/ >>>>>> / state?/ >>>>> Hi Tom, >>>>> The dominating effect of the refdip is indeed very problematic. I just >>>>> happened to have discussed this with Joachim Gross, and I have included >>>>> our email exchange below. Please first read that ... >>>>> Basically I agree with Joachim, and I don't trust the supdip that is >>>>> implemented in FieldTrip's sourceanalysis function. Better test and map >>>>> the significance of the difference in coherence between two conditions >>>>> using randomization of the trials before the coherence is beamed (that >>>>> is implemented in sourceanalysis + sourcestatistics). >>>>> Robert >>>>> -------------------------------------------------------------------- >>>>> my question to Joachim was >>>>> ---------------------------------------------------------------------- >>>>> Begin forwarded message: >>>>> >>>>>> / From: Robert Oostenveld >>>>> >>>>>> //>/ >>>>>> / Date: 1 October 2004 10:26:02 GMT+02:00/ >>>>>> / To: Joachim Gross >>>>> >>>>>> //>/ >>>>>> / Subject: dipole suppression/ >>>>>> / / >>>>>> / Hi Joachim,/ >>>>>> / / >>>>>> / What I always still had to ask you is how you do supression of >>>>>> dipoles/ >>>>>> / in DICS, especially in the case of coherence imaging. I have >>>>>> thought/ >>>>>> / of two ways of projecting them out:/ >>>>>> / / >>>>>> / 1) compute supdip leadfield and its projection on the COV/CSD >>>>>> matrix,/ >>>>>> / then project it out of the COV/CSD matrix (which looses 2 or 3 from/ >>>>>> / its rank)./ >>>>>> / / >>>>>> / 2) compute supdip leadfield and add it to the leadfield of the >>>>>> dipole/ >>>>>> / with which is scanned (scandip). Subsequently compute the source/ >>>>>> / COV/CSD on those 6 leadfield components and select the 3x3 >>>>>> submatrix/ >>>>>> / that corresponds with the scandip to continue the computations >>>>>> with./ >>>>>> / / >>>>>> / Both methods don't really gave me very convincing results. A third/ >>>>>> / approach would be to add the supdip leadfield to the (identity) >>>>>> noise/ >>>>>> / matrix and project it through the filters. Then nai=pow/noise is/ >>>>>> / corrected for the presence of the supdip, but that does not >>>>>> result in/ >>>>>> / a supressed source coherence distribution. What is your idea or/ >>>>>> / approach for this?/ >>>>>> / / >>>>>> / best regards/ >>>>>> / Robert/ >>>>>> / / >>>>> ---------------------------------------------------------------------- >>>>> and his answer (Joachim, I hope you don't mind me sharing this on the >>>>> list) >>>>> ---------------------------------------------------------------------- >>>>> Begin forwarded message: >>>>> >>>>>> / From: Joachim Gross >>>>> >>>>>> //>/ >>>>>> / Date: 14 October 2004 17:20:45 GMT+02:00/ >>>>>> / To: "//robert.oostenveld at fcdonders.kun.nl >>>>>> >>>>>> //"/ >>>>>> / >>>>> >>>>>> //>/ >>>>>> / Subject: dipole suppression/ >>>>>> / / >>>>>> / Hi Robert,/ >>>>>> / / >>>>>> / sorry for the delay./ >>>>>> / / >>>>>> / The dipole suppression is indeed a complex issue./ >>>>>> / We first implemented it because it facilitates visualization and >>>>>> the/ >>>>>> / exact identification of the first/ >>>>>> / strongest local maxima./ >>>>>> / Nevertheless, it is quite dangerous because the map is (locally)/ >>>>>> / distorted in a non-trivial way./ >>>>>> / We are now trying to move away from suppressing the sources. I >>>>>> think/ >>>>>> / it would be better to identify the/ >>>>>> / significant local maxima (significance based on/ >>>>>> / randomization/permutation)./ >>>>>> / But what we are doing at the moment is your approach 3./ >>>>>> / So we add the supdip leadfield to the noise covariance matrix >>>>>> and look/ >>>>>> / at pow/noise./ >>>>>> / / >>>>>> / For coherence we are basically doing the same thing./ >>>>>> / So we divide the coherence map (or actually the map of cross >>>>>> spectral/ >>>>>> / densities) by a noise map/ >>>>>> / that peaks at the locations of the "unwanted" dipoles./ >>>>>> / With this procedure we loose absolute coherence values./ >>>>>> / This is not so important for us since we get the absolute values >>>>>> from/ >>>>>> / the coherence and partial coherence spectra/ >>>>>> / that are computed afterwards./ >>>>>> / It works surprisingly well but should be used with care./ >>>>>> / / >>>>>> / A better approach would be to map partial coherence (with the >>>>>> unwanted/ >>>>>> / dipoles removed). But we have not implemented/ >>>>>> / this so far./ >>>>>> / / >>>>>> / Again, I think it is better to have regions of interest >>>>>> identified by/ >>>>>> / their significance./ >>>>>> / / >>>>>> / Joachim/ >>>>> ---------------------------------------------------------------------- >>>>> Robert Oostenveld, PhD >>>>> Center for Sensory-Motor Interaction (SMI) >>>>> Aalborg University, Denmark >>>>> and >>>>> F.C. Donders Centre for Cognitive Neuroimaging >>>>> University Nijmegen >>>>> P.O. Box 9101 >>>>> NL-6500 AH Nijmegen >>>>> The Netherlands >>>>> Tel: +31 (0)24 3619695 >>>>> Fax: +31 (0)24 3610989 >>>>> ---------------------------------------------------------------------- >>>>> N.B. Starting from 1 September 2004, the University of Nijmegen has >>>>> changed its name to Radboud University Nijmegen. All web- and >>>>> email-addresses ending in ".kun.nl" should therefore be changed into >>>>> ".ru.nl". Please update your address book and links. >>>>> Jan Hirschmann >>>>> MSc. Neuroscience >>>>> Insititute of Clinical Neuroscience and Medical Psychology >>>>> Heinrich Heine University Duesseldorf >>>>> Universitaetsstr. 1 >>>>> 40225 Duesseldorf >>>>> Tel: 0049 - (0)211 - 81 - 18415 >>>>> ------------------------------------------------------------------------ >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> -- >>>> "The test of a first-rate intelligence is the ability to hold two >>>> opposed ideas in the mind at the same time, and still retain the >>>> ability to function." — F. Scott Fitzgerald >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition >>> and Behaviour, Centre for Cognitive Neuroimaging, >>> Radboud University Nijmegen, The Netherlands >>> Max Planck Institute for Psycholinguistics, >>> Nijmegen, The Netherlands >>> J.Schoffelen at donders.ru.nl >>> Telephone: +31-24-3614793 >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> ------------------------------------------------------------------------ >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> "The test of a first-rate intelligence is the ability to hold two >> opposed ideas in the mind at the same time, and still retain the >> ability to function." — F. Scott Fitzgerald >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > ------------------------------------------------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- "The test of a first-rate intelligence is the ability to hold two opposed ideas in the mind at the same time, and still retain the ability to function." — F. Scott Fitzgerald From jan.schoffelen at donders.ru.nl Mon Dec 5 22:03:06 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 5 Dec 2011 22:03:06 +0100 Subject: [FieldTrip] source statistics, group level In-Reply-To: References: Message-ID: <2A18BE4D-384F-4EE3-8D57-F11C642A089B@donders.ru.nl> Hi Sonja I think you are almost there. What I am not sure about is the name of the field in the grandaverage structure which contains the concatenated individual subject data. Isn't this field called '.trial'? In that case you should specify cfg.parameter to be 'trial'. If this is not the cause of the problem, did you check the individual subject volumes? Do these contain colored data? What do you exactly mean by getting a blank mri? Does the stat.stat field contain only zeros, nans or something else? Best, Jan-Mathijs On Dec 2, 2011, at 12:16 PM, Sonja Suntrup wrote: > Dear fieldtrip users, > I would like to do sourcestatistics on a group level with meg data. I have a > pre and post intervention measurement for each of my 21 subjects > (within-subjects design). After source reconstruction using an LCMV beamformer > and volume normalization I calculated the sourcegrandaverage for the pre and > post condition with the parameter cfg.keepindividual = 'yes'. > However, when I use the grandaverage results in ft_sourcestatistics in the > configuration shown below and plot the result I just get a blank anatomical > mri. Do I have to set any additional parameters or do I make a general > mistake? Whould you recommend to use a cluster-based permutation test > comparable to ft_timelockstatistics and would I have to set the same > parameters in ft_sourcestatistics then? > > cfg=[]; > cfg.dim = grandAVGsourcePre.dim; > cfg.method = 'montecarlo'; > cfg.statistic = 'depsamplesT'; > cfg.parameter = 'avg.pow'; > cfg.correctm = 'cluster'; > cfg.numrandomization = 100; > cfg.alpha = 0.05; > cfg.tail = 0; > > nsubj=length(sourcePre.trial); > cfg.design(1,:) = [1:nsubj 1:nsubj]; > cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2]; > cfg.uvar = 1; > cfg.ivar = 2; > stat = ft_sourcestatistics(cfg, grandAVGsourcePre, grandAVGsourcePost); > > Your help is greatly appreciated! > Best, > Sonja > > > -- > Dr. med. Sonja Suntrup > Institute for Biomagnetism and Biosignalanalysis > University of Muenster > Malmedyweg 15 > 48149 Münster, Germany > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From dderiso at ucsd.edu Tue Dec 6 02:45:45 2011 From: dderiso at ucsd.edu (Dave Deriso) Date: Mon, 5 Dec 2011 17:45:45 -0800 Subject: [FieldTrip] Problem plotting independent components Message-ID: Dear Fieldtrip Users, I am trying to implement the tutorial on using ICA to extract eyeblink artifacts ( http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). Everything works, except that the labels from the IC data do not match the labels from the layout file, causing an error in the topoplotIC function. Your help in solving this is most appreciated. Layout labels (I am using a Neuromag 306 MEG): 'MEG0113' 'MEG0112' 'MEG0111' 'MEG0122' 'MEG0123' IC labels: 'runica001' 'runica002' 'runica003' 'runica004' 'runica005' Matlab Output: ft_topoplotIC(cfg, comp); creating layout from data.grad creating layout for neuromag306alt system Error using ft_topoplotTFR (line 659) labels in data and labels in layout do not match Error in ft_topoplotIC (line 122) ft_topoplotTFR(cfg, varargin{:}); Cheers, Dave Deriso -- UCSD Institute for Neural Computation UCSD Department of Neurosurgery -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Dec 6 07:46:17 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 6 Dec 2011 07:46:17 +0100 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: Message-ID: <195A02BE-0BCE-4A9A-B25B-15657D7DDC53@donders.ru.nl> Hi Dave, Could you try and report back what happens when you specify cfg.layout = 'NM306.lay', prior to calling ft_topoplotTFR? Cheers, JM On Dec 6, 2011, at 2:45 AM, Dave Deriso wrote: > Dear Fieldtrip Users, > > I am trying to implement the tutorial on using ICA to extract eyeblink artifacts (http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). Everything works, except that the labels from the IC data do not match the labels from the layout file, causing an error in the topoplotIC function. Your help in solving this is most appreciated. > > > Layout labels (I am using a Neuromag 306 MEG): > 'MEG0113' > 'MEG0112' > 'MEG0111' > 'MEG0122' > 'MEG0123' > > IC labels: > 'runica001' > 'runica002' > 'runica003' > 'runica004' > 'runica005' > > Matlab Output: > ft_topoplotIC(cfg, comp); > creating layout from data.grad > creating layout for neuromag306alt system > Error using ft_topoplotTFR (line 659) > labels in data and labels in layout do not match > Error in ft_topoplotIC (line 122) > ft_topoplotTFR(cfg, varargin{:}); > > > > Cheers, > Dave Deriso > > -- > UCSD Institute for Neural Computation > UCSD Department of Neurosurgery > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue Dec 6 12:55:31 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 06 Dec 2011 12:55:31 +0100 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: Message-ID: <4EDE02B3.1010103@donders.ru.nl> Dear Dave, the labels do not match indeed, because ICs do not correspond to single channel (obviously). I am not exactly sure how ft_topoplotIC is built, but you could try using ft_databrowser instead, with cfg.viewmode = 'component' Hope that at least circumvents your problem. Best, Jörn On 12/6/2011 2:45 AM, Dave Deriso wrote: > Dear Fieldtrip Users, > > I am trying to implement the tutorial on using ICA to extract eyeblink > artifacts > (http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). > Everything works, except that the labels from the IC data do not match > the labels from the layout file, causing an error in the topoplotIC > function. Your help in solving this is most appreciated. > > > Layout labels (I am using a Neuromag 306 MEG): > 'MEG0113' > 'MEG0112' > 'MEG0111' > 'MEG0122' > 'MEG0123' > > IC labels: > 'runica001' > 'runica002' > 'runica003' > 'runica004' > 'runica005' > > Matlab Output: > ft_topoplotIC(cfg, comp); > creating layout from data.grad > creating layout for neuromag306alt system > Error using ft_topoplotTFR (line 659) > labels in data and labels in layout do not match > Error in ft_topoplotIC (line 122) > ft_topoplotTFR(cfg, varargin{:}); > > > > Cheers, > Dave Deriso > > -- > UCSD Institute for Neural Computation > UCSD Department of Neurosurgery > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From h.rossiter at ucl.ac.uk Tue Dec 6 14:18:28 2011 From: h.rossiter at ucl.ac.uk (Rossiter, Holly) Date: Tue, 6 Dec 2011 13:18:28 +0000 Subject: [FieldTrip] DICS beamformer images Message-ID: Hi all, I am using DICS to assess coherence and viewing the beamformer images through SPM. What I want to know is what is the value given in the image and how is it calculated? I thought it was a coherence value but it is not bounded between 0 and 1. Also what do you think is the best way to threshold the images in order to get rid of low value peaks? Thanks, Holly -------------- next part -------------- An HTML attachment was scrubbed... URL: From dderiso at ucsd.edu Tue Dec 6 20:17:03 2011 From: dderiso at ucsd.edu (Dave Deriso) Date: Tue, 6 Dec 2011 11:17:03 -0800 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: <4EDE02B3.1010103@donders.ru.nl> References: <4EDE02B3.1010103@donders.ru.nl> Message-ID: Dear JM and Jörn, Thank you so much for your helpful suggestions. Matlab could not find/open layout file: *NM306.lay* with both *ft_topoplotTFR* and* ft_topoplotIC*. I have also tried each of the following layouts without success: cfg.layout =3D data.grad; cfg.layout =3D 'neuromag306all.lay'; cfg.layout =3D 'neuromag306cmb.lay'; cfg.layout =3D 'neuromag306mag.lay'; cfg.layout =3D 'neuromag306planar.lay'; (and no layout cfg, as prescribed by the bottom of http://fieldtrip.fcdonders.nl/reference/ft_topoplotic) As Jörn mentioned, the IC and sensor labels are different and, therefore, doing a string comparison will return an error. The question is then, how can I project the ICs back into sensor space and plot them topographically using the pre-existing sensor layouts? If this accomplished by the *ft_topoplotIC* function, shouldn't it expect the IC labels to be different from the layout labels? Thanks again for all of your help! Cheers, Dave Deriso -- UCSD Institute for Neural Computation UCSD Department of Neurosurgery On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" < jm.horschig at donders.ru.nl> wrote: > Dear Dave, > > the labels do not match indeed, because ICs do not correspond to single > channel (obviously). I am not exactly sure how ft_topoplotIC is built, but > you could try using ft_databrowser instead, with cfg.viewmode = 'component' > Hope that at least circumvents your problem. > > Best, > Jörn > > > On 12/6/2011 2:45 AM, Dave Deriso wrote: > > Dear Fieldtrip Users, > > I am trying to implement the tutorial on using ICA to extract eyeblink > artifacts ( > http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). > Everything works, except that the labels from the IC data do not match the > labels from the layout file, causing an error in the topoplotIC > function. Your help in solving this is most appreciated. > > > Layout labels (I am using a Neuromag 306 MEG): > 'MEG0113' > 'MEG0112' > 'MEG0111' > 'MEG0122' > 'MEG0123' > > IC labels: > 'runica001' > 'runica002' > 'runica003' > 'runica004' > 'runica005' > > Matlab Output: > ft_topoplotIC(cfg, comp); > creating layout from data.grad > creating layout for neuromag306alt system > Error using ft_topoplotTFR (line 659) > labels in data and labels in layout do not match > Error in ft_topoplotIC (line 122) > ft_topoplotTFR(cfg, varargin{:}); > > > > Cheers, > Dave Deriso > > -- > UCSD Institute for Neural Computation > UCSD Department of Neurosurgery > > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dderiso at ucsd.edu Wed Dec 7 02:07:55 2011 From: dderiso at ucsd.edu (Dave Deriso) Date: Tue, 6 Dec 2011 17:07:55 -0800 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: <4EDE02B3.1010103@donders.ru.nl> Message-ID: I should also note that when I tried the *ft_databrowser* function it was unable to plot the component topographies because there weren't enough grid points. Have you encountered this before? Thanks again for all of your great help!! My code: cfg = []; cfg.viewmode = 'component' ft_databrowser(cfg, comp); Output: creating layout from cfg.grad creating layout for neuromag306alt system the input is component data with 306 components and 306 original channels detected 0 visual artifacts redrawing with viewmode component fetching data... done fetching artifacts... done preprocessing data... done plotting artifacts... plotting events... plotting data... Warning: Imaginary parts of complex X and/or Y arguments ignored > In ft_plot_vector at 191 In ft_databrowser>redraw_cb at 1309 In ft_databrowser at 508 Warning: Imaginary parts of complex X and/or Y arguments ignored > In ft_plot_vector at 191 In ft_databrowser>redraw_cb at 1309 In ft_databrowser at 508 ****** these errors repeat about 10 times, then: plotting component topographies... Error using griddata (line 79) Not enough unique sample points specified. Error in ft_plot_topo (line 153) [Xi,Yi,Zi] = griddata(chanX', chanY, dat, xi', yi, interpmethod); % interpolate the topographic data Error in ft_databrowser>redraw_cb (line 1377) ft_plot_topo(chanx, chany, chanz, 'mask', laychan.mask, 'interplim', 'mask', 'outline', laychan.outline, 'tag', 'topography', ... Error in ft_databrowser (line 508) redraw_cb(h); Cheers, Dave On Tue, Dec 6, 2011 at 11:17 AM, Dave Deriso wrote: > Dear JM and Jörn, > > Thank you so much for your helpful suggestions. Matlab could not find/open > layout file: *NM306.lay* with both *ft_topoplotTFR* and* ft_topoplotIC*. > I have also tried each of the following layouts without success: > > cfg.layout =3D data.grad; > cfg.layout =3D 'neuromag306all.lay'; > cfg.layout =3D 'neuromag306cmb.lay'; > cfg.layout =3D 'neuromag306mag.lay'; > cfg.layout =3D 'neuromag306planar.lay'; > (and no layout cfg, as prescribed by the bottom of > http://fieldtrip.fcdonders.nl/reference/ft_topoplotic) > > > As Jörn mentioned, the IC and sensor labels are different and, > therefore, doing a string comparison will return an error. The question is > then, how can I project the ICs back into sensor space and plot them > topographically using the pre-existing sensor layouts? If this accomplished > by the *ft_topoplotIC* function, shouldn't it expect the IC labels to be > different from the layout labels? > > Thanks again for all of your help! > > Cheers, > Dave Deriso > > -- > UCSD Institute for Neural Computation > UCSD Department of Neurosurgery > > > > > On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" < > jm.horschig at donders.ru.nl> wrote: > >> Dear Dave, >> >> the labels do not match indeed, because ICs do not correspond to single >> channel (obviously). I am not exactly sure how ft_topoplotIC is built, but >> you could try using ft_databrowser instead, with cfg.viewmode = 'component' >> Hope that at least circumvents your problem. >> >> Best, >> Jörn >> >> >> On 12/6/2011 2:45 AM, Dave Deriso wrote: >> >> Dear Fieldtrip Users, >> >> I am trying to implement the tutorial on using ICA to extract eyeblink >> artifacts ( >> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). >> Everything works, except that the labels from the IC data do not match the >> labels from the layout file, causing an error in the topoplotIC >> function. Your help in solving this is most appreciated. >> >> >> Layout labels (I am using a Neuromag 306 MEG): >> 'MEG0113' >> 'MEG0112' >> 'MEG0111' >> 'MEG0122' >> 'MEG0123' >> >> IC labels: >> 'runica001' >> 'runica002' >> 'runica003' >> 'runica004' >> 'runica005' >> >> Matlab Output: >> ft_topoplotIC(cfg, comp); >> creating layout from data.grad >> creating layout for neuromag306alt system >> Error using ft_topoplotTFR (line 659) >> labels in data and labels in layout do not match >> Error in ft_topoplotIC (line 122) >> ft_topoplotTFR(cfg, varargin{:}); >> >> >> >> Cheers, >> Dave Deriso >> >> -- >> UCSD Institute for Neural Computation >> UCSD Department of Neurosurgery >> >> >> >> _______________________________________________ >> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Jörn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jarang.hahm at gmail.com Wed Dec 7 03:34:49 2011 From: jarang.hahm at gmail.com (Jarang Hahm) Date: Wed, 7 Dec 2011 11:34:49 +0900 Subject: [FieldTrip] Question about the identification of sensor type & proper timing of gradiometer selection Message-ID: Dear fieldtrip user. I'm newcomer on an MEG analysis and the fieldtrip. I have MEG data (.fif file) measured by Neuromag 306 channel system. Recently I got two problems on 1) identification of sensor type and 2) proper time to separate gradiometer in data processing. 1) First one is about identification of sensor type when using fieldtrip toolbox (20111204 version) After trial definition and preprocessing, I got some warnings in series when doing time-frequency analysis: Warning: could be Yokogawa system > In fileio\private\ft_senstype at 271 In ft_chantype at 71 In ft_chantype at 477 In ft_datatype_sens at 124 In ft_datatype_raw at 95 In ft_checkdata at 175 In ft_freqanalysis at 188 Warning: could be Yokogawa system > In fileio\private\ft_senstype at 271 In ft_chantype at 166 In ft_chantype at 477 In ft_datatype_sens at 124 In ft_datatype_raw at 95 In ft_checkdata at 175 In ft_freqanalysis at 188 (...There were also the other 12 warnings, which were simillar to above except for the specific line in ft_chantype.) As warning indicated, I've been ft_senstype at the line 271 and found that it couldn't recognize the data as a Neuromag 306 system although the sensor label of my data was matched with that of Neuromag 306. I wonder whether those warnings might affect overall analysis procedure or not and wish to fix this problem. 2) The second question is about a proper time for gradiometer selection. My analysis of interest is only gradiometer channels, not magnetometer one, so that the magnetometer can be removed at some time. In data processing, when is the proper time to separate the gradiometer channel from magnetometer? My data will be processed like this way: Trial definition -> preprocessing -> ICA for EOG rejection -> artifact rejection -> time-frequency analysis at sensor level & source analysis. Should I keep apart gradiometer channel from magnetometer after artifact rejection? or before ICA analysis? Need your help. Sincerely, Jarang Hahm -------------- next part -------------- An HTML attachment was scrubbed... URL: From miellet at psy.gla.ac.uk Wed Dec 7 07:52:28 2011 From: miellet at psy.gla.ac.uk (miellet at psy.gla.ac.uk) Date: Wed, 07 Dec 2011 06:52:28 +0000 Subject: [FieldTrip] second-level stats with TFR In-Reply-To: <4ECE596D.90504@psy.gla.ac.uk> References: <4ECE596D.90504@psy.gla.ac.uk> Message-ID: <20111207065228.27673d9bz74irz8s@horde.psy.gla.ac.uk> Hello, I've got problems doing second-level stats with TFR because of the data structure. I previously did it with ERF and didn't experience any difficulty. I'm just comparing 2 conditions so the design is very simple. The dimord for ERF was rpt_chan_time so I had access to the different trials. For ERF, I computed individual t-values between my conditions and across trials; then averaged the result across participants and compared the grand-average to zero. Do you think this strategy makes sense? For TFR, the dimord is chan_freq_time (with cfg.keeptrials='yes', before or after ft_freqbaseline). Obviously I don't want to compute the individual t-values across channels, freq bands or time points but across trials. Do you have any idea where I could find this information please? (I look in previous.....previous but couldn't find anything useful. I also specify keeptrials at each step of the process) Thank you very much for your help, Sebastien ---------------------------------------------- Dr. Sébastien Miellet, Lecturer Department of Psychology University of Fribourg Faucigny 2 1700 Fribourg Switzerland tel: +41 26 300 7666 ---------------------------------------------- Quoting Sara Bögels : > Hi all, > > I have been trying to do second-level statistical inference (as > described in one of the FAQs) on ERFs, but I am not sure whether I > am doing everything correctly. > > In the first step I calculate the T-values for the difference > between two conditions (twice), which are between items, with > ft_timelockstatistics. I put the output of all participants in a > cell (called 'stat1a' and 'stat1b'). (I tried to use > ft_timelockgrandaverage to combine the subjects together but it > needs a field avg). > > Then I use ft_timelockstatistics again but subject level. I first > want to look at the difference between the two conditions. This > difference is reflected in the T-values of the first step so I > create a dummy which is the same as 'stat1' but I replace all the > values in the field 'stat' per participant with zeros. Then I call > (with appropriate cfg parameters): > > stat2a = ft_timelockstatistics(cfg,stat1a{:},dummy{:}); > stat2b = ft_timelockstatistics(cfg,stat1b{:},dummy{:}); > > To compare the two differences (stat1a and stat1b) and thereby look > at an interaction, I call: > > stat2a-b = ft_timelockstatistics(cfg,stat1a{:},stat1b{:}); > > I am uncertain whether the dummy works (or is there a way to compare > the t-values to zero directly?) and whether the stat1a{:} trick > works with ft_timelockstatistics. > > Thanks in advance for your answer. > > Sara > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > ---------------------------------------------------------------- This message was sent using the Web mail system for The University of Glasgow School of Psychology ------------------------------------------------------------------ From jm.horschig at donders.ru.nl Wed Dec 7 08:33:08 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 07 Dec 2011 08:33:08 +0100 Subject: [FieldTrip] Critical bug in ft_freqstatistic fixed Message-ID: <4EDF16B4.4030605@donders.ru.nl> Dear 'trippers, last week we fixed a *critical bug in freqstatistic *which might have caused wrong clustering on channel-level. You might have been affected by this *if your channel labels were not ordered alphabetically by default *(e.g. BTI system, EEG systems, etc.). In essence, the bug caused channelclusters which did not make sense (e.g. frontal channels and occipital channels in one cluster). You might have noticed already whether you were affected by critically looking at the plots. *This bug was introduced in May 2011*, so if you made a cluster-based permutation test on channel-level between May and now, *please make the effort to rerun *to be sure that your clusters are not due to this bug! Thanks to Gregor Volberg who reported this bug and Tobias Staudigl for also looking into this one and providing a fix. Our sincere apologies for this. On behalf of the FieldTrip team, Jörn -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Dec 7 08:52:21 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 7 Dec 2011 08:52:21 +0100 Subject: [FieldTrip] second-level stats with TFR In-Reply-To: <20111207065228.27673d9bz74irz8s@horde.psy.gla.ac.uk> References: <4ECE596D.90504@psy.gla.ac.uk> <20111207065228.27673d9bz74irz8s@horde.psy.gla.ac.uk> Message-ID: Cher Seb, In order to be able to compute a single subject T-statistic on the TFR you indeed need to specify cfg.keeptrials = 'yes', prior to calling ft_freqanalysis. Are you absolutely sure that you did this? If so, we need to look into this. Could you create yourself an account on our bugzilla file-server (bugzilla.fcdonders.nl) and file this as a bug. Just copy and paste your e-mail message and also upload some script+data facilitating the reproduction of the problem? Cheers, Jan-Mathijs On Dec 7, 2011, at 7:52 AM, miellet at psy.gla.ac.uk wrote: > Hello, > I've got problems doing second-level stats with TFR because of the data structure. > I previously did it with ERF and didn't experience any difficulty. I'm just comparing 2 conditions so the design is very simple. The dimord for ERF was rpt_chan_time so I had access to the different trials. > For ERF, I computed individual t-values between my conditions and across trials; then averaged the result across participants and compared the grand-average to zero. Do you think this strategy makes sense? > For TFR, the dimord is chan_freq_time (with cfg.keeptrials='yes', before or after ft_freqbaseline). Obviously I don't want to compute the individual t-values across channels, freq bands or time points but across trials. > Do you have any idea where I could find this information please? (I look in previous.....previous but couldn't find anything useful. I also specify keeptrials at each step of the process) > Thank you very much for your help, > Sebastien > > ---------------------------------------------- > Dr. Sébastien Miellet, Lecturer > > Department of Psychology > University of Fribourg > Faucigny 2 > 1700 Fribourg > Switzerland > > tel: +41 26 300 7666 > ---------------------------------------------- > > > > Quoting Sara Bögels : > >> Hi all, >> >> I have been trying to do second-level statistical inference (as described in one of the FAQs) on ERFs, but I am not sure whether I am doing everything correctly. >> >> In the first step I calculate the T-values for the difference between two conditions (twice), which are between items, with ft_timelockstatistics. I put the output of all participants in a cell (called 'stat1a' and 'stat1b'). (I tried to use ft_timelockgrandaverage to combine the subjects together but it needs a field avg). >> >> Then I use ft_timelockstatistics again but subject level. I first want to look at the difference between the two conditions. This difference is reflected in the T-values of the first step so I create a dummy which is the same as 'stat1' but I replace all the values in the field 'stat' per participant with zeros. Then I call (with appropriate cfg parameters): >> >> stat2a = ft_timelockstatistics(cfg,stat1a{:},dummy{:}); >> stat2b = ft_timelockstatistics(cfg,stat1b{:},dummy{:}); >> >> To compare the two differences (stat1a and stat1b) and thereby look at an interaction, I call: >> >> stat2a-b = ft_timelockstatistics(cfg,stat1a{:},stat1b{:}); >> >> I am uncertain whether the dummy works (or is there a way to compare the t-values to zero directly?) and whether the stat1a{:} trick works with ft_timelockstatistics. >> >> Thanks in advance for your answer. >> >> Sara >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > ---------------------------------------------------------------- > This message was sent using the Web mail system for > The University of Glasgow School of Psychology > ------------------------------------------------------------------ > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed Dec 7 10:42:12 2011 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 7 Dec 2011 10:42:12 +0100 Subject: [FieldTrip] Interactive Plotting in ft_rejectvisual Message-ID: <1C5AEC7D-4B54-428E-BE54-B408171837FC@gmail.com> Hi, Not really a bug report, so I put this on the discussion List. I noticed that when plotting single trials in the ft_rejectivusal function, the figure popping up is not interactive which makes a closer inspection of the trials somewhat harder. Maybe this is intentional, but I can't see a reason for it. However, simply adding "cfg_mp.interactive='yes';" at line 510 of "reject visual_summary" fixes this. Best, Julian Dipl. Psych. Julian Keil OBOB-Lab University of Konstanz Department of Psychology P.O. Box D25 78457 Konstanz Germany Tel: ++49 - (0)7531 - 88 42 50 Fax: ++49 - (0)7531 - 88 28 91 Email: julian.keil at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at donders.ru.nl Wed Dec 7 12:59:48 2011 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Wed, 7 Dec 2011 12:59:48 +0100 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: <4EDE02B3.1010103@donders.ru.nl> Message-ID: Hi Dave, Perhaps this error is due to the complex data that ft_databrowser cannot plot? If you re-calculate the components and get out real-only values, do you still get this error? Best, Johanna On 7 December 2011 02:07, Dave Deriso wrote: > I should also note that when I tried the *ft_databrowser* function it was > unable to plot the component topographies because there weren't enough grid > points. Have you encountered this before? Thanks again for all of your > great help!! > > My code: > > cfg = []; > cfg.viewmode = 'component' > ft_databrowser(cfg, comp); > > > Output: > > creating layout from cfg.grad > creating layout for neuromag306alt system > the input is component data with 306 components and 306 original channels > detected 0 visual artifacts > redrawing with viewmode component > fetching data... done > fetching artifacts... done > preprocessing data... done > plotting artifacts... > plotting events... > plotting data... > > Warning: Imaginary parts of complex X and/or Y arguments ignored > > In ft_plot_vector at 191 > In ft_databrowser>redraw_cb at 1309 > In ft_databrowser at 508 > Warning: Imaginary parts of complex X and/or Y arguments ignored > > In ft_plot_vector at 191 > In ft_databrowser>redraw_cb at 1309 > In ft_databrowser at 508 > ****** these errors repeat about > 10 times, then: > plotting component topographies... > Error using griddata (line 79) > Not enough unique sample points specified. > > Error in ft_plot_topo (line 153) > [Xi,Yi,Zi] = griddata(chanX', chanY, dat, xi', yi, interpmethod); % > interpolate the topographic data > > Error in ft_databrowser>redraw_cb (line 1377) > ft_plot_topo(chanx, chany, chanz, 'mask', laychan.mask, 'interplim', > 'mask', 'outline', laychan.outline, 'tag', 'topography', > ... > > Error in ft_databrowser (line 508) > redraw_cb(h); > > > > > > Cheers, > Dave > > > On Tue, Dec 6, 2011 at 11:17 AM, Dave Deriso wrote: > >> Dear JM and Jörn, >> >> Thank you so much for your helpful suggestions. Matlab could not >> find/open layout file: *NM306.lay* with both *ft_topoplotTFR* and* >> ft_topoplotIC*. I have also tried each of the following layouts without >> success: >> >> cfg.layout =3D data.grad; >> cfg.layout =3D 'neuromag306all.lay'; >> cfg.layout =3D 'neuromag306cmb.lay'; >> cfg.layout =3D 'neuromag306mag.lay'; >> cfg.layout =3D 'neuromag306planar.lay'; >> (and no layout cfg, as prescribed by the bottom of >> http://fieldtrip.fcdonders.nl/reference/ft_topoplotic) >> >> >> As Jörn mentioned, the IC and sensor labels are different and, >> therefore, doing a string comparison will return an error. The question is >> then, how can I project the ICs back into sensor space and plot them >> topographically using the pre-existing sensor layouts? If this accomplished >> by the *ft_topoplotIC* function, shouldn't it expect the IC labels to be >> different from the layout labels? >> >> Thanks again for all of your help! >> >> Cheers, >> Dave Deriso >> >> -- >> UCSD Institute for Neural Computation >> UCSD Department of Neurosurgery >> >> >> >> >> On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" < >> jm.horschig at donders.ru.nl> wrote: >> >>> Dear Dave, >>> >>> the labels do not match indeed, because ICs do not correspond to single >>> channel (obviously). I am not exactly sure how ft_topoplotIC is built, but >>> you could try using ft_databrowser instead, with cfg.viewmode = 'component' >>> Hope that at least circumvents your problem. >>> >>> Best, >>> Jörn >>> >>> >>> On 12/6/2011 2:45 AM, Dave Deriso wrote: >>> >>> Dear Fieldtrip Users, >>> >>> I am trying to implement the tutorial on using ICA to extract eyeblink >>> artifacts ( >>> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). >>> Everything works, except that the labels from the IC data do not match the >>> labels from the layout file, causing an error in the topoplotIC >>> function. Your help in solving this is most appreciated. >>> >>> >>> Layout labels (I am using a Neuromag 306 MEG): >>> 'MEG0113' >>> 'MEG0112' >>> 'MEG0111' >>> 'MEG0122' >>> 'MEG0123' >>> >>> IC labels: >>> 'runica001' >>> 'runica002' >>> 'runica003' >>> 'runica004' >>> 'runica005' >>> >>> Matlab Output: >>> ft_topoplotIC(cfg, comp); >>> creating layout from data.grad >>> creating layout for neuromag306alt system >>> Error using ft_topoplotTFR (line 659) >>> labels in data and labels in layout do not match >>> Error in ft_topoplotIC (line 122) >>> ft_topoplotTFR(cfg, varargin{:}); >>> >>> >>> >>> Cheers, >>> Dave Deriso >>> >>> -- >>> UCSD Institute for Neural Computation >>> UCSD Department of Neurosurgery >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> -- >>> Jörn M. Horschig >>> PhD Student >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognitive Neuroimaging >>> Radboud University Nijmegen >>> Neuronal Oscillations Group >>> >>> P.O. Box 9101 >>> NL-6500 HB Nijmegen >>> The Netherlands >>> >>> Contact: >>> E-Mail: jm.horschig at donders.ru.nl >>> Tel: +31-(0)24-36-68493 >>> Web: http://www.ru.nl/donders >>> >>> Visiting address: >>> Trigon, room 2.30 >>> Kapittelweg 29 >>> NL-6525 EN Nijmegen >>> The Netherlands >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed Dec 7 22:51:48 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 7 Dec 2011 22:51:48 +0100 Subject: [FieldTrip] how to avoid displaying function info In-Reply-To: References: Message-ID: <5A6D62F9-DD15-4683-B212-72517DB4AE3D@donders.ru.nl> Dear Marco This is now possible, see http://bugzilla.fcdonders.nl/show_bug.cgi?id=1191 and especially the last comment for details. Note that in case the callinfo is printed, the memory estimate only returns something useful on Linux and OS X. On Windows the memory useage cannot be estimated yet. best regards, Robert PS the main reason for printing the callinfo is to educate users about the memory and time requirements, so that users can more easily get reasonable lower-bound estimates for the resources required when doing distributed computing on a torque/sge linux cluster. On 25 Nov 2011, at 12:27, Marco Buiatti wrote: > Dear FTrippers, > > an aesthetic question: When I plot several topoplots, I would like to > avoid displaying information about the duration and RAM used by the > plotting functions, as: > the call to "ft_topoplotTFR" took 0 seconds and an estimated 0 MB > the call to "ft_prepare_layout" took 0 seconds and an estimated 0 MB > > Is there a simple way to do this? > > Thanks, > > Marco > > > -- > Marco Buiatti, PhD > > CEA/DSV/I2BM / NeuroSpin > INSERM U992 - Cognitive Neuroimaging Unit > Bât 145 - Point Courrier 156 > Gif sur Yvette F-91191 FRANCE > Ph: +33(0)169.08.65.21 > Fax: +33(0)169.08.79.73 > E-mail: marco.buiatti at gmail.com > http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti > > *********************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From dderiso at ucsd.edu Wed Dec 7 23:34:48 2011 From: dderiso at ucsd.edu (Dave Deriso) Date: Wed, 7 Dec 2011 14:34:48 -0800 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: <4EDE02B3.1010103@donders.ru.nl> Message-ID: Hi Johanna, Thanks for taking a look. I could not find a method inside * ft_componentanalysis* that extracts real values (although using real() could also accomplish this), however the warning seems to indicate that the complex values are ignored. Do you think this is still an issue? The error with *ft_databrowser* indicates a lack of "unique sample points" from some kind of grid, which is perhaps a bigger problem. Any thoughts? Thanks again! Cheers, Dave On Wed, Dec 7, 2011 at 3:59 AM, Johanna Zumer wrote: > Hi Dave, > Perhaps this error is due to the complex data that ft_databrowser cannot > plot? If you re-calculate the components and get out real-only values, do > you still get this error? > > Best, > Johanna > > > On 7 December 2011 02:07, Dave Deriso wrote: > >> I should also note that when I tried the *ft_databrowser* function it >> was unable to plot the component topographies because there weren't enough >> grid points. Have you encountered this before? Thanks again for all of your >> great help!! >> >> My code: >> >> cfg = []; >> cfg.viewmode = 'component' >> ft_databrowser(cfg, comp); >> >> >> Output: >> >> creating layout from cfg.grad >> creating layout for neuromag306alt system >> the input is component data with 306 components and 306 original channels >> detected 0 visual artifacts >> redrawing with viewmode component >> fetching data... done >> fetching artifacts... done >> preprocessing data... done >> plotting artifacts... >> plotting events... >> plotting data... >> >> Warning: Imaginary parts of complex X and/or Y arguments ignored >> > In ft_plot_vector at 191 >> In ft_databrowser>redraw_cb at 1309 >> In ft_databrowser at 508 >> Warning: Imaginary parts of complex X and/or Y arguments ignored >> > In ft_plot_vector at 191 >> In ft_databrowser>redraw_cb at 1309 >> In ft_databrowser at 508 >> ****** these errors repeat >> about 10 times, then: >> plotting component topographies... >> Error using griddata (line 79) >> Not enough unique sample points specified. >> >> Error in ft_plot_topo (line 153) >> [Xi,Yi,Zi] = griddata(chanX', chanY, dat, xi', yi, interpmethod); % >> interpolate the topographic data >> >> Error in ft_databrowser>redraw_cb (line 1377) >> ft_plot_topo(chanx, chany, chanz, 'mask', laychan.mask, >> 'interplim', 'mask', 'outline', laychan.outline, 'tag', 'topography', >> ... >> >> Error in ft_databrowser (line 508) >> redraw_cb(h); >> >> >> >> >> >> Cheers, >> Dave >> >> >> On Tue, Dec 6, 2011 at 11:17 AM, Dave Deriso wrote: >> >>> Dear JM and Jörn, >>> >>> Thank you so much for your helpful suggestions. Matlab could not >>> find/open layout file: *NM306.lay* with both *ft_topoplotTFR* and* >>> ft_topoplotIC*. I have also tried each of the following layouts >>> without success: >>> >>> cfg.layout =3D data.grad; >>> cfg.layout =3D 'neuromag306all.lay'; >>> cfg.layout =3D 'neuromag306cmb.lay'; >>> cfg.layout =3D 'neuromag306mag.lay'; >>> cfg.layout =3D 'neuromag306planar.lay'; >>> (and no layout cfg, as prescribed by the bottom of >>> http://fieldtrip.fcdonders.nl/reference/ft_topoplotic) >>> >>> >>> As Jörn mentioned, the IC and sensor labels are different and, >>> therefore, doing a string comparison will return an error. The question is >>> then, how can I project the ICs back into sensor space and plot them >>> topographically using the pre-existing sensor layouts? If this accomplished >>> by the *ft_topoplotIC* function, shouldn't it expect the IC labels to >>> be different from the layout labels? >>> >>> Thanks again for all of your help! >>> >>> Cheers, >>> Dave Deriso >>> >>> -- >>> UCSD Institute for Neural Computation >>> UCSD Department of Neurosurgery >>> >>> >>> >>> >>> On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" < >>> jm.horschig at donders.ru.nl> wrote: >>> >>>> Dear Dave, >>>> >>>> the labels do not match indeed, because ICs do not correspond to single >>>> channel (obviously). I am not exactly sure how ft_topoplotIC is built, but >>>> you could try using ft_databrowser instead, with cfg.viewmode = 'component' >>>> Hope that at least circumvents your problem. >>>> >>>> Best, >>>> Jörn >>>> >>>> >>>> On 12/6/2011 2:45 AM, Dave Deriso wrote: >>>> >>>> Dear Fieldtrip Users, >>>> >>>> I am trying to implement the tutorial on using ICA to extract >>>> eyeblink artifacts ( >>>> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). >>>> Everything works, except that the labels from the IC data do not match the >>>> labels from the layout file, causing an error in the topoplotIC >>>> function. Your help in solving this is most appreciated. >>>> >>>> >>>> Layout labels (I am using a Neuromag 306 MEG): >>>> 'MEG0113' >>>> 'MEG0112' >>>> 'MEG0111' >>>> 'MEG0122' >>>> 'MEG0123' >>>> >>>> IC labels: >>>> 'runica001' >>>> 'runica002' >>>> 'runica003' >>>> 'runica004' >>>> 'runica005' >>>> >>>> Matlab Output: >>>> ft_topoplotIC(cfg, comp); >>>> creating layout from data.grad >>>> creating layout for neuromag306alt system >>>> Error using ft_topoplotTFR (line 659) >>>> labels in data and labels in layout do not match >>>> Error in ft_topoplotIC (line 122) >>>> ft_topoplotTFR(cfg, varargin{:}); >>>> >>>> >>>> >>>> Cheers, >>>> Dave Deriso >>>> >>>> -- >>>> UCSD Institute for Neural Computation >>>> UCSD Department of Neurosurgery >>>> >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> >>>> -- >>>> Jörn M. Horschig >>>> PhD Student >>>> Donders Institute for Brain, Cognition and Behaviour >>>> Centre for Cognitive Neuroimaging >>>> Radboud University Nijmegen >>>> Neuronal Oscillations Group >>>> >>>> P.O. Box 9101 >>>> NL-6500 HB Nijmegen >>>> The Netherlands >>>> >>>> Contact: >>>> E-Mail: jm.horschig at donders.ru.nl >>>> Tel: +31-(0)24-36-68493 >>>> Web: http://www.ru.nl/donders >>>> >>>> Visiting address: >>>> Trigon, room 2.30 >>>> Kapittelweg 29 >>>> NL-6525 EN Nijmegen >>>> The Netherlands >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Dec 8 07:58:13 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 8 Dec 2011 07:58:13 +0100 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: <4EDE02B3.1010103@donders.ru.nl> Message-ID: Dear Dave, The output of an ICA should actually not contain complex numbers. It can happen though, and this is indicative of a problem. You should probably have a look at this FAQ: http://fieldtrip.fcdonders.nl/faq/why_does_my_ica_output_contain_complex_numbers Best, Eelke 2011/12/7 Dave Deriso : > Hi Johanna, > > Thanks for taking a look. I could not find a method inside > ft_componentanalysis that extracts real values (although using real() could > also accomplish this), however the warning seems to indicate that the > complex values are ignored. Do you think this is still an issue? The error > with ft_databrowser indicates a lack of "unique sample points" from some > kind of grid, which is perhaps a bigger problem. Any thoughts? Thanks again! > > Cheers, > Dave > > On Wed, Dec 7, 2011 at 3:59 AM, Johanna Zumer > wrote: >> >> Hi Dave, >> Perhaps this error is due to the complex data that ft_databrowser cannot >> plot?  If you re-calculate the components and get out real-only values, do >> you still get this error? >> >> Best, >> Johanna >> >> >> On 7 December 2011 02:07, Dave Deriso wrote: >>> >>> I should also note that when I tried the ft_databrowser function it was >>> unable to plot the component topographies because there weren't enough grid >>> points. Have you encountered this before? Thanks again for all of your great >>> help!! >>> >>> My code: >>> >>> cfg = []; >>> cfg.viewmode = 'component' >>> ft_databrowser(cfg, comp); >>> >>> >>> Output: >>> >>> creating layout from cfg.grad >>> creating layout for neuromag306alt system >>> the input is component data with 306 components and 306 original channels >>> detected   0 visual artifacts >>> redrawing with viewmode component >>> fetching data... done >>> fetching artifacts... done >>> preprocessing data... done >>> plotting artifacts... >>> plotting events... >>> plotting data... >>> >>> Warning: Imaginary parts of complex X and/or Y arguments ignored >>> > In ft_plot_vector at 191 >>>   In ft_databrowser>redraw_cb at 1309 >>>   In ft_databrowser at 508 >>> Warning: Imaginary parts of complex X and/or Y arguments ignored >>> > In ft_plot_vector at 191 >>>   In ft_databrowser>redraw_cb at 1309 >>>   In ft_databrowser at 508 >>>                                           ****** these errors repeat >>> about 10 times, then: >>> plotting component topographies... >>> Error using griddata (line 79) >>> Not enough unique sample points specified. >>> >>> Error in ft_plot_topo (line 153) >>> [Xi,Yi,Zi] = griddata(chanX', chanY, dat, xi', yi, interpmethod); % >>> interpolate the topographic data >>> >>> Error in ft_databrowser>redraw_cb (line 1377) >>>       ft_plot_topo(chanx, chany, chanz, 'mask', laychan.mask, >>> 'interplim', 'mask', 'outline', laychan.outline, 'tag', 'topography', >>>       ... >>> >>> Error in ft_databrowser (line 508) >>> redraw_cb(h); >>> >>> >>> >>> >>> >>> Cheers, >>> Dave >>> >>> >>> On Tue, Dec 6, 2011 at 11:17 AM, Dave Deriso wrote: >>>> >>>> Dear JM and Jörn, >>>> >>>> Thank you so much for your helpful suggestions. Matlab could not >>>> find/open layout file: NM306.lay with both ft_topoplotTFR and ft_topoplotIC. >>>> I have also tried each of the following layouts without success: >>>> >>>> cfg.layout    =3D data.grad; >>>> cfg.layout    =3D 'neuromag306all.lay'; >>>> cfg.layout    =3D 'neuromag306cmb.lay'; >>>> cfg.layout    =3D 'neuromag306mag.lay'; >>>> cfg.layout    =3D 'neuromag306planar.lay'; >>>> (and no layout cfg, as prescribed by the bottom >>>> of http://fieldtrip.fcdonders.nl/reference/ft_topoplotic) >>>> >>>> >>>> As Jörn mentioned, the IC and sensor labels are different and, >>>> therefore, doing a string comparison will return an error. The question is >>>> then, how can I project the ICs back into sensor space and plot them >>>> topographically using the pre-existing sensor layouts? If this accomplished >>>> by the ft_topoplotIC function, shouldn't it expect the IC labels to be >>>> different from the layout labels? >>>> >>>> Thanks again for all of your help! >>>> >>>> Cheers, >>>> Dave Deriso >>>> >>>> -- >>>> UCSD Institute for Neural Computation >>>> UCSD Department of Neurosurgery >>>> >>>> >>>> >>>> >>>> On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" >>>> wrote: >>>>> >>>>> Dear Dave, >>>>> >>>>> the labels do not match indeed, because ICs do not correspond to single >>>>> channel (obviously). I am not exactly sure how ft_topoplotIC is built, but >>>>> you could try using ft_databrowser instead, with cfg.viewmode = 'component' >>>>> Hope that at least circumvents your problem. >>>>> >>>>> Best, >>>>> Jörn >>>>> >>>>> >>>>> On 12/6/2011 2:45 AM, Dave Deriso wrote: >>>>> >>>>> Dear Fieldtrip Users, >>>>> >>>>> I am trying to implement the tutorial on using ICA to extract eyeblink >>>>> artifacts >>>>> (http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). >>>>> Everything works, except that the labels from the IC data do not match the >>>>> labels from the layout file, causing an error in the topoplotIC >>>>> function. Your help in solving this is most appreciated. >>>>> >>>>> >>>>> Layout labels (I am using a Neuromag 306 MEG): >>>>> 'MEG0113' >>>>> 'MEG0112' >>>>> 'MEG0111' >>>>> 'MEG0122' >>>>> 'MEG0123' >>>>> >>>>> IC labels: >>>>> 'runica001' >>>>> 'runica002' >>>>> 'runica003' >>>>> 'runica004' >>>>> 'runica005' >>>>> >>>>> Matlab Output: >>>>> ft_topoplotIC(cfg, comp); >>>>> creating layout from data.grad >>>>> creating layout for neuromag306alt system >>>>> Error using ft_topoplotTFR (line 659) >>>>> labels in data and labels in layout do not match >>>>> Error in ft_topoplotIC (line 122) >>>>> ft_topoplotTFR(cfg, varargin{:}); >>>>> >>>>> >>>>> >>>>> Cheers, >>>>> Dave Deriso >>>>> >>>>> -- >>>>> UCSD Institute for Neural Computation >>>>> UCSD Department of Neurosurgery >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>> >>>>> >>>>> >>>>> -- >>>>> Jörn M. Horschig >>>>> PhD Student >>>>> Donders Institute for Brain, Cognition and Behaviour >>>>> Centre for Cognitive Neuroimaging >>>>> Radboud University Nijmegen >>>>> Neuronal Oscillations Group >>>>> >>>>> P.O. Box 9101 >>>>> NL-6500 HB Nijmegen >>>>> The Netherlands >>>>> >>>>> Contact: >>>>> E-Mail: jm.horschig at donders.ru.nl >>>>> Tel: +31-(0)24-36-68493 >>>>> Web: http://www.ru.nl/donders >>>>> >>>>> Visiting address: >>>>> Trigon, room 2.30 >>>>> Kapittelweg 29 >>>>> NL-6525 EN Nijmegen >>>>> The Netherlands >>>>> >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From ole.jensen at donders.ru.nl Thu Dec 8 10:14:44 2011 From: ole.jensen at donders.ru.nl (Ole Jensen) Date: Thu, 08 Dec 2011 10:14:44 +0100 Subject: [FieldTrip] PhD position at the Donders Institute, Nijmegen Message-ID: <4EE08004.9020903@donders.ru.nl> Dear colleagues, If you know of potential PhD candidates please forward them the job listing below. All the best, Ole Jensen -- Ole Jensen http://www.neuosc.com ------- PhD position on 'Bridging the Gap between Neuronal Activity and Neuroimaging' (1,0 fte) *Donders Institute, Centre for Cognitive Neuroimaging* *Maximum salary: EUR 2,612 gross/month* *Vacancy number: 30.08.11* *Closing date: 1 January 2012* *Responsibilities* The Neuronal Oscillation group and the MR Techniques in Brain Function group at the Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, have funding available for a PhD position, aimed at quantitative evaluation of neuroimaging signal characteristics resulting from activity of neurons in the working human brain. The human brain is composed of multiple regions that are flexibly engaged and disengaged depending on the cognitive task performed. Each of these regions comprises large numbers of neurons that interact non-linearly. A fundamental question in cognitive neuroscience is how the connections and interactions of the neurons shape the functional architecture of the working brain. At the Donders Institute this question is addressed experimentally by measuring cognitive signals by means of magneto-encephalography (MEG), electro-encephalography (EEG) and functional magnetic resonance imaging (fMRI). You will work on this project from a complementary perspective, using computer simulation to investigate which plausible networks of neurons can explain measured signals. You will use and extend numerical software developed at the institute and elsewhere. Your results will improve the interpretation of measured cognitive signals. You will focus on positive and negative spatial and temporal correlations between various signals obtained in cognitive experiments. *Work environment* The Donders Institute for Brain, Cognition and Behaviour consists of the Centre for Cognition, the Centre for Cognitive Neuroimaging and the Centre for Neuroscience. The mission of the Centre for Cognitive Neuroimaging is to conduct cutting-edge fundamental research in cognitive neuroscience. Much of the rapid progress in this field is being driven by the development of complex neuroimaging techniques for measuring activity in the human working brain - an area in which the Centre plays a leading role. The research themes cover central cognitive functions such as perception, action, control, decision making, attention, memory, language, learning and plasticity. The Centre also aims to establish how the different brain areas coordinate their activity with very high temporal precision to enable human and animal cognition. This internationally renowned centre currently employs more than 100 PhD students and post-doctoral researchers of more than 20 different nationalities, offering a stimulating and multidisciplinary research environment. The centre is equipped with three MRI scanners (7T, 3T, 1.5T), a 275-channel MEG system, an EEG-TMS laboratory, several (MR-compatible) EEG systems, and high-performance computational facilities. English is the lingua franca at the centre. You will work within a joint project of the Neuronal Oscillations group and the MR Methods for Cognitive Neuroscience group at the Centre for Cognitive Neuroimaging, and the Neuroinformatics department at the Centre for Neuroscience. *What we expect from you* You should have a Master's degree (or equivalent). Applicants with a background in neuroscience should be willing to acquire the mathematical and numerical skills required to simulate complex systems. Applicants with a background in mathematics, physics or computer science should be willing to develop in-depth knowledge of cognitive neuroscience and physiology. You are enthusiastic to understand the dynamic properties of the human brain and to probe the interaction between different regions, all on the basis of what is known of the physiology of the brain. Furthermore, you are prepared to take courses and workshops offered at the Donders Graduate School for Cognitive Neuroscience to bring your knowledge of cognitive neuroscience up to the standard required. You should be willing to work in a multidisciplinary environment in which the results and methods from various disciplines, ranging from natural to behavioural sciences, are integrated. And you are eager to work with us at the cutting edge of science, where your personal commitment and skills are both essential and appreciated. Proficiency in oral and written English is essential. You are expected to work in a team, sharing technical know-how and ideas. *What we have to offer* We offer you: - employment: 1,0 fte; - a maximum gross monthly salary of EUR 2,612 based on a 38-hour working week; - in addition to the salary: an 8% holiday allowance and an 8.3% end-of-year bonus; - The starting salary is EUR2,042 per month and will increase to EUR2,612 per month in the fourth year; - duration of the contract: 4 years. Are you interested in our excellent employment conditions ? *Other Information* This vacancy was advertised earlier this year in July/August. If you applied for this position at the time and were rejected, please do not apply again. *Would you like to know more?* Further information on: DCCN Prof. dr. Jan van der Eerden, project leader Telephone:+31 24 3614602 E-mail: j.vandereerden at donders.ru.nl Dr. Ole Jensen, PI Neuronal Oscillation group Telephone:+31 24 3610884 E-mail: ole.jensen at donders.ru.nl * * *Applications* Are you interested? Please submit an application letter, a CV, and the names of two persons who can provide references. Please explain your interest in neuroscience and the above mentioned scientific approaches in your application letter. It is Radboud University Nijmegen's policy to only accept applications by e-mail. Please send your application, /stating vacancy number 30.08.11/, to vacatures at dpo.ru.nl , for the attention of Prof. dr. Jan van der Eerden, before 1 January 2012. For more information on the application procedure:+ 31 24 3611173 -- Ole Jensen http://www.neuosc.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.leszczynski.m at googlemail.com Thu Dec 8 17:33:45 2011 From: m.leszczynski.m at googlemail.com (Marcin Leszczynski) Date: Thu, 8 Dec 2011 17:33:45 +0100 Subject: [FieldTrip] 2x3 anova in cluster analysis In-Reply-To: References: Message-ID: Hi Jan-Mathijs and Fieldtrippers, I have a follow up question refering to statistical inference about monotonic trends in the permutation framework. I have four conditions A, B, C, D and I would like to test whether there is a monotonic change in the ERP/TF among the conditions (i.e. A > 2011/12/5 jan-mathijs schoffelen > >> Hi Stan et al, >> >> Actually FieldTrip allows in a very straightforward way to plug-in one's >> favourite statistic. The idea is the following: when specifying >> cfg.statistic you need to specify a string that under the hood points to a >> function, e.g. 'indepsamplesT' eventually causes a function to be called, >> answering to the aptly chosen name: 'statfun_indepsamplesT' which is doing >> the legwork. As long as the statfun_younameit has properly defined input >> and output arguments, you can let it do whatever you want. FieldTrip >> contains a bunch of 'statfuns' in the statfun directory but there's no >> reason not to implement any yourself (and ideally contribute them to the >> repository). >> Another discussion altogether is the question whether the test statistic >> of interest is an appropriate one that allows for statistical inference >> using the permutation framework. Over the past years there have been >> various threads on this mailing list regarding the possibility to test for >> interactions using a permutation test. You can look this up in the archive. >> Strictly speaking this is statistically not possible this way. The >> permutation-framework tests the null-hypothesis of exchangeability of data >> across allocated conditions, whereas when one wants to test for an >> interaction effect tests one tests for a particular linear (parametric) >> model of the dependent variables explaining variance in the dependent >> variable. Inferring that exchangeability across conditions is unlikely >> (i.e. obtaining a small p-value through permutation) does not necessarily >> lead to the conclusion that there is an actual interaction effect. Though >> opinions among the statisticians about this seem to vary, there may be a >> way out: one could either use bootstrapping to obtain confidence intervals >> for the interaction F under the null-hypothesis. The recipe for this would >> be to do a cell-specific demeaning of the data to impose the >> null-hypothesis of no interaction, and then through bootstrap resampling >> obtain a reference distribution of the interaction F. Alternatively, >> although I haven't thought this one through for any case other than a 2x2 >> anova, one could reduce the interaction effect to a two-condition contrast >> where observations belonging to the 'main diagonal' of the 2x2 conditions >> design are labeled as condition 1, and the observations belonging to the >> other diagonal are labeled as condition 2. One could then proceed with >> using a T-statistic as a descriptive statistic across these two >> 'conditions' on which inference can be done. >> >> Cheers and a happy Sinterklaas to you all, >> >> Jan-Mathijs >> >> >> On Dec 5, 2011, at 8:17 PM, Stanley Klein wrote: >> >> Nico, >> >> Your question gives me the chance to ask something I've been curious >> about. It seems to me that one of the nifty things about permutation >> cluster analysis is that it allows you to do anything that seems reasonable >> as long you decide on the process ahead of time and don't do any future >> tweaking other than fixing coding errors. I'm curious whether the Fieldtrip >> code make it easy to insert new statistics modules. >> >> I presume your actual question had to do with whether Fieldtrip already >> has the possibility of doing that 2x3 ANOVA. I suspect it doesn't have >> that capability. However, it would be nice if the permutation cluster >> analysis could be made sufficiently modular that one could make use of all >> the complicated clustering and permuting and all, but enable the user to >> substitute their own statistical method. I haven't actually watched my >> students doing the nitty-gritty use of Fieldtrip's version of the >> permutation test (other than knowing that is is very nice and well >> documented) so I don't know how easy it is to stick in one's own favorite >> statistic, but I'm hoping it is easy. >> >> Stan >> >> On Mon, Dec 5, 2011 at 4:58 AM, Nico Alexander Willi Kremers < >> nkremers at uni-bonn.de> wrote: >> >>> >>> Hi, >>> >>> I followed the discussion about implementing a 2x2 within subjects >>> design into a cluster statistic with much interest. I want to implement a >>> 2x3 repeated measure anova in a cluster analysis using fieldtrip. I think >>> for this type of analysis subracting two conditions from each other and >>> then calculate a ttest is not appropriate. Is there another way of >>> calculating the interaction effect between the two factors and generate >>> clusters for real and permutation data? What specifications must be set and >>> how? >>> >>> Thank you very much for your answer, >>> >>> Nico >>> ______________________________**_________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.m.groppe at gmail.com Fri Dec 9 20:18:21 2011 From: david.m.groppe at gmail.com (David Groppe) Date: Fri, 9 Dec 2011 14:18:21 -0500 Subject: [FieldTrip] 2x3 anova in cluster analysis In-Reply-To: References: Message-ID: Hi Marcin, You could use a permutation test based on a rank correlation statistic (e.g., Kendall's tau or Spearman's rho) to test for such a monotonic relationship. I do not know if FieldTrip currently implements this or not though. cheers, -D On Thu, Dec 8, 2011 at 11:33 AM, Marcin Leszczynski wrote: > Hi Jan-Mathijs and Fieldtrippers, > > I have a follow up question refering to statistical inference about > monotonic trends in the permutation framework. > > I have four conditions A, B, C, D and I would like to test whether there is > a monotonic change in the ERP/TF among the conditions (i.e. A possibly also A < B <= C < D). I guess one way would be to run multiple t > tests. However it seems a bit unconvenient as one needs to correct for > multiple comparisons. Furtheremore, the second case (A < B <= C < D) might > not be well captured. > > I found a thread from 31 Aug 2011 ("[FieldTrip] depsamplesregrT help" by > Jonas Obleser) suggesting that depsamplesregrT will be the way to go. > However, your reply to Nico somehow destroyed my confidence. If I got the > reply correctly this is not that easy as I would be testing a particular > linear model which is a bit of a problem. Thus, the question: > > How would you suggest testing for such a monotonic effect in the permutation > framework? > > Best, > Marcin > >> >> >> 2011/12/5 jan-mathijs schoffelen >>> >>> Hi Stan et al, >>> >>> Actually FieldTrip allows in a very straightforward way to plug-in one's >>> favourite statistic. The idea is the following: when specifying >>> cfg.statistic you need to specify a string that under the hood points to a >>> function, e.g. 'indepsamplesT' eventually causes a function to be called, >>> answering to the aptly chosen name: 'statfun_indepsamplesT' which is doing >>> the legwork. As long as the statfun_younameit has properly defined input and >>> output arguments, you can let it do whatever you want. FieldTrip contains a >>> bunch of 'statfuns' in the statfun directory but there's no reason not to >>> implement any yourself (and ideally contribute them to the repository). >>> Another discussion altogether is the question whether the test statistic >>> of interest is an appropriate one that allows for statistical inference >>> using the permutation framework. Over the past years there have been various >>> threads on this mailing list regarding the possibility to test for >>> interactions using a permutation test. You can look this up in the archive. >>> Strictly speaking this is statistically not possible this way. The >>> permutation-framework tests the null-hypothesis of exchangeability of data >>> across allocated conditions, whereas when one wants to test for an >>> interaction effect tests one tests for a particular linear (parametric) >>> model of the dependent variables explaining variance in the dependent >>> variable. Inferring that exchangeability across conditions is unlikely (i.e. >>> obtaining a small p-value through permutation) does not necessarily lead to >>> the conclusion that there is an actual interaction effect. Though opinions >>> among the statisticians about this seem to vary, there may be a way out: one >>> could either use bootstrapping to obtain confidence intervals for the >>> interaction F under the null-hypothesis. The recipe for this would be to do >>> a cell-specific demeaning of the data to impose the null-hypothesis of no >>> interaction, and then through bootstrap resampling obtain a reference >>> distribution of the interaction F. Alternatively, although I haven't thought >>> this one through for any case other than a 2x2 anova, one could reduce the >>> interaction effect to a two-condition contrast where observations belonging >>> to the 'main diagonal' of the 2x2 conditions design are labeled as condition >>> 1, and the observations belonging to the other diagonal are labeled as >>> condition 2. One could then proceed with using a T-statistic as a >>> descriptive statistic across these two 'conditions' on which inference can >>> be done. >>> >>> Cheers and a happy Sinterklaas to you all, >>> >>> Jan-Mathijs >>> >>> >>> On Dec 5, 2011, at 8:17 PM, Stanley Klein wrote: >>> >>> Nico, >>> >>> Your question gives me the chance to ask something I've been curious >>> about. It seems to me that one of the nifty things about permutation cluster >>> analysis is that it allows you to do anything that seems reasonable as long >>> you decide on the process ahead of time and don't do any future tweaking >>> other than fixing coding errors. I'm curious whether the Fieldtrip code make >>> it easy to insert new statistics modules. >>> >>> I presume your actual question had to do with whether Fieldtrip already >>> has the possibility of doing that 2x3 ANOVA.  I suspect it doesn't have that >>> capability. However, it would be nice if the permutation cluster analysis >>> could be made sufficiently modular that one could make use of all the >>> complicated clustering and permuting and all, but enable the user to >>> substitute their own statistical method.  I haven't actually watched my >>> students doing the nitty-gritty use of Fieldtrip's version of the >>> permutation test (other than knowing that is is very nice and well >>> documented) so I don't know how easy it is to stick in one's own favorite >>> statistic, but I'm hoping it is easy. >>> >>> Stan >>> >>> On Mon, Dec 5, 2011 at 4:58 AM, Nico Alexander Willi Kremers >>> wrote: >>>> >>>> >>>> Hi, >>>> >>>> I followed the discussion about implementing a 2x2 within subjects >>>> design into a cluster statistic with much interest. I want to implement a >>>> 2x3 repeated measure anova in a cluster analysis using fieldtrip. I think >>>> for this type of analysis subracting two conditions from each other and then >>>> calculate a ttest is not appropriate. Is there another way of calculating >>>> the interaction effect between the two factors and generate clusters for >>>> real and permutation data? What specifications must be set and how? >>>> >>>> Thank you very much for your answer, >>>> >>>> Nico >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> Jan-Mathijs Schoffelen, MD PhD >>> >>> Donders Institute for Brain, Cognition and Behaviour, >>> Centre for Cognitive Neuroimaging, >>> Radboud University Nijmegen, The Netherlands >>> >>> Max Planck Institute for Psycholinguistics, >>> Nijmegen, The Netherlands >>> >>> J.Schoffelen at donders.ru.nl >>> Telephone: +31-24-3614793 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- David Groppe, Ph.D. Postdoctoral Researcher North Shore LIJ Health System New Hyde Park, New York http://www.cogsci.ucsd.edu/~dgroppe/ From eva.patai at psy.ox.ac.uk Sun Dec 11 20:28:51 2011 From: eva.patai at psy.ox.ac.uk (Zita Eva Patai) Date: Sun, 11 Dec 2011 19:28:51 +0000 Subject: [FieldTrip] clusterstat on multiple frequencies Message-ID: Dear FT-ers, I have tried to run a permutation test on time-frequency data, and would have like to see a statistical evealuation over a set of frequencies (ex: 4-8Hz) It seems that the test itself runs, but it crashes when i try to plot the data, saying that 'stat' must not contain multiple frequencies. I was wondering if there was a way to evaluate the difference between two conditions over a set range of frequencies? Thank you! zita -- Zita Patai DPhil Candidate, Experimental Psychology University of Oxford bcl.psy.ox.ac.uk/people/zita-eva-patai/ eva.patai at psy.ox.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From inieuwenhuis at berkeley.edu Sun Dec 11 21:06:11 2011 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Sun, 11 Dec 2011 12:06:11 -0800 Subject: [FieldTrip] rereference to repaired channel Message-ID: <4EE50D33.8030500@berkeley.edu> Hi all, I've measured EEG data with Cz as the reference. I now want to rereference to linked mastoids. However, in one participant one of the mastoid electrodes is really noisy. Is it valid to throw out the noisy channel, then fix it (with ft_channelrepair), and then rereference to this fixed mastoid channel? In other words, is channelrepair a linear operation? Or would I be mixing (a little) Cz into all channels now...? Any other options? Or another way of asking: do I get the same result if I first rereference and then fix bad channels, compared to first fixing bad channels and then rereference? In the participant with the bad mastoid chan, I don't have a choice, I have to first fix the channel first, or I'd be mixing noise into all channels. But, in other participants, where I also have bad channels (but not the mastoid ones), does the order matter, which order is better? I'd think first rereference, then fix... Correct? Thanks!! Ingrid -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 From jan.schoffelen at donders.ru.nl Mon Dec 12 08:59:38 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 12 Dec 2011 08:59:38 +0100 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: References: Message-ID: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> Hi Zita, Could you provide some more information please? What plotting function are you using? What does the stat-structure look like etc.? With sufficient additional information we can try and reproduce the problem, and if it's a bug fix it. If it's not a bug, we may give you some hints to fool the system... BW, Jan-Mathijs On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: > Dear FT-ers, > > I have tried to run a permutation test on time-frequency data, and would have like to see a statistical evealuation over a set of frequencies (ex: 4-8Hz) > > It seems that the test itself runs, but it crashes when i try to plot the data, saying that 'stat' must not contain multiple frequencies. > > I was wondering if there was a way to evaluate the difference between two conditions over a set range of frequencies? > > Thank you! > zita > > > -- > > Zita Patai > DPhil Candidate, Experimental Psychology > University of Oxford > bcl.psy.ox.ac.uk/people/zita-eva-patai/ > eva.patai at psy.ox.ac.uk > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From boracbci at gmail.com Mon Dec 12 09:18:17 2011 From: boracbci at gmail.com (Bora Cebeci) Date: Mon, 12 Dec 2011 10:18:17 +0200 Subject: [FieldTrip] Brainvision recorder RDA Message-ID: Hi, I want to use the Fieldtrip functions for real-time data processing. I'm testing the delay. Neither rda2ft.exe nor ft_realtime_brainampproxy.m is working properly. If you don't get an event, ft_realtime_brainampproxy.m can be usable. I found three messages about Brain Vision Recorder in the mail list. I have similar problems as mentioned in those messages. 1) I think that using rda2ft.exe is faster than ft_realtime_brainampproxy.m, so finding a solution for rda2ft.exe problem will be enough. I have the same error message as *Casper van Heck. Casper *said: " >* When running rda2ft.exe (with the parameters localhost and 51244) it does seem to connect; it shows the list of channels (all channels), their resolution, and their names, and some other assorted stuff. However, it then says: *>* "Unrecognized packet type (10000), has size 24 - exiting"* " My parameters : " rda2ft.exe localhost 51234" and I tried it in a different PC: " rda2ft.exe 10.1.54.160 51234" I got the same error message. 2) Secondly, I tried to use ft_realtime_brainampproxy.m, but I cannot use it efficiently. When an event occurs, buffering freezes and there is no error message. I have a bad solution for this problem. I'm stopping the program by "Ctrl+C" then I start it again. Meanwhile I measured 179ms delay (average of 45 trials), it is really big ?? 3) Even the above problem is solved, the events cannot read. Khalid mentioned before about this problem. I couldn't find the reading code for events in the ft_realtime_brainampproxy.m file. Here is the related part of the code: % convert the RDA message into data and/or events dat = []; event = []; if msg.nType==2 && msg.nPoints>0 % FIXME should I apply the calibration here? dat = msg.nData(chanindx,:); end if msg.nType==4 && msg.nPoints>0 % FIXME should I apply the calibration here? dat = msg.fData(chanindx,:); end if (msg.nType==2 || msg.nType==4) && msg.nMarkers>0 % FIXME convert the message to events end The variable 'event' doesn't get any value here. So by using ft_read_event function , you get an empty vector. Thanks -- Bora Cebeci -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Mon Dec 12 10:40:49 2011 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Mon, 12 Dec 2011 10:40:49 +0100 Subject: [FieldTrip] Brainvision recorder RDA In-Reply-To: References: Message-ID: Dear Bora Cebeci, Thank your for reporting this issue. There are indeed other reports that reading the RDA protocol is not working properly: http://bugzilla.fcdonders.nl/show_bug.cgi?id=1172 http://bugzilla.fcdonders.nl/show_bug.cgi?id=1164 The packet that causes rda2ft.exe to crash is not documented in the RDA protocol, and we are in contact with BrainProducts in order to resolve this issue. The problem you mention in (3) is unforgivable, and I would like to ask you to report this as a separate bug on http:/bugzilla.fcdonders.nl (just copy and past the email). You can then also subscribe to the other two bugs, which allows you to track our progress on fixing this issue. Best regards, Boris Reuderink On Mon, Dec 12, 2011 at 9:18 AM, Bora Cebeci wrote: > Hi, > > I want to use the Fieldtrip functions for real-time data processing. I'm > testing the delay. Neither rda2ft.exe nor ft_realtime_brainampproxy.m is > working properly. If you don't get an event, ft_realtime_brainampproxy.m can > be usable. > I found three messages about Brain Vision Recorder in the mail list. I have > similar problems as mentioned in those messages. > > 1) I think that using rda2ft.exe is faster than ft_realtime_brainampproxy.m, > so finding a solution for rda2ft.exe problem will be enough. I have the same > error message as Casper van Heck. > Casper  said: > " > >> When running rda2ft.exe (with the parameters localhost and 51244) it does >> seem to connect; it shows the list of channels (all channels), their >> resolution, and their names, and some other assorted stuff. However, it then >> says: > > >> "Unrecognized packet type (10000), has size 24 - exiting" > > " > My parameters : " rda2ft.exe localhost 51234" > and I tried it in a different PC: " rda2ft.exe 10.1.54.160 51234" > I got the same error message. > > > 2) Secondly, I tried to use ft_realtime_brainampproxy.m, but I cannot use it > efficiently. When an event occurs, buffering freezes and there is no error > message. > > I have a bad solution for this problem. I'm stopping the program by "Ctrl+C" > then I start it again. > Meanwhile I measured 179ms delay (average of 45 trials), it is really big ?? > > > 3) Even the above problem is solved, the events cannot read. Khalid > mentioned before about this problem. I couldn't find the reading code for > events in the ft_realtime_brainampproxy.m file. Here is the related part of > the code: > >  % convert the RDA message into data and/or events >   dat   = []; >   event = []; > >   if msg.nType==2 && msg.nPoints>0 >     % FIXME should I apply the calibration here? >     dat = msg.nData(chanindx,:); >   end > >   if msg.nType==4 && msg.nPoints>0 >     % FIXME should I apply the calibration here? >     dat = msg.fData(chanindx,:); >   end > >   if (msg.nType==2 || msg.nType==4) && msg.nMarkers>0 >     % FIXME convert the message to events >   end > > The variable 'event' doesn't get any value here. So by using ft_read_event > function , you get an empty vector. > > Thanks > > > -- > Bora Cebeci > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From eva.patai at psy.ox.ac.uk Mon Dec 12 12:22:57 2011 From: eva.patai at psy.ox.ac.uk (Zita Eva Patai) Date: Mon, 12 Dec 2011 11:22:57 +0000 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> Message-ID: Dear Jan-Mathijs, Sorry I was so vague, i thought maybe it was a common problem... OK, so i was running a clusterstat with the following input ( main point, i want to look at the difference between conditions over a set of frequencies) *** load blk1_tf_avg load blk3_tf_avg cfg = []; cfg.latency = [1.0 1.5 ]; cfg.frequency = [4 8]; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 1000; cfg.feedback = 'yes'; cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg); subj = 15; design = zeros(2,2*subj); for i = 1:subj design(1,i) = i; end for i = 1:subj design(1,subj+i) = i; end design(2,1:subj) = 1; design(2,subj+1:2*subj) = 2; cfg.design = design; cfg.uvar = 1; cfg.ivar = 2; [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg); save stat_tf_theta_1000_1500_bkey3vsbkey1 stat *** The error comes during the plotting phase when it says that i should not have multiple frequencies, as the data should be averaged across frequencies. And it does save my file (stat_theta....) but and i can see the pos/neg clusters in the data structure...but i can't plot with : cfg = []; cfg.highlightsymbolseries = ['*','*','.','.','.']; cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay'; cfg.contournum = 0; cfg.markersymbol = '.'; cfg.alpha = 0.05; cfg.zparam = 'stat'; ft_clusterplot(cfg,stat); I have also tried plotting with the script from the tutorial pos_cluster_pvals = [stat.posclusters(:).prob]; pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha); pos = ismember(stat.posclusterslabelmat, pos_signif_clust); neg_cluster_pvals = [stat.negclusters(:).prob]; neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha); neg = ismember(stat.negclusterslabelmat, neg_signif_clust); for k = 1:20; etc. but this makes the plot really weird looking...and i am not sure how i can only plot the data from the frequencies i would like to display (in this case 4-8Hz). I know how to make the subtraction image (between my two conditions), but not how to specify the frequency range that i want displayed... If this is too complicated, is there a way to average over a set of frequencies in the data, and then just input files into the permutation test that are already collapsed across the frequency range i am interested in? Thank you! z On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Zita, > > Could you provide some more information please? What plotting function are > you using? What does the stat-structure look like etc.? With sufficient > additional information we can try and reproduce the problem, and if it's a > bug fix it. If it's not a bug, we may give you some hints to fool the > system... > > BW, > > Jan-Mathijs > > On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: > > Dear FT-ers, > > I have tried to run a permutation test on time-frequency data, and would > have like to see a statistical evealuation over a set of frequencies (ex: > 4-8Hz) > > It seems that the test itself runs, but it crashes when i try to plot the > data, saying that 'stat' must not contain multiple frequencies. > > I was wondering if there was a way to evaluate the difference between two > conditions over a set range of frequencies? > > Thank you! > zita > > > -- > > Zita Patai > DPhil Candidate, Experimental Psychology > University of Oxford > bcl.psy.ox.ac.uk/people/zita-eva-patai/ > eva.patai at psy.ox.ac.uk > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Zita Patai DPhil Candidate, Experimental Psychology University of Oxford bcl.psy.ox.ac.uk/people/zita-eva-patai/ eva.patai at psy.ox.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From dporada at uos.de Mon Dec 12 16:16:01 2011 From: dporada at uos.de (Porada Danja) Date: Mon, 12 Dec 2011 16:16:01 +0100 Subject: [FieldTrip] Automatic artifact rejection Message-ID: <5BCBAF3A-26D5-4B64-BC0C-DD8284D6551D@uos.de> Hi, I want to use automatic artifact detection to clean my MEG-data. Does it make sense to clean the data visually first, remove very odd trials (like very huge slow waveforms which were caused by a passing car) and then apply the ft_artifact_zvalue function? I went step by step through the ft_artifact_zvalue function using the same parameters as proposed in the "automatic artifact rejection" tutorial for jump artifacts. It seems to me that the function doesn't use the parameter "absdiff" which is specified in cfg.artfctdef.zvalue.absdiff = 'yes'. Is this right? I am using the fieldtrip-20111115-version. Best, Danja From jm.horschig at donders.ru.nl Mon Dec 12 16:18:34 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 12 Dec 2011 16:18:34 +0100 Subject: [FieldTrip] rereference to repaired channel In-Reply-To: <4EE50D33.8030500@berkeley.edu> References: <4EE50D33.8030500@berkeley.edu> Message-ID: <4EE61B4A.4050208@donders.ru.nl> Hi Ingrid, ft_channelrepair is simply taking the average of the neighbouring channels. So, you would need to specify your neighbours and based on this, and it just gets the average of the neighbours of your mastoid. However, imho, you cannot really define neighbours for a mastoid channel. There is a method to interpolate not using nearest neighbours but spherical splines, however this is not (yet) part of FieldTrip, see also here: http://bugzilla.fcdonders.nl/show_bug.cgi?id=634 But, I am not sure if this would help in this case either. If you really want to use linked mastoid as a reference, I would probably reject that subject due to bad signal quality. I don't know if anyone on the list has a better idea (or more experience). Second, if you first rereference, all noise from this one channel will leak into all other channels, as you said. As long as your mastoid is not a bad channel, there should be no difference whether you first rereference or then interpolate bad channels or the other way around (assuming that I got no mathematical blackout right now). Should be easy to verify, e.g. if you have channels A, B, and C (all neighbours) and want to reference to R, then your referenced channels would be A-R, B-R and C-R. If B is a bad channel, and you interpolate first, you get B=(A+C)/2 (i.e. just the average of the neighbouring sensors). If you then rereference you will obtain (A+C)/2 - R, which is the same as (A+C) /2 - (R+R)/2 = (A-R + C-R) /2. If you first rereference and then interpolate you obtain B-R = (A-R + C-R) /2 immediately (because A-R and C-R are the only neighbours of B-R). Hope it helps! Best, Jörn On 12/11/2011 9:06 PM, Ingrid Nieuwenhuis wrote: > Hi all, > > I've measured EEG data with Cz as the reference. I now want to > rereference to linked mastoids. However, in one participant one of the > mastoid electrodes is really noisy. Is it valid to throw out the noisy > channel, then fix it (with ft_channelrepair), and then rereference to > this fixed mastoid channel? In other words, is channelrepair a linear > operation? Or would I be mixing (a little) Cz into all channels > now...? Any other options? > > Or another way of asking: do I get the same result if I first > rereference and then fix bad channels, compared to first fixing bad > channels and then rereference? In the participant with the bad mastoid > chan, I don't have a choice, I have to first fix the channel first, or > I'd be mixing noise into all channels. But, in other participants, > where I also have bad channels (but not the mastoid ones), does the > order matter, which order is better? I'd think first rereference, then > fix... Correct? > > Thanks!! > Ingrid > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From inieuwenhuis at berkeley.edu Mon Dec 12 18:00:06 2011 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Mon, 12 Dec 2011 09:00:06 -0800 Subject: [FieldTrip] rereference to repaired channel In-Reply-To: <4EE61B4A.4050208@donders.ru.nl> References: <4EE50D33.8030500@berkeley.edu> <4EE61B4A.4050208@donders.ru.nl> Message-ID: <4EE63316.40104@berkeley.edu> Hi Jorn, Thanks a lot! And fortunately, the mastoid has plenty neighbours ('E95' 'E96' 'E99' 'E101' 'E107' 'E108'), since I'm using high density EEG (128 EGI). The spherical spline method sounds pretty cool as well. Would be cool to implement one day indeed! Cheers, Ingrid On 12/12/2011 7:18 AM, "Jörn M. Horschig" wrote: > Hi Ingrid, > > ft_channelrepair is simply taking the average of the neighbouring > channels. So, you would need to specify your neighbours and based on > this, and it just gets the average of the neighbours of your mastoid. > However, imho, you cannot really define neighbours for a mastoid > channel. There is a method to interpolate not using nearest neighbours > but spherical splines, however this is not (yet) part of FieldTrip, > see also here: > http://bugzilla.fcdonders.nl/show_bug.cgi?id=634 > But, I am not sure if this would help in this case either. If you > really want to use linked mastoid as a reference, I would probably > reject that subject due to bad signal quality. I don't know if anyone > on the list has a better idea (or more experience). > > Second, if you first rereference, all noise from this one channel will > leak into all other channels, as you said. As long as your mastoid is > not a bad channel, there should be no difference whether you first > rereference or then interpolate bad channels or the other way around > (assuming that I got no mathematical blackout right now). > Should be easy to verify, e.g. if you have channels A, B, and C (all > neighbours) and want to reference to R, then your referenced channels > would be A-R, B-R and C-R. > If B is a bad channel, and you interpolate first, you get B=(A+C)/2 > (i.e. just the average of the neighbouring sensors). If you then > rereference you will obtain (A+C)/2 - R, which is the same as (A+C) /2 > - (R+R)/2 = (A-R + C-R) /2. > If you first rereference and then interpolate you obtain B-R = (A-R + > C-R) /2 immediately (because A-R and C-R are the only neighbours of B-R). > > Hope it helps! Best, > Jörn > > On 12/11/2011 9:06 PM, Ingrid Nieuwenhuis wrote: >> Hi all, >> >> I've measured EEG data with Cz as the reference. I now want to >> rereference to linked mastoids. However, in one participant one of >> the mastoid electrodes is really noisy. Is it valid to throw out the >> noisy channel, then fix it (with ft_channelrepair), and then >> rereference to this fixed mastoid channel? In other words, is >> channelrepair a linear operation? Or would I be mixing (a little) Cz >> into all channels now...? Any other options? >> >> Or another way of asking: do I get the same result if I first >> rereference and then fix bad channels, compared to first fixing bad >> channels and then rereference? In the participant with the bad >> mastoid chan, I don't have a choice, I have to first fix the channel >> first, or I'd be mixing noise into all channels. But, in other >> participants, where I also have bad channels (but not the mastoid >> ones), does the order matter, which order is better? I'd think first >> rereference, then fix... Correct? >> >> Thanks!! >> Ingrid >> > > -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 From jan.schoffelen at donders.ru.nl Tue Dec 13 09:27:45 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 13 Dec 2011 09:27:45 +0100 Subject: [FieldTrip] PhD studentship available in cortical networks of aging at CCNi Glasgow References: <218D83BF-2F53-4471-881B-0AF4CE682E97@glasgow.ac.uk> Message-ID: <875C1820-4679-49F6-8952-85ABF6C24EC9@donders.ru.nl> Dear all, Please see below a PhD-position available at Glasgow university. Cheers, JM A 4-year PhD studentship is available to work with Philippe Schyns & Guillaume Rousselet in the Institute of Neuroscience and Psychology. Understanding age-related changes in the processing of emotion information Deadline: Friday 27th January 2012 Stipend: £13,848 per annum The start date is October 2012 and applicants will normally be expected to reside (or have residency) within the UK or EU. The financial package will include a four year stipend, approved University fees, Research Training Support Grant and a Conference Allowance. Information about the training and how to apply is available here: http://www.gla.ac.uk/colleges/mvls/graduateschool/informationforprospectivestudents/phdandmresscholarships/phdprogrammes/ Contact us directly for inquiries about the project: Philippe Schyns Guillaume Rousselet Abstract: It is estimated that, by 2060, one quarter of the British population will be over 65, many of whom will still be working. Over a lifetime, the brain ages as dramatically as the body, manifesting itself in the decline of the basic and essential task of interpreting social signals. Research has established that ageing adults show specific differences in the emotional interpretation of facial expressions, particularly anger. These perceptual differences could have drastic impacts on everyday social interactions and decision-making. Failure to accurately interpret social signals may lead to vulnerabilities in critical social interactions such as identifying deception and predicting the behavioural intentions of others. With the development of new methods in computational neuroscience, it has become possible to further understand why the ageing brain fails in what are deceptively simple information processing tasks—i.e. interpreting the emotions of others. We will study how oscillatory networks in the ageing brain extract and further process visual information to recognize facial expressions of emotion at different intensities. Our framework will combine a unique platform that precisely controls the photo-realistic biological motion of faces with other developments in applications of information theoretic mathematics to analyses of brain signals. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Dec 13 17:06:53 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 13 Dec 2011 17:06:53 +0100 Subject: [FieldTrip] DICS beamformer images In-Reply-To: References: Message-ID: <3A18CB06-2B78-41C6-8F9C-BC21C0147BEF@donders.ru.nl> Hi Holly, DICS can also be used to compute univariate power in a given frequency band. This yields not a bounded quantity. Depending on your analysis settings you will observe a depth bias which is not physiologically relevant. Best way to deal with this is to compute the beamformer maps using an experimental contrast. Best Jan-Mathijs On Dec 6, 2011, at 2:18 PM, Rossiter, Holly wrote: > Hi all, > > I am using DICS to assess coherence and viewing the beamformer images through SPM. What I want to know is what is the value given in the image and how is it calculated? I thought it was a coherence value but it is not bounded between 0 and 1. > > Also what do you think is the best way to threshold the images in order to get rid of low value peaks? > > Thanks, > > Holly > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Dec 13 17:10:22 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 13 Dec 2011 17:10:22 +0100 Subject: [FieldTrip] Interactive Plotting in ft_rejectvisual In-Reply-To: <1C5AEC7D-4B54-428E-BE54-B408171837FC@gmail.com> References: <1C5AEC7D-4B54-428E-BE54-B408171837FC@gmail.com> Message-ID: <31D7B637-547A-4C66-ADE1-351F59CAD83B@donders.ru.nl> Dear Julian, Thanks for reporting this. We will look into the issue. If you want to stay informed about this you can consider creating yourself a bugzilla account on www.bugzilla.fcdonders.nl. People who have an account can add themselves in the CC for a particular bug/feature request. The issue you sketched has been filed by me as bug 1230. Best wishes, Jan-Mathijs On Dec 7, 2011, at 10:42 AM, Julian Keil wrote: > Hi, > > Not really a bug report, so I put this on the discussion List. > I noticed that when plotting single trials in the ft_rejectivusal function, the figure popping up is not interactive which makes a closer inspection of the trials somewhat harder. > Maybe this is intentional, but I can't see a reason for it. > However, simply adding "cfg_mp.interactive='yes';" at line 510 of "reject visual_summary" fixes this. > > Best, > > Julian > > > Dipl. Psych. Julian Keil > > OBOB-Lab > University of Konstanz > Department of Psychology > P.O. Box D25 > 78457 Konstanz > Germany > > Tel: ++49 - (0)7531 - 88 42 50 > Fax: ++49 - (0)7531 - 88 28 91 > Email: julian.keil at uni-konstanz.de > Homepage: http://www.uni-konstanz.de/obob > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Dec 13 17:22:42 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 13 Dec 2011 17:22:42 +0100 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> Message-ID: <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> Hi Zita, OK. I now understand the point. ft_clusterplot throws an error because it does not know how to collapse across frequencies. If the clusters have spectral extent (as well as spatial extent) it's a non-trivial question what are the channels to be plotted, because different channels can contribute different time and frequency points to the significant cluster. The time points are dealt with because ft_clusterplot shows the cluster evolving over time; the frequencies are not dealt with. FieldTrip does not make the choice of which channels to highlight for you (should all frequencies be significant for a given time point, or only one, or just a few?) and thus throws an error. However, if you have a priori reasons to expect your effect to occur in a particular frequency range (as you seem to do, because of your specification of the cfg before calling ft_freqstatistics), you can also specify cfg.avgoverfreq to 'yes', yielding a single observation per channel (and by construction the clustering only occurs over channels), making the plotting trivial. I hope this helps. BW, JM On Dec 12, 2011, at 12:22 PM, Zita Eva Patai wrote: > Dear Jan-Mathijs, > > Sorry I was so vague, i thought maybe it was a common problem... > > OK, so i was running a clusterstat with the following input ( main point, i want to look at the difference between conditions over a set of frequencies) > *** > load blk1_tf_avg > load blk3_tf_avg > > cfg = []; > cfg.latency = [1.0 1.5 ]; > cfg.frequency = [4 8]; > cfg.method = 'montecarlo'; > cfg.statistic = 'depsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 1000; > cfg.feedback = 'yes'; > cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg); > subj = 15; > design = zeros(2,2*subj); > for i = 1:subj > design(1,i) = i; > end > for i = 1:subj > design(1,subj+i) = i; > end > design(2,1:subj) = 1; > design(2,subj+1:2*subj) = 2; > > > cfg.design = design; > cfg.uvar = 1; > cfg.ivar = 2; > > [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg); > > save stat_tf_theta_1000_1500_bkey3vsbkey1 stat > > > *** > > The error comes during the plotting phase when it says that i should not have multiple frequencies, as the data should be averaged across frequencies. And it does save my file (stat_theta....) but and i can see the pos/neg clusters in the data structure...but i can't plot with : > > cfg = []; > cfg.highlightsymbolseries = ['*','*','.','.','.']; > cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay'; > cfg.contournum = 0; > cfg.markersymbol = '.'; > cfg.alpha = 0.05; > cfg.zparam = 'stat'; > ft_clusterplot(cfg,stat); > > > I have also tried plotting with the script from the tutorial > > pos_cluster_pvals = [stat.posclusters(:).prob]; > pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha); > pos = ismember(stat.posclusterslabelmat, pos_signif_clust); > > neg_cluster_pvals = [stat.negclusters(:).prob]; > neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha); > neg = ismember(stat.negclusterslabelmat, neg_signif_clust); > > for k = 1:20; > > etc. > but this makes the plot really weird looking...and i am not sure how i can only plot the data from the frequencies i would like to display (in this case 4-8Hz). I know how to make the subtraction image (between my two conditions), but not how to specify the frequency range that i want displayed... > > If this is too complicated, is there a way to average over a set of frequencies in the data, and then just input files into the permutation test that are already collapsed across the frequency range i am interested in? > > > Thank you! > z > > > On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen wrote: > Hi Zita, > > Could you provide some more information please? What plotting function are you using? What does the stat-structure look like etc.? With sufficient additional information we can try and reproduce the problem, and if it's a bug fix it. If it's not a bug, we may give you some hints to fool the system... > > BW, > > Jan-Mathijs > > On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: > >> Dear FT-ers, >> >> I have tried to run a permutation test on time-frequency data, and would have like to see a statistical evealuation over a set of frequencies (ex: 4-8Hz) >> >> It seems that the test itself runs, but it crashes when i try to plot the data, saying that 'stat' must not contain multiple frequencies. >> >> I was wondering if there was a way to evaluate the difference between two conditions over a set range of frequencies? >> >> Thank you! >> zita >> >> >> -- >> >> Zita Patai >> DPhil Candidate, Experimental Psychology >> University of Oxford >> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >> eva.patai at psy.ox.ac.uk >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > > Zita Patai > DPhil Candidate, Experimental Psychology > University of Oxford > bcl.psy.ox.ac.uk/people/zita-eva-patai/ > eva.patai at psy.ox.ac.uk > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From eva.patai at psy.ox.ac.uk Tue Dec 13 18:10:58 2011 From: eva.patai at psy.ox.ac.uk (Zita Eva Patai) Date: Tue, 13 Dec 2011 17:10:58 +0000 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> Message-ID: Dear Jan-Mathijs, Thank you for that, it makes a lot more sense. I figured the data was too complex for display, so I will average over frequencies as you suggested, as I am interested in an effect that would encompass that range anyway... Thank you again and happy holidays! z On Tue, Dec 13, 2011 at 4:22 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Zita, > > OK. I now understand the point. ft_clusterplot throws an error because it > does not know how to collapse across frequencies. If the clusters have > spectral extent (as well as spatial extent) it's a non-trivial question > what are the channels to be plotted, because different channels can > contribute different time and frequency points to the significant cluster. > The time points are dealt with because ft_clusterplot shows the cluster > evolving over time; the frequencies are not dealt with. FieldTrip does not > make the choice of which channels to highlight for you (should all > frequencies be significant for a given time point, or only one, or just a > few?) and thus throws an error. However, if you have a priori reasons to > expect your effect to occur in a particular frequency range (as you seem to > do, because of your specification of the cfg before calling > ft_freqstatistics), you can also specify cfg.avgoverfreq to 'yes', yielding > a single observation per channel (and by construction the clustering only > occurs over channels), making the plotting trivial. > > I hope this helps. > > BW, > > JM > > > > On Dec 12, 2011, at 12:22 PM, Zita Eva Patai wrote: > > Dear Jan-Mathijs, > > Sorry I was so vague, i thought maybe it was a common problem... > > OK, so i was running a clusterstat with the following input ( main point, > i want to look at the difference between conditions over a set of > frequencies) > *** > load blk1_tf_avg > load blk3_tf_avg > > cfg = []; > cfg.latency = [1.0 1.5 ]; > cfg.frequency = [4 8]; > cfg.method = 'montecarlo'; > cfg.statistic = 'depsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 1000; > cfg.feedback = 'yes'; > cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg); > subj = 15; > design = zeros(2,2*subj); > for i = 1:subj > design(1,i) = i; > end > for i = 1:subj > design(1,subj+i) = i; > end > design(2,1:subj) = 1; > design(2,subj+1:2*subj) = 2; > > > cfg.design = design; > cfg.uvar = 1; > cfg.ivar = 2; > > > [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg); > > > save stat_tf_theta_1000_1500_bkey3vsbkey1 stat > > > *** > > The error comes during the plotting phase when it says that i should not > have multiple frequencies, as the data should be averaged across > frequencies. And it does save my file (stat_theta....) but and i can see > the pos/neg clusters in the data structure...but i can't plot with : > > cfg = []; > cfg.highlightsymbolseries = ['*','*','.','.','.']; > cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay'; > cfg.contournum = 0; > cfg.markersymbol = '.'; > cfg.alpha = 0.05; > cfg.zparam = 'stat'; > ft_clusterplot(cfg,stat); > > > > I have also tried plotting with the script from the tutorial > > > pos_cluster_pvals = [stat.posclusters(:).prob]; > pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha); > pos = ismember(stat.posclusterslabelmat, pos_signif_clust); > > > neg_cluster_pvals = [stat.negclusters(:).prob]; > neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha); > neg = ismember(stat.negclusterslabelmat, neg_signif_clust); > > for k = 1:20; > > etc. > but this makes the plot really weird looking...and i am not sure how i can > only plot the data from the frequencies i would like to display (in this > case 4-8Hz). I know how to make the subtraction image (between my two > conditions), but not how to specify the frequency range that i want > displayed... > > If this is too complicated, is there a way to average over a set of > frequencies in the data, and then just input files into the permutation > test that are already collapsed across the frequency range i am interested > in? > > > Thank you! > z > > > On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Zita, >> >> Could you provide some more information please? What plotting function >> are you using? What does the stat-structure look like etc.? With sufficient >> additional information we can try and reproduce the problem, and if it's a >> bug fix it. If it's not a bug, we may give you some hints to fool the >> system... >> >> BW, >> >> Jan-Mathijs >> >> On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: >> >> Dear FT-ers, >> >> I have tried to run a permutation test on time-frequency data, and would >> have like to see a statistical evealuation over a set of frequencies (ex: >> 4-8Hz) >> >> It seems that the test itself runs, but it crashes when i try to plot the >> data, saying that 'stat' must not contain multiple frequencies. >> >> I was wondering if there was a way to evaluate the difference between two >> conditions over a set range of frequencies? >> >> Thank you! >> zita >> >> >> -- >> >> Zita Patai >> DPhil Candidate, Experimental Psychology >> University of Oxford >> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >> eva.patai at psy.ox.ac.uk >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > > Zita Patai > DPhil Candidate, Experimental Psychology > University of Oxford > bcl.psy.ox.ac.uk/people/zita-eva-patai/ > eva.patai at psy.ox.ac.uk > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Zita Patai DPhil Candidate, Experimental Psychology University of Oxford bcl.psy.ox.ac.uk/people/zita-eva-patai/ eva.patai at psy.ox.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Tue Dec 13 18:47:40 2011 From: matt.mollison at gmail.com (Matt Mollison) Date: Tue, 13 Dec 2011 10:47:40 -0700 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> Message-ID: Hi Zita, I have not used this method much, but it actually is possible to plot clusters without averaging over the frequency dimension using ft_multiplotTFR (where cfg.avgoverchan = 'no'; cfg.avgovertime = 'no'; cfg.avgoverfreq='no'; in your statistical test—so you'll get space, time, and frequency information). You can also highlight the significant portions of time and frequency space, using cfg.mask='yes', cfg.maskparameter='mask', and set a cfg.maskalpha. Do keep in mind that there are important reasons for averaging over frequency, as Dr. Maris described in this post (specifically, to increase power): < http://mailman.science.ru.nl/pipermail/fieldtrip/2010-November/003312.html>. Cheers, Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Tue, Dec 13, 2011 at 10:10 AM, Zita Eva Patai wrote: > Dear Jan-Mathijs, > > Thank you for that, it makes a lot more sense. I figured the data was too > complex for display, so I will average over frequencies as you suggested, > as I am interested in an effect that would encompass that range anyway... > > Thank you again and happy holidays! > z > > On Tue, Dec 13, 2011 at 4:22 PM, jan-mathijs schoffelen < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Zita, >> >> OK. I now understand the point. ft_clusterplot throws an error because it >> does not know how to collapse across frequencies. If the clusters have >> spectral extent (as well as spatial extent) it's a non-trivial question >> what are the channels to be plotted, because different channels can >> contribute different time and frequency points to the significant cluster. >> The time points are dealt with because ft_clusterplot shows the cluster >> evolving over time; the frequencies are not dealt with. FieldTrip does not >> make the choice of which channels to highlight for you (should all >> frequencies be significant for a given time point, or only one, or just a >> few?) and thus throws an error. However, if you have a priori reasons to >> expect your effect to occur in a particular frequency range (as you seem to >> do, because of your specification of the cfg before calling >> ft_freqstatistics), you can also specify cfg.avgoverfreq to 'yes', yielding >> a single observation per channel (and by construction the clustering only >> occurs over channels), making the plotting trivial. >> >> I hope this helps. >> >> BW, >> >> JM >> >> >> >> On Dec 12, 2011, at 12:22 PM, Zita Eva Patai wrote: >> >> Dear Jan-Mathijs, >> >> Sorry I was so vague, i thought maybe it was a common problem... >> >> OK, so i was running a clusterstat with the following input ( main point, >> i want to look at the difference between conditions over a set of >> frequencies) >> *** >> load blk1_tf_avg >> load blk3_tf_avg >> >> cfg = []; >> cfg.latency = [1.0 1.5 ]; >> cfg.frequency = [4 8]; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'depsamplesT'; >> cfg.correctm = 'cluster'; >> cfg.clusteralpha = 0.05; >> cfg.clusterstatistic = 'maxsum'; >> cfg.minnbchan = 2; >> cfg.tail = 0; >> cfg.clustertail = 0; >> cfg.alpha = 0.025; >> cfg.numrandomization = 1000; >> cfg.feedback = 'yes'; >> cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg); >> subj = 15; >> design = zeros(2,2*subj); >> for i = 1:subj >> design(1,i) = i; >> end >> for i = 1:subj >> design(1,subj+i) = i; >> end >> design(2,1:subj) = 1; >> design(2,subj+1:2*subj) = 2; >> >> >> cfg.design = design; >> cfg.uvar = 1; >> cfg.ivar = 2; >> >> >> [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg); >> >> >> save stat_tf_theta_1000_1500_bkey3vsbkey1 stat >> >> >> *** >> >> The error comes during the plotting phase when it says that i should not >> have multiple frequencies, as the data should be averaged across >> frequencies. And it does save my file (stat_theta....) but and i can see >> the pos/neg clusters in the data structure...but i can't plot with : >> >> cfg = []; >> cfg.highlightsymbolseries = ['*','*','.','.','.']; >> cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay'; >> cfg.contournum = 0; >> cfg.markersymbol = '.'; >> cfg.alpha = 0.05; >> cfg.zparam = 'stat'; >> ft_clusterplot(cfg,stat); >> >> >> >> I have also tried plotting with the script from the tutorial >> >> >> pos_cluster_pvals = [stat.posclusters(:).prob]; >> pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha); >> pos = ismember(stat.posclusterslabelmat, pos_signif_clust); >> >> >> neg_cluster_pvals = [stat.negclusters(:).prob]; >> neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha); >> neg = ismember(stat.negclusterslabelmat, neg_signif_clust); >> >> for k = 1:20; >> >> etc. >> but this makes the plot really weird looking...and i am not sure how i >> can only plot the data from the frequencies i would like to display (in >> this case 4-8Hz). I know how to make the subtraction image (between my two >> conditions), but not how to specify the frequency range that i want >> displayed... >> >> If this is too complicated, is there a way to average over a set of >> frequencies in the data, and then just input files into the permutation >> test that are already collapsed across the frequency range i am interested >> in? >> >> >> Thank you! >> z >> >> >> On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen < >> jan.schoffelen at donders.ru.nl> wrote: >> >>> Hi Zita, >>> >>> Could you provide some more information please? What plotting function >>> are you using? What does the stat-structure look like etc.? With sufficient >>> additional information we can try and reproduce the problem, and if it's a >>> bug fix it. If it's not a bug, we may give you some hints to fool the >>> system... >>> >>> BW, >>> >>> Jan-Mathijs >>> >>> On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: >>> >>> Dear FT-ers, >>> >>> I have tried to run a permutation test on time-frequency data, and would >>> have like to see a statistical evealuation over a set of frequencies (ex: >>> 4-8Hz) >>> >>> It seems that the test itself runs, but it crashes when i try to plot >>> the data, saying that 'stat' must not contain multiple frequencies. >>> >>> I was wondering if there was a way to evaluate the difference between >>> two conditions over a set range of frequencies? >>> >>> Thank you! >>> zita >>> >>> >>> -- >>> >>> Zita Patai >>> DPhil Candidate, Experimental Psychology >>> University of Oxford >>> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >>> eva.patai at psy.ox.ac.uk >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> Jan-Mathijs Schoffelen, MD PhD >>> >>> Donders Institute for Brain, Cognition and Behaviour, >>> Centre for Cognitive Neuroimaging, >>> Radboud University Nijmegen, The Netherlands >>> >>> Max Planck Institute for Psycholinguistics, >>> Nijmegen, The Netherlands >>> >>> J.Schoffelen at donders.ru.nl >>> Telephone: +31-24-3614793 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> >> Zita Patai >> DPhil Candidate, Experimental Psychology >> University of Oxford >> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >> eva.patai at psy.ox.ac.uk >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > > Zita Patai > DPhil Candidate, Experimental Psychology > University of Oxford > bcl.psy.ox.ac.uk/people/zita-eva-patai/ > eva.patai at psy.ox.ac.uk > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eva.patai at psy.ox.ac.uk Tue Dec 13 19:18:36 2011 From: eva.patai at psy.ox.ac.uk (Zita Eva Patai) Date: Tue, 13 Dec 2011 18:18:36 +0000 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> Message-ID: Thank you Matt, that further makes my situation more clear to me! On Tue, Dec 13, 2011 at 5:47 PM, Matt Mollison wrote: > Hi Zita, > > I have not used this method much, but it actually is possible to plot > clusters without averaging over the frequency dimension > using ft_multiplotTFR (where cfg.avgoverchan = 'no'; cfg.avgovertime = > 'no'; cfg.avgoverfreq='no'; in your statistical test—so you'll get space, > time, and frequency information). You can also highlight the significant > portions of time and frequency space, using cfg.mask='yes', > cfg.maskparameter='mask', and set a cfg.maskalpha. Do keep in mind that > there are important reasons for averaging over frequency, as Dr. Maris > described in this post (specifically, to increase power): < > http://mailman.science.ru.nl/pipermail/fieldtrip/2010-November/003312.html > >. > > Cheers, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > > On Tue, Dec 13, 2011 at 10:10 AM, Zita Eva Patai wrote: > >> Dear Jan-Mathijs, >> >> Thank you for that, it makes a lot more sense. I figured the data was too >> complex for display, so I will average over frequencies as you suggested, >> as I am interested in an effect that would encompass that range anyway... >> >> Thank you again and happy holidays! >> z >> >> On Tue, Dec 13, 2011 at 4:22 PM, jan-mathijs schoffelen < >> jan.schoffelen at donders.ru.nl> wrote: >> >>> Hi Zita, >>> >>> OK. I now understand the point. ft_clusterplot throws an error because >>> it does not know how to collapse across frequencies. If the clusters have >>> spectral extent (as well as spatial extent) it's a non-trivial question >>> what are the channels to be plotted, because different channels can >>> contribute different time and frequency points to the significant cluster. >>> The time points are dealt with because ft_clusterplot shows the cluster >>> evolving over time; the frequencies are not dealt with. FieldTrip does not >>> make the choice of which channels to highlight for you (should all >>> frequencies be significant for a given time point, or only one, or just a >>> few?) and thus throws an error. However, if you have a priori reasons to >>> expect your effect to occur in a particular frequency range (as you seem to >>> do, because of your specification of the cfg before calling >>> ft_freqstatistics), you can also specify cfg.avgoverfreq to 'yes', yielding >>> a single observation per channel (and by construction the clustering only >>> occurs over channels), making the plotting trivial. >>> >>> I hope this helps. >>> >>> BW, >>> >>> JM >>> >>> >>> >>> On Dec 12, 2011, at 12:22 PM, Zita Eva Patai wrote: >>> >>> Dear Jan-Mathijs, >>> >>> Sorry I was so vague, i thought maybe it was a common problem... >>> >>> OK, so i was running a clusterstat with the following input ( main >>> point, i want to look at the difference between conditions over a set of >>> frequencies) >>> *** >>> load blk1_tf_avg >>> load blk3_tf_avg >>> >>> cfg = []; >>> cfg.latency = [1.0 1.5 ]; >>> cfg.frequency = [4 8]; >>> cfg.method = 'montecarlo'; >>> cfg.statistic = 'depsamplesT'; >>> cfg.correctm = 'cluster'; >>> cfg.clusteralpha = 0.05; >>> cfg.clusterstatistic = 'maxsum'; >>> cfg.minnbchan = 2; >>> cfg.tail = 0; >>> cfg.clustertail = 0; >>> cfg.alpha = 0.025; >>> cfg.numrandomization = 1000; >>> cfg.feedback = 'yes'; >>> cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg); >>> subj = 15; >>> design = zeros(2,2*subj); >>> for i = 1:subj >>> design(1,i) = i; >>> end >>> for i = 1:subj >>> design(1,subj+i) = i; >>> end >>> design(2,1:subj) = 1; >>> design(2,subj+1:2*subj) = 2; >>> >>> >>> cfg.design = design; >>> cfg.uvar = 1; >>> cfg.ivar = 2; >>> >>> >>> [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg); >>> >>> >>> save stat_tf_theta_1000_1500_bkey3vsbkey1 stat >>> >>> >>> *** >>> >>> The error comes during the plotting phase when it says that i should not >>> have multiple frequencies, as the data should be averaged across >>> frequencies. And it does save my file (stat_theta....) but and i can see >>> the pos/neg clusters in the data structure...but i can't plot with : >>> >>> cfg = []; >>> cfg.highlightsymbolseries = ['*','*','.','.','.']; >>> cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay'; >>> cfg.contournum = 0; >>> cfg.markersymbol = '.'; >>> cfg.alpha = 0.05; >>> cfg.zparam = 'stat'; >>> ft_clusterplot(cfg,stat); >>> >>> >>> >>> I have also tried plotting with the script from the tutorial >>> >>> >>> pos_cluster_pvals = [stat.posclusters(:).prob]; >>> pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha); >>> pos = ismember(stat.posclusterslabelmat, pos_signif_clust); >>> >>> >>> neg_cluster_pvals = [stat.negclusters(:).prob]; >>> neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha); >>> neg = ismember(stat.negclusterslabelmat, neg_signif_clust); >>> >>> for k = 1:20; >>> >>> etc. >>> but this makes the plot really weird looking...and i am not sure how i >>> can only plot the data from the frequencies i would like to display (in >>> this case 4-8Hz). I know how to make the subtraction image (between my two >>> conditions), but not how to specify the frequency range that i want >>> displayed... >>> >>> If this is too complicated, is there a way to average over a set of >>> frequencies in the data, and then just input files into the permutation >>> test that are already collapsed across the frequency range i am interested >>> in? >>> >>> >>> Thank you! >>> z >>> >>> >>> On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen < >>> jan.schoffelen at donders.ru.nl> wrote: >>> >>>> Hi Zita, >>>> >>>> Could you provide some more information please? What plotting function >>>> are you using? What does the stat-structure look like etc.? With sufficient >>>> additional information we can try and reproduce the problem, and if it's a >>>> bug fix it. If it's not a bug, we may give you some hints to fool the >>>> system... >>>> >>>> BW, >>>> >>>> Jan-Mathijs >>>> >>>> On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: >>>> >>>> Dear FT-ers, >>>> >>>> I have tried to run a permutation test on time-frequency data, and >>>> would have like to see a statistical evealuation over a set of frequencies >>>> (ex: 4-8Hz) >>>> >>>> It seems that the test itself runs, but it crashes when i try to plot >>>> the data, saying that 'stat' must not contain multiple frequencies. >>>> >>>> I was wondering if there was a way to evaluate the difference between >>>> two conditions over a set range of frequencies? >>>> >>>> Thank you! >>>> zita >>>> >>>> >>>> -- >>>> >>>> Zita Patai >>>> DPhil Candidate, Experimental Psychology >>>> University of Oxford >>>> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >>>> eva.patai at psy.ox.ac.uk >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> Jan-Mathijs Schoffelen, MD PhD >>>> >>>> Donders Institute for Brain, Cognition and Behaviour, >>>> Centre for Cognitive Neuroimaging, >>>> Radboud University Nijmegen, The Netherlands >>>> >>>> Max Planck Institute for Psycholinguistics, >>>> Nijmegen, The Netherlands >>>> >>>> J.Schoffelen at donders.ru.nl >>>> Telephone: +31-24-3614793 >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> >>> Zita Patai >>> DPhil Candidate, Experimental Psychology >>> University of Oxford >>> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >>> eva.patai at psy.ox.ac.uk >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> Jan-Mathijs Schoffelen, MD PhD >>> >>> Donders Institute for Brain, Cognition and Behaviour, >>> Centre for Cognitive Neuroimaging, >>> Radboud University Nijmegen, The Netherlands >>> >>> Max Planck Institute for Psycholinguistics, >>> Nijmegen, The Netherlands >>> >>> J.Schoffelen at donders.ru.nl >>> Telephone: +31-24-3614793 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> >> Zita Patai >> DPhil Candidate, Experimental Psychology >> University of Oxford >> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >> eva.patai at psy.ox.ac.uk >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Zita Patai DPhil Candidate, Experimental Psychology University of Oxford bcl.psy.ox.ac.uk/people/zita-eva-patai/ eva.patai at psy.ox.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From Gregor.Volberg at psychologie.uni-regensburg.de Wed Dec 14 10:32:17 2011 From: Gregor.Volberg at psychologie.uni-regensburg.de (Gregor Volberg) Date: Wed, 14 Dec 2011 10:32:17 +0100 Subject: [FieldTrip] read_eeglab, header file? In-Reply-To: References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> Message-ID: <4EE87B31020000570000BF1A@gwsmtp1.uni-regensburg.de> Dear Fieldtrip developers, I encountered an error warning when reading in an eeglab *.set - file for preprocessing (version fieldtrip-20111206), where the call to ft_preprocessing says ??? Undefined function or variable "hdr". Error in ==> read_eeglabdata at 52 if isempty(hdr) Shouldn't code lines 52 to 54 read if isempty(header) header = read_eeglabheader(filename); end instead of if isempty(hdr) hdr = read_eeglabheader(filename); end Not really a problem, just to bring it to your attention... Best regards, Gregor -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.hesselmann at gmail.com Wed Dec 14 18:53:46 2011 From: g.hesselmann at gmail.com (Guido Hesselmann) Date: Wed, 14 Dec 2011 18:53:46 +0100 Subject: [FieldTrip] Time-frequency analysis: based on single trials or on average? Message-ID: Hi all, I am new to fieldtrip and have a very simple question. I have EEG data and would like to run a time-frequency analysis (e.g., using a Hanning taper with fixed window length). If I have 100 trials, how is this analysis performed? On a trial-by-trial basis, or based on the average? Can I choose between these options in fieldtrip? Thanks a lot! Guido Hesselmann Visual Perception Lab Department of Psychiatry & Psychotherapy Charité Berlin -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Wed Dec 14 19:03:49 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Wed, 14 Dec 2011 19:03:49 +0100 Subject: [FieldTrip] Time-frequency analysis: based on single trials or on average? In-Reply-To: References: Message-ID: Hi Guido, The FieldTrip method that performs time-frequency analyses is called ft_freqanalysis. By default, ft_freqanalysis gives you power averaged over trials as output. You can easily override this default behaviour by specifying cfg.keeptrials='yes', you will then get a power estimate for each individual trial. You might want to take a look at the following tutorial, which covers the basics of how to do time-frequency analysis in FieldTrip: http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis The reference documentation for ft_freqanalysis also might be of use: http://fieldtrip.fcdonders.nl/reference/ft_freqanalysis (which is the same information you get when you type 'help ft_freqanalysis' or 'doc ft_freqanalysis' at the matlab prompt). Hope this was of help. Best, Eelke 2011/12/14 Guido Hesselmann : > Hi all, > > I am new to fieldtrip and have a very simple question. I have EEG data and > would like to run a > time-frequency analysis (e.g., using a Hanning taper with fixed window > length). If I have 100 trials, > how is this analysis performed? On a trial-by-trial basis, or based on the > average? Can I choose > between these options in fieldtrip? > > Thanks a lot! > > Guido Hesselmann > Visual Perception Lab > Department of Psychiatry & Psychotherapy > Charité Berlin > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From lihqih at gmail.com Wed Dec 14 19:04:37 2011 From: lihqih at gmail.com (qi li) Date: Wed, 14 Dec 2011 13:04:37 -0500 Subject: [FieldTrip] remove trials after ft_preprocessing Message-ID: I am new to fieldtrip. After I processed the data, I got triggered_trials = hdr: [1x1 struct] label: {273x1 cell} time: {1x20 cell} trial: {1x20 cell} fsample: 600 sampleinfo: [20x2 double] grad: [1x1 struct] cfg: [1x1 struct] Now I want to remove a few trials with trial no 1 3 5 8. What command do I need to remove the trials and keep the structure of triggered_trials unchanged? Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From ucbtmba at ucl.ac.uk Wed Dec 14 19:08:48 2011 From: ucbtmba at ucl.ac.uk (Markus Bauer) Date: Wed, 14 Dec 2011 18:08:48 +0000 Subject: [FieldTrip] Time-frequency analysis: based on single trials or on average? In-Reply-To: References: Message-ID: <4EE8E630.2050600@ucl.ac.uk> An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Wed Dec 14 19:15:06 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Wed, 14 Dec 2011 19:15:06 +0100 Subject: [FieldTrip] remove trials after ft_preprocessing In-Reply-To: References: Message-ID: Dear Qi Li, There are several ways to achieve this. Both ft_selectdata and ft_preprocessing allow you to select a subset of trials without altering anything else in the data. Both of these functions require a vector as input that contains the indices of the trials to be *retained*, so you need to create this yourself. For instance: trialsToKeep = 1:20; % initialize vector with all trial indices trialsToKeep([1 3 5 8]) = []; % remove the trials that should go After this you can call either: data = ft_selectdata(data, 'rpt', trialsToKeep); Or: cfg = []; cfg.trials = trialsToKeep; data = ft_preprocessing(cfg, data); Best, Eelke 2011/12/14 qi li : > I am new to fieldtrip. After I processed the data, I got > triggered_trials = > >            hdr: [1x1 struct] >          label: {273x1 cell} >           time: {1x20 cell} >          trial: {1x20 cell} >        fsample: 600 >     sampleinfo: [20x2 double] >           grad: [1x1 struct] >            cfg: [1x1 struct] > Now I want to remove a few trials with trial no 1 3 5 8. What command do I > need to remove the trials and keep the structure of triggered_trials > unchanged? Thanks! > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Thu Dec 15 10:15:56 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 15 Dec 2011 10:15:56 +0100 Subject: [FieldTrip] read_eeglab, header file? In-Reply-To: <4EE87B31020000570000BF1A@gwsmtp1.uni-regensburg.de> References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> <4EE87B31020000570000BF1A@gwsmtp1.uni-regensburg.de> Message-ID: <4EE9BACC.7040809@donders.ru.nl> Hi Gregor, thanks for reporting this. It looks indeed like it should be like that, so I changed it to what you suggested (otherwise, if-clause does not make any sense at all). Best, Jörn On 12/14/2011 10:32 AM, Gregor Volberg wrote: > > Dear Fieldtrip developers, > > > I encountered an error warning when reading in an eeglab *.set - file > for preprocessing (version fieldtrip-20111206), where the call to > ft_preprocessing says > > > ??? Undefined function or variable "hdr". > > Error in ==> read_eeglabdata at 52 > > if isempty(hdr) > > > > Shouldn't code lines 52 to 54 read > > > if isempty(header) > > header = read_eeglabheader(filename); > > end > > > instead of > > > if isempty(hdr) > > hdr = read_eeglabheader(filename); > > end > > > > Not really a problem, just to bring it to your attention... > > > Best regards, > > Gregor > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Thu Dec 15 21:00:59 2011 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Thu, 15 Dec 2011 14:00:59 -0600 Subject: [FieldTrip] Topographic scaling of ERP data Message-ID: Hello, Our lab is interested in performing the topographic scaling method described in the following paper to compare ERP topographies: Jing, H., Pivik, R., & Dykman, R. (2006). A new scaling method for topographic comparisons of event-related potentials. *Journal of Neuroscience Methods 151*. Are there any FieldTrip functions available that implement this method? Thank you,, Steve Politzer-Ahles -- Stephen Politzer-Ahles University of Kansas Linguistics Department http://www.linguistics.ku.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From chenzuyue at live.cn Fri Dec 16 13:14:22 2011 From: chenzuyue at live.cn (chenzuyue) Date: Fri, 16 Dec 2011 12:14:22 +0000 Subject: [FieldTrip] Problems time-frequency analysis of Local Field Potential Message-ID: Hi, everyone, I am a new user of FieldTrip. In my study, I want to computes the difference of time-frequency representations of event-related LFP in two conditions. The data in the first condition is a 4 X 1100 X 103 matrix (Nchan X Nsamples X Ntrials). The data in the second condition is a 4 X 1100 X 107 matrix. The data reformatted are as follows: dataset1.label (4 X 1 cell ); dataset1.fsample 1000; dataset1.trial (1 X 103 cell ); dataset1.time (1X 103 cell); % time is from -100ms to 999ms. dataset2.label (4 X 1 cell ); dataset2.fsample 1000; dataset2.trial (1 X 107 cell ); dataset2.time (1X 107 cell ); % time is from -100ms to 999ms. The frequency interested is 0-100Hz. The method to calculate TFRs is the multitaper method. The configuration is as below: cfg = []; cfg.output = 'pow'; cfg.method = 'mtmconvol'; cfg.foi = 1:2:100; cfg.t_ftimwin = 5./cfg.foi; cfg.tapsmofrq = 0.4 *cfg.foi; cfg.toi = -0.1:0.05:1; cfg.pad = 'maxperlen'; TFRmult1 = ft_freqanalysis(cfg, dataset1); But after running, I can not get the right results. When I use ft_singleplotTFR to plot graph, there is only blue color. I wonder whether the process and configuration is right. The method is from one paper of E Maris and R Oostenvels published on the Journal of Neuroscience Methods.164(2007), 177-190; Figure 3. http://www.ncbi.nlm.nih.gov/pubmed/17517438 Any help is much appreciated. Yours Sincerely, Zuyue -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Fri Dec 16 13:44:51 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Fri, 16 Dec 2011 13:44:51 +0100 Subject: [FieldTrip] Problems time-frequency analysis of Local Field Potential In-Reply-To: References: Message-ID: Dear Zuyue, When you invoke ft_singleplotTFR, do you specify a means of baseline correction and/or explicit z-limits (i.e., limits of the color axis)? When looking at raw power (i.e., not contrasted), it is advisable to use a baseline correction in order to see something. Also, specifying z-limits of a different order of magnitude than your data will of course lead to all blue plots. You should take a look at the time-frequency analysis tutorial, particularly the part about visualization: http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis#visualization If you still don't see anything after you use baseline correction (or plot a contrast instead) and have proper z-limits, there might be something else wrong. Best, Eelke 2011/12/16 chenzuyue : > Hi, everyone, > > I am a new user of FieldTrip. In my study, I want to computes the difference > of time-frequency representations of event-related LFP in two conditions. > > The data in the first condition is a 4 X 1100 X 103 matrix (Nchan X Nsamples > X Ntrials). The data in the second condition is a 4 X 1100 X 107 matrix. The > data reformatted are as follows: > > dataset1.label (4 X 1 cell ); > > dataset1.fsample 1000; > > dataset1.trial (1 X 103 cell ); > > dataset1.time (1X 103 cell); % time is from -100ms to 999ms. > > > dataset2.label (4 X 1 cell ); > > dataset2.fsample 1000; > > dataset2.trial (1 X 107 cell ); > > dataset2.time (1X 107 cell ); % time is from -100ms to 999ms. > > > The frequency interested is 0-100Hz. The method to calculate TFRs is the > multitaper method. The configuration is as below: > > cfg = []; > cfg.output = 'pow'; > cfg.method = 'mtmconvol'; > cfg.foi = 1:2:100; > cfg.t_ftimwin = 5./cfg.foi; > cfg.tapsmofrq = 0.4 *cfg.foi; > cfg.toi = -0.1:0.05:1; > cfg.pad = 'maxperlen'; > TFRmult1 = ft_freqanalysis(cfg, dataset1); > > But after running, I can not get the right results. When I use > ft_singleplotTFR to plot graph, there is only blue color. I wonder whether > the process and configuration is right. > > The method is from one paper of E Maris and R Oostenvels published on the > Journal of Neuroscience Methods.164(2007), 177-190; Figure 3. > http://www.ncbi.nlm.nih.gov/pubmed/17517438 > > Any help is much appreciated. > > Yours Sincerely, > > Zuyue > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Fri Dec 16 14:02:36 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 16 Dec 2011 14:02:36 +0100 Subject: [FieldTrip] Problems time-frequency analysis of Local Field Potential In-Reply-To: References: Message-ID: <46831F4B-7707-496E-B55C-DDE4E4E5BB15@donders.ru.nl> Dear Zuyue, I agree with Eelke. One thing you need to check is whether the time axis (in data.time{}) is in seconds or milliseconds. In the cfg to ft_freqanalysis you specify it in seconds. FieldTrip does not care about the exact units, so you need to ensure that the units in the time-axis correspond. BW, Jan-Mathijs On Dec 16, 2011, at 1:44 PM, Eelke Spaak wrote: > Dear Zuyue, > > When you invoke ft_singleplotTFR, do you specify a means of baseline > correction and/or explicit z-limits (i.e., limits of the color axis)? > When looking at raw power (i.e., not contrasted), it is advisable to > use a baseline correction in order to see something. Also, specifying > z-limits of a different order of magnitude than your data will of > course lead to all blue plots. > > You should take a look at the time-frequency analysis tutorial, > particularly the part about visualization: > http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis#visualization > > If you still don't see anything after you use baseline correction (or > plot a contrast instead) and have proper z-limits, there might be > something else wrong. > > Best, > Eelke > > 2011/12/16 chenzuyue : >> Hi, everyone, >> >> I am a new user of FieldTrip. In my study, I want to computes the difference >> of time-frequency representations of event-related LFP in two conditions. >> >> The data in the first condition is a 4 X 1100 X 103 matrix (Nchan X Nsamples >> X Ntrials). The data in the second condition is a 4 X 1100 X 107 matrix. The >> data reformatted are as follows: >> >> dataset1.label (4 X 1 cell ); >> >> dataset1.fsample 1000; >> >> dataset1.trial (1 X 103 cell ); >> >> dataset1.time (1X 103 cell); % time is from -100ms to 999ms. >> >> >> dataset2.label (4 X 1 cell ); >> >> dataset2.fsample 1000; >> >> dataset2.trial (1 X 107 cell ); >> >> dataset2.time (1X 107 cell ); % time is from -100ms to 999ms. >> >> >> The frequency interested is 0-100Hz. The method to calculate TFRs is the >> multitaper method. The configuration is as below: >> >> cfg = []; >> cfg.output = 'pow'; >> cfg.method = 'mtmconvol'; >> cfg.foi = 1:2:100; >> cfg.t_ftimwin = 5./cfg.foi; >> cfg.tapsmofrq = 0.4 *cfg.foi; >> cfg.toi = -0.1:0.05:1; >> cfg.pad = 'maxperlen'; >> TFRmult1 = ft_freqanalysis(cfg, dataset1); >> >> But after running, I can not get the right results. When I use >> ft_singleplotTFR to plot graph, there is only blue color. I wonder whether >> the process and configuration is right. >> >> The method is from one paper of E Maris and R Oostenvels published on the >> Journal of Neuroscience Methods.164(2007), 177-190; Figure 3. >> http://www.ncbi.nlm.nih.gov/pubmed/17517438 >> >> Any help is much appreciated. >> >> Yours Sincerely, >> >> Zuyue >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Mon Dec 19 10:03:51 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Mon, 19 Dec 2011 11:03:51 +0200 Subject: [FieldTrip] Address of biosemi device Message-ID: Hello, I'd tried to use the biosemi2ft function for realtime acquiring. But the following message appears: "Could not connect to buffer server at localhost: 1972". Should I change the Hostname and the Port, if yes what should they be? Best, -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Dec 19 11:04:47 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 19 Dec 2011 11:04:47 +0100 Subject: [FieldTrip] Topographic scaling of ERP data In-Reply-To: References: Message-ID: Dear Stephen, I am not aware of any FieldTrip function that achieves this scaling. Looking at the method, it seems that it should be able to implement this is not too many lines of matlab code. Maybe someone else on the list has some code lying around. Best wishes, Jan-Mathijs On Dec 15, 2011, at 9:00 PM, Stephen Politzer-Ahles wrote: > Hello, > > Our lab is interested in performing the topographic scaling method described in the following paper to compare ERP topographies: > > Jing, H., Pivik, R., & Dykman, R. (2006). A new scaling method for topographic comparisons of event-related potentials. Journal of Neuroscience Methods 151. > > Are there any FieldTrip functions available that implement this method? > > Thank you,, > Steve Politzer-Ahles > > -- > Stephen Politzer-Ahles > University of Kansas > Linguistics Department > http://www.linguistics.ku.edu/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Tue Dec 20 02:54:53 2011 From: lihqih at gmail.com (qi li) Date: Mon, 19 Dec 2011 20:54:53 -0500 Subject: [FieldTrip] operation order difference Message-ID: Hi, I have a CTF axial data. Is the result of timelock first then do the ft_megplanar same as ft_megplanar first then timelock? I think both method should get the same result. Qi -------------- next part -------------- An HTML attachment was scrubbed... URL: From adam at adamcsnyder.com Tue Dec 20 04:54:39 2011 From: adam at adamcsnyder.com (Adam C. Snyder) Date: Mon, 19 Dec 2011 22:54:39 -0500 Subject: [FieldTrip] Problem detecting triggers with real time synchronous analysis Message-ID: <29E38593-B980-47D1-9E86-E197EF62994E@adamcsnyder.com> Hello, I'm trying to perform a real time synchronous analysis in response to a particular trigger, but it isn't working. Here are some brief details of the setup: we're using BioSemi ActiveTwo, a December 2011 version of FieldTrip and MATLAB 2010b. I've managed to get the biosemi2ft executable running, and if I send a trigger through the BioSemi system, the details are noted in the command window. However, within the ft_realtime_synchronous function, the trigger events are not being found. The built-in status updates (e.g., "CMS_IN_RANGE", etc.), in contrast, are picked up by the ft_read_event call within ft_realtime_synchronous function, which adds to my confusion. My configurations are something like these: cfg.dataset = 'buffer://localhost:1972'; cfg.bcifun = @hello_world; cfg.blocksize = 1; cfg.trigger = [4 2]; cfg.jumptoeof = 'yes'; cfg.bufferdata = 'last'; %maybe the name of this option was different -- I'm typing from memory I hope someone can kindly help me to figure this out, and thank you in advance for whatever help you can provide. In Science, Adam C. Snyder Postdoctoral Fellow Cognitive Neurophysiology Lab Albert Einstein College of Medicine Bronx, NY From eelke.spaak at donders.ru.nl Tue Dec 20 10:56:13 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 20 Dec 2011 10:56:13 +0100 Subject: [FieldTrip] operation order difference In-Reply-To: References: Message-ID: Hi Qi, I think so too. Have you tried it? Best, Eelke 2011/12/20 qi li : > Hi, > > I have a CTF axial data. Is the result of timelock first then do the > ft_megplanar same as ft_megplanar first then timelock? > > I think both method should get the same result. > > Qi > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From lihqih at gmail.com Tue Dec 20 17:39:19 2011 From: lihqih at gmail.com (qi li) Date: Tue, 20 Dec 2011 11:39:19 -0500 Subject: [FieldTrip] operation order difference In-Reply-To: References: Message-ID: Hi Eelke, Thanks for your reply. I tried a particular sample and the difference between these two methods are small. However, timelock first is faster whereas ft_megplanar first makes much more sense. Qi On Tue, Dec 20, 2011 at 4:56 AM, Eelke Spaak wrote: > Hi Qi, > > I think so too. Have you tried it? > > Best, > Eelke > > 2011/12/20 qi li : > > Hi, > > > > I have a CTF axial data. Is the result of timelock first then do the > > ft_megplanar same as ft_megplanar first then timelock? > > > > I think both method should get the same result. > > > > Qi > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Wed Dec 21 11:56:26 2011 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Wed, 21 Dec 2011 11:56:26 +0100 Subject: [FieldTrip] Address of biosemi device In-Reply-To: References: Message-ID: Dear Hamza, I think this message appears when you specify a specific buffer server to connect to. The biosemi2ft.exe can be run in two modes, 1) it starts an baked-in buffer server (default), or 2) it can can use a buffer server that is run in a separate process. The default mode is probably a good choice. You can select the default mode *by not specifying a server of port*. Best regards, Boris On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) wrote: > Hello, > > I'd tried to use the biosemi2ft function for realtime acquiring. But the > following message appears: > > "Could not connect to buffer server at localhost: 1972". > > Should I change the Hostname and the Port, if yes what should they be? > > Best, > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From hamzaf at sabanciuniv.edu Wed Dec 21 15:36:21 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Wed, 21 Dec 2011 16:36:21 +0200 Subject: [FieldTrip] Address of biosemi device In-Reply-To: References: Message-ID: Thank you Boris. Well, I tried the default mode (just by specifying the configuration file and the gdf file in the cmd). But this message appeared. Could you or anyone just tell me exactly what should I do or modify. Thanks a lot On Wed, Dec 21, 2011 at 12:56 PM, Boris Reuderink wrote: > Dear Hamza, > > I think this message appears when you specify a specific buffer server > to connect to. The biosemi2ft.exe can be run in two modes, 1) it > starts an baked-in buffer server (default), or 2) it can can use a > buffer server that is run in a separate process. > > The default mode is probably a good choice. You can select the default > mode *by not specifying a server of port*. > > Best regards, > > Boris > > On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) > wrote: > > Hello, > > > > I'd tried to use the biosemi2ft function for realtime acquiring. But the > > following message appears: > > > > "Could not connect to buffer server at localhost: 1972". > > > > Should I change the Hostname and the Port, if yes what should they be? > > > > Best, > > > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Wed Dec 21 16:48:02 2011 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Wed, 21 Dec 2011 16:48:02 +0100 Subject: [FieldTrip] Address of biosemi device In-Reply-To: References: Message-ID: Could you perhaps send me the exact command you executed? Tomorrow I'll have access to a windows machine --- maybe I can find out what went wrong. Best regards, Boris 2011/12/21 Hamza Fawzi Altakroury (Student) : > Thank you Boris. > > Well, I tried the default mode (just by specifying the configuration file > and the gdf file in the cmd). But this message appeared. > Could you or anyone just tell me exactly what should I do or modify. > > Thanks a lot > > > On Wed, Dec 21, 2011 at 12:56 PM, Boris Reuderink > wrote: >> >> Dear Hamza, >> >> I think this message appears when you specify a specific buffer server >> to connect to. The biosemi2ft.exe can be run in two modes, 1) it >> starts an baked-in buffer server (default), or 2) it can can use a >> buffer server that is run in a separate process. >> >> The default mode is probably a good choice. You can select the default >> mode *by not specifying a server of port*. >> >> Best regards, >> >> Boris >> >> On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) >> wrote: >> > Hello, >> > >> > I'd tried to use the biosemi2ft function for realtime acquiring. But the >> > following message appears: >> > >> > "Could not connect to buffer server at localhost: 1972". >> > >> > Should I change the Hostname and the Port, if yes what should they be? >> > >> > Best, >> > >> > >> > -- >> > Hamza Fawzi Altakroury >> > Graduate student - MA >> > Faculty of Engineering and Natural Sciences >> > Sabancı University >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From johemart at gmail.com Wed Dec 21 16:50:42 2011 From: johemart at gmail.com (=?ISO-8859-1?Q?Johann_Heinz_Mart=EDnez_Huartos?=) Date: Wed, 21 Dec 2011 16:50:42 +0100 Subject: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? Message-ID: Hello dear fieldtripers Currently im using ft_topoplotER() function in order to visualize a cluster of channels in the head. But i cant fill the marker im using to highlight those channels. I know that the commend to chage this opction in matlab is markerfacecolor = 'k'. if i want to fill it up with black color, but this option does not makes anything happend and the markers are not filled. So, anyone knows how to fill the marker in ft_topoplotER() funtion? Thanks -- Atentamente: Johann Martínez. M.Sc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Wed Dec 21 17:50:03 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Wed, 21 Dec 2011 18:50:03 +0200 Subject: [FieldTrip] Address of biosemi device In-Reply-To: References: Message-ID: The directory: fieldtrip-20111211\realtime\acquisition\biosemi The command: biosemi2ft config.txt ex.gdf Output : could not connect to buffer server at localhost:1972. Thank a lot On Wed, Dec 21, 2011 at 5:48 PM, Boris Reuderink wrote: > Could you perhaps send me the exact command you executed? Tomorrow > I'll have access to a windows machine --- maybe I can find out what > went wrong. > > Best regards, > > Boris > > 2011/12/21 Hamza Fawzi Altakroury (Student) : > > Thank you Boris. > > > > Well, I tried the default mode (just by specifying the configuration file > > and the gdf file in the cmd). But this message appeared. > > Could you or anyone just tell me exactly what should I do or modify. > > > > Thanks a lot > > > > > > On Wed, Dec 21, 2011 at 12:56 PM, Boris Reuderink > > wrote: > >> > >> Dear Hamza, > >> > >> I think this message appears when you specify a specific buffer server > >> to connect to. The biosemi2ft.exe can be run in two modes, 1) it > >> starts an baked-in buffer server (default), or 2) it can can use a > >> buffer server that is run in a separate process. > >> > >> The default mode is probably a good choice. You can select the default > >> mode *by not specifying a server of port*. > >> > >> Best regards, > >> > >> Boris > >> > >> On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) > >> wrote: > >> > Hello, > >> > > >> > I'd tried to use the biosemi2ft function for realtime acquiring. But > the > >> > following message appears: > >> > > >> > "Could not connect to buffer server at localhost: 1972". > >> > > >> > Should I change the Hostname and the Port, if yes what should they be? > >> > > >> > Best, > >> > > >> > > >> > -- > >> > Hamza Fawzi Altakroury > >> > Graduate student - MA > >> > Faculty of Engineering and Natural Sciences > >> > Sabancı University > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > fieldtrip at donders.ru.nl > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Wed Dec 21 19:19:24 2011 From: lihqih at gmail.com (qi li) Date: Wed, 21 Dec 2011 13:19:24 -0500 Subject: [FieldTrip] how to plot the selected trials in the same plot Message-ID: Hi, I am trying to plot a single plot for a particular sensor with multiple trials by ft_singleplotER. Even I set the cfg.trials='all', it only gives one curve. If I want to use ft_multiplotER for the various sensors and multiple trials, what should I do? The multiplotER dosen't show the axes ticks and labels, how to fix it? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed Dec 21 20:58:10 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 21 Dec 2011 20:58:10 +0100 Subject: [FieldTrip] Address of biosemi device In-Reply-To: References: Message-ID: <28B62884-7633-4554-A460-31E1BF711582@donders.ru.nl> Dear Hamza According to the documentation on http://fieldtrip.fcdonders.nl/development/realtime/biosemi the full command line is biosemi2ft and "The first argument must be the name of a configuration file (see below). The second argument determines the base name of a GDF file that data is written to. The .gdf will be added automatically, as well as session counters (see below) and additional file name parts _1, _2 and so on for splitting the data over multiple files (to avoid 2 GB limits). The optional third and fourth argument are the hostname and port of the FieldTrip buffer. Defaults are localhost and 1972. Replacinghostname by a minus (-) tells the software to spawn its own buffer server on the given port." If you did not start buffer.exe prior to biosemi2ft.exe, you don't have a buffer server running and the error message makes sense because the buffer cannot be found. If you specify "-" as 3rd argument then biosemi2ft.exe will spawn its own buffer server in a separate thread and will connect to that. See http://fieldtrip.fcdonders.nl/development/realtime/biosemi and http://fieldtrip.fcdonders.nl/development/realtime/buffer. Note that you should name the output file "ex", not "ex.gdf". best Robert On 21 Dec 2011, at 17:50, Hamza Fawzi Altakroury (Student) wrote: > The directory: fieldtrip-20111211\realtime\acquisition\biosemi > > The command: biosemi2ft config.txt ex.gdf > > Output : could not connect to buffer server at localhost:1972. > > Thank a lot > > > > On Wed, Dec 21, 2011 at 5:48 PM, Boris Reuderink wrote: > Could you perhaps send me the exact command you executed? Tomorrow > I'll have access to a windows machine --- maybe I can find out what > went wrong. > > Best regards, > > Boris > > 2011/12/21 Hamza Fawzi Altakroury (Student) : > > Thank you Boris. > > > > Well, I tried the default mode (just by specifying the configuration file > > and the gdf file in the cmd). But this message appeared. > > Could you or anyone just tell me exactly what should I do or modify. > > > > Thanks a lot > > > > > > On Wed, Dec 21, 2011 at 12:56 PM, Boris Reuderink > > wrote: > >> > >> Dear Hamza, > >> > >> I think this message appears when you specify a specific buffer server > >> to connect to. The biosemi2ft.exe can be run in two modes, 1) it > >> starts an baked-in buffer server (default), or 2) it can can use a > >> buffer server that is run in a separate process. > >> > >> The default mode is probably a good choice. You can select the default > >> mode *by not specifying a server of port*. > >> > >> Best regards, > >> > >> Boris > >> > >> On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) > >> wrote: > >> > Hello, > >> > > >> > I'd tried to use the biosemi2ft function for realtime acquiring. But the > >> > following message appears: > >> > > >> > "Could not connect to buffer server at localhost: 1972". > >> > > >> > Should I change the Hostname and the Port, if yes what should they be? > >> > > >> > Best, > >> > > >> > > >> > -- > >> > Hamza Fawzi Altakroury > >> > Graduate student - MA > >> > Faculty of Engineering and Natural Sciences > >> > Sabancı University > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > fieldtrip at donders.ru.nl > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From s.bogels at psy.gla.ac.uk Thu Dec 22 10:26:57 2011 From: s.bogels at psy.gla.ac.uk (Sara =?iso-8859-1?b?QvZnZWxz?=) Date: Thu, 22 Dec 2011 09:26:57 +0000 Subject: [FieldTrip] problems with ft_multiplotTFR Message-ID: <20111222092657.846462fkkxbzywgx@horde.psy.gla.ac.uk> Hi all, I have performed a cluster-based permutation test on time-frequency data and I am trying to plot the significant clusters. Since I used multiple frequencies I cannot use ft_clusterplot but I should use ft_multiplotTFR if I understand correctly. I also did not average over time and I used all channels. The analysis resulted in 1 significant positive cluster and 1 significant negative cluster. I have tried ft_multiplotTFR with the following settings (plus a correct cfg.layout): cfg = []: cfg.maskparameter = 'mask'; cfg.parameter = 'stat'; cfg.maskalpha = 0.025; figure, ft_multiplotTFR(cfg,stats) This gives me plots on the head for all channels but they are all black. If I outcomment cfg.maskparameter I do get nicely coloured plots (of the teststatistic I assume) but of course without the significant cluster(s). Any help is appreciated. Thank you, Sara ---------------------------------------------------------------- This message was sent using the Web mail system for The University of Glasgow School of Psychology ------------------------------------------------------------------ From r.vandermeij at donders.ru.nl Thu Dec 22 10:37:43 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Thu, 22 Dec 2011 10:37:43 +0100 Subject: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? In-Reply-To: References: Message-ID: <4EF2FA67.8010108@donders.ru.nl> Hi Johann, If you update to the newest fieldtrip version, you can use the option cfg.highlightsymbol or cfg.markersymbol to pick a marker that is filled, like '.'. Best, Roemer On 21-12-11 16:50, Johann Heinz Martínez Huartos wrote: > Hello dear fieldtripers > > Currently im using ft_topoplotER() function in order to visualize a > cluster of channels in the head. But i cant fill the marker im using > to highlight those channels. I know that the commend to chage this > opction in matlab is markerfacecolor = 'k'. > if i want to fill it up with black color, but this option does not > makes anything happend and the markers are not filled. So, anyone > knows how to fill the marker in ft_topoplotER() funtion? > > Thanks > > -- > Atentamente: > Johann Martínez. M.Sc. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Thu Dec 22 14:36:31 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 22 Dec 2011 15:36:31 +0200 Subject: [FieldTrip] Address of biosemi device In-Reply-To: <28B62884-7633-4554-A460-31E1BF711582@donders.ru.nl> References: <28B62884-7633-4554-A460-31E1BF711582@donders.ru.nl> Message-ID: Dear Mr Robert Thanks a lot for your help. It works. Best On Wed, Dec 21, 2011 at 9:58 PM, Robert Oostenveld < r.oostenveld at donders.ru.nl> wrote: > Dear Hamza > > According to the documentation on > http://fieldtrip.fcdonders.nl/development/realtime/biosemi the full > command line is > biosemi2ft > and "The first argument must be the name of a configuration file (see > below). The second argument determines the base name of a GDF file that > data is written to. The .gdf will be added automatically, as well as > session counters (see below) and additional file name parts _1, _2 and so > on for splitting the data over multiple files (to avoid 2 GB limits). The > optional third and fourth argument are the hostname and port of the > FieldTrip buffer. Defaults are localhost and 1972. Replacinghostname by a > minus (-) tells the software to spawn its own buffer server on the given > port." > > If you did not start buffer.exe prior to biosemi2ft.exe, you don't have a > buffer server running and the error message makes sense because the buffer > cannot be found. > > If you specify "-" as 3rd argument then biosemi2ft.exe will spawn its own > buffer server in a separate thread and will connect to that. See > http://fieldtrip.fcdonders.nl/development/realtime/biosemi and > http://fieldtrip.fcdonders.nl/development/realtime/buffer. Note that you > should name the output file "ex", not "ex.gdf". > > best > Robert > > > On 21 Dec 2011, at 17:50, Hamza Fawzi Altakroury (Student) wrote: > > > The directory: fieldtrip-20111211\realtime\acquisition\biosemi > > > > The command: biosemi2ft config.txt ex.gdf > > > > Output : could not connect to buffer server at localhost:1972. > > > > Thank a lot > > > > > > > > On Wed, Dec 21, 2011 at 5:48 PM, Boris Reuderink < > b.reuderink at donders.ru.nl> wrote: > > Could you perhaps send me the exact command you executed? Tomorrow > > I'll have access to a windows machine --- maybe I can find out what > > went wrong. > > > > Best regards, > > > > Boris > > > > 2011/12/21 Hamza Fawzi Altakroury (Student) : > > > Thank you Boris. > > > > > > Well, I tried the default mode (just by specifying the configuration > file > > > and the gdf file in the cmd). But this message appeared. > > > Could you or anyone just tell me exactly what should I do or modify. > > > > > > Thanks a lot > > > > > > > > > On Wed, Dec 21, 2011 at 12:56 PM, Boris Reuderink > > > wrote: > > >> > > >> Dear Hamza, > > >> > > >> I think this message appears when you specify a specific buffer server > > >> to connect to. The biosemi2ft.exe can be run in two modes, 1) it > > >> starts an baked-in buffer server (default), or 2) it can can use a > > >> buffer server that is run in a separate process. > > >> > > >> The default mode is probably a good choice. You can select the default > > >> mode *by not specifying a server of port*. > > >> > > >> Best regards, > > >> > > >> Boris > > >> > > >> On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) > > >> wrote: > > >> > Hello, > > >> > > > >> > I'd tried to use the biosemi2ft function for realtime acquiring. > But the > > >> > following message appears: > > >> > > > >> > "Could not connect to buffer server at localhost: 1972". > > >> > > > >> > Should I change the Hostname and the Port, if yes what should they > be? > > >> > > > >> > Best, > > >> > > > >> > > > >> > -- > > >> > Hamza Fawzi Altakroury > > >> > Graduate student - MA > > >> > Faculty of Engineering and Natural Sciences > > >> > Sabancı University > > >> > > > >> > _______________________________________________ > > >> > fieldtrip mailing list > > >> > fieldtrip at donders.ru.nl > > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > >> > > >> _______________________________________________ > > >> fieldtrip mailing list > > >> fieldtrip at donders.ru.nl > > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > -- > > > Hamza Fawzi Altakroury > > > Graduate student - MA > > > Faculty of Engineering and Natural Sciences > > > Sabancı University > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Thu Dec 22 19:47:56 2011 From: lihqih at gmail.com (qi li) Date: Thu, 22 Dec 2011 13:47:56 -0500 Subject: [FieldTrip] artifact removal Message-ID: Hi, I am following the automatic_artifact_rejection tutorial but the interactive graphic window doesn't show. I am using fieldtrip 1014 version. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sat Dec 24 20:37:27 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sat, 24 Dec 2011 21:37:27 +0200 Subject: [FieldTrip] offset2time function Message-ID: Hello I tried to run the "ft_realtime_synchronous" function but, the following error appeared. ??? Undefined function or method 'offset2time' for input arguments of type 'double'. How can I get the offset2time function. Note: I read the "resampledata/offset2time" email and updated the folder but I same problem appeared. Best -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sun Dec 25 18:48:24 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sun, 25 Dec 2011 19:48:24 +0200 Subject: [FieldTrip] Reading online-data from a file Message-ID: Hello, I am using biosemi2ft for saving data into a gdf file online. I want to process the data as the acquiring is taking place. The "ft_read_event" function give me an easy way to get the triggers values. But as I think it reads the file each time from the beginning. Unfortunately the sread function which keep track of the file, does not extract the triggers' values. Any suggestions. -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sun Dec 25 20:46:33 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sun, 25 Dec 2011 21:46:33 +0200 Subject: [FieldTrip] Trigger values in data matrix Message-ID: Hello, I can't get the real trigger values if use sopen function (or ft_read_data), even after adding the min value -1.7281e+009 to get a positive values. Note: I plotted the triggers and their proportion is right but I can't get their exact values, what should I do. Best, -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From johemart at gmail.com Wed Dec 28 14:39:14 2011 From: johemart at gmail.com (=?ISO-8859-1?Q?Johann_Heinz_Mart=EDnez_Huartos?=) Date: Wed, 28 Dec 2011 14:39:14 +0100 Subject: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? In-Reply-To: <4EF2FA67.8010108@donders.ru.nl> References: <4EF2FA67.8010108@donders.ru.nl> Message-ID: Hi Roemer. Thnkx 4 ur answer. But Im using the fieldtrip version October 2011 and in this version cfg.highlightsymbol already appear just for ft_topoplotER() and cfg.markersymbol just appear for ft.singleplot() nor in ft_topoplotER(). In fact, I looking for a way to fill whichever marker i want to use for. (i.e. ^ > < o) not neccesarilly with '.' Do you know how to do that? thnx again for ur answer or comments. Johann On 22 December 2011 10:37, Roemer van der Meij wrote: > Hi Johann, > > If you update to the newest fieldtrip version, you can use the option > cfg.highlightsymbol or cfg.markersymbol to pick a marker that is filled, > like '.'. > > Best, > Roemer > > > > On 21-12-11 16:50, Johann Heinz Martínez Huartos wrote: > > Hello dear fieldtripers > > Currently im using ft_topoplotER() function in order to visualize a > cluster of channels in the head. But i cant fill the marker im using to > highlight those channels. I know that the commend to chage this opction in > matlab is markerfacecolor = 'k'. > if i want to fill it up with black color, but this option does not makes > anything happend and the markers are not filled. So, anyone knows how to > fill the marker in ft_topoplotER() funtion? > > Thanks > > -- > Atentamente: > Johann Martínez. M.Sc. > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Atentamente: Johann Martínez. M.Sc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Wed Dec 28 16:43:19 2011 From: lihqih at gmail.com (qi li) Date: Wed, 28 Dec 2011 10:43:19 -0500 Subject: [FieldTrip] combine sessions Message-ID: Hi, I have 3 identical sessions. Each of them has 40 trials. Is there any command to combine the 3 sessions into one 120 trials? Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at mac.com Wed Dec 28 16:48:39 2011 From: nathanweisz at mac.com (Nathan Weisz) Date: Wed, 28 Dec 2011 16:48:39 +0100 Subject: [FieldTrip] combine sessions In-Reply-To: References: Message-ID: hi, ft_appenddata.m is likely what you need. best, nathan On 28.12.2011, at 16:43, qi li wrote: > Hi, > > I have 3 identical sessions. Each of them has 40 trials. Is there any command to combine the 3 sessions into one 120 trials? > > Thanks! > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From adam at adamcsnyder.com Thu Dec 29 13:33:21 2011 From: adam at adamcsnyder.com (Adam C. Snyder) Date: Thu, 29 Dec 2011 07:33:21 -0500 Subject: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? In-Reply-To: References: Message-ID: <4EFC5E11.8090404@adamcsnyder.com> What about just using a command such as the following: set(findobj(gca,'type','hggroup'),'markerfacecolor','k'); -Adam C. Snyder P.s., on another note, I asked for some help some time ago with a problem I was having using triggers from BioSemi to instigate online analysis using ft_realtime_synchronous. Does anyone have any thoughts about that? I can restate the problem, if needed. Your help would be greatly appreciated. On 29-Dec-2011 06:00, fieldtrip-request at donders.ru.nl wrote: > Send fieldtrip mailing list submissions to > fieldtrip at donders.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at donders.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at donders.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: How to fill the markers in FT_TOPOPLOTER?? > (Johann Heinz Mart?nez Huartos) > 2. combine sessions (qi li) > 3. Re: combine sessions (Nathan Weisz) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 28 Dec 2011 14:39:14 +0100 > From: Johann Heinz Mart?nez Huartos > To: r.vandermeij at donders.ru.nl, Email discussion list for the > FieldTrip project > Subject: Re: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Roemer. > > Thnkx 4 ur answer. But Im using the fieldtrip version October 2011 and in > this version cfg.highlightsymbol already appear just for ft_topoplotER() > and cfg.markersymbol just appear for ft.singleplot() nor in > ft_topoplotER(). > In fact, I looking for a way to fill whichever marker i want to use for. > (i.e. ^> < o) not neccesarilly with '.' > > Do you know how to do that? > > thnx again for ur answer or comments. > > Johann > > > On 22 December 2011 10:37, Roemer van der Meij > wrote: > >> Hi Johann, >> >> If you update to the newest fieldtrip version, you can use the option >> cfg.highlightsymbol or cfg.markersymbol to pick a marker that is filled, >> like '.'. >> >> Best, >> Roemer >> >> >> >> On 21-12-11 16:50, Johann Heinz Mart?nez Huartos wrote: >> >> Hello dear fieldtripers >> >> Currently im using ft_topoplotER() function in order to visualize a >> cluster of channels in the head. But i cant fill the marker im using to >> highlight those channels. I know that the commend to chage this opction in >> matlab is markerfacecolor = 'k'. >> if i want to fill it up with black color, but this option does not makes >> anything happend and the markers are not filled. So, anyone knows how to >> fill the marker in ft_topoplotER() funtion? >> >> Thanks >> >> -- >> Atentamente: >> Johann Mart?nez. M.Sc. >> >> >> _______________________________________________ >> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> Roemer van der Meij M.Sc. >> PhD student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> P.O. Box 9104 >> 6500 HE Nijmegen >> The Netherlands >> Tel: +31(0)24 3655932 >> E-mail: r.vandermeij at donders.ru.nl >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > From johemart at gmail.com Thu Dec 29 16:44:03 2011 From: johemart at gmail.com (=?ISO-8859-1?Q?Johann_Heinz_Mart=EDnez_Huartos?=) Date: Thu, 29 Dec 2011 16:44:03 +0100 Subject: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? In-Reply-To: <4EFC5E11.8090404@adamcsnyder.com> References: <4EFC5E11.8090404@adamcsnyder.com> Message-ID: thnkx Adam. I,ll try to use that command. good luck with your question! Johann. On 29 December 2011 13:33, Adam C. Snyder wrote: > What about just using a command such as the following: > > set(findobj(gca,'type','**hggroup'),'markerfacecolor','**k'); > > -Adam C. Snyder > > P.s., on another note, I asked for some help some time ago with a problem > I was having using triggers from BioSemi to instigate online analysis using > ft_realtime_synchronous. Does anyone have any thoughts about that? I can > restate the problem, if needed. Your help would be greatly appreciated. > > On 29-Dec-2011 06:00, fieldtrip-request at donders.ru.**nlwrote: > >> Send fieldtrip mailing list submissions to >> fieldtrip at donders.ru.nl >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >> or, via email, send a message with subject or body 'help' to >> fieldtrip-request at donders.ru.**nl >> >> You can reach the person managing the list at >> fieldtrip-owner at donders.ru.nl >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of fieldtrip digest..." >> >> >> Today's Topics: >> >> 1. Re: How to fill the markers in FT_TOPOPLOTER?? >> (Johann Heinz Mart?nez Huartos) >> 2. combine sessions (qi li) >> 3. Re: combine sessions (Nathan Weisz) >> >> >> ------------------------------**------------------------------** >> ---------- >> >> Message: 1 >> Date: Wed, 28 Dec 2011 14:39:14 +0100 >> From: Johann Heinz Mart?nez Huartos >> To: r.vandermeij at donders.ru.nl, Email discussion list for the >> FieldTrip project >> Subject: Re: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? >> Message-ID: >> > gmail.com <75UhLSw at mail.gmail.com>> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Hi Roemer. >> >> Thnkx 4 ur answer. But Im using the fieldtrip version October 2011 and in >> this version cfg.highlightsymbol already appear just for ft_topoplotER() >> and cfg.markersymbol just appear for ft.singleplot() nor in >> ft_topoplotER(). >> In fact, I looking for a way to fill whichever marker i want to use for. >> (i.e. ^> < o) not neccesarilly with '.' >> >> Do you know how to do that? >> >> thnx again for ur answer or comments. >> >> Johann >> >> >> On 22 December 2011 10:37, Roemer van der Meij >> **wrote: >> >> Hi Johann, >>> >>> If you update to the newest fieldtrip version, you can use the option >>> cfg.highlightsymbol or cfg.markersymbol to pick a marker that is filled, >>> like '.'. >>> >>> Best, >>> Roemer >>> >>> >>> >>> On 21-12-11 16:50, Johann Heinz Mart?nez Huartos wrote: >>> >>> Hello dear fieldtripers >>> >>> Currently im using ft_topoplotER() function in order to visualize a >>> cluster of channels in the head. But i cant fill the marker im using to >>> highlight those channels. I know that the commend to chage this opction >>> in >>> matlab is markerfacecolor = 'k'. >>> if i want to fill it up with black color, but this option does not makes >>> anything happend and the markers are not filled. So, anyone knows how to >>> fill the marker in ft_topoplotER() funtion? >>> >>> Thanks >>> >>> -- >>> Atentamente: >>> Johann Mart?nez. M.Sc. >>> >>> >>> ______________________________**_________________ >>> fieldtrip mailing listfieldtrip at donders.ru.**nlhttp:// >>> mailman.science.ru.**nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> -- >>> Roemer van der Meij M.Sc. >>> PhD student >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognition >>> P.O. Box 9104 >>> 6500 HE Nijmegen >>> The Netherlands >>> Tel: +31(0)24 3655932 >>> E-mail: r.vandermeij at donders.ru.nl >>> >>> ______________________________**_________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >>> >>> >> >> > ______________________________**_________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip > -- Atentamente: Johann Martínez. M.Sc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eva.patai at psy.ox.ac.uk Thu Dec 29 23:22:16 2011 From: eva.patai at psy.ox.ac.uk (Zita Eva Patai) Date: Thu, 29 Dec 2011 22:22:16 +0000 Subject: [FieldTrip] clusterplot not plotting for gradiometeres Message-ID: Dear All (happy holidays) when plotting significant clusters of tf/erf output of permutation test, i can plot sig. clusters for magnetometers but not gradiometers please see attached image...there are indications that there should be highlights...yet not visible...i am using exact same script, everything, difference is the layout file i use (neuromag306mag vs neuromag306cmb) thank you! z -- Zita Patai DPhil Candidate, Experimental Psychology University of Oxford bcl.psy.ox.ac.uk/people/zita-eva-patai/ eva.patai at psy.ox.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: wherearethehighlights Type: application/octet-stream Size: 30527 bytes Desc: not available URL: From marco.rotonda at gmail.com Fri Dec 30 13:07:15 2011 From: marco.rotonda at gmail.com (Marco Rotonda) Date: Fri, 30 Dec 2011 13:07:15 +0100 Subject: [FieldTrip] Strange path problem? Message-ID: Hi fieldtrippers, yesterday I moved to a win7 64bit version, installed latest matlab (2011b) and updated fieldtrip to the latest version (fieldtrip-20111223). After setting up all I tried to run a script I used until yesterday and I get a strange error: Invalid MEX-file 'C:\Program Files\fieldtrip\fileio\private\read_16bit.mexw64': The specified module could not be found. fileio is in the path, so I thought it was about the x86 program and I moved fieldtrip there, but same result: Invalid MEX-file 'C:\Program Files (x86)\fieldtrip\fileio\private\read_16bit.mexw64': The specified module could not be found. I think I miss a stupid thing. Sorry to disturb you, Marco From bibi.raquel at gmail.com Fri Dec 30 15:18:12 2011 From: bibi.raquel at gmail.com (Raquel Bibi) Date: Fri, 30 Dec 2011 09:18:12 -0500 Subject: [FieldTrip] Strange path problem? In-Reply-To: References: Message-ID: Hi, Marco. As a first test I would run "mbuild -setup" at the Matlab command line and select a C/C++ compiler. If this doesn't fix problem see: http://fieldtrip.fcdonders.nl/faq/how_can_i_compile_the_mex_files_on_64_bit_windows. This should fix the problems your having. Best, Raquel On Fri, Dec 30, 2011 at 7:07 AM, Marco Rotonda wrote: > Hi fieldtrippers, > yesterday I moved to a win7 64bit version, installed latest matlab > (2011b) and updated fieldtrip to the latest version > (fieldtrip-20111223). > After setting up all I tried to run a script I used until yesterday > and I get a strange error: > > Invalid MEX-file 'C:\Program > Files\fieldtrip\fileio\private\read_16bit.mexw64': The > specified module could not be found. > > fileio is in the path, so I thought it was about the x86 program and I > moved fieldtrip there, but same result: > > Invalid MEX-file 'C:\Program Files > (x86)\fieldtrip\fileio\private\read_16bit.mexw64': The > specified module could not be found. > > I think I miss a stupid thing. > > Sorry to disturb you, > > Marco > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Fri Dec 30 17:04:35 2011 From: lihqih at gmail.com (qi li) Date: Fri, 30 Dec 2011 11:04:35 -0500 Subject: [FieldTrip] question of planar gradient decomposition Message-ID: Hi, We have a axial ctf 1st order gradiometer. So it measures the axial gradient of the the magnetic field-(dB/dr). If I do the planar gradient transformation by 'sincos ,distance,' your codes looks like computing d^2B/d(theta) and d^2B/d(phi) where theta and phi are azimuth angle and polar angle respectively. It is well known in a spherical coordinate, there is no way to derive the tangential components from axial component, so what is the purpose of your linear transformation? Compared to neuromag which does pick up the planar gradient, is there any advantage for you to do so? Thanks a lot! Happy new year! Qi * * -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.rotonda at gmail.com Fri Dec 30 17:20:34 2011 From: marco.rotonda at gmail.com (Marco Rotonda) Date: Fri, 30 Dec 2011 17:20:34 +0100 Subject: [FieldTrip] Strange path problem? In-Reply-To: References: Message-ID: Thanks, I know it was a quite simple problem... sorry to disturb not reading the faq :( 2011/12/30 Raquel Bibi : > Hi, Marco. > > As a first test I would run "mbuild -setup" at the Matlab command line and > select a C/C++ compiler.  If this doesn't fix problem see: > > http://fieldtrip.fcdonders.nl/faq/how_can_i_compile_the_mex_files_on_64_bit_windows. >  This should fix the problems your having. > > Best, > > Raquel > > On Fri, Dec 30, 2011 at 7:07 AM, Marco Rotonda > wrote: >> >> Hi fieldtrippers, >> yesterday I moved to a win7 64bit version, installed latest matlab >> (2011b) and updated fieldtrip to the latest version >> (fieldtrip-20111223). >> After setting up all I tried to run a script I used until yesterday >> and I get a strange error: >> >> Invalid MEX-file 'C:\Program >> Files\fieldtrip\fileio\private\read_16bit.mexw64': The >> specified module could not be found. >> >> fileio is in the path, so I thought it was about the x86 program and I >> moved fieldtrip there, but same result: >> >> Invalid MEX-file 'C:\Program Files >> (x86)\fieldtrip\fileio\private\read_16bit.mexw64': The >> specified module could not be found. >> >> I think I miss a stupid thing. >> >> Sorry to disturb you, >> >> Marco >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Christos.Papadelis at childrens.harvard.edu Sat Dec 31 18:31:18 2011 From: Christos.Papadelis at childrens.harvard.edu (Papadelis, Christos) Date: Sat, 31 Dec 2011 17:31:18 +0000 Subject: [FieldTrip] Special issue in Advances on Human-Computer Interaction In-Reply-To: <876E0E5B34DB6A4DBD0E65B9091B4350027E0A@CHEXMBX2A.CHBOSTON.ORG> References: <876E0E5B34DB6A4DBD0E65B9091B4350027CAD@CHEXMBX2A.CHBOSTON.ORG>, <876E0E5B34DB6A4DBD0E65B9091B4350027E0A@CHEXMBX2A.CHBOSTON.ORG> Message-ID: <876E0E5B34DB6A4DBD0E65B9091B4350027E95@CHEXMBX2A.CHBOSTON.ORG> Dear Collegues, We would like to draw your attention to the following special issue in Advances on Human-Computer Interaction journal, entitled "Using Brain Waves to Control Computers and Machines" (http://www.hindawi.com/journals/ahci/si/ubw/). We invite authors to submit original research and review articles that explore all aspects of Brain Computer Interfaces (BCIs). My best wishes for Happy New Year. On behalf of all the Editors Christos Papadelis, PhD Instructor in Neurology, Harvard Medical School MEG Lab Manager, Children's Hospital Boston 9 Hope Avenue, Waltham, MA 02453, USA christos.papadelis at childrens.harvard.edu Phone: +1-781-216-1128 Fax: +1-781-216-1172 From s.bogels at psy.gla.ac.uk Thu Dec 1 10:34:20 2011 From: s.bogels at psy.gla.ac.uk (=?UTF-8?B?U2FyYSBCw7ZnZWxz?=) Date: Thu, 01 Dec 2011 09:34:20 +0000 Subject: [FieldTrip] second-level statistical inference In-Reply-To: <007e01ccaf95$536c0dc0$fa442940$@maris@psych.ru.nl> References: <744936625.46871.1322211858651.JavaMail.root@sculptor.zimbra.ru.nl> <4ECF8144.4010706@psy.gla.ac.uk> <007e01ccaf95$536c0dc0$fa442940$@maris@psych.ru.nl> Message-ID: <4ED74A1C.40701@psy.gla.ac.uk> Hi Eric, I understand that is another option. However, I do not see how to look at an interaction between two variables in this way. Do you have any advice if I want to do that? Thanks, Sara On 30/11/2011 19:21, Eric Maris wrote: > Hi Sara, > > > I'm replying to your initial question (somewhere below in this email). > > Why don't you calculate per-subject averages in the two within-subject > experimental conditions (using timelockgrandaverage with > keepindividual='yes'), and then do your second-level inference on these > averages? See also the Fieldtrip statistics tutorials. > > Best, > > Eric Maris > > >> -----Original Message----- >> From: Sara Bögels [mailto:s.bogels at psy.gla.ac.uk] >> Sent: vrijdag 25 november 2011 12:52 >> To: fieldtrip at donders.ru.nl >> Subject: Re: [FieldTrip] second-level statistical inference >> >> Hi Arjen, >> >> Thank you very much for your answer. That sounds good, but step 2 does >> not work straightforwardly, since matlab gives the error message that it >> cannot find an avg field (which would not be in the structure created by >> ft_timelockstatistics). Just saying cfg.parameter = 'stat' does not >> work. I tried to get around that by inserting an avg field which is the >> same as the stat field for each participant. Matlab also asked for an >> fsample field, which I inserted from an earlier datafile. Then it >> worked. Is it ok to do this? >> >> I did step 3 as well, using the field individual (which you get by >> keepindividuals = 'yes'). In step 4, I should just use cfg.statistic = >> 'depsamplesT', right (because the variables are within subject)? >> >> Thank you! >> Sara >> >> On 25/11/2011 09:04, Stolk, A. wrote: >>> Hi Sara, >>> >>> If I understand correctly, you want to test intra-subject differences >> (between conditions) at the second level? This would require the following >> steps: >>> 1) subject-level statistics, which you have done already >>> >>> 2) grandaverage all these, with keepindividuals=yes. >>> >>> 3) copy the output of the grandaverage (into a dummy variable), and >> replace the fields containing the subject T-values with zeros (for >> timelock >> data this may be the trial fields?) >>> 4) again timelockstatistics, as in step 1, now with the variables >>> following >> step 3. this should give you the resulting statistics of contrasting >> intra- >> subject differences vs. null at the group level. >>> Hope this helps, >>> >>> Arjen >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ----- "Sara Bögels" schreef: >>> >>>> Van: "Sara Bögels" >>>> Aan: fieldtrip at donders.ru.nl >>>> Verzonden: Donderdag 24 november 2011 15:49:17 >>>> Onderwerp: [FieldTrip] second-level statistical inference >>>> >>>> Hi all, >>>> >>>> I have been trying to do second-level statistical inference (as >>>> described in one of the FAQs) on ERFs, but I am not sure whether I am >>>> >>>> doing everything correctly. >>>> >>>> In the first step I calculate the T-values for the difference between >>>> >>>> two conditions (twice), which are between items, with >>>> ft_timelockstatistics. I put the output of all participants in a cell >>>> >>>> (called 'stat1a' and 'stat1b'). (I tried to use >>>> ft_timelockgrandaverage >>>> to combine the subjects together but it needs a field avg). >>>> >>>> Then I use ft_timelockstatistics again but subject level. I first >>>> want >>>> to look at the difference between the two conditions. This difference >>>> is >>>> reflected in the T-values of the first step so I create a dummy which >>>> is >>>> the same as 'stat1' but I replace all the values in the field 'stat' >>>> per >>>> participant with zeros. Then I call (with appropriate cfg >>>> parameters): >>>> >>>> stat2a = ft_timelockstatistics(cfg,stat1a{:},dummy{:}); >>>> stat2b = ft_timelockstatistics(cfg,stat1b{:},dummy{:}); >>>> >>>> To compare the two differences (stat1a and stat1b) and thereby look at >>>> >>>> an interaction, I call: >>>> >>>> stat2a-b = ft_timelockstatistics(cfg,stat1a{:},stat1b{:}); >>>> >>>> I am uncertain whether the dummy works (or is there a way to compare >>>> the >>>> t-values to zero directly?) and whether the stat1a{:} trick works with >>>> >>>> ft_timelockstatistics. >>>> >>>> Thanks in advance for your answer. >>>> >>>> Sara >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From max-philipp.stenner at med.ovgu.de Thu Dec 1 14:22:52 2011 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 01 Dec 2011 13:22:52 +0000 Subject: [FieldTrip] readCTFds Message-ID: Dear fieldtrip users, as a beginner I am encountering a rather fundamental problem even when trying to read the tutorial data (Subject01.ds): ft_read_data reports readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) and Matlab adds index exceeding matrix dimension errors ft_read_hdr reports nTrials = -1 The same happens with my own CTF data. I would be very grateful for any help on this very basic problem thanks! Best Max From jan.schoffelen at donders.ru.nl Thu Dec 1 14:54:08 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 1 Dec 2011 14:54:08 +0100 Subject: [FieldTrip] readCTFds In-Reply-To: References: Message-ID: <9F142CD3-12CB-4184-AF91-3233D42AE3FA@donders.ru.nl> Dear Max, Before we can think along with you, could you please give some more details? Some basic things such as the fieldtrip version you are using, matlab version and operating system? Thanks, Jan-Mathijs On Dec 1, 2011, at 2:22 PM, Stenner, Max-Philipp wrote: > Dear fieldtrip users, > > > > as a beginner I am encountering a rather fundamental problem even when trying to read the tutorial data (Subject01.ds): > > > > ft_read_data reports > > > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > > > and Matlab adds index exceeding matrix dimension errors > > > > ft_read_hdr reports > > > > nTrials = -1 > > > > The same happens with my own CTF data. > > > > I would be very grateful for any help on this very basic problem > > > > thanks! > > Best > > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Heng-RuMay.Tan at glasgow.ac.uk Thu Dec 1 15:52:52 2011 From: Heng-RuMay.Tan at glasgow.ac.uk (May (Heng-Ru May TAN)) Date: Thu, 01 Dec 2011 14:52:52 +0000 Subject: [FieldTrip] Grad and labels Message-ID: <4ED794C4.5070909@glasgow.ac.uk> Hello I would like to plot the grad.pnt for a few channels but realised that there are fewer labels (271) than grad.pnt rows (276) Presumably some of the channels have more than 1 grad.pnt > D = > > hdr: [1x1 struct] > label: {248x1 cell} > time: {1x9 cell} > trial: {1x9 cell} > fsample: 1.0172e+003 > grad: [1x1 struct] > cfg: [1x1 struct] > > >> D.grad > > ans = > > pnt: [276x3 double] > ori: [276x3 double] > tra: [271x276 double] > label: {271x1 cell} > unit: 'm' > balance: [1x1 struct] But how do the grad labels correspond to the grad.pnt with the numbers don't match? Can someone help? Thanks! May The above was derived using the following: > cfg = []; > > cfg.subjNUM = subjNUM; > cfg.irun=irun; > > cfg.headerfile = 'c,rfDC'; > cfg.datafile = cfg.headerfile; > cfg.trialfun ='trialfun_general'; > cfg.channel={'MEG'}; > cfg.continuous='yes'; > cfg.trialdef.eventtype = '?'; > > cfg=ft_definetrial(cfg); %--->cfg.events > cfg.header = ft_read_header(cfg.headerfile); > % just to be sure > cfg = rmfield(cfg,'trl'); > > > %% specify 'trial' information for 'epoching' > cfg.detrend='yes'; %no other filtering at the moment. > > cfg.trialdef.stimulusSETnum = [iset]; > cfg.trialdef.eventtype = 'PostStimTriggerIdx'; %% > cfg.trialdef.eventinfo = 'PostStimSampleTime'; > cfg.trialdef.eventvalue = [iset].*2 + 128; > > cfg.trialdef.response_time=[1]; % to include RXNtime in the > definetrial procedure... > cfg.trialdef.CorrectWrong = [1]; %only correct ones > > cfg.trialdef.prestim = 2; % duration in secs before '0' > cfg.trialdef.poststim = 2; % duration in secs after '0' > > cfg.trialfun ='trialfun_readEventgetRespInfo'; %%CHANGE 3rd > Column!!! > > cfg=ft_definetrial(cfg); > % cfg.trl ==//// [begsam endsam off runN stimN ] > > D=ft_preprocessing(cfg); From Heng-RuMay.Tan at glasgow.ac.uk Thu Dec 1 16:08:56 2011 From: Heng-RuMay.Tan at glasgow.ac.uk (May (Heng-Ru May TAN)) Date: Thu, 01 Dec 2011 15:08:56 +0000 Subject: [FieldTrip] change in ft_definetrial event output? Message-ID: <4ED79888.4020907@glasgow.ac.uk> Hi again, Another question -- possibly me missing out on all the updates! Was wondering if there has been changes to how events are output in newer versions of FT because previously using fieldtrip-20100419 > cfg = > > subjNUM: 1 > irun: 1 > headerfile: 'c,rfDC' > datafile: 'c,rfDC' > trialfun: 'trialfun_general' > channel: {'MEG'} > continuous: 'yes' > trialdef: [1x1 struct] > trackconfig: 'off' > checkconfig: 'loose' > checksize: 100000 > _ event: [850x1 struct] > _ trl: [] > version: [1x1 struct] > header: [1x1 struct] Now the newer versions only give _event: [849x1 struct]_ Is the 'trial' heading in the previous first row removed by default now? Thanks, May -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Thu Dec 1 16:15:56 2011 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Thu, 01 Dec 2011 15:15:56 +0000 Subject: [FieldTrip] readCTFds In-Reply-To: References: Message-ID: Dear all, in addition to my email sent earlier today (see below) here's some information on the OS, fieldtrip and MatLab versions: Windows7 Fieldtrip version 20111130 (20111129 caused the same error) Matlab R2011a Whereas readCTFds reports 'Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file)' a direct call to the dir command of the .meg4 file returns ' bytes: 179071208' for the number of trials ft_read_header('Subject01.ds') returns ' nTrials: -1' Thanks, best Max ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]" im Auftrag von "Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de] Gesendet: Donnerstag, 1. Dezember 2011 14:22 Bis: fieldtrip at donders.ru.nl Betreff: [FieldTrip] readCTFds Dear fieldtrip users, as a beginner I am encountering a rather fundamental problem even when trying to read the tutorial data (Subject01.ds): ft_read_data reports readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) and Matlab adds index exceeding matrix dimension errors ft_read_hdr reports nTrials = -1 The same happens with my own CTF data. I would be very grateful for any help on this very basic problem thanks! Best Max _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From b.reuderink at donders.ru.nl Thu Dec 1 17:58:45 2011 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Thu, 1 Dec 2011 17:58:45 +0100 Subject: [FieldTrip] Error in Java buffer reader and fakebiosemiclient.cc In-Reply-To: References: Message-ID: Dear Jacob, I have created bug 1209 (http://bugzilla.fcdonders.nl/show_bug.cgi?id=1209) for your issue. Could you provide some additional details to reproduce the bug on that page? And, could you (perhaps privately --- bypassing the list) explain how you are planning to use the FieldTrip buffer? We might find a workaround for you problem. Best regards, Boris On Tue, Nov 29, 2011 at 12:13 AM, Jacob Martin wrote: > Ok, seems like it has to do with exceeding the maximum number of > samples.  Not sure what to do here though yet: > > http://code.google.com/p/fieldtrip/source/browse/trunk/realtime/buffer/src/dmarequest.c?r=1218#413 > > On Mon, Nov 28, 2011 at 6:10 PM, Jacob Martin wrote: >> Hi, >> >> After letting the server run for a while (see below size at 512hz), I >> get an "err3": >> >> data: >> size = 176960 x 34 >> dmarequest: err3 >> Exception in thread "main" java.io.IOException: Error returned from >> FieldTrip buffer server. >>        at nl.fcdonders.fieldtrip.BufferClient.readResponse(BufferClient.java:646) >>        at nl.fcdonders.fieldtrip.BufferClient.getEvents(BufferClient.java:386) >>        at testclient.main(testclient.java:71) >> >> >> >> Any ideas? >> >> Thanks, >> Jake >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Fri Dec 2 10:03:40 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 02 Dec 2011 10:03:40 +0100 Subject: [FieldTrip] readCTFds In-Reply-To: References: Message-ID: <4ED8946C.2050209@donders.ru.nl> Hi Max, I usually encounter similar problems when CTF data is not fully saved, i.e. aborted the saving and forgot to click on 'OK' in the next dialog or something else went wrong. Maybe ther went something wrong when downloading the data? Since it says 0 bytes in dir, it could maybe also be that you something more basic wrong. Just to be sure, you could check whether Subject01.ds is a folder and whether it contains all the relevant files, and none of these have size 0. Best, Jörn On 12/1/2011 4:15 PM, Stenner, Max-Philipp wrote: > Dear all, > > in addition to my email sent earlier today (see below) here's some information on the OS, fieldtrip and MatLab versions: > > Windows7 > Fieldtrip version 20111130 (20111129 caused the same error) > Matlab R2011a > > Whereas readCTFds reports > > 'Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file)' > > a direct call to the dir command of the .meg4 file returns > > ' bytes: 179071208' > > for the number of trials ft_read_header('Subject01.ds') returns > > ' nTrials: -1' > > Thanks, > best > Max > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]" im Auftrag von"Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de] > Gesendet: Donnerstag, 1. Dezember 2011 14:22 > Bis: fieldtrip at donders.ru.nl > Betreff: [FieldTrip] readCTFds > > Dear fieldtrip users, > > > > as a beginner I am encountering a rather fundamental problem even when trying to read the tutorial data (Subject01.ds): > > > > ft_read_data reports > > > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > > > and Matlab adds index exceeding matrix dimension errors > > > > ft_read_hdr reports > > > > nTrials = -1 > > > > The same happens with my own CTF data. > > > > I would be very grateful for any help on this very basic problem > > > > thanks! > > Best > > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From sonjasuntrup at uni-muenster.de Fri Dec 2 12:16:20 2011 From: sonjasuntrup at uni-muenster.de (Sonja Suntrup) Date: Fri, 02 Dec 2011 12:16:20 +0100 (CET) Subject: [FieldTrip] source statistics, group level Message-ID: Dear fieldtrip users, I would like to do sourcestatistics on a group level with meg data. I have a pre and post intervention measurement for each of my 21 subjects (within-subjects design). After source reconstruction using an LCMV beamformer and volume normalization I calculated the sourcegrandaverage for the pre and post condition with the parameter cfg.keepindividual = 'yes'. However, when I use the grandaverage results in ft_sourcestatistics in the configuration shown below and plot the result I just get a blank anatomical mri. Do I have to set any additional parameters or do I make a general mistake? Whould you recommend to use a cluster-based permutation test comparable to ft_timelockstatistics and would I have to set the same parameters in ft_sourcestatistics then? cfg=[]; cfg.dim = grandAVGsourcePre.dim; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.parameter = 'avg.pow'; cfg.correctm = 'cluster'; cfg.numrandomization = 100; cfg.alpha = 0.05; cfg.tail = 0; nsubj=length(sourcePre.trial); cfg.design(1,:) = [1:nsubj 1:nsubj]; cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2]; cfg.uvar = 1; cfg.ivar = 2; stat = ft_sourcestatistics(cfg, grandAVGsourcePre, grandAVGsourcePost); Your help is greatly appreciated! Best, Sonja -- Dr. med. Sonja Suntrup Institute for Biomagnetism and Biosignalanalysis University of Muenster Malmedyweg 15 48149 Münster, Germany From max-philipp.stenner at med.ovgu.de Fri Dec 2 12:28:38 2011 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Fri, 02 Dec 2011 11:28:38 +0000 Subject: [FieldTrip] readCTFds In-Reply-To: <4ED8946C.2050209@donders.ru.nl> References: <4ED8946C.2050209@donders.ru.nl> Message-ID: Hi Joern, thank you very much for your reply, the (rather trivial) problem turned out to be indeed that the path wasn't added correctly, best Max ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]" im Auftrag von ""Jörn M. Horschig" [jm.horschig at donders.ru.nl] Gesendet: Freitag, 2. Dezember 2011 10:03 Bis: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] readCTFds Hi Max, I usually encounter similar problems when CTF data is not fully saved, i.e. aborted the saving and forgot to click on 'OK' in the next dialog or something else went wrong. Maybe ther went something wrong when downloading the data? Since it says 0 bytes in dir, it could maybe also be that you something more basic wrong. Just to be sure, you could check whether Subject01.ds is a folder and whether it contains all the relevant files, and none of these have size 0. Best, Jörn On 12/1/2011 4:15 PM, Stenner, Max-Philipp wrote: > Dear all, > > in addition to my email sent earlier today (see below) here's some information on the OS, fieldtrip and MatLab versions: > > Windows7 > Fieldtrip version 20111130 (20111129 caused the same error) > Matlab R2011a > > Whereas readCTFds reports > > 'Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file)' > > a direct call to the dir command of the .meg4 file returns > > ' bytes: 179071208' > > for the number of trials ft_read_header('Subject01.ds') returns > > ' nTrials: -1' > > Thanks, > best > Max > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]" im Auftrag von"Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de] > Gesendet: Donnerstag, 1. Dezember 2011 14:22 > Bis: fieldtrip at donders.ru.nl > Betreff: [FieldTrip] readCTFds > > Dear fieldtrip users, > > > > as a beginner I am encountering a rather fundamental problem even when trying to read the tutorial data (Subject01.ds): > > > > ft_read_data reports > > > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > > > and Matlab adds index exceeding matrix dimension errors > > > > ft_read_hdr reports > > > > nTrials = -1 > > > > The same happens with my own CTF data. > > > > I would be very grateful for any help on this very basic problem > > > > thanks! > > Best > > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Jan.Hirschmann at med.uni-duesseldorf.de Fri Dec 2 18:20:43 2011 From: Jan.Hirschmann at med.uni-duesseldorf.de (Jan.Hirschmann at med.uni-duesseldorf.de) Date: Fri, 2 Dec 2011 18:20:43 +0100 Subject: [FieldTrip] coherence normalization Message-ID: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> Hi community, Regarding this thread on suppressing the reference dipole from 2004, what is the current status? Has anybody found and implemented a recommendable way to project out activity from unwanted dipoles? Thank you for any comments/opinions! Best, Jan Hirschmann On 21 Oct 2004, at 17:23, Tom Holroyd wrote: > When running a coherence volume using a reference dipole, one > naturally expects the coherence will be high around the reference > dipole. > > This effect tends to dominate the images. > > Is there a way to normalize the coherence volume to eliminate > this effect? Perhaps by dividing by the coherence in a "control" > state? Hi Tom, The dominating effect of the refdip is indeed very problematic. I just happened to have discussed this with Joachim Gross, and I have included our email exchange below. Please first read that ... Basically I agree with Joachim, and I don't trust the supdip that is implemented in FieldTrip's sourceanalysis function. Better test and map the significance of the difference in coherence between two conditions using randomization of the trials before the coherence is beamed (that is implemented in sourceanalysis + sourcestatistics). Robert -------------------------------------------------------------------- my question to Joachim was ---------------------------------------------------------------------- Begin forwarded message: > From: Robert Oostenveld > > Date: 1 October 2004 10:26:02 GMT+02:00 > To: Joachim Gross > > Subject: dipole suppression > > Hi Joachim, > > What I always still had to ask you is how you do supression of dipoles > in DICS, especially in the case of coherence imaging. I have thought > of two ways of projecting them out: > > 1) compute supdip leadfield and its projection on the COV/CSD matrix, > then project it out of the COV/CSD matrix (which looses 2 or 3 from > its rank). > > 2) compute supdip leadfield and add it to the leadfield of the dipole > with which is scanned (scandip). Subsequently compute the source > COV/CSD on those 6 leadfield components and select the 3x3 submatrix > that corresponds with the scandip to continue the computations with. > > Both methods don't really gave me very convincing results. A third > approach would be to add the supdip leadfield to the (identity) noise > matrix and project it through the filters. Then nai=pow/noise is > corrected for the presence of the supdip, but that does not result in > a supressed source coherence distribution. What is your idea or > approach for this? > > best regards > Robert > ---------------------------------------------------------------------- and his answer (Joachim, I hope you don't mind me sharing this on the list) ---------------------------------------------------------------------- Begin forwarded message: > From: Joachim Gross > > Date: 14 October 2004 17:20:45 GMT+02:00 > To: "robert.oostenveld at fcdonders.kun.nl " > > > Subject: dipole suppression > > Hi Robert, > > sorry for the delay. > > The dipole suppression is indeed a complex issue. > We first implemented it because it facilitates visualization and the > exact identification of the first > strongest local maxima. > Nevertheless, it is quite dangerous because the map is (locally) > distorted in a non-trivial way. > We are now trying to move away from suppressing the sources. I think > it would be better to identify the > significant local maxima (significance based on > randomization/permutation). > But what we are doing at the moment is your approach 3. > So we add the supdip leadfield to the noise covariance matrix and look > at pow/noise. > > For coherence we are basically doing the same thing. > So we divide the coherence map (or actually the map of cross spectral > densities) by a noise map > that peaks at the locations of the "unwanted" dipoles. > With this procedure we loose absolute coherence values. > This is not so important for us since we get the absolute values from > the coherence and partial coherence spectra > that are computed afterwards. > It works surprisingly well but should be used with care. > > A better approach would be to map partial coherence (with the unwanted > dipoles removed). But we have not implemented > this so far. > > Again, I think it is better to have regions of interest identified by > their significance. > > Joachim ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. Jan Hirschmann MSc. Neuroscience Insititute of Clinical Neuroscience and Medical Psychology Heinrich Heine University Duesseldorf Universitaetsstr. 1 40225 Duesseldorf Tel: 0049 - (0)211 - 81 - 18415 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at kurage.nimh.nih.gov Fri Dec 2 18:52:07 2011 From: tomh at kurage.nimh.nih.gov (Tom Holroyd (NIH/NIMH) [E]) Date: Fri, 02 Dec 2011 12:52:07 -0500 Subject: [FieldTrip] coherence normalization In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> Message-ID: <4ED91047.6050107@kurage.nimh.nih.gov> The solution I have adopted is to always look at coherence contrasts. Make two volumes using the same reference dipole in two different conditions, then subtract the volumes. The self-coherence of the reference will disappear. Mostly. Then use stats, like a U-test. Jan.Hirschmann at med.uni-duesseldorf.de wrote: > Hi community, > > > > Regarding this thread on suppressing the reference dipole from 2004, what is the current status? Has anybody found and implemented a recommendable way to project out activity from unwanted dipoles? Thank you for any comments/opinions! > > > > Best, > > Jan Hirschmann > > > > > > > > On 21 Oct 2004, at 17:23, Tom Holroyd wrote: > > > >>/ When running a coherence volume using a reference dipole, one/ > >>/ naturally expects the coherence will be high around the reference/ > >>/ dipole./ > >>/ / > >>/ This effect tends to dominate the images./ > >>/ / > >>/ Is there a way to normalize the coherence volume to eliminate/ > >>/ this effect? Perhaps by dividing by the coherence in a "control"/ > >>/ state?/ > > > > Hi Tom, > > > > The dominating effect of the refdip is indeed very problematic. I just > > happened to have discussed this with Joachim Gross, and I have included > > our email exchange below. Please first read that ... > > > > Basically I agree with Joachim, and I don't trust the supdip that is > > implemented in FieldTrip's sourceanalysis function. Better test and map > > the significance of the difference in coherence between two conditions > > using randomization of the trials before the coherence is beamed (that > > is implemented in sourceanalysis + sourcestatistics). > > > > Robert > > > > -------------------------------------------------------------------- > > my question to Joachim was > > ---------------------------------------------------------------------- > > > > Begin forwarded message: > > > >>/ From: Robert Oostenveld //>/ > >>/ Date: 1 October 2004 10:26:02 GMT+02:00/ > >>/ To: Joachim Gross //>/ > >>/ Subject: dipole suppression/ > >>/ / > >>/ Hi Joachim,/ > >>/ / > >>/ What I always still had to ask you is how you do supression of dipoles/ > >>/ in DICS, especially in the case of coherence imaging. I have thought/ > >>/ of two ways of projecting them out:/ > >>/ / > >>/ 1) compute supdip leadfield and its projection on the COV/CSD matrix,/ > >>/ then project it out of the COV/CSD matrix (which looses 2 or 3 from/ > >>/ its rank)./ > >>/ / > >>/ 2) compute supdip leadfield and add it to the leadfield of the dipole/ > >>/ with which is scanned (scandip). Subsequently compute the source/ > >>/ COV/CSD on those 6 leadfield components and select the 3x3 submatrix/ > >>/ that corresponds with the scandip to continue the computations with./ > >>/ / > >>/ Both methods don't really gave me very convincing results. A third/ > >>/ approach would be to add the supdip leadfield to the (identity) noise/ > >>/ matrix and project it through the filters. Then nai=pow/noise is/ > >>/ corrected for the presence of the supdip, but that does not result in/ > >>/ a supressed source coherence distribution. What is your idea or/ > >>/ approach for this?/ > >>/ / > >>/ best regards/ > >>/ Robert/ > >>/ / > > > > ---------------------------------------------------------------------- > > and his answer (Joachim, I hope you don't mind me sharing this on the > > list) > > ---------------------------------------------------------------------- > > > > Begin forwarded message: > > > >>/ From: Joachim Gross //>/ > >>/ Date: 14 October 2004 17:20:45 GMT+02:00/ > >>/ To: "//robert.oostenveld at fcdonders.kun.nl //"/ > >>/ //>/ > >>/ Subject: dipole suppression/ > >>/ / > >>/ Hi Robert,/ > >>/ / > >>/ sorry for the delay./ > >>/ / > >>/ The dipole suppression is indeed a complex issue./ > >>/ We first implemented it because it facilitates visualization and the/ > >>/ exact identification of the first/ > >>/ strongest local maxima./ > >>/ Nevertheless, it is quite dangerous because the map is (locally)/ > >>/ distorted in a non-trivial way./ > >>/ We are now trying to move away from suppressing the sources. I think/ > >>/ it would be better to identify the/ > >>/ significant local maxima (significance based on/ > >>/ randomization/permutation)./ > >>/ But what we are doing at the moment is your approach 3./ > >>/ So we add the supdip leadfield to the noise covariance matrix and look/ > >>/ at pow/noise./ > >>/ / > >>/ For coherence we are basically doing the same thing./ > >>/ So we divide the coherence map (or actually the map of cross spectral/ > >>/ densities) by a noise map/ > >>/ that peaks at the locations of the "unwanted" dipoles./ > >>/ With this procedure we loose absolute coherence values./ > >>/ This is not so important for us since we get the absolute values from/ > >>/ the coherence and partial coherence spectra/ > >>/ that are computed afterwards./ > >>/ It works surprisingly well but should be used with care./ > >>/ / > >>/ A better approach would be to map partial coherence (with the unwanted/ > >>/ dipoles removed). But we have not implemented/ > >>/ this so far./ > >>/ / > >>/ Again, I think it is better to have regions of interest identified by/ > >>/ their significance./ > >>/ / > >>/ Joachim/ > > > > > > ---------------------------------------------------------------------- > > Robert Oostenveld, PhD > > Center for Sensory-Motor Interaction (SMI) > > Aalborg University, Denmark > > > > and > > > > F.C. Donders Centre for Cognitive Neuroimaging > > University Nijmegen > > P.O. Box 9101 > > NL-6500 AH Nijmegen > > The Netherlands > > > > Tel: +31 (0)24 3619695 > > Fax: +31 (0)24 3610989 > > ---------------------------------------------------------------------- > > N.B. Starting from 1 September 2004, the University of Nijmegen has > > changed its name to Radboud University Nijmegen. All web- and > > email-addresses ending in ".kun.nl" should therefore be changed into > > ".ru.nl". Please update your address book and links. > > > > > > Jan Hirschmann > > MSc. Neuroscience > > Insititute of Clinical Neuroscience and Medical Psychology > > Heinrich Heine University Duesseldorf > > Universitaetsstr. 1 > 40225 Duesseldorf > > Tel: 0049 - (0)211 - 81 - 18415 > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- "The test of a first-rate intelligence is the ability to hold two opposed ideas in the mind at the same time, and still retain the ability to function." — F. Scott Fitzgerald From jan.schoffelen at donders.ru.nl Fri Dec 2 19:49:33 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 2 Dec 2011 19:49:33 +0100 Subject: [FieldTrip] coherence normalization In-Reply-To: <4ED91047.6050107@kurage.nimh.nih.gov> References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> <4ED91047.6050107@kurage.nimh.nih.gov> Message-ID: <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> Hi Jan, Tom and the rest, I agree with Tom, but would like to strongly emphasize that differences in power across conditions more often than not will affect the coherence landscape in a non-trivial way. This does not only count for power changes in the reference dipole, but also for changes in power for third party dipoles (i.e. any potential other source). Therefore the interpretation of the subtracted coherence volumes should be done with care. BW, JM On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote: > The solution I have adopted is to always look at coherence contrasts. Make two volumes using the same reference dipole in two different conditions, then subtract the volumes. The self-coherence of the reference will disappear. Mostly. Then use stats, like a U-test. > > Jan.Hirschmann at med.uni-duesseldorf.de wrote: >> Hi community, >> Regarding this thread on suppressing the reference dipole from 2004, what is the current status? Has anybody found and implemented a recommendable way to project out activity from unwanted dipoles? Thank you for any comments/opinions! >> Best, >> Jan Hirschmann >> On 21 Oct 2004, at 17:23, Tom Holroyd wrote: >> >>> / When running a coherence volume using a reference dipole, one/ >>> / naturally expects the coherence will be high around the reference/ >>> / dipole./ >>> / / >>> / This effect tends to dominate the images./ >>> / / >>> / Is there a way to normalize the coherence volume to eliminate/ >>> / this effect? Perhaps by dividing by the coherence in a "control"/ >>> / state?/ >> Hi Tom, >> The dominating effect of the refdip is indeed very problematic. I just >> happened to have discussed this with Joachim Gross, and I have included >> our email exchange below. Please first read that ... >> Basically I agree with Joachim, and I don't trust the supdip that is >> implemented in FieldTrip's sourceanalysis function. Better test and map >> the significance of the difference in coherence between two conditions >> using randomization of the trials before the coherence is beamed (that >> is implemented in sourceanalysis + sourcestatistics). >> Robert >> -------------------------------------------------------------------- >> my question to Joachim was >> ---------------------------------------------------------------------- >> Begin forwarded message: >> >>> / From: Robert Oostenveld //>/ >>> / Date: 1 October 2004 10:26:02 GMT+02:00/ >>> / To: Joachim Gross //>/ >>> / Subject: dipole suppression/ >>> / / >>> / Hi Joachim,/ >>> / / >>> / What I always still had to ask you is how you do supression of dipoles/ >>> / in DICS, especially in the case of coherence imaging. I have thought/ >>> / of two ways of projecting them out:/ >>> / / >>> / 1) compute supdip leadfield and its projection on the COV/CSD matrix,/ >>> / then project it out of the COV/CSD matrix (which looses 2 or 3 from/ >>> / its rank)./ >>> / / >>> / 2) compute supdip leadfield and add it to the leadfield of the dipole/ >>> / with which is scanned (scandip). Subsequently compute the source/ >>> / COV/CSD on those 6 leadfield components and select the 3x3 submatrix/ >>> / that corresponds with the scandip to continue the computations with./ >>> / / >>> / Both methods don't really gave me very convincing results. A third/ >>> / approach would be to add the supdip leadfield to the (identity) noise/ >>> / matrix and project it through the filters. Then nai=pow/noise is/ >>> / corrected for the presence of the supdip, but that does not result in/ >>> / a supressed source coherence distribution. What is your idea or/ >>> / approach for this?/ >>> / / >>> / best regards/ >>> / Robert/ >>> / / >> ---------------------------------------------------------------------- >> and his answer (Joachim, I hope you don't mind me sharing this on the >> list) >> ---------------------------------------------------------------------- >> Begin forwarded message: >> >>> / From: Joachim Gross //>/ >>> / Date: 14 October 2004 17:20:45 GMT+02:00/ >>> / To: "//robert.oostenveld at fcdonders.kun.nl //"/ >>> / //>/ >>> / Subject: dipole suppression/ >>> / / >>> / Hi Robert,/ >>> / / >>> / sorry for the delay./ >>> / / >>> / The dipole suppression is indeed a complex issue./ >>> / We first implemented it because it facilitates visualization and the/ >>> / exact identification of the first/ >>> / strongest local maxima./ >>> / Nevertheless, it is quite dangerous because the map is (locally)/ >>> / distorted in a non-trivial way./ >>> / We are now trying to move away from suppressing the sources. I think/ >>> / it would be better to identify the/ >>> / significant local maxima (significance based on/ >>> / randomization/permutation)./ >>> / But what we are doing at the moment is your approach 3./ >>> / So we add the supdip leadfield to the noise covariance matrix and look/ >>> / at pow/noise./ >>> / / >>> / For coherence we are basically doing the same thing./ >>> / So we divide the coherence map (or actually the map of cross spectral/ >>> / densities) by a noise map/ >>> / that peaks at the locations of the "unwanted" dipoles./ >>> / With this procedure we loose absolute coherence values./ >>> / This is not so important for us since we get the absolute values from/ >>> / the coherence and partial coherence spectra/ >>> / that are computed afterwards./ >>> / It works surprisingly well but should be used with care./ >>> / / >>> / A better approach would be to map partial coherence (with the unwanted/ >>> / dipoles removed). But we have not implemented/ >>> / this so far./ >>> / / >>> / Again, I think it is better to have regions of interest identified by/ >>> / their significance./ >>> / / >>> / Joachim/ >> ---------------------------------------------------------------------- >> Robert Oostenveld, PhD >> Center for Sensory-Motor Interaction (SMI) >> Aalborg University, Denmark >> and >> F.C. Donders Centre for Cognitive Neuroimaging >> University Nijmegen >> P.O. Box 9101 >> NL-6500 AH Nijmegen >> The Netherlands >> Tel: +31 (0)24 3619695 >> Fax: +31 (0)24 3610989 >> ---------------------------------------------------------------------- >> N.B. Starting from 1 September 2004, the University of Nijmegen has >> changed its name to Radboud University Nijmegen. All web- and >> email-addresses ending in ".kun.nl" should therefore be changed into >> ".ru.nl". Please update your address book and links. >> Jan Hirschmann >> MSc. Neuroscience >> Insititute of Clinical Neuroscience and Medical Psychology >> Heinrich Heine University Duesseldorf >> Universitaetsstr. 1 >> 40225 Duesseldorf >> Tel: 0049 - (0)211 - 81 - 18415 >> ------------------------------------------------------------------------ >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- > "The test of a first-rate intelligence is the ability to hold two > opposed ideas in the mind at the same time, and still retain the > ability to function." — F. Scott Fitzgerald > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tolgacan1 at yahoo.com Sun Dec 4 15:00:40 2011 From: tolgacan1 at yahoo.com (=?utf-8?B?VG9sZ2Egw5Z6a3VydA==?=) Date: Sun, 4 Dec 2011 06:00:40 -0800 (PST) Subject: [FieldTrip] coherence normalization In-Reply-To: <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> <4ED91047.6050107@kurage.nimh.nih.gov> <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> Message-ID: <1323007240.37048.YahooMailNeo@web111505.mail.gq1.yahoo.com> Regarding the discussion here, I've gotten onto a recent paper (Sekihara et al., 2011) talking about "imaginary coherence" to prevent the seed region effects.  Even though imaginary coherence does not contain total connectivity information, it might at least be used to select the coherent regions that you want to project on your brain image and ignore the rest. Tolga ________________________________ From: jan-mathijs schoffelen To: Email discussion list for the FieldTrip project Sent: Friday, December 2, 2011 8:49 PM Subject: Re: [FieldTrip] coherence normalization Hi Jan, Tom and the rest, I agree with Tom, but would like to strongly emphasize that differences in power across conditions more often than not will affect the coherence landscape in a non-trivial way. This does not only count for power changes in the reference dipole, but also for changes in power for third party dipoles (i.e. any potential other source). Therefore the interpretation of the subtracted  coherence volumes should be done with care. BW, JM On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote: The solution I have adopted is to always look at coherence contrasts. Make two volumes using the same reference dipole in two different conditions, then subtract the volumes. The self-coherence of the reference will disappear. Mostly. Then use stats, like a U-test. > >Jan.Hirschmann at med.uni-duesseldorf.de wrote: > >Hi community, >> >Regarding this thread on suppressing the reference dipole from 2004, what is the current status? Has anybody found and implemented a recommendable way to project out activity from unwanted dipoles? Thank you for any comments/opinions! >> >Best, >> >Jan Hirschmann >> >  On 21 Oct 2004, at 17:23, Tom Holroyd wrote: >> > >> >/ When running a coherence volume using a reference dipole, one/ >>> >/ naturally expects the coherence will be high around the reference/ >>> >/ dipole./ >>> >/ / >>> >/ This effect tends to dominate the images./ >>> >/ / >>> >/ Is there a way to normalize the coherence volume to eliminate/ >>> >/ this effect?  Perhaps by dividing by the coherence in a "control"/ >>> >/ state?/ >>> >Hi Tom, >> >The dominating effect of the refdip is indeed very problematic. I just >> >happened to have discussed this with Joachim Gross, and I have included >> >our email exchange below. Please first read that ... >> >Basically I agree with Joachim, and I don't trust the supdip that is >> >implemented in FieldTrip's sourceanalysis function. Better test and map >> >the significance of the difference in coherence between two conditions >> >using randomization of the trials before the coherence is beamed (that >> >is implemented in sourceanalysis + sourcestatistics). >> >Robert >> >-------------------------------------------------------------------- >> >my question to Joachim was >> >---------------------------------------------------------------------- >> >Begin forwarded message: >> > >> >/ From: Robert Oostenveld //>/ >>> >/ Date: 1 October 2004 10:26:02 GMT+02:00/ >>> >/ To: Joachim Gross //>/ >>> >/ Subject: dipole suppression/ >>> >/ / >>> >/ Hi Joachim,/ >>> >/ / >>> >/ What I always still had to ask you is how you do supression of dipoles/ >>> >/ in DICS, especially in the case of coherence imaging. I have thought/ >>> >/ of two ways of projecting them out:/ >>> >/ / >>> >/ 1) compute supdip leadfield and its projection on the COV/CSD matrix,/ >>> >/ then project it out of the COV/CSD matrix (which looses 2 or 3 from/ >>> >/ its rank)./ >>> >/ / >>> >/ 2) compute supdip leadfield and add it to the leadfield of the dipole/ >>> >/ with which is scanned (scandip). Subsequently compute the source/ >>> >/ COV/CSD on those 6 leadfield components and select the 3x3 submatrix/ >>> >/ that corresponds with the scandip to continue the computations with./ >>> >/ / >>> >/ Both methods don't really gave me very convincing results. A third/ >>> >/ approach would be to add the supdip leadfield to the (identity) noise/ >>> >/ matrix and project it through the filters. Then nai=pow/noise is/ >>> >/ corrected for the presence of the supdip, but that does not result in/ >>> >/ a supressed source coherence distribution. What is your idea or/ >>> >/ approach for this?/ >>> >/ / >>> >/ best regards/ >>> >/ Robert/ >>> >/ / >>> >---------------------------------------------------------------------- >> >and his answer (Joachim, I hope you don't mind me sharing this on the >> >list) >> >---------------------------------------------------------------------- >> >Begin forwarded message: >> > >> >/ From: Joachim Gross //>/ >>> >/ Date: 14 October 2004 17:20:45 GMT+02:00/ >>> >/ To: "//robert.oostenveld at fcdonders.kun.nl //"/ >>> >/ //>/ >>> >/ Subject: dipole suppression/ >>> >/ / >>> >/ Hi Robert,/ >>> >/ / >>> >/ sorry for the delay./ >>> >/ / >>> >/ The dipole suppression is indeed a complex issue./ >>> >/ We first implemented it because it facilitates visualization and the/ >>> >/ exact identification of the first/ >>> >/ strongest local maxima./ >>> >/ Nevertheless, it is quite dangerous because the map is (locally)/ >>> >/ distorted in a non-trivial way./ >>> >/ We are now trying to move away from suppressing the sources. I think/ >>> >/ it would be better to identify the/ >>> >/ significant local maxima (significance based on/ >>> >/ randomization/permutation)./ >>> >/ But what we are doing at the moment is your approach 3./ >>> >/ So we add the supdip leadfield to the noise covariance matrix and look/ >>> >/ at pow/noise./ >>> >/ / >>> >/ For coherence we are basically doing the same thing./ >>> >/ So we divide the coherence map (or actually the map of cross spectral/ >>> >/ densities) by a noise map/ >>> >/ that peaks at the locations of the "unwanted" dipoles./ >>> >/ With this procedure we loose absolute coherence values./ >>> >/ This is not so important for us since we get the absolute values from/ >>> >/ the coherence and partial coherence spectra/ >>> >/ that are computed afterwards./ >>> >/ It works surprisingly well but should be used with care./ >>> >/ / >>> >/ A better approach would be to map partial coherence (with the unwanted/ >>> >/ dipoles removed). But we have not implemented/ >>> >/ this so far./ >>> >/ / >>> >/ Again, I think it is better to have regions of interest identified by/ >>> >/ their significance./ >>> >/ / >>> >/ Joachim/ >>> > ---------------------------------------------------------------------- >> >Robert Oostenveld, PhD >> >Center for Sensory-Motor Interaction (SMI) >> >Aalborg University, Denmark >> >and >> >F.C. Donders Centre for Cognitive Neuroimaging >> >University Nijmegen >> >P.O. Box 9101 >> >NL-6500 AH Nijmegen >> >The Netherlands >> >Tel: +31 (0)24 3619695 >> >Fax: +31 (0)24 3610989 >> >---------------------------------------------------------------------- >> >N.B. Starting from 1 September 2004, the University of Nijmegen has >> >changed its name to Radboud University Nijmegen. All web- and >> >email-addresses ending in ".kun.nl" should therefore be changed into >> >".ru.nl". Please update your address book and links. >> > Jan Hirschmann >> >MSc. Neuroscience >> >Insititute of Clinical Neuroscience and Medical Psychology >> >Heinrich Heine University Duesseldorf >> >Universitaetsstr.  1 >> >40225  Duesseldorf >> >Tel: 0049 - (0)211 - 81 - 18415 >> >------------------------------------------------------------------------ >> >_______________________________________________ >> >fieldtrip mailing list >> >fieldtrip at donders.ru.nl >> >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >-- >"The test of a first-rate intelligence is the ability to hold two >opposed ideas in the mind at the same time, and still retain the >ability to function." — F. Scott Fitzgerald >_______________________________________________ >fieldtrip mailing list >fieldtrip at donders.ru.nl >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > Jan-Mathijs Schoffelen, MD PhD  Donders Institute for Brain, Cognition and Behaviour,  Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From nkremers at uni-bonn.de Mon Dec 5 13:58:58 2011 From: nkremers at uni-bonn.de (Nico Alexander Willi Kremers) Date: Mon, 05 Dec 2011 13:58:58 +0100 Subject: [FieldTrip] 2x3 anova in cluster analysis Message-ID: Hi, I followed the discussion about implementing a 2x2 within subjects design into a cluster statistic with much interest. I want to implement a 2x3 repeated measure anova in a cluster analysis using fieldtrip. I think for this type of analysis subracting two conditions from each other and then calculate a ttest is not appropriate. Is there another way of calculating the interaction effect between the two factors and generate clusters for real and permutation data? What specifications must be set and how? Thank you very much for your answer, Nico From tomh at kurage.nimh.nih.gov Mon Dec 5 19:56:02 2011 From: tomh at kurage.nimh.nih.gov (Tom Holroyd (NIH/NIMH) [E]) Date: Mon, 05 Dec 2011 13:56:02 -0500 Subject: [FieldTrip] coherence normalization In-Reply-To: <1323007240.37048.YahooMailNeo@web111505.mail.gq1.yahoo.com> References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> <4ED91047.6050107@kurage.nimh.nih.gov> <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> <1323007240.37048.YahooMailNeo@web111505.mail.gq1.yahoo.com> Message-ID: <4EDD13C2.3000305@kurage.nimh.nih.gov> Yes, Guido Nolte came up with that around the same time (2004). I found this link by google, there might be a better one http://keck.ucsf.edu/~houde/sensorimotor_jc/GNolte04a.pdf Imaginary coherence is insensitive to volume conduction in EEG. I think the interpretation is different for MEG, but you can certainly easily compute it; you might still want to contrast different conditions. Tolga Özkurt wrote: > Regarding the discussion here, I've gotten onto a recent paper (Sekihara > et al., 2011) talking about "imaginary coherence" to prevent the seed > region effects. > > Even though imaginary coherence does not contain total connectivity > information, it might at least be used to select the coherent regions > that you want to project on your brain image and ignore the rest. > > Tolga > > > ------------------------------------------------------------------------ > *From:* jan-mathijs schoffelen > *To:* Email discussion list for the FieldTrip project > > *Sent:* Friday, December 2, 2011 8:49 PM > *Subject:* Re: [FieldTrip] coherence normalization > > Hi Jan, Tom and the rest, > > I agree with Tom, but would like to strongly emphasize that differences > in power across conditions more often than not will affect the coherence > landscape in a non-trivial way. This does not only count for power > changes in the reference dipole, but also for changes in power for third > party dipoles (i.e. any potential other source). Therefore the > interpretation of the subtracted coherence volumes should be done with > care. > > BW, > > JM > > On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote: > >> The solution I have adopted is to always look at coherence contrasts. >> Make two volumes using the same reference dipole in two different >> conditions, then subtract the volumes. The self-coherence of the >> reference will disappear. Mostly. Then use stats, like a U-test. >> >> Jan.Hirschmann at med.uni-duesseldorf.de >> wrote: >>> Hi community, >>> Regarding this thread on suppressing the reference dipole from 2004, >>> what is the current status? Has anybody found and implemented a >>> recommendable way to project out activity from unwanted dipoles? >>> Thank you for any comments/opinions! >>> Best, >>> Jan Hirschmann >>> On 21 Oct 2004, at 17:23, Tom Holroyd wrote: >>> >>>> / When running a coherence volume using a reference dipole, one/ >>>> / naturally expects the coherence will be high around the reference/ >>>> / dipole./ >>>> / / >>>> / This effect tends to dominate the images./ >>>> / / >>>> / Is there a way to normalize the coherence volume to eliminate/ >>>> / this effect? Perhaps by dividing by the coherence in a "control"/ >>>> / state?/ >>> Hi Tom, >>> The dominating effect of the refdip is indeed very problematic. I just >>> happened to have discussed this with Joachim Gross, and I have included >>> our email exchange below. Please first read that ... >>> Basically I agree with Joachim, and I don't trust the supdip that is >>> implemented in FieldTrip's sourceanalysis function. Better test and map >>> the significance of the difference in coherence between two conditions >>> using randomization of the trials before the coherence is beamed (that >>> is implemented in sourceanalysis + sourcestatistics). >>> Robert >>> -------------------------------------------------------------------- >>> my question to Joachim was >>> ---------------------------------------------------------------------- >>> Begin forwarded message: >>> >>>> / From: Robert Oostenveld >>> >>>> //>/ >>>> / Date: 1 October 2004 10:26:02 GMT+02:00/ >>>> / To: Joachim Gross >>> >>>> //>/ >>>> / Subject: dipole suppression/ >>>> / / >>>> / Hi Joachim,/ >>>> / / >>>> / What I always still had to ask you is how you do supression of >>>> dipoles/ >>>> / in DICS, especially in the case of coherence imaging. I have thought/ >>>> / of two ways of projecting them out:/ >>>> / / >>>> / 1) compute supdip leadfield and its projection on the COV/CSD matrix,/ >>>> / then project it out of the COV/CSD matrix (which looses 2 or 3 from/ >>>> / its rank)./ >>>> / / >>>> / 2) compute supdip leadfield and add it to the leadfield of the dipole/ >>>> / with which is scanned (scandip). Subsequently compute the source/ >>>> / COV/CSD on those 6 leadfield components and select the 3x3 submatrix/ >>>> / that corresponds with the scandip to continue the computations with./ >>>> / / >>>> / Both methods don't really gave me very convincing results. A third/ >>>> / approach would be to add the supdip leadfield to the (identity) noise/ >>>> / matrix and project it through the filters. Then nai=pow/noise is/ >>>> / corrected for the presence of the supdip, but that does not result in/ >>>> / a supressed source coherence distribution. What is your idea or/ >>>> / approach for this?/ >>>> / / >>>> / best regards/ >>>> / Robert/ >>>> / / >>> ---------------------------------------------------------------------- >>> and his answer (Joachim, I hope you don't mind me sharing this on the >>> list) >>> ---------------------------------------------------------------------- >>> Begin forwarded message: >>> >>>> / From: Joachim Gross >>> >>>> //>/ >>>> / Date: 14 October 2004 17:20:45 GMT+02:00/ >>>> / To: "//robert.oostenveld at fcdonders.kun.nl >>>> >>>> //"/ >>>> / >>>> //>/ >>>> / Subject: dipole suppression/ >>>> / / >>>> / Hi Robert,/ >>>> / / >>>> / sorry for the delay./ >>>> / / >>>> / The dipole suppression is indeed a complex issue./ >>>> / We first implemented it because it facilitates visualization and the/ >>>> / exact identification of the first/ >>>> / strongest local maxima./ >>>> / Nevertheless, it is quite dangerous because the map is (locally)/ >>>> / distorted in a non-trivial way./ >>>> / We are now trying to move away from suppressing the sources. I think/ >>>> / it would be better to identify the/ >>>> / significant local maxima (significance based on/ >>>> / randomization/permutation)./ >>>> / But what we are doing at the moment is your approach 3./ >>>> / So we add the supdip leadfield to the noise covariance matrix and >>>> look/ >>>> / at pow/noise./ >>>> / / >>>> / For coherence we are basically doing the same thing./ >>>> / So we divide the coherence map (or actually the map of cross spectral/ >>>> / densities) by a noise map/ >>>> / that peaks at the locations of the "unwanted" dipoles./ >>>> / With this procedure we loose absolute coherence values./ >>>> / This is not so important for us since we get the absolute values from/ >>>> / the coherence and partial coherence spectra/ >>>> / that are computed afterwards./ >>>> / It works surprisingly well but should be used with care./ >>>> / / >>>> / A better approach would be to map partial coherence (with the >>>> unwanted/ >>>> / dipoles removed). But we have not implemented/ >>>> / this so far./ >>>> / / >>>> / Again, I think it is better to have regions of interest identified by/ >>>> / their significance./ >>>> / / >>>> / Joachim/ >>> ---------------------------------------------------------------------- >>> Robert Oostenveld, PhD >>> Center for Sensory-Motor Interaction (SMI) >>> Aalborg University, Denmark >>> and >>> F.C. Donders Centre for Cognitive Neuroimaging >>> University Nijmegen >>> P.O. Box 9101 >>> NL-6500 AH Nijmegen >>> The Netherlands >>> Tel: +31 (0)24 3619695 >>> Fax: +31 (0)24 3610989 >>> ---------------------------------------------------------------------- >>> N.B. Starting from 1 September 2004, the University of Nijmegen has >>> changed its name to Radboud University Nijmegen. All web- and >>> email-addresses ending in ".kun.nl" should therefore be changed into >>> ".ru.nl". Please update your address book and links. >>> Jan Hirschmann >>> MSc. Neuroscience >>> Insititute of Clinical Neuroscience and Medical Psychology >>> Heinrich Heine University Duesseldorf >>> Universitaetsstr. 1 >>> 40225 Duesseldorf >>> Tel: 0049 - (0)211 - 81 - 18415 >>> ------------------------------------------------------------------------ >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> "The test of a first-rate intelligence is the ability to hold two >> opposed ideas in the mind at the same time, and still retain the >> ability to function." — F. Scott Fitzgerald >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > ------------------------------------------------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- "The test of a first-rate intelligence is the ability to hold two opposed ideas in the mind at the same time, and still retain the ability to function." — F. Scott Fitzgerald From dualitystan at gmail.com Mon Dec 5 20:17:04 2011 From: dualitystan at gmail.com (Stanley Klein) Date: Mon, 5 Dec 2011 11:17:04 -0800 Subject: [FieldTrip] 2x3 anova in cluster analysis In-Reply-To: References: Message-ID: Nico, Your question gives me the chance to ask something I've been curious about. It seems to me that one of the nifty things about permutation cluster analysis is that it allows you to do anything that seems reasonable as long you decide on the process ahead of time and don't do any future tweaking other than fixing coding errors. I'm curious whether the Fieldtrip code make it easy to insert new statistics modules. I presume your actual question had to do with whether Fieldtrip already has the possibility of doing that 2x3 ANOVA. I suspect it doesn't have that capability. However, it would be nice if the permutation cluster analysis could be made sufficiently modular that one could make use of all the complicated clustering and permuting and all, but enable the user to substitute their own statistical method. I haven't actually watched my students doing the nitty-gritty use of Fieldtrip's version of the permutation test (other than knowing that is is very nice and well documented) so I don't know how easy it is to stick in one's own favorite statistic, but I'm hoping it is easy. Stan On Mon, Dec 5, 2011 at 4:58 AM, Nico Alexander Willi Kremers < nkremers at uni-bonn.de> wrote: > > Hi, > > I followed the discussion about implementing a 2x2 within subjects design > into a cluster statistic with much interest. I want to implement a 2x3 > repeated measure anova in a cluster analysis using fieldtrip. I think for > this type of analysis subracting two conditions from each other and then > calculate a ttest is not appropriate. Is there another way of calculating > the interaction effect between the two factors and generate clusters for > real and permutation data? What specifications must be set and how? > > Thank you very much for your answer, > > Nico > ______________________________**_________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Dec 5 21:01:39 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 5 Dec 2011 21:01:39 +0100 Subject: [FieldTrip] 2x3 anova in cluster analysis In-Reply-To: References: Message-ID: <6A25053C-2EB2-437A-A96F-2C1047DC862F@donders.ru.nl> Hi Stan et al, Actually FieldTrip allows in a very straightforward way to plug-in one's favourite statistic. The idea is the following: when specifying cfg.statistic you need to specify a string that under the hood points to a function, e.g. 'indepsamplesT' eventually causes a function to be called, answering to the aptly chosen name: 'statfun_indepsamplesT' which is doing the legwork. As long as the statfun_younameit has properly defined input and output arguments, you can let it do whatever you want. FieldTrip contains a bunch of 'statfuns' in the statfun directory but there's no reason not to implement any yourself (and ideally contribute them to the repository). Another discussion altogether is the question whether the test statistic of interest is an appropriate one that allows for statistical inference using the permutation framework. Over the past years there have been various threads on this mailing list regarding the possibility to test for interactions using a permutation test. You can look this up in the archive. Strictly speaking this is statistically not possible this way. The permutation-framework tests the null-hypothesis of exchangeability of data across allocated conditions, whereas when one wants to test for an interaction effect tests one tests for a particular linear (parametric) model of the dependent variables explaining variance in the dependent variable. Inferring that exchangeability across conditions is unlikely (i.e. obtaining a small p-value through permutation) does not necessarily lead to the conclusion that there is an actual interaction effect. Though opinions among the statisticians about this seem to vary, there may be a way out: one could either use bootstrapping to obtain confidence intervals for the interaction F under the null-hypothesis. The recipe for this would be to do a cell-specific demeaning of the data to impose the null-hypothesis of no interaction, and then through bootstrap resampling obtain a reference distribution of the interaction F. Alternatively, although I haven't thought this one through for any case other than a 2x2 anova, one could reduce the interaction effect to a two-condition contrast where observations belonging to the 'main diagonal' of the 2x2 conditions design are labeled as condition 1, and the observations belonging to the other diagonal are labeled as condition 2. One could then proceed with using a T-statistic as a descriptive statistic across these two 'conditions' on which inference can be done. Cheers and a happy Sinterklaas to you all, Jan-Mathijs On Dec 5, 2011, at 8:17 PM, Stanley Klein wrote: > Nico, > > Your question gives me the chance to ask something I've been curious about. It seems to me that one of the nifty things about permutation cluster analysis is that it allows you to do anything that seems reasonable as long you decide on the process ahead of time and don't do any future tweaking other than fixing coding errors. I'm curious whether the Fieldtrip code make it easy to insert new statistics modules. > > I presume your actual question had to do with whether Fieldtrip already has the possibility of doing that 2x3 ANOVA. I suspect it doesn't have that capability. However, it would be nice if the permutation cluster analysis could be made sufficiently modular that one could make use of all the complicated clustering and permuting and all, but enable the user to substitute their own statistical method. I haven't actually watched my students doing the nitty-gritty use of Fieldtrip's version of the permutation test (other than knowing that is is very nice and well documented) so I don't know how easy it is to stick in one's own favorite statistic, but I'm hoping it is easy. > > Stan > > > On Mon, Dec 5, 2011 at 4:58 AM, Nico Alexander Willi Kremers wrote: > > Hi, > > I followed the discussion about implementing a 2x2 within subjects design into a cluster statistic with much interest. I want to implement a 2x3 repeated measure anova in a cluster analysis using fieldtrip. I think for this type of analysis subracting two conditions from each other and then calculate a ttest is not appropriate. Is there another way of calculating the interaction effect between the two factors and generate clusters for real and permutation data? What specifications must be set and how? > > Thank you very much for your answer, > > Nico > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Dec 5 21:13:30 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 5 Dec 2011 21:13:30 +0100 Subject: [FieldTrip] coherence normalization In-Reply-To: <4EDD13C2.3000305@kurage.nimh.nih.gov> References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> <4ED91047.6050107@kurage.nimh.nih.gov> <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> <1323007240.37048.YahooMailNeo@web111505.mail.gq1.yahoo.com> <4EDD13C2.3000305@kurage.nimh.nih.gov> Message-ID: Hi all, I would not venture to interpret a conditional difference in the imaginary part of the coherency. When this quantity changes, it could either be due to a change in the phase or to a change of the magnitude of the coherency (or of any combination of the two). BW, JM On Dec 5, 2011, at 7:56 PM, Tom Holroyd (NIH/NIMH) [E] wrote: > Yes, Guido Nolte came up with that around the same time (2004). > > I found this link by google, there might be a better one > > http://keck.ucsf.edu/~houde/sensorimotor_jc/GNolte04a.pdf > > Imaginary coherence is insensitive to volume conduction in EEG. > > I think the interpretation is different for MEG, but you can certainly easily compute it; you might still want to contrast different conditions. > > Tolga Özkurt wrote: >> Regarding the discussion here, I've gotten onto a recent paper (Sekihara et al., 2011) talking about "imaginary coherence" to prevent the seed region effects. Even though imaginary coherence does not contain total connectivity information, it might at least be used to select the coherent regions that you want to project on your brain image and ignore the rest. >> Tolga >> ------------------------------------------------------------------------ >> *From:* jan-mathijs schoffelen >> *To:* Email discussion list for the FieldTrip project >> *Sent:* Friday, December 2, 2011 8:49 PM >> *Subject:* Re: [FieldTrip] coherence normalization >> Hi Jan, Tom and the rest, >> I agree with Tom, but would like to strongly emphasize that differences in power across conditions more often than not will affect the coherence landscape in a non-trivial way. This does not only count for power changes in the reference dipole, but also for changes in power for third party dipoles (i.e. any potential other source). Therefore the interpretation of the subtracted coherence volumes should be done with care. >> BW, >> JM >> On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote: >>> The solution I have adopted is to always look at coherence contrasts. Make two volumes using the same reference dipole in two different conditions, then subtract the volumes. The self-coherence of the reference will disappear. Mostly. Then use stats, like a U-test. >>> >>> Jan.Hirschmann at med.uni-duesseldorf.de wrote: >>>> Hi community, >>>> Regarding this thread on suppressing the reference dipole from 2004, what is the current status? Has anybody found and implemented a recommendable way to project out activity from unwanted dipoles? Thank you for any comments/opinions! >>>> Best, >>>> Jan Hirschmann >>>> On 21 Oct 2004, at 17:23, Tom Holroyd wrote: >>>> >>>>> / When running a coherence volume using a reference dipole, one/ >>>>> / naturally expects the coherence will be high around the reference/ >>>>> / dipole./ >>>>> / / >>>>> / This effect tends to dominate the images./ >>>>> / / >>>>> / Is there a way to normalize the coherence volume to eliminate/ >>>>> / this effect? Perhaps by dividing by the coherence in a "control"/ >>>>> / state?/ >>>> Hi Tom, >>>> The dominating effect of the refdip is indeed very problematic. I just >>>> happened to have discussed this with Joachim Gross, and I have included >>>> our email exchange below. Please first read that ... >>>> Basically I agree with Joachim, and I don't trust the supdip that is >>>> implemented in FieldTrip's sourceanalysis function. Better test and map >>>> the significance of the difference in coherence between two conditions >>>> using randomization of the trials before the coherence is beamed (that >>>> is implemented in sourceanalysis + sourcestatistics). >>>> Robert >>>> -------------------------------------------------------------------- >>>> my question to Joachim was >>>> ---------------------------------------------------------------------- >>>> Begin forwarded message: >>>> >>>>> / From: Robert Oostenveld //>/ >>>>> / Date: 1 October 2004 10:26:02 GMT+02:00/ >>>>> / To: Joachim Gross //>/ >>>>> / Subject: dipole suppression/ >>>>> / / >>>>> / Hi Joachim,/ >>>>> / / >>>>> / What I always still had to ask you is how you do supression of dipoles/ >>>>> / in DICS, especially in the case of coherence imaging. I have thought/ >>>>> / of two ways of projecting them out:/ >>>>> / / >>>>> / 1) compute supdip leadfield and its projection on the COV/CSD matrix,/ >>>>> / then project it out of the COV/CSD matrix (which looses 2 or 3 from/ >>>>> / its rank)./ >>>>> / / >>>>> / 2) compute supdip leadfield and add it to the leadfield of the dipole/ >>>>> / with which is scanned (scandip). Subsequently compute the source/ >>>>> / COV/CSD on those 6 leadfield components and select the 3x3 submatrix/ >>>>> / that corresponds with the scandip to continue the computations with./ >>>>> / / >>>>> / Both methods don't really gave me very convincing results. A third/ >>>>> / approach would be to add the supdip leadfield to the (identity) noise/ >>>>> / matrix and project it through the filters. Then nai=pow/noise is/ >>>>> / corrected for the presence of the supdip, but that does not result in/ >>>>> / a supressed source coherence distribution. What is your idea or/ >>>>> / approach for this?/ >>>>> / / >>>>> / best regards/ >>>>> / Robert/ >>>>> / / >>>> ---------------------------------------------------------------------- >>>> and his answer (Joachim, I hope you don't mind me sharing this on the >>>> list) >>>> ---------------------------------------------------------------------- >>>> Begin forwarded message: >>>> >>>>> / From: Joachim Gross //>/ >>>>> / Date: 14 October 2004 17:20:45 GMT+02:00/ >>>>> / To: "//robert.oostenveld at fcdonders.kun.nl //"/ >>>>> / //>/ >>>>> / Subject: dipole suppression/ >>>>> / / >>>>> / Hi Robert,/ >>>>> / / >>>>> / sorry for the delay./ >>>>> / / >>>>> / The dipole suppression is indeed a complex issue./ >>>>> / We first implemented it because it facilitates visualization and the/ >>>>> / exact identification of the first/ >>>>> / strongest local maxima./ >>>>> / Nevertheless, it is quite dangerous because the map is (locally)/ >>>>> / distorted in a non-trivial way./ >>>>> / We are now trying to move away from suppressing the sources. I think/ >>>>> / it would be better to identify the/ >>>>> / significant local maxima (significance based on/ >>>>> / randomization/permutation)./ >>>>> / But what we are doing at the moment is your approach 3./ >>>>> / So we add the supdip leadfield to the noise covariance matrix and look/ >>>>> / at pow/noise./ >>>>> / / >>>>> / For coherence we are basically doing the same thing./ >>>>> / So we divide the coherence map (or actually the map of cross spectral/ >>>>> / densities) by a noise map/ >>>>> / that peaks at the locations of the "unwanted" dipoles./ >>>>> / With this procedure we loose absolute coherence values./ >>>>> / This is not so important for us since we get the absolute values from/ >>>>> / the coherence and partial coherence spectra/ >>>>> / that are computed afterwards./ >>>>> / It works surprisingly well but should be used with care./ >>>>> / / >>>>> / A better approach would be to map partial coherence (with the unwanted/ >>>>> / dipoles removed). But we have not implemented/ >>>>> / this so far./ >>>>> / / >>>>> / Again, I think it is better to have regions of interest identified by/ >>>>> / their significance./ >>>>> / / >>>>> / Joachim/ >>>> ---------------------------------------------------------------------- >>>> Robert Oostenveld, PhD >>>> Center for Sensory-Motor Interaction (SMI) >>>> Aalborg University, Denmark >>>> and >>>> F.C. Donders Centre for Cognitive Neuroimaging >>>> University Nijmegen >>>> P.O. Box 9101 >>>> NL-6500 AH Nijmegen >>>> The Netherlands >>>> Tel: +31 (0)24 3619695 >>>> Fax: +31 (0)24 3610989 >>>> ---------------------------------------------------------------------- >>>> N.B. Starting from 1 September 2004, the University of Nijmegen has >>>> changed its name to Radboud University Nijmegen. All web- and >>>> email-addresses ending in ".kun.nl" should therefore be changed into >>>> ".ru.nl". Please update your address book and links. >>>> Jan Hirschmann >>>> MSc. Neuroscience >>>> Insititute of Clinical Neuroscience and Medical Psychology >>>> Heinrich Heine University Duesseldorf >>>> Universitaetsstr. 1 >>>> 40225 Duesseldorf >>>> Tel: 0049 - (0)211 - 81 - 18415 >>>> ------------------------------------------------------------------------ >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> -- >>> "The test of a first-rate intelligence is the ability to hold two >>> opposed ideas in the mind at the same time, and still retain the >>> ability to function." — F. Scott Fitzgerald >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> ------------------------------------------------------------------------ >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- > "The test of a first-rate intelligence is the ability to hold two > opposed ideas in the mind at the same time, and still retain the > ability to function." — F. Scott Fitzgerald > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at kurage.nimh.nih.gov Mon Dec 5 21:38:55 2011 From: tomh at kurage.nimh.nih.gov (Tom Holroyd (NIH/NIMH) [E]) Date: Mon, 05 Dec 2011 15:38:55 -0500 Subject: [FieldTrip] coherence normalization In-Reply-To: References: <72E993C35FB11743B79FF9286E5B6D8B033CA518@Mail2-UKD.VMED.UKD> <4ED91047.6050107@kurage.nimh.nih.gov> <5492A720-8DC2-4B77-8ED7-EF5CA2C9608F@donders.ru.nl> <1323007240.37048.YahooMailNeo@web111505.mail.gq1.yahoo.com> <4EDD13C2.3000305@kurage.nimh.nih.gov> Message-ID: <4EDD2BDF.6090506@kurage.nimh.nih.gov> Yes. Nolte mentions that although one often computes coherency relative to a baseline, one must be careful because of this and random flips of pi making hash of it if you just blindly subtract. Same thing for any relative phase calculation. Also, I was misunderstanding things below; the interpretation is the same for MEG as it is for EEG, any source affects multiple sensors simultaneously. It is this spatial correlation that allows us to see it as a source after all, and what makes the imaginary part positive. If there were no spatial correlations there would be no imaginary part in the coherence. heh, yes, it took me that long to understand this paper ... :-) jan-mathijs schoffelen wrote: > Hi all, > > I would not venture to interpret a conditional difference in the > imaginary part of the coherency. When this quantity changes, it could > either be due to a change in the phase or to a change of the magnitude > of the coherency (or of any combination of the two). > > BW, > > JM > > > On Dec 5, 2011, at 7:56 PM, Tom Holroyd (NIH/NIMH) [E] wrote: > >> Yes, Guido Nolte came up with that around the same time (2004). >> >> I found this link by google, there might be a better one >> >> http://keck.ucsf.edu/~houde/sensorimotor_jc/GNolte04a.pdf >> >> Imaginary coherence is insensitive to volume conduction in EEG. >> >> I think the interpretation is different for MEG, but you can certainly >> easily compute it; you might still want to contrast different conditions. >> >> Tolga Özkurt wrote: >>> Regarding the discussion here, I've gotten onto a recent paper >>> (Sekihara et al., 2011) talking about "imaginary coherence" to >>> prevent the seed region effects. Even though imaginary coherence does >>> not contain total connectivity information, it might at least be used >>> to select the coherent regions that you want to project on your brain >>> image and ignore the rest. >>> Tolga >>> ------------------------------------------------------------------------ >>> *From:* jan-mathijs schoffelen >>> *To:* Email discussion list for the FieldTrip project >>> >>> *Sent:* Friday, December 2, 2011 8:49 PM >>> *Subject:* Re: [FieldTrip] coherence normalization >>> Hi Jan, Tom and the rest, >>> I agree with Tom, but would like to strongly emphasize that >>> differences in power across conditions more often than not will >>> affect the coherence landscape in a non-trivial way. This does not >>> only count for power changes in the reference dipole, but also for >>> changes in power for third party dipoles (i.e. any potential other >>> source). Therefore the interpretation of the subtracted coherence >>> volumes should be done with care. >>> BW, >>> JM >>> On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote: >>>> The solution I have adopted is to always look at coherence >>>> contrasts. Make two volumes using the same reference dipole in two >>>> different conditions, then subtract the volumes. The self-coherence >>>> of the reference will disappear. Mostly. Then use stats, like a U-test. >>>> >>>> Jan.Hirschmann at med.uni-duesseldorf.de >>>> wrote: >>>>> Hi community, >>>>> Regarding this thread on suppressing the reference dipole from >>>>> 2004, what is the current status? Has anybody found and implemented >>>>> a recommendable way to project out activity from unwanted dipoles? >>>>> Thank you for any comments/opinions! >>>>> Best, >>>>> Jan Hirschmann >>>>> On 21 Oct 2004, at 17:23, Tom Holroyd wrote: >>>>> >>>>>> / When running a coherence volume using a reference dipole, one/ >>>>>> / naturally expects the coherence will be high around the reference/ >>>>>> / dipole./ >>>>>> / / >>>>>> / This effect tends to dominate the images./ >>>>>> / / >>>>>> / Is there a way to normalize the coherence volume to eliminate/ >>>>>> / this effect? Perhaps by dividing by the coherence in a "control"/ >>>>>> / state?/ >>>>> Hi Tom, >>>>> The dominating effect of the refdip is indeed very problematic. I just >>>>> happened to have discussed this with Joachim Gross, and I have included >>>>> our email exchange below. Please first read that ... >>>>> Basically I agree with Joachim, and I don't trust the supdip that is >>>>> implemented in FieldTrip's sourceanalysis function. Better test and map >>>>> the significance of the difference in coherence between two conditions >>>>> using randomization of the trials before the coherence is beamed (that >>>>> is implemented in sourceanalysis + sourcestatistics). >>>>> Robert >>>>> -------------------------------------------------------------------- >>>>> my question to Joachim was >>>>> ---------------------------------------------------------------------- >>>>> Begin forwarded message: >>>>> >>>>>> / From: Robert Oostenveld >>>>> >>>>>> //>/ >>>>>> / Date: 1 October 2004 10:26:02 GMT+02:00/ >>>>>> / To: Joachim Gross >>>>> >>>>>> //>/ >>>>>> / Subject: dipole suppression/ >>>>>> / / >>>>>> / Hi Joachim,/ >>>>>> / / >>>>>> / What I always still had to ask you is how you do supression of >>>>>> dipoles/ >>>>>> / in DICS, especially in the case of coherence imaging. I have >>>>>> thought/ >>>>>> / of two ways of projecting them out:/ >>>>>> / / >>>>>> / 1) compute supdip leadfield and its projection on the COV/CSD >>>>>> matrix,/ >>>>>> / then project it out of the COV/CSD matrix (which looses 2 or 3 from/ >>>>>> / its rank)./ >>>>>> / / >>>>>> / 2) compute supdip leadfield and add it to the leadfield of the >>>>>> dipole/ >>>>>> / with which is scanned (scandip). Subsequently compute the source/ >>>>>> / COV/CSD on those 6 leadfield components and select the 3x3 >>>>>> submatrix/ >>>>>> / that corresponds with the scandip to continue the computations >>>>>> with./ >>>>>> / / >>>>>> / Both methods don't really gave me very convincing results. A third/ >>>>>> / approach would be to add the supdip leadfield to the (identity) >>>>>> noise/ >>>>>> / matrix and project it through the filters. Then nai=pow/noise is/ >>>>>> / corrected for the presence of the supdip, but that does not >>>>>> result in/ >>>>>> / a supressed source coherence distribution. What is your idea or/ >>>>>> / approach for this?/ >>>>>> / / >>>>>> / best regards/ >>>>>> / Robert/ >>>>>> / / >>>>> ---------------------------------------------------------------------- >>>>> and his answer (Joachim, I hope you don't mind me sharing this on the >>>>> list) >>>>> ---------------------------------------------------------------------- >>>>> Begin forwarded message: >>>>> >>>>>> / From: Joachim Gross >>>>> >>>>>> //>/ >>>>>> / Date: 14 October 2004 17:20:45 GMT+02:00/ >>>>>> / To: "//robert.oostenveld at fcdonders.kun.nl >>>>>> >>>>>> //"/ >>>>>> / >>>>> >>>>>> //>/ >>>>>> / Subject: dipole suppression/ >>>>>> / / >>>>>> / Hi Robert,/ >>>>>> / / >>>>>> / sorry for the delay./ >>>>>> / / >>>>>> / The dipole suppression is indeed a complex issue./ >>>>>> / We first implemented it because it facilitates visualization and >>>>>> the/ >>>>>> / exact identification of the first/ >>>>>> / strongest local maxima./ >>>>>> / Nevertheless, it is quite dangerous because the map is (locally)/ >>>>>> / distorted in a non-trivial way./ >>>>>> / We are now trying to move away from suppressing the sources. I >>>>>> think/ >>>>>> / it would be better to identify the/ >>>>>> / significant local maxima (significance based on/ >>>>>> / randomization/permutation)./ >>>>>> / But what we are doing at the moment is your approach 3./ >>>>>> / So we add the supdip leadfield to the noise covariance matrix >>>>>> and look/ >>>>>> / at pow/noise./ >>>>>> / / >>>>>> / For coherence we are basically doing the same thing./ >>>>>> / So we divide the coherence map (or actually the map of cross >>>>>> spectral/ >>>>>> / densities) by a noise map/ >>>>>> / that peaks at the locations of the "unwanted" dipoles./ >>>>>> / With this procedure we loose absolute coherence values./ >>>>>> / This is not so important for us since we get the absolute values >>>>>> from/ >>>>>> / the coherence and partial coherence spectra/ >>>>>> / that are computed afterwards./ >>>>>> / It works surprisingly well but should be used with care./ >>>>>> / / >>>>>> / A better approach would be to map partial coherence (with the >>>>>> unwanted/ >>>>>> / dipoles removed). But we have not implemented/ >>>>>> / this so far./ >>>>>> / / >>>>>> / Again, I think it is better to have regions of interest >>>>>> identified by/ >>>>>> / their significance./ >>>>>> / / >>>>>> / Joachim/ >>>>> ---------------------------------------------------------------------- >>>>> Robert Oostenveld, PhD >>>>> Center for Sensory-Motor Interaction (SMI) >>>>> Aalborg University, Denmark >>>>> and >>>>> F.C. Donders Centre for Cognitive Neuroimaging >>>>> University Nijmegen >>>>> P.O. Box 9101 >>>>> NL-6500 AH Nijmegen >>>>> The Netherlands >>>>> Tel: +31 (0)24 3619695 >>>>> Fax: +31 (0)24 3610989 >>>>> ---------------------------------------------------------------------- >>>>> N.B. Starting from 1 September 2004, the University of Nijmegen has >>>>> changed its name to Radboud University Nijmegen. All web- and >>>>> email-addresses ending in ".kun.nl" should therefore be changed into >>>>> ".ru.nl". Please update your address book and links. >>>>> Jan Hirschmann >>>>> MSc. Neuroscience >>>>> Insititute of Clinical Neuroscience and Medical Psychology >>>>> Heinrich Heine University Duesseldorf >>>>> Universitaetsstr. 1 >>>>> 40225 Duesseldorf >>>>> Tel: 0049 - (0)211 - 81 - 18415 >>>>> ------------------------------------------------------------------------ >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> -- >>>> "The test of a first-rate intelligence is the ability to hold two >>>> opposed ideas in the mind at the same time, and still retain the >>>> ability to function." — F. Scott Fitzgerald >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition >>> and Behaviour, Centre for Cognitive Neuroimaging, >>> Radboud University Nijmegen, The Netherlands >>> Max Planck Institute for Psycholinguistics, >>> Nijmegen, The Netherlands >>> J.Schoffelen at donders.ru.nl >>> Telephone: +31-24-3614793 >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> ------------------------------------------------------------------------ >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> "The test of a first-rate intelligence is the ability to hold two >> opposed ideas in the mind at the same time, and still retain the >> ability to function." — F. Scott Fitzgerald >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > ------------------------------------------------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- "The test of a first-rate intelligence is the ability to hold two opposed ideas in the mind at the same time, and still retain the ability to function." — F. Scott Fitzgerald From jan.schoffelen at donders.ru.nl Mon Dec 5 22:03:06 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 5 Dec 2011 22:03:06 +0100 Subject: [FieldTrip] source statistics, group level In-Reply-To: References: Message-ID: <2A18BE4D-384F-4EE3-8D57-F11C642A089B@donders.ru.nl> Hi Sonja I think you are almost there. What I am not sure about is the name of the field in the grandaverage structure which contains the concatenated individual subject data. Isn't this field called '.trial'? In that case you should specify cfg.parameter to be 'trial'. If this is not the cause of the problem, did you check the individual subject volumes? Do these contain colored data? What do you exactly mean by getting a blank mri? Does the stat.stat field contain only zeros, nans or something else? Best, Jan-Mathijs On Dec 2, 2011, at 12:16 PM, Sonja Suntrup wrote: > Dear fieldtrip users, > I would like to do sourcestatistics on a group level with meg data. I have a > pre and post intervention measurement for each of my 21 subjects > (within-subjects design). After source reconstruction using an LCMV beamformer > and volume normalization I calculated the sourcegrandaverage for the pre and > post condition with the parameter cfg.keepindividual = 'yes'. > However, when I use the grandaverage results in ft_sourcestatistics in the > configuration shown below and plot the result I just get a blank anatomical > mri. Do I have to set any additional parameters or do I make a general > mistake? Whould you recommend to use a cluster-based permutation test > comparable to ft_timelockstatistics and would I have to set the same > parameters in ft_sourcestatistics then? > > cfg=[]; > cfg.dim = grandAVGsourcePre.dim; > cfg.method = 'montecarlo'; > cfg.statistic = 'depsamplesT'; > cfg.parameter = 'avg.pow'; > cfg.correctm = 'cluster'; > cfg.numrandomization = 100; > cfg.alpha = 0.05; > cfg.tail = 0; > > nsubj=length(sourcePre.trial); > cfg.design(1,:) = [1:nsubj 1:nsubj]; > cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2]; > cfg.uvar = 1; > cfg.ivar = 2; > stat = ft_sourcestatistics(cfg, grandAVGsourcePre, grandAVGsourcePost); > > Your help is greatly appreciated! > Best, > Sonja > > > -- > Dr. med. Sonja Suntrup > Institute for Biomagnetism and Biosignalanalysis > University of Muenster > Malmedyweg 15 > 48149 Münster, Germany > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From dderiso at ucsd.edu Tue Dec 6 02:45:45 2011 From: dderiso at ucsd.edu (Dave Deriso) Date: Mon, 5 Dec 2011 17:45:45 -0800 Subject: [FieldTrip] Problem plotting independent components Message-ID: Dear Fieldtrip Users, I am trying to implement the tutorial on using ICA to extract eyeblink artifacts ( http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). Everything works, except that the labels from the IC data do not match the labels from the layout file, causing an error in the topoplotIC function. Your help in solving this is most appreciated. Layout labels (I am using a Neuromag 306 MEG): 'MEG0113' 'MEG0112' 'MEG0111' 'MEG0122' 'MEG0123' IC labels: 'runica001' 'runica002' 'runica003' 'runica004' 'runica005' Matlab Output: ft_topoplotIC(cfg, comp); creating layout from data.grad creating layout for neuromag306alt system Error using ft_topoplotTFR (line 659) labels in data and labels in layout do not match Error in ft_topoplotIC (line 122) ft_topoplotTFR(cfg, varargin{:}); Cheers, Dave Deriso -- UCSD Institute for Neural Computation UCSD Department of Neurosurgery -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Dec 6 07:46:17 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 6 Dec 2011 07:46:17 +0100 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: Message-ID: <195A02BE-0BCE-4A9A-B25B-15657D7DDC53@donders.ru.nl> Hi Dave, Could you try and report back what happens when you specify cfg.layout = 'NM306.lay', prior to calling ft_topoplotTFR? Cheers, JM On Dec 6, 2011, at 2:45 AM, Dave Deriso wrote: > Dear Fieldtrip Users, > > I am trying to implement the tutorial on using ICA to extract eyeblink artifacts (http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). Everything works, except that the labels from the IC data do not match the labels from the layout file, causing an error in the topoplotIC function. Your help in solving this is most appreciated. > > > Layout labels (I am using a Neuromag 306 MEG): > 'MEG0113' > 'MEG0112' > 'MEG0111' > 'MEG0122' > 'MEG0123' > > IC labels: > 'runica001' > 'runica002' > 'runica003' > 'runica004' > 'runica005' > > Matlab Output: > ft_topoplotIC(cfg, comp); > creating layout from data.grad > creating layout for neuromag306alt system > Error using ft_topoplotTFR (line 659) > labels in data and labels in layout do not match > Error in ft_topoplotIC (line 122) > ft_topoplotTFR(cfg, varargin{:}); > > > > Cheers, > Dave Deriso > > -- > UCSD Institute for Neural Computation > UCSD Department of Neurosurgery > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue Dec 6 12:55:31 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 06 Dec 2011 12:55:31 +0100 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: Message-ID: <4EDE02B3.1010103@donders.ru.nl> Dear Dave, the labels do not match indeed, because ICs do not correspond to single channel (obviously). I am not exactly sure how ft_topoplotIC is built, but you could try using ft_databrowser instead, with cfg.viewmode = 'component' Hope that at least circumvents your problem. Best, Jörn On 12/6/2011 2:45 AM, Dave Deriso wrote: > Dear Fieldtrip Users, > > I am trying to implement the tutorial on using ICA to extract eyeblink > artifacts > (http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). > Everything works, except that the labels from the IC data do not match > the labels from the layout file, causing an error in the topoplotIC > function. Your help in solving this is most appreciated. > > > Layout labels (I am using a Neuromag 306 MEG): > 'MEG0113' > 'MEG0112' > 'MEG0111' > 'MEG0122' > 'MEG0123' > > IC labels: > 'runica001' > 'runica002' > 'runica003' > 'runica004' > 'runica005' > > Matlab Output: > ft_topoplotIC(cfg, comp); > creating layout from data.grad > creating layout for neuromag306alt system > Error using ft_topoplotTFR (line 659) > labels in data and labels in layout do not match > Error in ft_topoplotIC (line 122) > ft_topoplotTFR(cfg, varargin{:}); > > > > Cheers, > Dave Deriso > > -- > UCSD Institute for Neural Computation > UCSD Department of Neurosurgery > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From h.rossiter at ucl.ac.uk Tue Dec 6 14:18:28 2011 From: h.rossiter at ucl.ac.uk (Rossiter, Holly) Date: Tue, 6 Dec 2011 13:18:28 +0000 Subject: [FieldTrip] DICS beamformer images Message-ID: Hi all, I am using DICS to assess coherence and viewing the beamformer images through SPM. What I want to know is what is the value given in the image and how is it calculated? I thought it was a coherence value but it is not bounded between 0 and 1. Also what do you think is the best way to threshold the images in order to get rid of low value peaks? Thanks, Holly -------------- next part -------------- An HTML attachment was scrubbed... URL: From dderiso at ucsd.edu Tue Dec 6 20:17:03 2011 From: dderiso at ucsd.edu (Dave Deriso) Date: Tue, 6 Dec 2011 11:17:03 -0800 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: <4EDE02B3.1010103@donders.ru.nl> References: <4EDE02B3.1010103@donders.ru.nl> Message-ID: Dear JM and Jörn, Thank you so much for your helpful suggestions. Matlab could not find/open layout file: *NM306.lay* with both *ft_topoplotTFR* and* ft_topoplotIC*. I have also tried each of the following layouts without success: cfg.layout =3D data.grad; cfg.layout =3D 'neuromag306all.lay'; cfg.layout =3D 'neuromag306cmb.lay'; cfg.layout =3D 'neuromag306mag.lay'; cfg.layout =3D 'neuromag306planar.lay'; (and no layout cfg, as prescribed by the bottom of http://fieldtrip.fcdonders.nl/reference/ft_topoplotic) As Jörn mentioned, the IC and sensor labels are different and, therefore, doing a string comparison will return an error. The question is then, how can I project the ICs back into sensor space and plot them topographically using the pre-existing sensor layouts? If this accomplished by the *ft_topoplotIC* function, shouldn't it expect the IC labels to be different from the layout labels? Thanks again for all of your help! Cheers, Dave Deriso -- UCSD Institute for Neural Computation UCSD Department of Neurosurgery On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" < jm.horschig at donders.ru.nl> wrote: > Dear Dave, > > the labels do not match indeed, because ICs do not correspond to single > channel (obviously). I am not exactly sure how ft_topoplotIC is built, but > you could try using ft_databrowser instead, with cfg.viewmode = 'component' > Hope that at least circumvents your problem. > > Best, > Jörn > > > On 12/6/2011 2:45 AM, Dave Deriso wrote: > > Dear Fieldtrip Users, > > I am trying to implement the tutorial on using ICA to extract eyeblink > artifacts ( > http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). > Everything works, except that the labels from the IC data do not match the > labels from the layout file, causing an error in the topoplotIC > function. Your help in solving this is most appreciated. > > > Layout labels (I am using a Neuromag 306 MEG): > 'MEG0113' > 'MEG0112' > 'MEG0111' > 'MEG0122' > 'MEG0123' > > IC labels: > 'runica001' > 'runica002' > 'runica003' > 'runica004' > 'runica005' > > Matlab Output: > ft_topoplotIC(cfg, comp); > creating layout from data.grad > creating layout for neuromag306alt system > Error using ft_topoplotTFR (line 659) > labels in data and labels in layout do not match > Error in ft_topoplotIC (line 122) > ft_topoplotTFR(cfg, varargin{:}); > > > > Cheers, > Dave Deriso > > -- > UCSD Institute for Neural Computation > UCSD Department of Neurosurgery > > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dderiso at ucsd.edu Wed Dec 7 02:07:55 2011 From: dderiso at ucsd.edu (Dave Deriso) Date: Tue, 6 Dec 2011 17:07:55 -0800 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: <4EDE02B3.1010103@donders.ru.nl> Message-ID: I should also note that when I tried the *ft_databrowser* function it was unable to plot the component topographies because there weren't enough grid points. Have you encountered this before? Thanks again for all of your great help!! My code: cfg = []; cfg.viewmode = 'component' ft_databrowser(cfg, comp); Output: creating layout from cfg.grad creating layout for neuromag306alt system the input is component data with 306 components and 306 original channels detected 0 visual artifacts redrawing with viewmode component fetching data... done fetching artifacts... done preprocessing data... done plotting artifacts... plotting events... plotting data... Warning: Imaginary parts of complex X and/or Y arguments ignored > In ft_plot_vector at 191 In ft_databrowser>redraw_cb at 1309 In ft_databrowser at 508 Warning: Imaginary parts of complex X and/or Y arguments ignored > In ft_plot_vector at 191 In ft_databrowser>redraw_cb at 1309 In ft_databrowser at 508 ****** these errors repeat about 10 times, then: plotting component topographies... Error using griddata (line 79) Not enough unique sample points specified. Error in ft_plot_topo (line 153) [Xi,Yi,Zi] = griddata(chanX', chanY, dat, xi', yi, interpmethod); % interpolate the topographic data Error in ft_databrowser>redraw_cb (line 1377) ft_plot_topo(chanx, chany, chanz, 'mask', laychan.mask, 'interplim', 'mask', 'outline', laychan.outline, 'tag', 'topography', ... Error in ft_databrowser (line 508) redraw_cb(h); Cheers, Dave On Tue, Dec 6, 2011 at 11:17 AM, Dave Deriso wrote: > Dear JM and Jörn, > > Thank you so much for your helpful suggestions. Matlab could not find/open > layout file: *NM306.lay* with both *ft_topoplotTFR* and* ft_topoplotIC*. > I have also tried each of the following layouts without success: > > cfg.layout =3D data.grad; > cfg.layout =3D 'neuromag306all.lay'; > cfg.layout =3D 'neuromag306cmb.lay'; > cfg.layout =3D 'neuromag306mag.lay'; > cfg.layout =3D 'neuromag306planar.lay'; > (and no layout cfg, as prescribed by the bottom of > http://fieldtrip.fcdonders.nl/reference/ft_topoplotic) > > > As Jörn mentioned, the IC and sensor labels are different and, > therefore, doing a string comparison will return an error. The question is > then, how can I project the ICs back into sensor space and plot them > topographically using the pre-existing sensor layouts? If this accomplished > by the *ft_topoplotIC* function, shouldn't it expect the IC labels to be > different from the layout labels? > > Thanks again for all of your help! > > Cheers, > Dave Deriso > > -- > UCSD Institute for Neural Computation > UCSD Department of Neurosurgery > > > > > On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" < > jm.horschig at donders.ru.nl> wrote: > >> Dear Dave, >> >> the labels do not match indeed, because ICs do not correspond to single >> channel (obviously). I am not exactly sure how ft_topoplotIC is built, but >> you could try using ft_databrowser instead, with cfg.viewmode = 'component' >> Hope that at least circumvents your problem. >> >> Best, >> Jörn >> >> >> On 12/6/2011 2:45 AM, Dave Deriso wrote: >> >> Dear Fieldtrip Users, >> >> I am trying to implement the tutorial on using ICA to extract eyeblink >> artifacts ( >> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). >> Everything works, except that the labels from the IC data do not match the >> labels from the layout file, causing an error in the topoplotIC >> function. Your help in solving this is most appreciated. >> >> >> Layout labels (I am using a Neuromag 306 MEG): >> 'MEG0113' >> 'MEG0112' >> 'MEG0111' >> 'MEG0122' >> 'MEG0123' >> >> IC labels: >> 'runica001' >> 'runica002' >> 'runica003' >> 'runica004' >> 'runica005' >> >> Matlab Output: >> ft_topoplotIC(cfg, comp); >> creating layout from data.grad >> creating layout for neuromag306alt system >> Error using ft_topoplotTFR (line 659) >> labels in data and labels in layout do not match >> Error in ft_topoplotIC (line 122) >> ft_topoplotTFR(cfg, varargin{:}); >> >> >> >> Cheers, >> Dave Deriso >> >> -- >> UCSD Institute for Neural Computation >> UCSD Department of Neurosurgery >> >> >> >> _______________________________________________ >> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Jörn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jarang.hahm at gmail.com Wed Dec 7 03:34:49 2011 From: jarang.hahm at gmail.com (Jarang Hahm) Date: Wed, 7 Dec 2011 11:34:49 +0900 Subject: [FieldTrip] Question about the identification of sensor type & proper timing of gradiometer selection Message-ID: Dear fieldtrip user. I'm newcomer on an MEG analysis and the fieldtrip. I have MEG data (.fif file) measured by Neuromag 306 channel system. Recently I got two problems on 1) identification of sensor type and 2) proper time to separate gradiometer in data processing. 1) First one is about identification of sensor type when using fieldtrip toolbox (20111204 version) After trial definition and preprocessing, I got some warnings in series when doing time-frequency analysis: Warning: could be Yokogawa system > In fileio\private\ft_senstype at 271 In ft_chantype at 71 In ft_chantype at 477 In ft_datatype_sens at 124 In ft_datatype_raw at 95 In ft_checkdata at 175 In ft_freqanalysis at 188 Warning: could be Yokogawa system > In fileio\private\ft_senstype at 271 In ft_chantype at 166 In ft_chantype at 477 In ft_datatype_sens at 124 In ft_datatype_raw at 95 In ft_checkdata at 175 In ft_freqanalysis at 188 (...There were also the other 12 warnings, which were simillar to above except for the specific line in ft_chantype.) As warning indicated, I've been ft_senstype at the line 271 and found that it couldn't recognize the data as a Neuromag 306 system although the sensor label of my data was matched with that of Neuromag 306. I wonder whether those warnings might affect overall analysis procedure or not and wish to fix this problem. 2) The second question is about a proper time for gradiometer selection. My analysis of interest is only gradiometer channels, not magnetometer one, so that the magnetometer can be removed at some time. In data processing, when is the proper time to separate the gradiometer channel from magnetometer? My data will be processed like this way: Trial definition -> preprocessing -> ICA for EOG rejection -> artifact rejection -> time-frequency analysis at sensor level & source analysis. Should I keep apart gradiometer channel from magnetometer after artifact rejection? or before ICA analysis? Need your help. Sincerely, Jarang Hahm -------------- next part -------------- An HTML attachment was scrubbed... URL: From miellet at psy.gla.ac.uk Wed Dec 7 07:52:28 2011 From: miellet at psy.gla.ac.uk (miellet at psy.gla.ac.uk) Date: Wed, 07 Dec 2011 06:52:28 +0000 Subject: [FieldTrip] second-level stats with TFR In-Reply-To: <4ECE596D.90504@psy.gla.ac.uk> References: <4ECE596D.90504@psy.gla.ac.uk> Message-ID: <20111207065228.27673d9bz74irz8s@horde.psy.gla.ac.uk> Hello, I've got problems doing second-level stats with TFR because of the data structure. I previously did it with ERF and didn't experience any difficulty. I'm just comparing 2 conditions so the design is very simple. The dimord for ERF was rpt_chan_time so I had access to the different trials. For ERF, I computed individual t-values between my conditions and across trials; then averaged the result across participants and compared the grand-average to zero. Do you think this strategy makes sense? For TFR, the dimord is chan_freq_time (with cfg.keeptrials='yes', before or after ft_freqbaseline). Obviously I don't want to compute the individual t-values across channels, freq bands or time points but across trials. Do you have any idea where I could find this information please? (I look in previous.....previous but couldn't find anything useful. I also specify keeptrials at each step of the process) Thank you very much for your help, Sebastien ---------------------------------------------- Dr. Sébastien Miellet, Lecturer Department of Psychology University of Fribourg Faucigny 2 1700 Fribourg Switzerland tel: +41 26 300 7666 ---------------------------------------------- Quoting Sara Bögels : > Hi all, > > I have been trying to do second-level statistical inference (as > described in one of the FAQs) on ERFs, but I am not sure whether I > am doing everything correctly. > > In the first step I calculate the T-values for the difference > between two conditions (twice), which are between items, with > ft_timelockstatistics. I put the output of all participants in a > cell (called 'stat1a' and 'stat1b'). (I tried to use > ft_timelockgrandaverage to combine the subjects together but it > needs a field avg). > > Then I use ft_timelockstatistics again but subject level. I first > want to look at the difference between the two conditions. This > difference is reflected in the T-values of the first step so I > create a dummy which is the same as 'stat1' but I replace all the > values in the field 'stat' per participant with zeros. Then I call > (with appropriate cfg parameters): > > stat2a = ft_timelockstatistics(cfg,stat1a{:},dummy{:}); > stat2b = ft_timelockstatistics(cfg,stat1b{:},dummy{:}); > > To compare the two differences (stat1a and stat1b) and thereby look > at an interaction, I call: > > stat2a-b = ft_timelockstatistics(cfg,stat1a{:},stat1b{:}); > > I am uncertain whether the dummy works (or is there a way to compare > the t-values to zero directly?) and whether the stat1a{:} trick > works with ft_timelockstatistics. > > Thanks in advance for your answer. > > Sara > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > ---------------------------------------------------------------- This message was sent using the Web mail system for The University of Glasgow School of Psychology ------------------------------------------------------------------ From jm.horschig at donders.ru.nl Wed Dec 7 08:33:08 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 07 Dec 2011 08:33:08 +0100 Subject: [FieldTrip] Critical bug in ft_freqstatistic fixed Message-ID: <4EDF16B4.4030605@donders.ru.nl> Dear 'trippers, last week we fixed a *critical bug in freqstatistic *which might have caused wrong clustering on channel-level. You might have been affected by this *if your channel labels were not ordered alphabetically by default *(e.g. BTI system, EEG systems, etc.). In essence, the bug caused channelclusters which did not make sense (e.g. frontal channels and occipital channels in one cluster). You might have noticed already whether you were affected by critically looking at the plots. *This bug was introduced in May 2011*, so if you made a cluster-based permutation test on channel-level between May and now, *please make the effort to rerun *to be sure that your clusters are not due to this bug! Thanks to Gregor Volberg who reported this bug and Tobias Staudigl for also looking into this one and providing a fix. Our sincere apologies for this. On behalf of the FieldTrip team, Jörn -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Dec 7 08:52:21 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 7 Dec 2011 08:52:21 +0100 Subject: [FieldTrip] second-level stats with TFR In-Reply-To: <20111207065228.27673d9bz74irz8s@horde.psy.gla.ac.uk> References: <4ECE596D.90504@psy.gla.ac.uk> <20111207065228.27673d9bz74irz8s@horde.psy.gla.ac.uk> Message-ID: Cher Seb, In order to be able to compute a single subject T-statistic on the TFR you indeed need to specify cfg.keeptrials = 'yes', prior to calling ft_freqanalysis. Are you absolutely sure that you did this? If so, we need to look into this. Could you create yourself an account on our bugzilla file-server (bugzilla.fcdonders.nl) and file this as a bug. Just copy and paste your e-mail message and also upload some script+data facilitating the reproduction of the problem? Cheers, Jan-Mathijs On Dec 7, 2011, at 7:52 AM, miellet at psy.gla.ac.uk wrote: > Hello, > I've got problems doing second-level stats with TFR because of the data structure. > I previously did it with ERF and didn't experience any difficulty. I'm just comparing 2 conditions so the design is very simple. The dimord for ERF was rpt_chan_time so I had access to the different trials. > For ERF, I computed individual t-values between my conditions and across trials; then averaged the result across participants and compared the grand-average to zero. Do you think this strategy makes sense? > For TFR, the dimord is chan_freq_time (with cfg.keeptrials='yes', before or after ft_freqbaseline). Obviously I don't want to compute the individual t-values across channels, freq bands or time points but across trials. > Do you have any idea where I could find this information please? (I look in previous.....previous but couldn't find anything useful. I also specify keeptrials at each step of the process) > Thank you very much for your help, > Sebastien > > ---------------------------------------------- > Dr. Sébastien Miellet, Lecturer > > Department of Psychology > University of Fribourg > Faucigny 2 > 1700 Fribourg > Switzerland > > tel: +41 26 300 7666 > ---------------------------------------------- > > > > Quoting Sara Bögels : > >> Hi all, >> >> I have been trying to do second-level statistical inference (as described in one of the FAQs) on ERFs, but I am not sure whether I am doing everything correctly. >> >> In the first step I calculate the T-values for the difference between two conditions (twice), which are between items, with ft_timelockstatistics. I put the output of all participants in a cell (called 'stat1a' and 'stat1b'). (I tried to use ft_timelockgrandaverage to combine the subjects together but it needs a field avg). >> >> Then I use ft_timelockstatistics again but subject level. I first want to look at the difference between the two conditions. This difference is reflected in the T-values of the first step so I create a dummy which is the same as 'stat1' but I replace all the values in the field 'stat' per participant with zeros. Then I call (with appropriate cfg parameters): >> >> stat2a = ft_timelockstatistics(cfg,stat1a{:},dummy{:}); >> stat2b = ft_timelockstatistics(cfg,stat1b{:},dummy{:}); >> >> To compare the two differences (stat1a and stat1b) and thereby look at an interaction, I call: >> >> stat2a-b = ft_timelockstatistics(cfg,stat1a{:},stat1b{:}); >> >> I am uncertain whether the dummy works (or is there a way to compare the t-values to zero directly?) and whether the stat1a{:} trick works with ft_timelockstatistics. >> >> Thanks in advance for your answer. >> >> Sara >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > ---------------------------------------------------------------- > This message was sent using the Web mail system for > The University of Glasgow School of Psychology > ------------------------------------------------------------------ > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Wed Dec 7 10:42:12 2011 From: julian.keil at gmail.com (Julian Keil) Date: Wed, 7 Dec 2011 10:42:12 +0100 Subject: [FieldTrip] Interactive Plotting in ft_rejectvisual Message-ID: <1C5AEC7D-4B54-428E-BE54-B408171837FC@gmail.com> Hi, Not really a bug report, so I put this on the discussion List. I noticed that when plotting single trials in the ft_rejectivusal function, the figure popping up is not interactive which makes a closer inspection of the trials somewhat harder. Maybe this is intentional, but I can't see a reason for it. However, simply adding "cfg_mp.interactive='yes';" at line 510 of "reject visual_summary" fixes this. Best, Julian Dipl. Psych. Julian Keil OBOB-Lab University of Konstanz Department of Psychology P.O. Box D25 78457 Konstanz Germany Tel: ++49 - (0)7531 - 88 42 50 Fax: ++49 - (0)7531 - 88 28 91 Email: julian.keil at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at donders.ru.nl Wed Dec 7 12:59:48 2011 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Wed, 7 Dec 2011 12:59:48 +0100 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: <4EDE02B3.1010103@donders.ru.nl> Message-ID: Hi Dave, Perhaps this error is due to the complex data that ft_databrowser cannot plot? If you re-calculate the components and get out real-only values, do you still get this error? Best, Johanna On 7 December 2011 02:07, Dave Deriso wrote: > I should also note that when I tried the *ft_databrowser* function it was > unable to plot the component topographies because there weren't enough grid > points. Have you encountered this before? Thanks again for all of your > great help!! > > My code: > > cfg = []; > cfg.viewmode = 'component' > ft_databrowser(cfg, comp); > > > Output: > > creating layout from cfg.grad > creating layout for neuromag306alt system > the input is component data with 306 components and 306 original channels > detected 0 visual artifacts > redrawing with viewmode component > fetching data... done > fetching artifacts... done > preprocessing data... done > plotting artifacts... > plotting events... > plotting data... > > Warning: Imaginary parts of complex X and/or Y arguments ignored > > In ft_plot_vector at 191 > In ft_databrowser>redraw_cb at 1309 > In ft_databrowser at 508 > Warning: Imaginary parts of complex X and/or Y arguments ignored > > In ft_plot_vector at 191 > In ft_databrowser>redraw_cb at 1309 > In ft_databrowser at 508 > ****** these errors repeat about > 10 times, then: > plotting component topographies... > Error using griddata (line 79) > Not enough unique sample points specified. > > Error in ft_plot_topo (line 153) > [Xi,Yi,Zi] = griddata(chanX', chanY, dat, xi', yi, interpmethod); % > interpolate the topographic data > > Error in ft_databrowser>redraw_cb (line 1377) > ft_plot_topo(chanx, chany, chanz, 'mask', laychan.mask, 'interplim', > 'mask', 'outline', laychan.outline, 'tag', 'topography', > ... > > Error in ft_databrowser (line 508) > redraw_cb(h); > > > > > > Cheers, > Dave > > > On Tue, Dec 6, 2011 at 11:17 AM, Dave Deriso wrote: > >> Dear JM and Jörn, >> >> Thank you so much for your helpful suggestions. Matlab could not >> find/open layout file: *NM306.lay* with both *ft_topoplotTFR* and* >> ft_topoplotIC*. I have also tried each of the following layouts without >> success: >> >> cfg.layout =3D data.grad; >> cfg.layout =3D 'neuromag306all.lay'; >> cfg.layout =3D 'neuromag306cmb.lay'; >> cfg.layout =3D 'neuromag306mag.lay'; >> cfg.layout =3D 'neuromag306planar.lay'; >> (and no layout cfg, as prescribed by the bottom of >> http://fieldtrip.fcdonders.nl/reference/ft_topoplotic) >> >> >> As Jörn mentioned, the IC and sensor labels are different and, >> therefore, doing a string comparison will return an error. The question is >> then, how can I project the ICs back into sensor space and plot them >> topographically using the pre-existing sensor layouts? If this accomplished >> by the *ft_topoplotIC* function, shouldn't it expect the IC labels to be >> different from the layout labels? >> >> Thanks again for all of your help! >> >> Cheers, >> Dave Deriso >> >> -- >> UCSD Institute for Neural Computation >> UCSD Department of Neurosurgery >> >> >> >> >> On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" < >> jm.horschig at donders.ru.nl> wrote: >> >>> Dear Dave, >>> >>> the labels do not match indeed, because ICs do not correspond to single >>> channel (obviously). I am not exactly sure how ft_topoplotIC is built, but >>> you could try using ft_databrowser instead, with cfg.viewmode = 'component' >>> Hope that at least circumvents your problem. >>> >>> Best, >>> Jörn >>> >>> >>> On 12/6/2011 2:45 AM, Dave Deriso wrote: >>> >>> Dear Fieldtrip Users, >>> >>> I am trying to implement the tutorial on using ICA to extract eyeblink >>> artifacts ( >>> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). >>> Everything works, except that the labels from the IC data do not match the >>> labels from the layout file, causing an error in the topoplotIC >>> function. Your help in solving this is most appreciated. >>> >>> >>> Layout labels (I am using a Neuromag 306 MEG): >>> 'MEG0113' >>> 'MEG0112' >>> 'MEG0111' >>> 'MEG0122' >>> 'MEG0123' >>> >>> IC labels: >>> 'runica001' >>> 'runica002' >>> 'runica003' >>> 'runica004' >>> 'runica005' >>> >>> Matlab Output: >>> ft_topoplotIC(cfg, comp); >>> creating layout from data.grad >>> creating layout for neuromag306alt system >>> Error using ft_topoplotTFR (line 659) >>> labels in data and labels in layout do not match >>> Error in ft_topoplotIC (line 122) >>> ft_topoplotTFR(cfg, varargin{:}); >>> >>> >>> >>> Cheers, >>> Dave Deriso >>> >>> -- >>> UCSD Institute for Neural Computation >>> UCSD Department of Neurosurgery >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> -- >>> Jörn M. Horschig >>> PhD Student >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognitive Neuroimaging >>> Radboud University Nijmegen >>> Neuronal Oscillations Group >>> >>> P.O. Box 9101 >>> NL-6500 HB Nijmegen >>> The Netherlands >>> >>> Contact: >>> E-Mail: jm.horschig at donders.ru.nl >>> Tel: +31-(0)24-36-68493 >>> Web: http://www.ru.nl/donders >>> >>> Visiting address: >>> Trigon, room 2.30 >>> Kapittelweg 29 >>> NL-6525 EN Nijmegen >>> The Netherlands >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed Dec 7 22:51:48 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 7 Dec 2011 22:51:48 +0100 Subject: [FieldTrip] how to avoid displaying function info In-Reply-To: References: Message-ID: <5A6D62F9-DD15-4683-B212-72517DB4AE3D@donders.ru.nl> Dear Marco This is now possible, see http://bugzilla.fcdonders.nl/show_bug.cgi?id=1191 and especially the last comment for details. Note that in case the callinfo is printed, the memory estimate only returns something useful on Linux and OS X. On Windows the memory useage cannot be estimated yet. best regards, Robert PS the main reason for printing the callinfo is to educate users about the memory and time requirements, so that users can more easily get reasonable lower-bound estimates for the resources required when doing distributed computing on a torque/sge linux cluster. On 25 Nov 2011, at 12:27, Marco Buiatti wrote: > Dear FTrippers, > > an aesthetic question: When I plot several topoplots, I would like to > avoid displaying information about the duration and RAM used by the > plotting functions, as: > the call to "ft_topoplotTFR" took 0 seconds and an estimated 0 MB > the call to "ft_prepare_layout" took 0 seconds and an estimated 0 MB > > Is there a simple way to do this? > > Thanks, > > Marco > > > -- > Marco Buiatti, PhD > > CEA/DSV/I2BM / NeuroSpin > INSERM U992 - Cognitive Neuroimaging Unit > Bât 145 - Point Courrier 156 > Gif sur Yvette F-91191 FRANCE > Ph: +33(0)169.08.65.21 > Fax: +33(0)169.08.79.73 > E-mail: marco.buiatti at gmail.com > http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti > > *********************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From dderiso at ucsd.edu Wed Dec 7 23:34:48 2011 From: dderiso at ucsd.edu (Dave Deriso) Date: Wed, 7 Dec 2011 14:34:48 -0800 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: <4EDE02B3.1010103@donders.ru.nl> Message-ID: Hi Johanna, Thanks for taking a look. I could not find a method inside * ft_componentanalysis* that extracts real values (although using real() could also accomplish this), however the warning seems to indicate that the complex values are ignored. Do you think this is still an issue? The error with *ft_databrowser* indicates a lack of "unique sample points" from some kind of grid, which is perhaps a bigger problem. Any thoughts? Thanks again! Cheers, Dave On Wed, Dec 7, 2011 at 3:59 AM, Johanna Zumer wrote: > Hi Dave, > Perhaps this error is due to the complex data that ft_databrowser cannot > plot? If you re-calculate the components and get out real-only values, do > you still get this error? > > Best, > Johanna > > > On 7 December 2011 02:07, Dave Deriso wrote: > >> I should also note that when I tried the *ft_databrowser* function it >> was unable to plot the component topographies because there weren't enough >> grid points. Have you encountered this before? Thanks again for all of your >> great help!! >> >> My code: >> >> cfg = []; >> cfg.viewmode = 'component' >> ft_databrowser(cfg, comp); >> >> >> Output: >> >> creating layout from cfg.grad >> creating layout for neuromag306alt system >> the input is component data with 306 components and 306 original channels >> detected 0 visual artifacts >> redrawing with viewmode component >> fetching data... done >> fetching artifacts... done >> preprocessing data... done >> plotting artifacts... >> plotting events... >> plotting data... >> >> Warning: Imaginary parts of complex X and/or Y arguments ignored >> > In ft_plot_vector at 191 >> In ft_databrowser>redraw_cb at 1309 >> In ft_databrowser at 508 >> Warning: Imaginary parts of complex X and/or Y arguments ignored >> > In ft_plot_vector at 191 >> In ft_databrowser>redraw_cb at 1309 >> In ft_databrowser at 508 >> ****** these errors repeat >> about 10 times, then: >> plotting component topographies... >> Error using griddata (line 79) >> Not enough unique sample points specified. >> >> Error in ft_plot_topo (line 153) >> [Xi,Yi,Zi] = griddata(chanX', chanY, dat, xi', yi, interpmethod); % >> interpolate the topographic data >> >> Error in ft_databrowser>redraw_cb (line 1377) >> ft_plot_topo(chanx, chany, chanz, 'mask', laychan.mask, >> 'interplim', 'mask', 'outline', laychan.outline, 'tag', 'topography', >> ... >> >> Error in ft_databrowser (line 508) >> redraw_cb(h); >> >> >> >> >> >> Cheers, >> Dave >> >> >> On Tue, Dec 6, 2011 at 11:17 AM, Dave Deriso wrote: >> >>> Dear JM and Jörn, >>> >>> Thank you so much for your helpful suggestions. Matlab could not >>> find/open layout file: *NM306.lay* with both *ft_topoplotTFR* and* >>> ft_topoplotIC*. I have also tried each of the following layouts >>> without success: >>> >>> cfg.layout =3D data.grad; >>> cfg.layout =3D 'neuromag306all.lay'; >>> cfg.layout =3D 'neuromag306cmb.lay'; >>> cfg.layout =3D 'neuromag306mag.lay'; >>> cfg.layout =3D 'neuromag306planar.lay'; >>> (and no layout cfg, as prescribed by the bottom of >>> http://fieldtrip.fcdonders.nl/reference/ft_topoplotic) >>> >>> >>> As Jörn mentioned, the IC and sensor labels are different and, >>> therefore, doing a string comparison will return an error. The question is >>> then, how can I project the ICs back into sensor space and plot them >>> topographically using the pre-existing sensor layouts? If this accomplished >>> by the *ft_topoplotIC* function, shouldn't it expect the IC labels to >>> be different from the layout labels? >>> >>> Thanks again for all of your help! >>> >>> Cheers, >>> Dave Deriso >>> >>> -- >>> UCSD Institute for Neural Computation >>> UCSD Department of Neurosurgery >>> >>> >>> >>> >>> On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" < >>> jm.horschig at donders.ru.nl> wrote: >>> >>>> Dear Dave, >>>> >>>> the labels do not match indeed, because ICs do not correspond to single >>>> channel (obviously). I am not exactly sure how ft_topoplotIC is built, but >>>> you could try using ft_databrowser instead, with cfg.viewmode = 'component' >>>> Hope that at least circumvents your problem. >>>> >>>> Best, >>>> Jörn >>>> >>>> >>>> On 12/6/2011 2:45 AM, Dave Deriso wrote: >>>> >>>> Dear Fieldtrip Users, >>>> >>>> I am trying to implement the tutorial on using ICA to extract >>>> eyeblink artifacts ( >>>> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). >>>> Everything works, except that the labels from the IC data do not match the >>>> labels from the layout file, causing an error in the topoplotIC >>>> function. Your help in solving this is most appreciated. >>>> >>>> >>>> Layout labels (I am using a Neuromag 306 MEG): >>>> 'MEG0113' >>>> 'MEG0112' >>>> 'MEG0111' >>>> 'MEG0122' >>>> 'MEG0123' >>>> >>>> IC labels: >>>> 'runica001' >>>> 'runica002' >>>> 'runica003' >>>> 'runica004' >>>> 'runica005' >>>> >>>> Matlab Output: >>>> ft_topoplotIC(cfg, comp); >>>> creating layout from data.grad >>>> creating layout for neuromag306alt system >>>> Error using ft_topoplotTFR (line 659) >>>> labels in data and labels in layout do not match >>>> Error in ft_topoplotIC (line 122) >>>> ft_topoplotTFR(cfg, varargin{:}); >>>> >>>> >>>> >>>> Cheers, >>>> Dave Deriso >>>> >>>> -- >>>> UCSD Institute for Neural Computation >>>> UCSD Department of Neurosurgery >>>> >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> >>>> -- >>>> Jörn M. Horschig >>>> PhD Student >>>> Donders Institute for Brain, Cognition and Behaviour >>>> Centre for Cognitive Neuroimaging >>>> Radboud University Nijmegen >>>> Neuronal Oscillations Group >>>> >>>> P.O. Box 9101 >>>> NL-6500 HB Nijmegen >>>> The Netherlands >>>> >>>> Contact: >>>> E-Mail: jm.horschig at donders.ru.nl >>>> Tel: +31-(0)24-36-68493 >>>> Web: http://www.ru.nl/donders >>>> >>>> Visiting address: >>>> Trigon, room 2.30 >>>> Kapittelweg 29 >>>> NL-6525 EN Nijmegen >>>> The Netherlands >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Dec 8 07:58:13 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 8 Dec 2011 07:58:13 +0100 Subject: [FieldTrip] Problem plotting independent components In-Reply-To: References: <4EDE02B3.1010103@donders.ru.nl> Message-ID: Dear Dave, The output of an ICA should actually not contain complex numbers. It can happen though, and this is indicative of a problem. You should probably have a look at this FAQ: http://fieldtrip.fcdonders.nl/faq/why_does_my_ica_output_contain_complex_numbers Best, Eelke 2011/12/7 Dave Deriso : > Hi Johanna, > > Thanks for taking a look. I could not find a method inside > ft_componentanalysis that extracts real values (although using real() could > also accomplish this), however the warning seems to indicate that the > complex values are ignored. Do you think this is still an issue? The error > with ft_databrowser indicates a lack of "unique sample points" from some > kind of grid, which is perhaps a bigger problem. Any thoughts? Thanks again! > > Cheers, > Dave > > On Wed, Dec 7, 2011 at 3:59 AM, Johanna Zumer > wrote: >> >> Hi Dave, >> Perhaps this error is due to the complex data that ft_databrowser cannot >> plot?  If you re-calculate the components and get out real-only values, do >> you still get this error? >> >> Best, >> Johanna >> >> >> On 7 December 2011 02:07, Dave Deriso wrote: >>> >>> I should also note that when I tried the ft_databrowser function it was >>> unable to plot the component topographies because there weren't enough grid >>> points. Have you encountered this before? Thanks again for all of your great >>> help!! >>> >>> My code: >>> >>> cfg = []; >>> cfg.viewmode = 'component' >>> ft_databrowser(cfg, comp); >>> >>> >>> Output: >>> >>> creating layout from cfg.grad >>> creating layout for neuromag306alt system >>> the input is component data with 306 components and 306 original channels >>> detected   0 visual artifacts >>> redrawing with viewmode component >>> fetching data... done >>> fetching artifacts... done >>> preprocessing data... done >>> plotting artifacts... >>> plotting events... >>> plotting data... >>> >>> Warning: Imaginary parts of complex X and/or Y arguments ignored >>> > In ft_plot_vector at 191 >>>   In ft_databrowser>redraw_cb at 1309 >>>   In ft_databrowser at 508 >>> Warning: Imaginary parts of complex X and/or Y arguments ignored >>> > In ft_plot_vector at 191 >>>   In ft_databrowser>redraw_cb at 1309 >>>   In ft_databrowser at 508 >>>                                           ****** these errors repeat >>> about 10 times, then: >>> plotting component topographies... >>> Error using griddata (line 79) >>> Not enough unique sample points specified. >>> >>> Error in ft_plot_topo (line 153) >>> [Xi,Yi,Zi] = griddata(chanX', chanY, dat, xi', yi, interpmethod); % >>> interpolate the topographic data >>> >>> Error in ft_databrowser>redraw_cb (line 1377) >>>       ft_plot_topo(chanx, chany, chanz, 'mask', laychan.mask, >>> 'interplim', 'mask', 'outline', laychan.outline, 'tag', 'topography', >>>       ... >>> >>> Error in ft_databrowser (line 508) >>> redraw_cb(h); >>> >>> >>> >>> >>> >>> Cheers, >>> Dave >>> >>> >>> On Tue, Dec 6, 2011 at 11:17 AM, Dave Deriso wrote: >>>> >>>> Dear JM and Jörn, >>>> >>>> Thank you so much for your helpful suggestions. Matlab could not >>>> find/open layout file: NM306.lay with both ft_topoplotTFR and ft_topoplotIC. >>>> I have also tried each of the following layouts without success: >>>> >>>> cfg.layout    =3D data.grad; >>>> cfg.layout    =3D 'neuromag306all.lay'; >>>> cfg.layout    =3D 'neuromag306cmb.lay'; >>>> cfg.layout    =3D 'neuromag306mag.lay'; >>>> cfg.layout    =3D 'neuromag306planar.lay'; >>>> (and no layout cfg, as prescribed by the bottom >>>> of http://fieldtrip.fcdonders.nl/reference/ft_topoplotic) >>>> >>>> >>>> As Jörn mentioned, the IC and sensor labels are different and, >>>> therefore, doing a string comparison will return an error. The question is >>>> then, how can I project the ICs back into sensor space and plot them >>>> topographically using the pre-existing sensor layouts? If this accomplished >>>> by the ft_topoplotIC function, shouldn't it expect the IC labels to be >>>> different from the layout labels? >>>> >>>> Thanks again for all of your help! >>>> >>>> Cheers, >>>> Dave Deriso >>>> >>>> -- >>>> UCSD Institute for Neural Computation >>>> UCSD Department of Neurosurgery >>>> >>>> >>>> >>>> >>>> On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" >>>> wrote: >>>>> >>>>> Dear Dave, >>>>> >>>>> the labels do not match indeed, because ICs do not correspond to single >>>>> channel (obviously). I am not exactly sure how ft_topoplotIC is built, but >>>>> you could try using ft_databrowser instead, with cfg.viewmode = 'component' >>>>> Hope that at least circumvents your problem. >>>>> >>>>> Best, >>>>> Jörn >>>>> >>>>> >>>>> On 12/6/2011 2:45 AM, Dave Deriso wrote: >>>>> >>>>> Dear Fieldtrip Users, >>>>> >>>>> I am trying to implement the tutorial on using ICA to extract eyeblink >>>>> artifacts >>>>> (http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts). >>>>> Everything works, except that the labels from the IC data do not match the >>>>> labels from the layout file, causing an error in the topoplotIC >>>>> function. Your help in solving this is most appreciated. >>>>> >>>>> >>>>> Layout labels (I am using a Neuromag 306 MEG): >>>>> 'MEG0113' >>>>> 'MEG0112' >>>>> 'MEG0111' >>>>> 'MEG0122' >>>>> 'MEG0123' >>>>> >>>>> IC labels: >>>>> 'runica001' >>>>> 'runica002' >>>>> 'runica003' >>>>> 'runica004' >>>>> 'runica005' >>>>> >>>>> Matlab Output: >>>>> ft_topoplotIC(cfg, comp); >>>>> creating layout from data.grad >>>>> creating layout for neuromag306alt system >>>>> Error using ft_topoplotTFR (line 659) >>>>> labels in data and labels in layout do not match >>>>> Error in ft_topoplotIC (line 122) >>>>> ft_topoplotTFR(cfg, varargin{:}); >>>>> >>>>> >>>>> >>>>> Cheers, >>>>> Dave Deriso >>>>> >>>>> -- >>>>> UCSD Institute for Neural Computation >>>>> UCSD Department of Neurosurgery >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>>> >>>>> >>>>> >>>>> -- >>>>> Jörn M. Horschig >>>>> PhD Student >>>>> Donders Institute for Brain, Cognition and Behaviour >>>>> Centre for Cognitive Neuroimaging >>>>> Radboud University Nijmegen >>>>> Neuronal Oscillations Group >>>>> >>>>> P.O. Box 9101 >>>>> NL-6500 HB Nijmegen >>>>> The Netherlands >>>>> >>>>> Contact: >>>>> E-Mail: jm.horschig at donders.ru.nl >>>>> Tel: +31-(0)24-36-68493 >>>>> Web: http://www.ru.nl/donders >>>>> >>>>> Visiting address: >>>>> Trigon, room 2.30 >>>>> Kapittelweg 29 >>>>> NL-6525 EN Nijmegen >>>>> The Netherlands >>>>> >>>>> >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From ole.jensen at donders.ru.nl Thu Dec 8 10:14:44 2011 From: ole.jensen at donders.ru.nl (Ole Jensen) Date: Thu, 08 Dec 2011 10:14:44 +0100 Subject: [FieldTrip] PhD position at the Donders Institute, Nijmegen Message-ID: <4EE08004.9020903@donders.ru.nl> Dear colleagues, If you know of potential PhD candidates please forward them the job listing below. All the best, Ole Jensen -- Ole Jensen http://www.neuosc.com ------- PhD position on 'Bridging the Gap between Neuronal Activity and Neuroimaging' (1,0 fte) *Donders Institute, Centre for Cognitive Neuroimaging* *Maximum salary: EUR 2,612 gross/month* *Vacancy number: 30.08.11* *Closing date: 1 January 2012* *Responsibilities* The Neuronal Oscillation group and the MR Techniques in Brain Function group at the Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, have funding available for a PhD position, aimed at quantitative evaluation of neuroimaging signal characteristics resulting from activity of neurons in the working human brain. The human brain is composed of multiple regions that are flexibly engaged and disengaged depending on the cognitive task performed. Each of these regions comprises large numbers of neurons that interact non-linearly. A fundamental question in cognitive neuroscience is how the connections and interactions of the neurons shape the functional architecture of the working brain. At the Donders Institute this question is addressed experimentally by measuring cognitive signals by means of magneto-encephalography (MEG), electro-encephalography (EEG) and functional magnetic resonance imaging (fMRI). You will work on this project from a complementary perspective, using computer simulation to investigate which plausible networks of neurons can explain measured signals. You will use and extend numerical software developed at the institute and elsewhere. Your results will improve the interpretation of measured cognitive signals. You will focus on positive and negative spatial and temporal correlations between various signals obtained in cognitive experiments. *Work environment* The Donders Institute for Brain, Cognition and Behaviour consists of the Centre for Cognition, the Centre for Cognitive Neuroimaging and the Centre for Neuroscience. The mission of the Centre for Cognitive Neuroimaging is to conduct cutting-edge fundamental research in cognitive neuroscience. Much of the rapid progress in this field is being driven by the development of complex neuroimaging techniques for measuring activity in the human working brain - an area in which the Centre plays a leading role. The research themes cover central cognitive functions such as perception, action, control, decision making, attention, memory, language, learning and plasticity. The Centre also aims to establish how the different brain areas coordinate their activity with very high temporal precision to enable human and animal cognition. This internationally renowned centre currently employs more than 100 PhD students and post-doctoral researchers of more than 20 different nationalities, offering a stimulating and multidisciplinary research environment. The centre is equipped with three MRI scanners (7T, 3T, 1.5T), a 275-channel MEG system, an EEG-TMS laboratory, several (MR-compatible) EEG systems, and high-performance computational facilities. English is the lingua franca at the centre. You will work within a joint project of the Neuronal Oscillations group and the MR Methods for Cognitive Neuroscience group at the Centre for Cognitive Neuroimaging, and the Neuroinformatics department at the Centre for Neuroscience. *What we expect from you* You should have a Master's degree (or equivalent). Applicants with a background in neuroscience should be willing to acquire the mathematical and numerical skills required to simulate complex systems. Applicants with a background in mathematics, physics or computer science should be willing to develop in-depth knowledge of cognitive neuroscience and physiology. You are enthusiastic to understand the dynamic properties of the human brain and to probe the interaction between different regions, all on the basis of what is known of the physiology of the brain. Furthermore, you are prepared to take courses and workshops offered at the Donders Graduate School for Cognitive Neuroscience to bring your knowledge of cognitive neuroscience up to the standard required. You should be willing to work in a multidisciplinary environment in which the results and methods from various disciplines, ranging from natural to behavioural sciences, are integrated. And you are eager to work with us at the cutting edge of science, where your personal commitment and skills are both essential and appreciated. Proficiency in oral and written English is essential. You are expected to work in a team, sharing technical know-how and ideas. *What we have to offer* We offer you: - employment: 1,0 fte; - a maximum gross monthly salary of EUR 2,612 based on a 38-hour working week; - in addition to the salary: an 8% holiday allowance and an 8.3% end-of-year bonus; - The starting salary is EUR2,042 per month and will increase to EUR2,612 per month in the fourth year; - duration of the contract: 4 years. Are you interested in our excellent employment conditions ? *Other Information* This vacancy was advertised earlier this year in July/August. If you applied for this position at the time and were rejected, please do not apply again. *Would you like to know more?* Further information on: DCCN Prof. dr. Jan van der Eerden, project leader Telephone:+31 24 3614602 E-mail: j.vandereerden at donders.ru.nl Dr. Ole Jensen, PI Neuronal Oscillation group Telephone:+31 24 3610884 E-mail: ole.jensen at donders.ru.nl * * *Applications* Are you interested? Please submit an application letter, a CV, and the names of two persons who can provide references. Please explain your interest in neuroscience and the above mentioned scientific approaches in your application letter. It is Radboud University Nijmegen's policy to only accept applications by e-mail. Please send your application, /stating vacancy number 30.08.11/, to vacatures at dpo.ru.nl , for the attention of Prof. dr. Jan van der Eerden, before 1 January 2012. For more information on the application procedure:+ 31 24 3611173 -- Ole Jensen http://www.neuosc.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.leszczynski.m at googlemail.com Thu Dec 8 17:33:45 2011 From: m.leszczynski.m at googlemail.com (Marcin Leszczynski) Date: Thu, 8 Dec 2011 17:33:45 +0100 Subject: [FieldTrip] 2x3 anova in cluster analysis In-Reply-To: References: Message-ID: Hi Jan-Mathijs and Fieldtrippers, I have a follow up question refering to statistical inference about monotonic trends in the permutation framework. I have four conditions A, B, C, D and I would like to test whether there is a monotonic change in the ERP/TF among the conditions (i.e. A > 2011/12/5 jan-mathijs schoffelen > >> Hi Stan et al, >> >> Actually FieldTrip allows in a very straightforward way to plug-in one's >> favourite statistic. The idea is the following: when specifying >> cfg.statistic you need to specify a string that under the hood points to a >> function, e.g. 'indepsamplesT' eventually causes a function to be called, >> answering to the aptly chosen name: 'statfun_indepsamplesT' which is doing >> the legwork. As long as the statfun_younameit has properly defined input >> and output arguments, you can let it do whatever you want. FieldTrip >> contains a bunch of 'statfuns' in the statfun directory but there's no >> reason not to implement any yourself (and ideally contribute them to the >> repository). >> Another discussion altogether is the question whether the test statistic >> of interest is an appropriate one that allows for statistical inference >> using the permutation framework. Over the past years there have been >> various threads on this mailing list regarding the possibility to test for >> interactions using a permutation test. You can look this up in the archive. >> Strictly speaking this is statistically not possible this way. The >> permutation-framework tests the null-hypothesis of exchangeability of data >> across allocated conditions, whereas when one wants to test for an >> interaction effect tests one tests for a particular linear (parametric) >> model of the dependent variables explaining variance in the dependent >> variable. Inferring that exchangeability across conditions is unlikely >> (i.e. obtaining a small p-value through permutation) does not necessarily >> lead to the conclusion that there is an actual interaction effect. Though >> opinions among the statisticians about this seem to vary, there may be a >> way out: one could either use bootstrapping to obtain confidence intervals >> for the interaction F under the null-hypothesis. The recipe for this would >> be to do a cell-specific demeaning of the data to impose the >> null-hypothesis of no interaction, and then through bootstrap resampling >> obtain a reference distribution of the interaction F. Alternatively, >> although I haven't thought this one through for any case other than a 2x2 >> anova, one could reduce the interaction effect to a two-condition contrast >> where observations belonging to the 'main diagonal' of the 2x2 conditions >> design are labeled as condition 1, and the observations belonging to the >> other diagonal are labeled as condition 2. One could then proceed with >> using a T-statistic as a descriptive statistic across these two >> 'conditions' on which inference can be done. >> >> Cheers and a happy Sinterklaas to you all, >> >> Jan-Mathijs >> >> >> On Dec 5, 2011, at 8:17 PM, Stanley Klein wrote: >> >> Nico, >> >> Your question gives me the chance to ask something I've been curious >> about. It seems to me that one of the nifty things about permutation >> cluster analysis is that it allows you to do anything that seems reasonable >> as long you decide on the process ahead of time and don't do any future >> tweaking other than fixing coding errors. I'm curious whether the Fieldtrip >> code make it easy to insert new statistics modules. >> >> I presume your actual question had to do with whether Fieldtrip already >> has the possibility of doing that 2x3 ANOVA. I suspect it doesn't have >> that capability. However, it would be nice if the permutation cluster >> analysis could be made sufficiently modular that one could make use of all >> the complicated clustering and permuting and all, but enable the user to >> substitute their own statistical method. I haven't actually watched my >> students doing the nitty-gritty use of Fieldtrip's version of the >> permutation test (other than knowing that is is very nice and well >> documented) so I don't know how easy it is to stick in one's own favorite >> statistic, but I'm hoping it is easy. >> >> Stan >> >> On Mon, Dec 5, 2011 at 4:58 AM, Nico Alexander Willi Kremers < >> nkremers at uni-bonn.de> wrote: >> >>> >>> Hi, >>> >>> I followed the discussion about implementing a 2x2 within subjects >>> design into a cluster statistic with much interest. I want to implement a >>> 2x3 repeated measure anova in a cluster analysis using fieldtrip. I think >>> for this type of analysis subracting two conditions from each other and >>> then calculate a ttest is not appropriate. Is there another way of >>> calculating the interaction effect between the two factors and generate >>> clusters for real and permutation data? What specifications must be set and >>> how? >>> >>> Thank you very much for your answer, >>> >>> Nico >>> ______________________________**_________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.m.groppe at gmail.com Fri Dec 9 20:18:21 2011 From: david.m.groppe at gmail.com (David Groppe) Date: Fri, 9 Dec 2011 14:18:21 -0500 Subject: [FieldTrip] 2x3 anova in cluster analysis In-Reply-To: References: Message-ID: Hi Marcin, You could use a permutation test based on a rank correlation statistic (e.g., Kendall's tau or Spearman's rho) to test for such a monotonic relationship. I do not know if FieldTrip currently implements this or not though. cheers, -D On Thu, Dec 8, 2011 at 11:33 AM, Marcin Leszczynski wrote: > Hi Jan-Mathijs and Fieldtrippers, > > I have a follow up question refering to statistical inference about > monotonic trends in the permutation framework. > > I have four conditions A, B, C, D and I would like to test whether there is > a monotonic change in the ERP/TF among the conditions (i.e. A possibly also A < B <= C < D). I guess one way would be to run multiple t > tests. However it seems a bit unconvenient as one needs to correct for > multiple comparisons. Furtheremore, the second case (A < B <= C < D) might > not be well captured. > > I found a thread from 31 Aug 2011 ("[FieldTrip] depsamplesregrT help" by > Jonas Obleser) suggesting that depsamplesregrT will be the way to go. > However, your reply to Nico somehow destroyed my confidence. If I got the > reply correctly this is not that easy as I would be testing a particular > linear model which is a bit of a problem. Thus, the question: > > How would you suggest testing for such a monotonic effect in the permutation > framework? > > Best, > Marcin > >> >> >> 2011/12/5 jan-mathijs schoffelen >>> >>> Hi Stan et al, >>> >>> Actually FieldTrip allows in a very straightforward way to plug-in one's >>> favourite statistic. The idea is the following: when specifying >>> cfg.statistic you need to specify a string that under the hood points to a >>> function, e.g. 'indepsamplesT' eventually causes a function to be called, >>> answering to the aptly chosen name: 'statfun_indepsamplesT' which is doing >>> the legwork. As long as the statfun_younameit has properly defined input and >>> output arguments, you can let it do whatever you want. FieldTrip contains a >>> bunch of 'statfuns' in the statfun directory but there's no reason not to >>> implement any yourself (and ideally contribute them to the repository). >>> Another discussion altogether is the question whether the test statistic >>> of interest is an appropriate one that allows for statistical inference >>> using the permutation framework. Over the past years there have been various >>> threads on this mailing list regarding the possibility to test for >>> interactions using a permutation test. You can look this up in the archive. >>> Strictly speaking this is statistically not possible this way. The >>> permutation-framework tests the null-hypothesis of exchangeability of data >>> across allocated conditions, whereas when one wants to test for an >>> interaction effect tests one tests for a particular linear (parametric) >>> model of the dependent variables explaining variance in the dependent >>> variable. Inferring that exchangeability across conditions is unlikely (i.e. >>> obtaining a small p-value through permutation) does not necessarily lead to >>> the conclusion that there is an actual interaction effect. Though opinions >>> among the statisticians about this seem to vary, there may be a way out: one >>> could either use bootstrapping to obtain confidence intervals for the >>> interaction F under the null-hypothesis. The recipe for this would be to do >>> a cell-specific demeaning of the data to impose the null-hypothesis of no >>> interaction, and then through bootstrap resampling obtain a reference >>> distribution of the interaction F. Alternatively, although I haven't thought >>> this one through for any case other than a 2x2 anova, one could reduce the >>> interaction effect to a two-condition contrast where observations belonging >>> to the 'main diagonal' of the 2x2 conditions design are labeled as condition >>> 1, and the observations belonging to the other diagonal are labeled as >>> condition 2. One could then proceed with using a T-statistic as a >>> descriptive statistic across these two 'conditions' on which inference can >>> be done. >>> >>> Cheers and a happy Sinterklaas to you all, >>> >>> Jan-Mathijs >>> >>> >>> On Dec 5, 2011, at 8:17 PM, Stanley Klein wrote: >>> >>> Nico, >>> >>> Your question gives me the chance to ask something I've been curious >>> about. It seems to me that one of the nifty things about permutation cluster >>> analysis is that it allows you to do anything that seems reasonable as long >>> you decide on the process ahead of time and don't do any future tweaking >>> other than fixing coding errors. I'm curious whether the Fieldtrip code make >>> it easy to insert new statistics modules. >>> >>> I presume your actual question had to do with whether Fieldtrip already >>> has the possibility of doing that 2x3 ANOVA.  I suspect it doesn't have that >>> capability. However, it would be nice if the permutation cluster analysis >>> could be made sufficiently modular that one could make use of all the >>> complicated clustering and permuting and all, but enable the user to >>> substitute their own statistical method.  I haven't actually watched my >>> students doing the nitty-gritty use of Fieldtrip's version of the >>> permutation test (other than knowing that is is very nice and well >>> documented) so I don't know how easy it is to stick in one's own favorite >>> statistic, but I'm hoping it is easy. >>> >>> Stan >>> >>> On Mon, Dec 5, 2011 at 4:58 AM, Nico Alexander Willi Kremers >>> wrote: >>>> >>>> >>>> Hi, >>>> >>>> I followed the discussion about implementing a 2x2 within subjects >>>> design into a cluster statistic with much interest. I want to implement a >>>> 2x3 repeated measure anova in a cluster analysis using fieldtrip. I think >>>> for this type of analysis subracting two conditions from each other and then >>>> calculate a ttest is not appropriate. Is there another way of calculating >>>> the interaction effect between the two factors and generate clusters for >>>> real and permutation data? What specifications must be set and how? >>>> >>>> Thank you very much for your answer, >>>> >>>> Nico >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> Jan-Mathijs Schoffelen, MD PhD >>> >>> Donders Institute for Brain, Cognition and Behaviour, >>> Centre for Cognitive Neuroimaging, >>> Radboud University Nijmegen, The Netherlands >>> >>> Max Planck Institute for Psycholinguistics, >>> Nijmegen, The Netherlands >>> >>> J.Schoffelen at donders.ru.nl >>> Telephone: +31-24-3614793 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- David Groppe, Ph.D. Postdoctoral Researcher North Shore LIJ Health System New Hyde Park, New York http://www.cogsci.ucsd.edu/~dgroppe/ From eva.patai at psy.ox.ac.uk Sun Dec 11 20:28:51 2011 From: eva.patai at psy.ox.ac.uk (Zita Eva Patai) Date: Sun, 11 Dec 2011 19:28:51 +0000 Subject: [FieldTrip] clusterstat on multiple frequencies Message-ID: Dear FT-ers, I have tried to run a permutation test on time-frequency data, and would have like to see a statistical evealuation over a set of frequencies (ex: 4-8Hz) It seems that the test itself runs, but it crashes when i try to plot the data, saying that 'stat' must not contain multiple frequencies. I was wondering if there was a way to evaluate the difference between two conditions over a set range of frequencies? Thank you! zita -- Zita Patai DPhil Candidate, Experimental Psychology University of Oxford bcl.psy.ox.ac.uk/people/zita-eva-patai/ eva.patai at psy.ox.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From inieuwenhuis at berkeley.edu Sun Dec 11 21:06:11 2011 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Sun, 11 Dec 2011 12:06:11 -0800 Subject: [FieldTrip] rereference to repaired channel Message-ID: <4EE50D33.8030500@berkeley.edu> Hi all, I've measured EEG data with Cz as the reference. I now want to rereference to linked mastoids. However, in one participant one of the mastoid electrodes is really noisy. Is it valid to throw out the noisy channel, then fix it (with ft_channelrepair), and then rereference to this fixed mastoid channel? In other words, is channelrepair a linear operation? Or would I be mixing (a little) Cz into all channels now...? Any other options? Or another way of asking: do I get the same result if I first rereference and then fix bad channels, compared to first fixing bad channels and then rereference? In the participant with the bad mastoid chan, I don't have a choice, I have to first fix the channel first, or I'd be mixing noise into all channels. But, in other participants, where I also have bad channels (but not the mastoid ones), does the order matter, which order is better? I'd think first rereference, then fix... Correct? Thanks!! Ingrid -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 From jan.schoffelen at donders.ru.nl Mon Dec 12 08:59:38 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 12 Dec 2011 08:59:38 +0100 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: References: Message-ID: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> Hi Zita, Could you provide some more information please? What plotting function are you using? What does the stat-structure look like etc.? With sufficient additional information we can try and reproduce the problem, and if it's a bug fix it. If it's not a bug, we may give you some hints to fool the system... BW, Jan-Mathijs On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: > Dear FT-ers, > > I have tried to run a permutation test on time-frequency data, and would have like to see a statistical evealuation over a set of frequencies (ex: 4-8Hz) > > It seems that the test itself runs, but it crashes when i try to plot the data, saying that 'stat' must not contain multiple frequencies. > > I was wondering if there was a way to evaluate the difference between two conditions over a set range of frequencies? > > Thank you! > zita > > > -- > > Zita Patai > DPhil Candidate, Experimental Psychology > University of Oxford > bcl.psy.ox.ac.uk/people/zita-eva-patai/ > eva.patai at psy.ox.ac.uk > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From boracbci at gmail.com Mon Dec 12 09:18:17 2011 From: boracbci at gmail.com (Bora Cebeci) Date: Mon, 12 Dec 2011 10:18:17 +0200 Subject: [FieldTrip] Brainvision recorder RDA Message-ID: Hi, I want to use the Fieldtrip functions for real-time data processing. I'm testing the delay. Neither rda2ft.exe nor ft_realtime_brainampproxy.m is working properly. If you don't get an event, ft_realtime_brainampproxy.m can be usable. I found three messages about Brain Vision Recorder in the mail list. I have similar problems as mentioned in those messages. 1) I think that using rda2ft.exe is faster than ft_realtime_brainampproxy.m, so finding a solution for rda2ft.exe problem will be enough. I have the same error message as *Casper van Heck. Casper *said: " >* When running rda2ft.exe (with the parameters localhost and 51244) it does seem to connect; it shows the list of channels (all channels), their resolution, and their names, and some other assorted stuff. However, it then says: *>* "Unrecognized packet type (10000), has size 24 - exiting"* " My parameters : " rda2ft.exe localhost 51234" and I tried it in a different PC: " rda2ft.exe 10.1.54.160 51234" I got the same error message. 2) Secondly, I tried to use ft_realtime_brainampproxy.m, but I cannot use it efficiently. When an event occurs, buffering freezes and there is no error message. I have a bad solution for this problem. I'm stopping the program by "Ctrl+C" then I start it again. Meanwhile I measured 179ms delay (average of 45 trials), it is really big ?? 3) Even the above problem is solved, the events cannot read. Khalid mentioned before about this problem. I couldn't find the reading code for events in the ft_realtime_brainampproxy.m file. Here is the related part of the code: % convert the RDA message into data and/or events dat = []; event = []; if msg.nType==2 && msg.nPoints>0 % FIXME should I apply the calibration here? dat = msg.nData(chanindx,:); end if msg.nType==4 && msg.nPoints>0 % FIXME should I apply the calibration here? dat = msg.fData(chanindx,:); end if (msg.nType==2 || msg.nType==4) && msg.nMarkers>0 % FIXME convert the message to events end The variable 'event' doesn't get any value here. So by using ft_read_event function , you get an empty vector. Thanks -- Bora Cebeci -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Mon Dec 12 10:40:49 2011 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Mon, 12 Dec 2011 10:40:49 +0100 Subject: [FieldTrip] Brainvision recorder RDA In-Reply-To: References: Message-ID: Dear Bora Cebeci, Thank your for reporting this issue. There are indeed other reports that reading the RDA protocol is not working properly: http://bugzilla.fcdonders.nl/show_bug.cgi?id=1172 http://bugzilla.fcdonders.nl/show_bug.cgi?id=1164 The packet that causes rda2ft.exe to crash is not documented in the RDA protocol, and we are in contact with BrainProducts in order to resolve this issue. The problem you mention in (3) is unforgivable, and I would like to ask you to report this as a separate bug on http:/bugzilla.fcdonders.nl (just copy and past the email). You can then also subscribe to the other two bugs, which allows you to track our progress on fixing this issue. Best regards, Boris Reuderink On Mon, Dec 12, 2011 at 9:18 AM, Bora Cebeci wrote: > Hi, > > I want to use the Fieldtrip functions for real-time data processing. I'm > testing the delay. Neither rda2ft.exe nor ft_realtime_brainampproxy.m is > working properly. If you don't get an event, ft_realtime_brainampproxy.m can > be usable. > I found three messages about Brain Vision Recorder in the mail list. I have > similar problems as mentioned in those messages. > > 1) I think that using rda2ft.exe is faster than ft_realtime_brainampproxy.m, > so finding a solution for rda2ft.exe problem will be enough. I have the same > error message as Casper van Heck. > Casper  said: > " > >> When running rda2ft.exe (with the parameters localhost and 51244) it does >> seem to connect; it shows the list of channels (all channels), their >> resolution, and their names, and some other assorted stuff. However, it then >> says: > > >> "Unrecognized packet type (10000), has size 24 - exiting" > > " > My parameters : " rda2ft.exe localhost 51234" > and I tried it in a different PC: " rda2ft.exe 10.1.54.160 51234" > I got the same error message. > > > 2) Secondly, I tried to use ft_realtime_brainampproxy.m, but I cannot use it > efficiently. When an event occurs, buffering freezes and there is no error > message. > > I have a bad solution for this problem. I'm stopping the program by "Ctrl+C" > then I start it again. > Meanwhile I measured 179ms delay (average of 45 trials), it is really big ?? > > > 3) Even the above problem is solved, the events cannot read. Khalid > mentioned before about this problem. I couldn't find the reading code for > events in the ft_realtime_brainampproxy.m file. Here is the related part of > the code: > >  % convert the RDA message into data and/or events >   dat   = []; >   event = []; > >   if msg.nType==2 && msg.nPoints>0 >     % FIXME should I apply the calibration here? >     dat = msg.nData(chanindx,:); >   end > >   if msg.nType==4 && msg.nPoints>0 >     % FIXME should I apply the calibration here? >     dat = msg.fData(chanindx,:); >   end > >   if (msg.nType==2 || msg.nType==4) && msg.nMarkers>0 >     % FIXME convert the message to events >   end > > The variable 'event' doesn't get any value here. So by using ft_read_event > function , you get an empty vector. > > Thanks > > > -- > Bora Cebeci > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From eva.patai at psy.ox.ac.uk Mon Dec 12 12:22:57 2011 From: eva.patai at psy.ox.ac.uk (Zita Eva Patai) Date: Mon, 12 Dec 2011 11:22:57 +0000 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> Message-ID: Dear Jan-Mathijs, Sorry I was so vague, i thought maybe it was a common problem... OK, so i was running a clusterstat with the following input ( main point, i want to look at the difference between conditions over a set of frequencies) *** load blk1_tf_avg load blk3_tf_avg cfg = []; cfg.latency = [1.0 1.5 ]; cfg.frequency = [4 8]; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 1000; cfg.feedback = 'yes'; cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg); subj = 15; design = zeros(2,2*subj); for i = 1:subj design(1,i) = i; end for i = 1:subj design(1,subj+i) = i; end design(2,1:subj) = 1; design(2,subj+1:2*subj) = 2; cfg.design = design; cfg.uvar = 1; cfg.ivar = 2; [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg); save stat_tf_theta_1000_1500_bkey3vsbkey1 stat *** The error comes during the plotting phase when it says that i should not have multiple frequencies, as the data should be averaged across frequencies. And it does save my file (stat_theta....) but and i can see the pos/neg clusters in the data structure...but i can't plot with : cfg = []; cfg.highlightsymbolseries = ['*','*','.','.','.']; cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay'; cfg.contournum = 0; cfg.markersymbol = '.'; cfg.alpha = 0.05; cfg.zparam = 'stat'; ft_clusterplot(cfg,stat); I have also tried plotting with the script from the tutorial pos_cluster_pvals = [stat.posclusters(:).prob]; pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha); pos = ismember(stat.posclusterslabelmat, pos_signif_clust); neg_cluster_pvals = [stat.negclusters(:).prob]; neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha); neg = ismember(stat.negclusterslabelmat, neg_signif_clust); for k = 1:20; etc. but this makes the plot really weird looking...and i am not sure how i can only plot the data from the frequencies i would like to display (in this case 4-8Hz). I know how to make the subtraction image (between my two conditions), but not how to specify the frequency range that i want displayed... If this is too complicated, is there a way to average over a set of frequencies in the data, and then just input files into the permutation test that are already collapsed across the frequency range i am interested in? Thank you! z On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Zita, > > Could you provide some more information please? What plotting function are > you using? What does the stat-structure look like etc.? With sufficient > additional information we can try and reproduce the problem, and if it's a > bug fix it. If it's not a bug, we may give you some hints to fool the > system... > > BW, > > Jan-Mathijs > > On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: > > Dear FT-ers, > > I have tried to run a permutation test on time-frequency data, and would > have like to see a statistical evealuation over a set of frequencies (ex: > 4-8Hz) > > It seems that the test itself runs, but it crashes when i try to plot the > data, saying that 'stat' must not contain multiple frequencies. > > I was wondering if there was a way to evaluate the difference between two > conditions over a set range of frequencies? > > Thank you! > zita > > > -- > > Zita Patai > DPhil Candidate, Experimental Psychology > University of Oxford > bcl.psy.ox.ac.uk/people/zita-eva-patai/ > eva.patai at psy.ox.ac.uk > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Zita Patai DPhil Candidate, Experimental Psychology University of Oxford bcl.psy.ox.ac.uk/people/zita-eva-patai/ eva.patai at psy.ox.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From dporada at uos.de Mon Dec 12 16:16:01 2011 From: dporada at uos.de (Porada Danja) Date: Mon, 12 Dec 2011 16:16:01 +0100 Subject: [FieldTrip] Automatic artifact rejection Message-ID: <5BCBAF3A-26D5-4B64-BC0C-DD8284D6551D@uos.de> Hi, I want to use automatic artifact detection to clean my MEG-data. Does it make sense to clean the data visually first, remove very odd trials (like very huge slow waveforms which were caused by a passing car) and then apply the ft_artifact_zvalue function? I went step by step through the ft_artifact_zvalue function using the same parameters as proposed in the "automatic artifact rejection" tutorial for jump artifacts. It seems to me that the function doesn't use the parameter "absdiff" which is specified in cfg.artfctdef.zvalue.absdiff = 'yes'. Is this right? I am using the fieldtrip-20111115-version. Best, Danja From jm.horschig at donders.ru.nl Mon Dec 12 16:18:34 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 12 Dec 2011 16:18:34 +0100 Subject: [FieldTrip] rereference to repaired channel In-Reply-To: <4EE50D33.8030500@berkeley.edu> References: <4EE50D33.8030500@berkeley.edu> Message-ID: <4EE61B4A.4050208@donders.ru.nl> Hi Ingrid, ft_channelrepair is simply taking the average of the neighbouring channels. So, you would need to specify your neighbours and based on this, and it just gets the average of the neighbours of your mastoid. However, imho, you cannot really define neighbours for a mastoid channel. There is a method to interpolate not using nearest neighbours but spherical splines, however this is not (yet) part of FieldTrip, see also here: http://bugzilla.fcdonders.nl/show_bug.cgi?id=634 But, I am not sure if this would help in this case either. If you really want to use linked mastoid as a reference, I would probably reject that subject due to bad signal quality. I don't know if anyone on the list has a better idea (or more experience). Second, if you first rereference, all noise from this one channel will leak into all other channels, as you said. As long as your mastoid is not a bad channel, there should be no difference whether you first rereference or then interpolate bad channels or the other way around (assuming that I got no mathematical blackout right now). Should be easy to verify, e.g. if you have channels A, B, and C (all neighbours) and want to reference to R, then your referenced channels would be A-R, B-R and C-R. If B is a bad channel, and you interpolate first, you get B=(A+C)/2 (i.e. just the average of the neighbouring sensors). If you then rereference you will obtain (A+C)/2 - R, which is the same as (A+C) /2 - (R+R)/2 = (A-R + C-R) /2. If you first rereference and then interpolate you obtain B-R = (A-R + C-R) /2 immediately (because A-R and C-R are the only neighbours of B-R). Hope it helps! Best, Jörn On 12/11/2011 9:06 PM, Ingrid Nieuwenhuis wrote: > Hi all, > > I've measured EEG data with Cz as the reference. I now want to > rereference to linked mastoids. However, in one participant one of the > mastoid electrodes is really noisy. Is it valid to throw out the noisy > channel, then fix it (with ft_channelrepair), and then rereference to > this fixed mastoid channel? In other words, is channelrepair a linear > operation? Or would I be mixing (a little) Cz into all channels > now...? Any other options? > > Or another way of asking: do I get the same result if I first > rereference and then fix bad channels, compared to first fixing bad > channels and then rereference? In the participant with the bad mastoid > chan, I don't have a choice, I have to first fix the channel first, or > I'd be mixing noise into all channels. But, in other participants, > where I also have bad channels (but not the mastoid ones), does the > order matter, which order is better? I'd think first rereference, then > fix... Correct? > > Thanks!! > Ingrid > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From inieuwenhuis at berkeley.edu Mon Dec 12 18:00:06 2011 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Mon, 12 Dec 2011 09:00:06 -0800 Subject: [FieldTrip] rereference to repaired channel In-Reply-To: <4EE61B4A.4050208@donders.ru.nl> References: <4EE50D33.8030500@berkeley.edu> <4EE61B4A.4050208@donders.ru.nl> Message-ID: <4EE63316.40104@berkeley.edu> Hi Jorn, Thanks a lot! And fortunately, the mastoid has plenty neighbours ('E95' 'E96' 'E99' 'E101' 'E107' 'E108'), since I'm using high density EEG (128 EGI). The spherical spline method sounds pretty cool as well. Would be cool to implement one day indeed! Cheers, Ingrid On 12/12/2011 7:18 AM, "Jörn M. Horschig" wrote: > Hi Ingrid, > > ft_channelrepair is simply taking the average of the neighbouring > channels. So, you would need to specify your neighbours and based on > this, and it just gets the average of the neighbours of your mastoid. > However, imho, you cannot really define neighbours for a mastoid > channel. There is a method to interpolate not using nearest neighbours > but spherical splines, however this is not (yet) part of FieldTrip, > see also here: > http://bugzilla.fcdonders.nl/show_bug.cgi?id=634 > But, I am not sure if this would help in this case either. If you > really want to use linked mastoid as a reference, I would probably > reject that subject due to bad signal quality. I don't know if anyone > on the list has a better idea (or more experience). > > Second, if you first rereference, all noise from this one channel will > leak into all other channels, as you said. As long as your mastoid is > not a bad channel, there should be no difference whether you first > rereference or then interpolate bad channels or the other way around > (assuming that I got no mathematical blackout right now). > Should be easy to verify, e.g. if you have channels A, B, and C (all > neighbours) and want to reference to R, then your referenced channels > would be A-R, B-R and C-R. > If B is a bad channel, and you interpolate first, you get B=(A+C)/2 > (i.e. just the average of the neighbouring sensors). If you then > rereference you will obtain (A+C)/2 - R, which is the same as (A+C) /2 > - (R+R)/2 = (A-R + C-R) /2. > If you first rereference and then interpolate you obtain B-R = (A-R + > C-R) /2 immediately (because A-R and C-R are the only neighbours of B-R). > > Hope it helps! Best, > Jörn > > On 12/11/2011 9:06 PM, Ingrid Nieuwenhuis wrote: >> Hi all, >> >> I've measured EEG data with Cz as the reference. I now want to >> rereference to linked mastoids. However, in one participant one of >> the mastoid electrodes is really noisy. Is it valid to throw out the >> noisy channel, then fix it (with ft_channelrepair), and then >> rereference to this fixed mastoid channel? In other words, is >> channelrepair a linear operation? Or would I be mixing (a little) Cz >> into all channels now...? Any other options? >> >> Or another way of asking: do I get the same result if I first >> rereference and then fix bad channels, compared to first fixing bad >> channels and then rereference? In the participant with the bad >> mastoid chan, I don't have a choice, I have to first fix the channel >> first, or I'd be mixing noise into all channels. But, in other >> participants, where I also have bad channels (but not the mastoid >> ones), does the order matter, which order is better? I'd think first >> rereference, then fix... Correct? >> >> Thanks!! >> Ingrid >> > > -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 From jan.schoffelen at donders.ru.nl Tue Dec 13 09:27:45 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 13 Dec 2011 09:27:45 +0100 Subject: [FieldTrip] PhD studentship available in cortical networks of aging at CCNi Glasgow References: <218D83BF-2F53-4471-881B-0AF4CE682E97@glasgow.ac.uk> Message-ID: <875C1820-4679-49F6-8952-85ABF6C24EC9@donders.ru.nl> Dear all, Please see below a PhD-position available at Glasgow university. Cheers, JM A 4-year PhD studentship is available to work with Philippe Schyns & Guillaume Rousselet in the Institute of Neuroscience and Psychology. Understanding age-related changes in the processing of emotion information Deadline: Friday 27th January 2012 Stipend: £13,848 per annum The start date is October 2012 and applicants will normally be expected to reside (or have residency) within the UK or EU. The financial package will include a four year stipend, approved University fees, Research Training Support Grant and a Conference Allowance. Information about the training and how to apply is available here: http://www.gla.ac.uk/colleges/mvls/graduateschool/informationforprospectivestudents/phdandmresscholarships/phdprogrammes/ Contact us directly for inquiries about the project: Philippe Schyns Guillaume Rousselet Abstract: It is estimated that, by 2060, one quarter of the British population will be over 65, many of whom will still be working. Over a lifetime, the brain ages as dramatically as the body, manifesting itself in the decline of the basic and essential task of interpreting social signals. Research has established that ageing adults show specific differences in the emotional interpretation of facial expressions, particularly anger. These perceptual differences could have drastic impacts on everyday social interactions and decision-making. Failure to accurately interpret social signals may lead to vulnerabilities in critical social interactions such as identifying deception and predicting the behavioural intentions of others. With the development of new methods in computational neuroscience, it has become possible to further understand why the ageing brain fails in what are deceptively simple information processing tasks—i.e. interpreting the emotions of others. We will study how oscillatory networks in the ageing brain extract and further process visual information to recognize facial expressions of emotion at different intensities. Our framework will combine a unique platform that precisely controls the photo-realistic biological motion of faces with other developments in applications of information theoretic mathematics to analyses of brain signals. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Dec 13 17:06:53 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 13 Dec 2011 17:06:53 +0100 Subject: [FieldTrip] DICS beamformer images In-Reply-To: References: Message-ID: <3A18CB06-2B78-41C6-8F9C-BC21C0147BEF@donders.ru.nl> Hi Holly, DICS can also be used to compute univariate power in a given frequency band. This yields not a bounded quantity. Depending on your analysis settings you will observe a depth bias which is not physiologically relevant. Best way to deal with this is to compute the beamformer maps using an experimental contrast. Best Jan-Mathijs On Dec 6, 2011, at 2:18 PM, Rossiter, Holly wrote: > Hi all, > > I am using DICS to assess coherence and viewing the beamformer images through SPM. What I want to know is what is the value given in the image and how is it calculated? I thought it was a coherence value but it is not bounded between 0 and 1. > > Also what do you think is the best way to threshold the images in order to get rid of low value peaks? > > Thanks, > > Holly > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Dec 13 17:10:22 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 13 Dec 2011 17:10:22 +0100 Subject: [FieldTrip] Interactive Plotting in ft_rejectvisual In-Reply-To: <1C5AEC7D-4B54-428E-BE54-B408171837FC@gmail.com> References: <1C5AEC7D-4B54-428E-BE54-B408171837FC@gmail.com> Message-ID: <31D7B637-547A-4C66-ADE1-351F59CAD83B@donders.ru.nl> Dear Julian, Thanks for reporting this. We will look into the issue. If you want to stay informed about this you can consider creating yourself a bugzilla account on www.bugzilla.fcdonders.nl. People who have an account can add themselves in the CC for a particular bug/feature request. The issue you sketched has been filed by me as bug 1230. Best wishes, Jan-Mathijs On Dec 7, 2011, at 10:42 AM, Julian Keil wrote: > Hi, > > Not really a bug report, so I put this on the discussion List. > I noticed that when plotting single trials in the ft_rejectivusal function, the figure popping up is not interactive which makes a closer inspection of the trials somewhat harder. > Maybe this is intentional, but I can't see a reason for it. > However, simply adding "cfg_mp.interactive='yes';" at line 510 of "reject visual_summary" fixes this. > > Best, > > Julian > > > Dipl. Psych. Julian Keil > > OBOB-Lab > University of Konstanz > Department of Psychology > P.O. Box D25 > 78457 Konstanz > Germany > > Tel: ++49 - (0)7531 - 88 42 50 > Fax: ++49 - (0)7531 - 88 28 91 > Email: julian.keil at uni-konstanz.de > Homepage: http://www.uni-konstanz.de/obob > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Dec 13 17:22:42 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 13 Dec 2011 17:22:42 +0100 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> Message-ID: <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> Hi Zita, OK. I now understand the point. ft_clusterplot throws an error because it does not know how to collapse across frequencies. If the clusters have spectral extent (as well as spatial extent) it's a non-trivial question what are the channels to be plotted, because different channels can contribute different time and frequency points to the significant cluster. The time points are dealt with because ft_clusterplot shows the cluster evolving over time; the frequencies are not dealt with. FieldTrip does not make the choice of which channels to highlight for you (should all frequencies be significant for a given time point, or only one, or just a few?) and thus throws an error. However, if you have a priori reasons to expect your effect to occur in a particular frequency range (as you seem to do, because of your specification of the cfg before calling ft_freqstatistics), you can also specify cfg.avgoverfreq to 'yes', yielding a single observation per channel (and by construction the clustering only occurs over channels), making the plotting trivial. I hope this helps. BW, JM On Dec 12, 2011, at 12:22 PM, Zita Eva Patai wrote: > Dear Jan-Mathijs, > > Sorry I was so vague, i thought maybe it was a common problem... > > OK, so i was running a clusterstat with the following input ( main point, i want to look at the difference between conditions over a set of frequencies) > *** > load blk1_tf_avg > load blk3_tf_avg > > cfg = []; > cfg.latency = [1.0 1.5 ]; > cfg.frequency = [4 8]; > cfg.method = 'montecarlo'; > cfg.statistic = 'depsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 1000; > cfg.feedback = 'yes'; > cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg); > subj = 15; > design = zeros(2,2*subj); > for i = 1:subj > design(1,i) = i; > end > for i = 1:subj > design(1,subj+i) = i; > end > design(2,1:subj) = 1; > design(2,subj+1:2*subj) = 2; > > > cfg.design = design; > cfg.uvar = 1; > cfg.ivar = 2; > > [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg); > > save stat_tf_theta_1000_1500_bkey3vsbkey1 stat > > > *** > > The error comes during the plotting phase when it says that i should not have multiple frequencies, as the data should be averaged across frequencies. And it does save my file (stat_theta....) but and i can see the pos/neg clusters in the data structure...but i can't plot with : > > cfg = []; > cfg.highlightsymbolseries = ['*','*','.','.','.']; > cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay'; > cfg.contournum = 0; > cfg.markersymbol = '.'; > cfg.alpha = 0.05; > cfg.zparam = 'stat'; > ft_clusterplot(cfg,stat); > > > I have also tried plotting with the script from the tutorial > > pos_cluster_pvals = [stat.posclusters(:).prob]; > pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha); > pos = ismember(stat.posclusterslabelmat, pos_signif_clust); > > neg_cluster_pvals = [stat.negclusters(:).prob]; > neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha); > neg = ismember(stat.negclusterslabelmat, neg_signif_clust); > > for k = 1:20; > > etc. > but this makes the plot really weird looking...and i am not sure how i can only plot the data from the frequencies i would like to display (in this case 4-8Hz). I know how to make the subtraction image (between my two conditions), but not how to specify the frequency range that i want displayed... > > If this is too complicated, is there a way to average over a set of frequencies in the data, and then just input files into the permutation test that are already collapsed across the frequency range i am interested in? > > > Thank you! > z > > > On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen wrote: > Hi Zita, > > Could you provide some more information please? What plotting function are you using? What does the stat-structure look like etc.? With sufficient additional information we can try and reproduce the problem, and if it's a bug fix it. If it's not a bug, we may give you some hints to fool the system... > > BW, > > Jan-Mathijs > > On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: > >> Dear FT-ers, >> >> I have tried to run a permutation test on time-frequency data, and would have like to see a statistical evealuation over a set of frequencies (ex: 4-8Hz) >> >> It seems that the test itself runs, but it crashes when i try to plot the data, saying that 'stat' must not contain multiple frequencies. >> >> I was wondering if there was a way to evaluate the difference between two conditions over a set range of frequencies? >> >> Thank you! >> zita >> >> >> -- >> >> Zita Patai >> DPhil Candidate, Experimental Psychology >> University of Oxford >> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >> eva.patai at psy.ox.ac.uk >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > > Zita Patai > DPhil Candidate, Experimental Psychology > University of Oxford > bcl.psy.ox.ac.uk/people/zita-eva-patai/ > eva.patai at psy.ox.ac.uk > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From eva.patai at psy.ox.ac.uk Tue Dec 13 18:10:58 2011 From: eva.patai at psy.ox.ac.uk (Zita Eva Patai) Date: Tue, 13 Dec 2011 17:10:58 +0000 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> Message-ID: Dear Jan-Mathijs, Thank you for that, it makes a lot more sense. I figured the data was too complex for display, so I will average over frequencies as you suggested, as I am interested in an effect that would encompass that range anyway... Thank you again and happy holidays! z On Tue, Dec 13, 2011 at 4:22 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Zita, > > OK. I now understand the point. ft_clusterplot throws an error because it > does not know how to collapse across frequencies. If the clusters have > spectral extent (as well as spatial extent) it's a non-trivial question > what are the channels to be plotted, because different channels can > contribute different time and frequency points to the significant cluster. > The time points are dealt with because ft_clusterplot shows the cluster > evolving over time; the frequencies are not dealt with. FieldTrip does not > make the choice of which channels to highlight for you (should all > frequencies be significant for a given time point, or only one, or just a > few?) and thus throws an error. However, if you have a priori reasons to > expect your effect to occur in a particular frequency range (as you seem to > do, because of your specification of the cfg before calling > ft_freqstatistics), you can also specify cfg.avgoverfreq to 'yes', yielding > a single observation per channel (and by construction the clustering only > occurs over channels), making the plotting trivial. > > I hope this helps. > > BW, > > JM > > > > On Dec 12, 2011, at 12:22 PM, Zita Eva Patai wrote: > > Dear Jan-Mathijs, > > Sorry I was so vague, i thought maybe it was a common problem... > > OK, so i was running a clusterstat with the following input ( main point, > i want to look at the difference between conditions over a set of > frequencies) > *** > load blk1_tf_avg > load blk3_tf_avg > > cfg = []; > cfg.latency = [1.0 1.5 ]; > cfg.frequency = [4 8]; > cfg.method = 'montecarlo'; > cfg.statistic = 'depsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 1000; > cfg.feedback = 'yes'; > cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg); > subj = 15; > design = zeros(2,2*subj); > for i = 1:subj > design(1,i) = i; > end > for i = 1:subj > design(1,subj+i) = i; > end > design(2,1:subj) = 1; > design(2,subj+1:2*subj) = 2; > > > cfg.design = design; > cfg.uvar = 1; > cfg.ivar = 2; > > > [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg); > > > save stat_tf_theta_1000_1500_bkey3vsbkey1 stat > > > *** > > The error comes during the plotting phase when it says that i should not > have multiple frequencies, as the data should be averaged across > frequencies. And it does save my file (stat_theta....) but and i can see > the pos/neg clusters in the data structure...but i can't plot with : > > cfg = []; > cfg.highlightsymbolseries = ['*','*','.','.','.']; > cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay'; > cfg.contournum = 0; > cfg.markersymbol = '.'; > cfg.alpha = 0.05; > cfg.zparam = 'stat'; > ft_clusterplot(cfg,stat); > > > > I have also tried plotting with the script from the tutorial > > > pos_cluster_pvals = [stat.posclusters(:).prob]; > pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha); > pos = ismember(stat.posclusterslabelmat, pos_signif_clust); > > > neg_cluster_pvals = [stat.negclusters(:).prob]; > neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha); > neg = ismember(stat.negclusterslabelmat, neg_signif_clust); > > for k = 1:20; > > etc. > but this makes the plot really weird looking...and i am not sure how i can > only plot the data from the frequencies i would like to display (in this > case 4-8Hz). I know how to make the subtraction image (between my two > conditions), but not how to specify the frequency range that i want > displayed... > > If this is too complicated, is there a way to average over a set of > frequencies in the data, and then just input files into the permutation > test that are already collapsed across the frequency range i am interested > in? > > > Thank you! > z > > > On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Zita, >> >> Could you provide some more information please? What plotting function >> are you using? What does the stat-structure look like etc.? With sufficient >> additional information we can try and reproduce the problem, and if it's a >> bug fix it. If it's not a bug, we may give you some hints to fool the >> system... >> >> BW, >> >> Jan-Mathijs >> >> On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: >> >> Dear FT-ers, >> >> I have tried to run a permutation test on time-frequency data, and would >> have like to see a statistical evealuation over a set of frequencies (ex: >> 4-8Hz) >> >> It seems that the test itself runs, but it crashes when i try to plot the >> data, saying that 'stat' must not contain multiple frequencies. >> >> I was wondering if there was a way to evaluate the difference between two >> conditions over a set range of frequencies? >> >> Thank you! >> zita >> >> >> -- >> >> Zita Patai >> DPhil Candidate, Experimental Psychology >> University of Oxford >> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >> eva.patai at psy.ox.ac.uk >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > > Zita Patai > DPhil Candidate, Experimental Psychology > University of Oxford > bcl.psy.ox.ac.uk/people/zita-eva-patai/ > eva.patai at psy.ox.ac.uk > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Zita Patai DPhil Candidate, Experimental Psychology University of Oxford bcl.psy.ox.ac.uk/people/zita-eva-patai/ eva.patai at psy.ox.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Tue Dec 13 18:47:40 2011 From: matt.mollison at gmail.com (Matt Mollison) Date: Tue, 13 Dec 2011 10:47:40 -0700 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> Message-ID: Hi Zita, I have not used this method much, but it actually is possible to plot clusters without averaging over the frequency dimension using ft_multiplotTFR (where cfg.avgoverchan = 'no'; cfg.avgovertime = 'no'; cfg.avgoverfreq='no'; in your statistical test—so you'll get space, time, and frequency information). You can also highlight the significant portions of time and frequency space, using cfg.mask='yes', cfg.maskparameter='mask', and set a cfg.maskalpha. Do keep in mind that there are important reasons for averaging over frequency, as Dr. Maris described in this post (specifically, to increase power): < http://mailman.science.ru.nl/pipermail/fieldtrip/2010-November/003312.html>. Cheers, Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Tue, Dec 13, 2011 at 10:10 AM, Zita Eva Patai wrote: > Dear Jan-Mathijs, > > Thank you for that, it makes a lot more sense. I figured the data was too > complex for display, so I will average over frequencies as you suggested, > as I am interested in an effect that would encompass that range anyway... > > Thank you again and happy holidays! > z > > On Tue, Dec 13, 2011 at 4:22 PM, jan-mathijs schoffelen < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Zita, >> >> OK. I now understand the point. ft_clusterplot throws an error because it >> does not know how to collapse across frequencies. If the clusters have >> spectral extent (as well as spatial extent) it's a non-trivial question >> what are the channels to be plotted, because different channels can >> contribute different time and frequency points to the significant cluster. >> The time points are dealt with because ft_clusterplot shows the cluster >> evolving over time; the frequencies are not dealt with. FieldTrip does not >> make the choice of which channels to highlight for you (should all >> frequencies be significant for a given time point, or only one, or just a >> few?) and thus throws an error. However, if you have a priori reasons to >> expect your effect to occur in a particular frequency range (as you seem to >> do, because of your specification of the cfg before calling >> ft_freqstatistics), you can also specify cfg.avgoverfreq to 'yes', yielding >> a single observation per channel (and by construction the clustering only >> occurs over channels), making the plotting trivial. >> >> I hope this helps. >> >> BW, >> >> JM >> >> >> >> On Dec 12, 2011, at 12:22 PM, Zita Eva Patai wrote: >> >> Dear Jan-Mathijs, >> >> Sorry I was so vague, i thought maybe it was a common problem... >> >> OK, so i was running a clusterstat with the following input ( main point, >> i want to look at the difference between conditions over a set of >> frequencies) >> *** >> load blk1_tf_avg >> load blk3_tf_avg >> >> cfg = []; >> cfg.latency = [1.0 1.5 ]; >> cfg.frequency = [4 8]; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'depsamplesT'; >> cfg.correctm = 'cluster'; >> cfg.clusteralpha = 0.05; >> cfg.clusterstatistic = 'maxsum'; >> cfg.minnbchan = 2; >> cfg.tail = 0; >> cfg.clustertail = 0; >> cfg.alpha = 0.025; >> cfg.numrandomization = 1000; >> cfg.feedback = 'yes'; >> cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg); >> subj = 15; >> design = zeros(2,2*subj); >> for i = 1:subj >> design(1,i) = i; >> end >> for i = 1:subj >> design(1,subj+i) = i; >> end >> design(2,1:subj) = 1; >> design(2,subj+1:2*subj) = 2; >> >> >> cfg.design = design; >> cfg.uvar = 1; >> cfg.ivar = 2; >> >> >> [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg); >> >> >> save stat_tf_theta_1000_1500_bkey3vsbkey1 stat >> >> >> *** >> >> The error comes during the plotting phase when it says that i should not >> have multiple frequencies, as the data should be averaged across >> frequencies. And it does save my file (stat_theta....) but and i can see >> the pos/neg clusters in the data structure...but i can't plot with : >> >> cfg = []; >> cfg.highlightsymbolseries = ['*','*','.','.','.']; >> cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay'; >> cfg.contournum = 0; >> cfg.markersymbol = '.'; >> cfg.alpha = 0.05; >> cfg.zparam = 'stat'; >> ft_clusterplot(cfg,stat); >> >> >> >> I have also tried plotting with the script from the tutorial >> >> >> pos_cluster_pvals = [stat.posclusters(:).prob]; >> pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha); >> pos = ismember(stat.posclusterslabelmat, pos_signif_clust); >> >> >> neg_cluster_pvals = [stat.negclusters(:).prob]; >> neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha); >> neg = ismember(stat.negclusterslabelmat, neg_signif_clust); >> >> for k = 1:20; >> >> etc. >> but this makes the plot really weird looking...and i am not sure how i >> can only plot the data from the frequencies i would like to display (in >> this case 4-8Hz). I know how to make the subtraction image (between my two >> conditions), but not how to specify the frequency range that i want >> displayed... >> >> If this is too complicated, is there a way to average over a set of >> frequencies in the data, and then just input files into the permutation >> test that are already collapsed across the frequency range i am interested >> in? >> >> >> Thank you! >> z >> >> >> On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen < >> jan.schoffelen at donders.ru.nl> wrote: >> >>> Hi Zita, >>> >>> Could you provide some more information please? What plotting function >>> are you using? What does the stat-structure look like etc.? With sufficient >>> additional information we can try and reproduce the problem, and if it's a >>> bug fix it. If it's not a bug, we may give you some hints to fool the >>> system... >>> >>> BW, >>> >>> Jan-Mathijs >>> >>> On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: >>> >>> Dear FT-ers, >>> >>> I have tried to run a permutation test on time-frequency data, and would >>> have like to see a statistical evealuation over a set of frequencies (ex: >>> 4-8Hz) >>> >>> It seems that the test itself runs, but it crashes when i try to plot >>> the data, saying that 'stat' must not contain multiple frequencies. >>> >>> I was wondering if there was a way to evaluate the difference between >>> two conditions over a set range of frequencies? >>> >>> Thank you! >>> zita >>> >>> >>> -- >>> >>> Zita Patai >>> DPhil Candidate, Experimental Psychology >>> University of Oxford >>> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >>> eva.patai at psy.ox.ac.uk >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> Jan-Mathijs Schoffelen, MD PhD >>> >>> Donders Institute for Brain, Cognition and Behaviour, >>> Centre for Cognitive Neuroimaging, >>> Radboud University Nijmegen, The Netherlands >>> >>> Max Planck Institute for Psycholinguistics, >>> Nijmegen, The Netherlands >>> >>> J.Schoffelen at donders.ru.nl >>> Telephone: +31-24-3614793 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> >> Zita Patai >> DPhil Candidate, Experimental Psychology >> University of Oxford >> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >> eva.patai at psy.ox.ac.uk >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > > Zita Patai > DPhil Candidate, Experimental Psychology > University of Oxford > bcl.psy.ox.ac.uk/people/zita-eva-patai/ > eva.patai at psy.ox.ac.uk > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eva.patai at psy.ox.ac.uk Tue Dec 13 19:18:36 2011 From: eva.patai at psy.ox.ac.uk (Zita Eva Patai) Date: Tue, 13 Dec 2011 18:18:36 +0000 Subject: [FieldTrip] clusterstat on multiple frequencies In-Reply-To: References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> Message-ID: Thank you Matt, that further makes my situation more clear to me! On Tue, Dec 13, 2011 at 5:47 PM, Matt Mollison wrote: > Hi Zita, > > I have not used this method much, but it actually is possible to plot > clusters without averaging over the frequency dimension > using ft_multiplotTFR (where cfg.avgoverchan = 'no'; cfg.avgovertime = > 'no'; cfg.avgoverfreq='no'; in your statistical test—so you'll get space, > time, and frequency information). You can also highlight the significant > portions of time and frequency space, using cfg.mask='yes', > cfg.maskparameter='mask', and set a cfg.maskalpha. Do keep in mind that > there are important reasons for averaging over frequency, as Dr. Maris > described in this post (specifically, to increase power): < > http://mailman.science.ru.nl/pipermail/fieldtrip/2010-November/003312.html > >. > > Cheers, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > > On Tue, Dec 13, 2011 at 10:10 AM, Zita Eva Patai wrote: > >> Dear Jan-Mathijs, >> >> Thank you for that, it makes a lot more sense. I figured the data was too >> complex for display, so I will average over frequencies as you suggested, >> as I am interested in an effect that would encompass that range anyway... >> >> Thank you again and happy holidays! >> z >> >> On Tue, Dec 13, 2011 at 4:22 PM, jan-mathijs schoffelen < >> jan.schoffelen at donders.ru.nl> wrote: >> >>> Hi Zita, >>> >>> OK. I now understand the point. ft_clusterplot throws an error because >>> it does not know how to collapse across frequencies. If the clusters have >>> spectral extent (as well as spatial extent) it's a non-trivial question >>> what are the channels to be plotted, because different channels can >>> contribute different time and frequency points to the significant cluster. >>> The time points are dealt with because ft_clusterplot shows the cluster >>> evolving over time; the frequencies are not dealt with. FieldTrip does not >>> make the choice of which channels to highlight for you (should all >>> frequencies be significant for a given time point, or only one, or just a >>> few?) and thus throws an error. However, if you have a priori reasons to >>> expect your effect to occur in a particular frequency range (as you seem to >>> do, because of your specification of the cfg before calling >>> ft_freqstatistics), you can also specify cfg.avgoverfreq to 'yes', yielding >>> a single observation per channel (and by construction the clustering only >>> occurs over channels), making the plotting trivial. >>> >>> I hope this helps. >>> >>> BW, >>> >>> JM >>> >>> >>> >>> On Dec 12, 2011, at 12:22 PM, Zita Eva Patai wrote: >>> >>> Dear Jan-Mathijs, >>> >>> Sorry I was so vague, i thought maybe it was a common problem... >>> >>> OK, so i was running a clusterstat with the following input ( main >>> point, i want to look at the difference between conditions over a set of >>> frequencies) >>> *** >>> load blk1_tf_avg >>> load blk3_tf_avg >>> >>> cfg = []; >>> cfg.latency = [1.0 1.5 ]; >>> cfg.frequency = [4 8]; >>> cfg.method = 'montecarlo'; >>> cfg.statistic = 'depsamplesT'; >>> cfg.correctm = 'cluster'; >>> cfg.clusteralpha = 0.05; >>> cfg.clusterstatistic = 'maxsum'; >>> cfg.minnbchan = 2; >>> cfg.tail = 0; >>> cfg.clustertail = 0; >>> cfg.alpha = 0.025; >>> cfg.numrandomization = 1000; >>> cfg.feedback = 'yes'; >>> cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg); >>> subj = 15; >>> design = zeros(2,2*subj); >>> for i = 1:subj >>> design(1,i) = i; >>> end >>> for i = 1:subj >>> design(1,subj+i) = i; >>> end >>> design(2,1:subj) = 1; >>> design(2,subj+1:2*subj) = 2; >>> >>> >>> cfg.design = design; >>> cfg.uvar = 1; >>> cfg.ivar = 2; >>> >>> >>> [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg); >>> >>> >>> save stat_tf_theta_1000_1500_bkey3vsbkey1 stat >>> >>> >>> *** >>> >>> The error comes during the plotting phase when it says that i should not >>> have multiple frequencies, as the data should be averaged across >>> frequencies. And it does save my file (stat_theta....) but and i can see >>> the pos/neg clusters in the data structure...but i can't plot with : >>> >>> cfg = []; >>> cfg.highlightsymbolseries = ['*','*','.','.','.']; >>> cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay'; >>> cfg.contournum = 0; >>> cfg.markersymbol = '.'; >>> cfg.alpha = 0.05; >>> cfg.zparam = 'stat'; >>> ft_clusterplot(cfg,stat); >>> >>> >>> >>> I have also tried plotting with the script from the tutorial >>> >>> >>> pos_cluster_pvals = [stat.posclusters(:).prob]; >>> pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha); >>> pos = ismember(stat.posclusterslabelmat, pos_signif_clust); >>> >>> >>> neg_cluster_pvals = [stat.negclusters(:).prob]; >>> neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha); >>> neg = ismember(stat.negclusterslabelmat, neg_signif_clust); >>> >>> for k = 1:20; >>> >>> etc. >>> but this makes the plot really weird looking...and i am not sure how i >>> can only plot the data from the frequencies i would like to display (in >>> this case 4-8Hz). I know how to make the subtraction image (between my two >>> conditions), but not how to specify the frequency range that i want >>> displayed... >>> >>> If this is too complicated, is there a way to average over a set of >>> frequencies in the data, and then just input files into the permutation >>> test that are already collapsed across the frequency range i am interested >>> in? >>> >>> >>> Thank you! >>> z >>> >>> >>> On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen < >>> jan.schoffelen at donders.ru.nl> wrote: >>> >>>> Hi Zita, >>>> >>>> Could you provide some more information please? What plotting function >>>> are you using? What does the stat-structure look like etc.? With sufficient >>>> additional information we can try and reproduce the problem, and if it's a >>>> bug fix it. If it's not a bug, we may give you some hints to fool the >>>> system... >>>> >>>> BW, >>>> >>>> Jan-Mathijs >>>> >>>> On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote: >>>> >>>> Dear FT-ers, >>>> >>>> I have tried to run a permutation test on time-frequency data, and >>>> would have like to see a statistical evealuation over a set of frequencies >>>> (ex: 4-8Hz) >>>> >>>> It seems that the test itself runs, but it crashes when i try to plot >>>> the data, saying that 'stat' must not contain multiple frequencies. >>>> >>>> I was wondering if there was a way to evaluate the difference between >>>> two conditions over a set range of frequencies? >>>> >>>> Thank you! >>>> zita >>>> >>>> >>>> -- >>>> >>>> Zita Patai >>>> DPhil Candidate, Experimental Psychology >>>> University of Oxford >>>> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >>>> eva.patai at psy.ox.ac.uk >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> Jan-Mathijs Schoffelen, MD PhD >>>> >>>> Donders Institute for Brain, Cognition and Behaviour, >>>> Centre for Cognitive Neuroimaging, >>>> Radboud University Nijmegen, The Netherlands >>>> >>>> Max Planck Institute for Psycholinguistics, >>>> Nijmegen, The Netherlands >>>> >>>> J.Schoffelen at donders.ru.nl >>>> Telephone: +31-24-3614793 >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> >>> Zita Patai >>> DPhil Candidate, Experimental Psychology >>> University of Oxford >>> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >>> eva.patai at psy.ox.ac.uk >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> Jan-Mathijs Schoffelen, MD PhD >>> >>> Donders Institute for Brain, Cognition and Behaviour, >>> Centre for Cognitive Neuroimaging, >>> Radboud University Nijmegen, The Netherlands >>> >>> Max Planck Institute for Psycholinguistics, >>> Nijmegen, The Netherlands >>> >>> J.Schoffelen at donders.ru.nl >>> Telephone: +31-24-3614793 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> >> Zita Patai >> DPhil Candidate, Experimental Psychology >> University of Oxford >> bcl.psy.ox.ac.uk/people/zita-eva-patai/ >> eva.patai at psy.ox.ac.uk >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Zita Patai DPhil Candidate, Experimental Psychology University of Oxford bcl.psy.ox.ac.uk/people/zita-eva-patai/ eva.patai at psy.ox.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From Gregor.Volberg at psychologie.uni-regensburg.de Wed Dec 14 10:32:17 2011 From: Gregor.Volberg at psychologie.uni-regensburg.de (Gregor Volberg) Date: Wed, 14 Dec 2011 10:32:17 +0100 Subject: [FieldTrip] read_eeglab, header file? In-Reply-To: References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> Message-ID: <4EE87B31020000570000BF1A@gwsmtp1.uni-regensburg.de> Dear Fieldtrip developers, I encountered an error warning when reading in an eeglab *.set - file for preprocessing (version fieldtrip-20111206), where the call to ft_preprocessing says ??? Undefined function or variable "hdr". Error in ==> read_eeglabdata at 52 if isempty(hdr) Shouldn't code lines 52 to 54 read if isempty(header) header = read_eeglabheader(filename); end instead of if isempty(hdr) hdr = read_eeglabheader(filename); end Not really a problem, just to bring it to your attention... Best regards, Gregor -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.hesselmann at gmail.com Wed Dec 14 18:53:46 2011 From: g.hesselmann at gmail.com (Guido Hesselmann) Date: Wed, 14 Dec 2011 18:53:46 +0100 Subject: [FieldTrip] Time-frequency analysis: based on single trials or on average? Message-ID: Hi all, I am new to fieldtrip and have a very simple question. I have EEG data and would like to run a time-frequency analysis (e.g., using a Hanning taper with fixed window length). If I have 100 trials, how is this analysis performed? On a trial-by-trial basis, or based on the average? Can I choose between these options in fieldtrip? Thanks a lot! Guido Hesselmann Visual Perception Lab Department of Psychiatry & Psychotherapy Charité Berlin -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Wed Dec 14 19:03:49 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Wed, 14 Dec 2011 19:03:49 +0100 Subject: [FieldTrip] Time-frequency analysis: based on single trials or on average? In-Reply-To: References: Message-ID: Hi Guido, The FieldTrip method that performs time-frequency analyses is called ft_freqanalysis. By default, ft_freqanalysis gives you power averaged over trials as output. You can easily override this default behaviour by specifying cfg.keeptrials='yes', you will then get a power estimate for each individual trial. You might want to take a look at the following tutorial, which covers the basics of how to do time-frequency analysis in FieldTrip: http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis The reference documentation for ft_freqanalysis also might be of use: http://fieldtrip.fcdonders.nl/reference/ft_freqanalysis (which is the same information you get when you type 'help ft_freqanalysis' or 'doc ft_freqanalysis' at the matlab prompt). Hope this was of help. Best, Eelke 2011/12/14 Guido Hesselmann : > Hi all, > > I am new to fieldtrip and have a very simple question. I have EEG data and > would like to run a > time-frequency analysis (e.g., using a Hanning taper with fixed window > length). If I have 100 trials, > how is this analysis performed? On a trial-by-trial basis, or based on the > average? Can I choose > between these options in fieldtrip? > > Thanks a lot! > > Guido Hesselmann > Visual Perception Lab > Department of Psychiatry & Psychotherapy > Charité Berlin > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From lihqih at gmail.com Wed Dec 14 19:04:37 2011 From: lihqih at gmail.com (qi li) Date: Wed, 14 Dec 2011 13:04:37 -0500 Subject: [FieldTrip] remove trials after ft_preprocessing Message-ID: I am new to fieldtrip. After I processed the data, I got triggered_trials = hdr: [1x1 struct] label: {273x1 cell} time: {1x20 cell} trial: {1x20 cell} fsample: 600 sampleinfo: [20x2 double] grad: [1x1 struct] cfg: [1x1 struct] Now I want to remove a few trials with trial no 1 3 5 8. What command do I need to remove the trials and keep the structure of triggered_trials unchanged? Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From ucbtmba at ucl.ac.uk Wed Dec 14 19:08:48 2011 From: ucbtmba at ucl.ac.uk (Markus Bauer) Date: Wed, 14 Dec 2011 18:08:48 +0000 Subject: [FieldTrip] Time-frequency analysis: based on single trials or on average? In-Reply-To: References: Message-ID: <4EE8E630.2050600@ucl.ac.uk> An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Wed Dec 14 19:15:06 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Wed, 14 Dec 2011 19:15:06 +0100 Subject: [FieldTrip] remove trials after ft_preprocessing In-Reply-To: References: Message-ID: Dear Qi Li, There are several ways to achieve this. Both ft_selectdata and ft_preprocessing allow you to select a subset of trials without altering anything else in the data. Both of these functions require a vector as input that contains the indices of the trials to be *retained*, so you need to create this yourself. For instance: trialsToKeep = 1:20; % initialize vector with all trial indices trialsToKeep([1 3 5 8]) = []; % remove the trials that should go After this you can call either: data = ft_selectdata(data, 'rpt', trialsToKeep); Or: cfg = []; cfg.trials = trialsToKeep; data = ft_preprocessing(cfg, data); Best, Eelke 2011/12/14 qi li : > I am new to fieldtrip. After I processed the data, I got > triggered_trials = > >            hdr: [1x1 struct] >          label: {273x1 cell} >           time: {1x20 cell} >          trial: {1x20 cell} >        fsample: 600 >     sampleinfo: [20x2 double] >           grad: [1x1 struct] >            cfg: [1x1 struct] > Now I want to remove a few trials with trial no 1 3 5 8. What command do I > need to remove the trials and keep the structure of triggered_trials > unchanged? Thanks! > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Thu Dec 15 10:15:56 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 15 Dec 2011 10:15:56 +0100 Subject: [FieldTrip] read_eeglab, header file? In-Reply-To: <4EE87B31020000570000BF1A@gwsmtp1.uni-regensburg.de> References: <4AFA1595-9C1E-4937-951B-8F0FE6980FAA@donders.ru.nl> <733DE7A7-2C6A-4DB3-824E-B0E32C0F08B6@donders.ru.nl> <4EE87B31020000570000BF1A@gwsmtp1.uni-regensburg.de> Message-ID: <4EE9BACC.7040809@donders.ru.nl> Hi Gregor, thanks for reporting this. It looks indeed like it should be like that, so I changed it to what you suggested (otherwise, if-clause does not make any sense at all). Best, Jörn On 12/14/2011 10:32 AM, Gregor Volberg wrote: > > Dear Fieldtrip developers, > > > I encountered an error warning when reading in an eeglab *.set - file > for preprocessing (version fieldtrip-20111206), where the call to > ft_preprocessing says > > > ??? Undefined function or variable "hdr". > > Error in ==> read_eeglabdata at 52 > > if isempty(hdr) > > > > Shouldn't code lines 52 to 54 read > > > if isempty(header) > > header = read_eeglabheader(filename); > > end > > > instead of > > > if isempty(hdr) > > hdr = read_eeglabheader(filename); > > end > > > > Not really a problem, just to bring it to your attention... > > > Best regards, > > Gregor > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Thu Dec 15 21:00:59 2011 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Thu, 15 Dec 2011 14:00:59 -0600 Subject: [FieldTrip] Topographic scaling of ERP data Message-ID: Hello, Our lab is interested in performing the topographic scaling method described in the following paper to compare ERP topographies: Jing, H., Pivik, R., & Dykman, R. (2006). A new scaling method for topographic comparisons of event-related potentials. *Journal of Neuroscience Methods 151*. Are there any FieldTrip functions available that implement this method? Thank you,, Steve Politzer-Ahles -- Stephen Politzer-Ahles University of Kansas Linguistics Department http://www.linguistics.ku.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From chenzuyue at live.cn Fri Dec 16 13:14:22 2011 From: chenzuyue at live.cn (chenzuyue) Date: Fri, 16 Dec 2011 12:14:22 +0000 Subject: [FieldTrip] Problems time-frequency analysis of Local Field Potential Message-ID: Hi, everyone, I am a new user of FieldTrip. In my study, I want to computes the difference of time-frequency representations of event-related LFP in two conditions. The data in the first condition is a 4 X 1100 X 103 matrix (Nchan X Nsamples X Ntrials). The data in the second condition is a 4 X 1100 X 107 matrix. The data reformatted are as follows: dataset1.label (4 X 1 cell ); dataset1.fsample 1000; dataset1.trial (1 X 103 cell ); dataset1.time (1X 103 cell); % time is from -100ms to 999ms. dataset2.label (4 X 1 cell ); dataset2.fsample 1000; dataset2.trial (1 X 107 cell ); dataset2.time (1X 107 cell ); % time is from -100ms to 999ms. The frequency interested is 0-100Hz. The method to calculate TFRs is the multitaper method. The configuration is as below: cfg = []; cfg.output = 'pow'; cfg.method = 'mtmconvol'; cfg.foi = 1:2:100; cfg.t_ftimwin = 5./cfg.foi; cfg.tapsmofrq = 0.4 *cfg.foi; cfg.toi = -0.1:0.05:1; cfg.pad = 'maxperlen'; TFRmult1 = ft_freqanalysis(cfg, dataset1); But after running, I can not get the right results. When I use ft_singleplotTFR to plot graph, there is only blue color. I wonder whether the process and configuration is right. The method is from one paper of E Maris and R Oostenvels published on the Journal of Neuroscience Methods.164(2007), 177-190; Figure 3. http://www.ncbi.nlm.nih.gov/pubmed/17517438 Any help is much appreciated. Yours Sincerely, Zuyue -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Fri Dec 16 13:44:51 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Fri, 16 Dec 2011 13:44:51 +0100 Subject: [FieldTrip] Problems time-frequency analysis of Local Field Potential In-Reply-To: References: Message-ID: Dear Zuyue, When you invoke ft_singleplotTFR, do you specify a means of baseline correction and/or explicit z-limits (i.e., limits of the color axis)? When looking at raw power (i.e., not contrasted), it is advisable to use a baseline correction in order to see something. Also, specifying z-limits of a different order of magnitude than your data will of course lead to all blue plots. You should take a look at the time-frequency analysis tutorial, particularly the part about visualization: http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis#visualization If you still don't see anything after you use baseline correction (or plot a contrast instead) and have proper z-limits, there might be something else wrong. Best, Eelke 2011/12/16 chenzuyue : > Hi, everyone, > > I am a new user of FieldTrip. In my study, I want to computes the difference > of time-frequency representations of event-related LFP in two conditions. > > The data in the first condition is a 4 X 1100 X 103 matrix (Nchan X Nsamples > X Ntrials). The data in the second condition is a 4 X 1100 X 107 matrix. The > data reformatted are as follows: > > dataset1.label (4 X 1 cell ); > > dataset1.fsample 1000; > > dataset1.trial (1 X 103 cell ); > > dataset1.time (1X 103 cell); % time is from -100ms to 999ms. > > > dataset2.label (4 X 1 cell ); > > dataset2.fsample 1000; > > dataset2.trial (1 X 107 cell ); > > dataset2.time (1X 107 cell ); % time is from -100ms to 999ms. > > > The frequency interested is 0-100Hz. The method to calculate TFRs is the > multitaper method. The configuration is as below: > > cfg = []; > cfg.output = 'pow'; > cfg.method = 'mtmconvol'; > cfg.foi = 1:2:100; > cfg.t_ftimwin = 5./cfg.foi; > cfg.tapsmofrq = 0.4 *cfg.foi; > cfg.toi = -0.1:0.05:1; > cfg.pad = 'maxperlen'; > TFRmult1 = ft_freqanalysis(cfg, dataset1); > > But after running, I can not get the right results. When I use > ft_singleplotTFR to plot graph, there is only blue color. I wonder whether > the process and configuration is right. > > The method is from one paper of E Maris and R Oostenvels published on the > Journal of Neuroscience Methods.164(2007), 177-190; Figure 3. > http://www.ncbi.nlm.nih.gov/pubmed/17517438 > > Any help is much appreciated. > > Yours Sincerely, > > Zuyue > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Fri Dec 16 14:02:36 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 16 Dec 2011 14:02:36 +0100 Subject: [FieldTrip] Problems time-frequency analysis of Local Field Potential In-Reply-To: References: Message-ID: <46831F4B-7707-496E-B55C-DDE4E4E5BB15@donders.ru.nl> Dear Zuyue, I agree with Eelke. One thing you need to check is whether the time axis (in data.time{}) is in seconds or milliseconds. In the cfg to ft_freqanalysis you specify it in seconds. FieldTrip does not care about the exact units, so you need to ensure that the units in the time-axis correspond. BW, Jan-Mathijs On Dec 16, 2011, at 1:44 PM, Eelke Spaak wrote: > Dear Zuyue, > > When you invoke ft_singleplotTFR, do you specify a means of baseline > correction and/or explicit z-limits (i.e., limits of the color axis)? > When looking at raw power (i.e., not contrasted), it is advisable to > use a baseline correction in order to see something. Also, specifying > z-limits of a different order of magnitude than your data will of > course lead to all blue plots. > > You should take a look at the time-frequency analysis tutorial, > particularly the part about visualization: > http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis#visualization > > If you still don't see anything after you use baseline correction (or > plot a contrast instead) and have proper z-limits, there might be > something else wrong. > > Best, > Eelke > > 2011/12/16 chenzuyue : >> Hi, everyone, >> >> I am a new user of FieldTrip. In my study, I want to computes the difference >> of time-frequency representations of event-related LFP in two conditions. >> >> The data in the first condition is a 4 X 1100 X 103 matrix (Nchan X Nsamples >> X Ntrials). The data in the second condition is a 4 X 1100 X 107 matrix. The >> data reformatted are as follows: >> >> dataset1.label (4 X 1 cell ); >> >> dataset1.fsample 1000; >> >> dataset1.trial (1 X 103 cell ); >> >> dataset1.time (1X 103 cell); % time is from -100ms to 999ms. >> >> >> dataset2.label (4 X 1 cell ); >> >> dataset2.fsample 1000; >> >> dataset2.trial (1 X 107 cell ); >> >> dataset2.time (1X 107 cell ); % time is from -100ms to 999ms. >> >> >> The frequency interested is 0-100Hz. The method to calculate TFRs is the >> multitaper method. The configuration is as below: >> >> cfg = []; >> cfg.output = 'pow'; >> cfg.method = 'mtmconvol'; >> cfg.foi = 1:2:100; >> cfg.t_ftimwin = 5./cfg.foi; >> cfg.tapsmofrq = 0.4 *cfg.foi; >> cfg.toi = -0.1:0.05:1; >> cfg.pad = 'maxperlen'; >> TFRmult1 = ft_freqanalysis(cfg, dataset1); >> >> But after running, I can not get the right results. When I use >> ft_singleplotTFR to plot graph, there is only blue color. I wonder whether >> the process and configuration is right. >> >> The method is from one paper of E Maris and R Oostenvels published on the >> Journal of Neuroscience Methods.164(2007), 177-190; Figure 3. >> http://www.ncbi.nlm.nih.gov/pubmed/17517438 >> >> Any help is much appreciated. >> >> Yours Sincerely, >> >> Zuyue >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Mon Dec 19 10:03:51 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Mon, 19 Dec 2011 11:03:51 +0200 Subject: [FieldTrip] Address of biosemi device Message-ID: Hello, I'd tried to use the biosemi2ft function for realtime acquiring. But the following message appears: "Could not connect to buffer server at localhost: 1972". Should I change the Hostname and the Port, if yes what should they be? Best, -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Dec 19 11:04:47 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 19 Dec 2011 11:04:47 +0100 Subject: [FieldTrip] Topographic scaling of ERP data In-Reply-To: References: Message-ID: Dear Stephen, I am not aware of any FieldTrip function that achieves this scaling. Looking at the method, it seems that it should be able to implement this is not too many lines of matlab code. Maybe someone else on the list has some code lying around. Best wishes, Jan-Mathijs On Dec 15, 2011, at 9:00 PM, Stephen Politzer-Ahles wrote: > Hello, > > Our lab is interested in performing the topographic scaling method described in the following paper to compare ERP topographies: > > Jing, H., Pivik, R., & Dykman, R. (2006). A new scaling method for topographic comparisons of event-related potentials. Journal of Neuroscience Methods 151. > > Are there any FieldTrip functions available that implement this method? > > Thank you,, > Steve Politzer-Ahles > > -- > Stephen Politzer-Ahles > University of Kansas > Linguistics Department > http://www.linguistics.ku.edu/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Tue Dec 20 02:54:53 2011 From: lihqih at gmail.com (qi li) Date: Mon, 19 Dec 2011 20:54:53 -0500 Subject: [FieldTrip] operation order difference Message-ID: Hi, I have a CTF axial data. Is the result of timelock first then do the ft_megplanar same as ft_megplanar first then timelock? I think both method should get the same result. Qi -------------- next part -------------- An HTML attachment was scrubbed... URL: From adam at adamcsnyder.com Tue Dec 20 04:54:39 2011 From: adam at adamcsnyder.com (Adam C. Snyder) Date: Mon, 19 Dec 2011 22:54:39 -0500 Subject: [FieldTrip] Problem detecting triggers with real time synchronous analysis Message-ID: <29E38593-B980-47D1-9E86-E197EF62994E@adamcsnyder.com> Hello, I'm trying to perform a real time synchronous analysis in response to a particular trigger, but it isn't working. Here are some brief details of the setup: we're using BioSemi ActiveTwo, a December 2011 version of FieldTrip and MATLAB 2010b. I've managed to get the biosemi2ft executable running, and if I send a trigger through the BioSemi system, the details are noted in the command window. However, within the ft_realtime_synchronous function, the trigger events are not being found. The built-in status updates (e.g., "CMS_IN_RANGE", etc.), in contrast, are picked up by the ft_read_event call within ft_realtime_synchronous function, which adds to my confusion. My configurations are something like these: cfg.dataset = 'buffer://localhost:1972'; cfg.bcifun = @hello_world; cfg.blocksize = 1; cfg.trigger = [4 2]; cfg.jumptoeof = 'yes'; cfg.bufferdata = 'last'; %maybe the name of this option was different -- I'm typing from memory I hope someone can kindly help me to figure this out, and thank you in advance for whatever help you can provide. In Science, Adam C. Snyder Postdoctoral Fellow Cognitive Neurophysiology Lab Albert Einstein College of Medicine Bronx, NY From eelke.spaak at donders.ru.nl Tue Dec 20 10:56:13 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 20 Dec 2011 10:56:13 +0100 Subject: [FieldTrip] operation order difference In-Reply-To: References: Message-ID: Hi Qi, I think so too. Have you tried it? Best, Eelke 2011/12/20 qi li : > Hi, > > I have a CTF axial data. Is the result of timelock first then do the > ft_megplanar same as ft_megplanar first then timelock? > > I think both method should get the same result. > > Qi > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From lihqih at gmail.com Tue Dec 20 17:39:19 2011 From: lihqih at gmail.com (qi li) Date: Tue, 20 Dec 2011 11:39:19 -0500 Subject: [FieldTrip] operation order difference In-Reply-To: References: Message-ID: Hi Eelke, Thanks for your reply. I tried a particular sample and the difference between these two methods are small. However, timelock first is faster whereas ft_megplanar first makes much more sense. Qi On Tue, Dec 20, 2011 at 4:56 AM, Eelke Spaak wrote: > Hi Qi, > > I think so too. Have you tried it? > > Best, > Eelke > > 2011/12/20 qi li : > > Hi, > > > > I have a CTF axial data. Is the result of timelock first then do the > > ft_megplanar same as ft_megplanar first then timelock? > > > > I think both method should get the same result. > > > > Qi > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Wed Dec 21 11:56:26 2011 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Wed, 21 Dec 2011 11:56:26 +0100 Subject: [FieldTrip] Address of biosemi device In-Reply-To: References: Message-ID: Dear Hamza, I think this message appears when you specify a specific buffer server to connect to. The biosemi2ft.exe can be run in two modes, 1) it starts an baked-in buffer server (default), or 2) it can can use a buffer server that is run in a separate process. The default mode is probably a good choice. You can select the default mode *by not specifying a server of port*. Best regards, Boris On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) wrote: > Hello, > > I'd tried to use the biosemi2ft function for realtime acquiring. But the > following message appears: > > "Could not connect to buffer server at localhost: 1972". > > Should I change the Hostname and the Port, if yes what should they be? > > Best, > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From hamzaf at sabanciuniv.edu Wed Dec 21 15:36:21 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Wed, 21 Dec 2011 16:36:21 +0200 Subject: [FieldTrip] Address of biosemi device In-Reply-To: References: Message-ID: Thank you Boris. Well, I tried the default mode (just by specifying the configuration file and the gdf file in the cmd). But this message appeared. Could you or anyone just tell me exactly what should I do or modify. Thanks a lot On Wed, Dec 21, 2011 at 12:56 PM, Boris Reuderink wrote: > Dear Hamza, > > I think this message appears when you specify a specific buffer server > to connect to. The biosemi2ft.exe can be run in two modes, 1) it > starts an baked-in buffer server (default), or 2) it can can use a > buffer server that is run in a separate process. > > The default mode is probably a good choice. You can select the default > mode *by not specifying a server of port*. > > Best regards, > > Boris > > On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) > wrote: > > Hello, > > > > I'd tried to use the biosemi2ft function for realtime acquiring. But the > > following message appears: > > > > "Could not connect to buffer server at localhost: 1972". > > > > Should I change the Hostname and the Port, if yes what should they be? > > > > Best, > > > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Wed Dec 21 16:48:02 2011 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Wed, 21 Dec 2011 16:48:02 +0100 Subject: [FieldTrip] Address of biosemi device In-Reply-To: References: Message-ID: Could you perhaps send me the exact command you executed? Tomorrow I'll have access to a windows machine --- maybe I can find out what went wrong. Best regards, Boris 2011/12/21 Hamza Fawzi Altakroury (Student) : > Thank you Boris. > > Well, I tried the default mode (just by specifying the configuration file > and the gdf file in the cmd). But this message appeared. > Could you or anyone just tell me exactly what should I do or modify. > > Thanks a lot > > > On Wed, Dec 21, 2011 at 12:56 PM, Boris Reuderink > wrote: >> >> Dear Hamza, >> >> I think this message appears when you specify a specific buffer server >> to connect to. The biosemi2ft.exe can be run in two modes, 1) it >> starts an baked-in buffer server (default), or 2) it can can use a >> buffer server that is run in a separate process. >> >> The default mode is probably a good choice. You can select the default >> mode *by not specifying a server of port*. >> >> Best regards, >> >> Boris >> >> On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) >> wrote: >> > Hello, >> > >> > I'd tried to use the biosemi2ft function for realtime acquiring. But the >> > following message appears: >> > >> > "Could not connect to buffer server at localhost: 1972". >> > >> > Should I change the Hostname and the Port, if yes what should they be? >> > >> > Best, >> > >> > >> > -- >> > Hamza Fawzi Altakroury >> > Graduate student - MA >> > Faculty of Engineering and Natural Sciences >> > Sabancı University >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From johemart at gmail.com Wed Dec 21 16:50:42 2011 From: johemart at gmail.com (=?ISO-8859-1?Q?Johann_Heinz_Mart=EDnez_Huartos?=) Date: Wed, 21 Dec 2011 16:50:42 +0100 Subject: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? Message-ID: Hello dear fieldtripers Currently im using ft_topoplotER() function in order to visualize a cluster of channels in the head. But i cant fill the marker im using to highlight those channels. I know that the commend to chage this opction in matlab is markerfacecolor = 'k'. if i want to fill it up with black color, but this option does not makes anything happend and the markers are not filled. So, anyone knows how to fill the marker in ft_topoplotER() funtion? Thanks -- Atentamente: Johann Martínez. M.Sc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Wed Dec 21 17:50:03 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Wed, 21 Dec 2011 18:50:03 +0200 Subject: [FieldTrip] Address of biosemi device In-Reply-To: References: Message-ID: The directory: fieldtrip-20111211\realtime\acquisition\biosemi The command: biosemi2ft config.txt ex.gdf Output : could not connect to buffer server at localhost:1972. Thank a lot On Wed, Dec 21, 2011 at 5:48 PM, Boris Reuderink wrote: > Could you perhaps send me the exact command you executed? Tomorrow > I'll have access to a windows machine --- maybe I can find out what > went wrong. > > Best regards, > > Boris > > 2011/12/21 Hamza Fawzi Altakroury (Student) : > > Thank you Boris. > > > > Well, I tried the default mode (just by specifying the configuration file > > and the gdf file in the cmd). But this message appeared. > > Could you or anyone just tell me exactly what should I do or modify. > > > > Thanks a lot > > > > > > On Wed, Dec 21, 2011 at 12:56 PM, Boris Reuderink > > wrote: > >> > >> Dear Hamza, > >> > >> I think this message appears when you specify a specific buffer server > >> to connect to. The biosemi2ft.exe can be run in two modes, 1) it > >> starts an baked-in buffer server (default), or 2) it can can use a > >> buffer server that is run in a separate process. > >> > >> The default mode is probably a good choice. You can select the default > >> mode *by not specifying a server of port*. > >> > >> Best regards, > >> > >> Boris > >> > >> On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) > >> wrote: > >> > Hello, > >> > > >> > I'd tried to use the biosemi2ft function for realtime acquiring. But > the > >> > following message appears: > >> > > >> > "Could not connect to buffer server at localhost: 1972". > >> > > >> > Should I change the Hostname and the Port, if yes what should they be? > >> > > >> > Best, > >> > > >> > > >> > -- > >> > Hamza Fawzi Altakroury > >> > Graduate student - MA > >> > Faculty of Engineering and Natural Sciences > >> > Sabancı University > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > fieldtrip at donders.ru.nl > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Wed Dec 21 19:19:24 2011 From: lihqih at gmail.com (qi li) Date: Wed, 21 Dec 2011 13:19:24 -0500 Subject: [FieldTrip] how to plot the selected trials in the same plot Message-ID: Hi, I am trying to plot a single plot for a particular sensor with multiple trials by ft_singleplotER. Even I set the cfg.trials='all', it only gives one curve. If I want to use ft_multiplotER for the various sensors and multiple trials, what should I do? The multiplotER dosen't show the axes ticks and labels, how to fix it? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed Dec 21 20:58:10 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 21 Dec 2011 20:58:10 +0100 Subject: [FieldTrip] Address of biosemi device In-Reply-To: References: Message-ID: <28B62884-7633-4554-A460-31E1BF711582@donders.ru.nl> Dear Hamza According to the documentation on http://fieldtrip.fcdonders.nl/development/realtime/biosemi the full command line is biosemi2ft and "The first argument must be the name of a configuration file (see below). The second argument determines the base name of a GDF file that data is written to. The .gdf will be added automatically, as well as session counters (see below) and additional file name parts _1, _2 and so on for splitting the data over multiple files (to avoid 2 GB limits). The optional third and fourth argument are the hostname and port of the FieldTrip buffer. Defaults are localhost and 1972. Replacinghostname by a minus (-) tells the software to spawn its own buffer server on the given port." If you did not start buffer.exe prior to biosemi2ft.exe, you don't have a buffer server running and the error message makes sense because the buffer cannot be found. If you specify "-" as 3rd argument then biosemi2ft.exe will spawn its own buffer server in a separate thread and will connect to that. See http://fieldtrip.fcdonders.nl/development/realtime/biosemi and http://fieldtrip.fcdonders.nl/development/realtime/buffer. Note that you should name the output file "ex", not "ex.gdf". best Robert On 21 Dec 2011, at 17:50, Hamza Fawzi Altakroury (Student) wrote: > The directory: fieldtrip-20111211\realtime\acquisition\biosemi > > The command: biosemi2ft config.txt ex.gdf > > Output : could not connect to buffer server at localhost:1972. > > Thank a lot > > > > On Wed, Dec 21, 2011 at 5:48 PM, Boris Reuderink wrote: > Could you perhaps send me the exact command you executed? Tomorrow > I'll have access to a windows machine --- maybe I can find out what > went wrong. > > Best regards, > > Boris > > 2011/12/21 Hamza Fawzi Altakroury (Student) : > > Thank you Boris. > > > > Well, I tried the default mode (just by specifying the configuration file > > and the gdf file in the cmd). But this message appeared. > > Could you or anyone just tell me exactly what should I do or modify. > > > > Thanks a lot > > > > > > On Wed, Dec 21, 2011 at 12:56 PM, Boris Reuderink > > wrote: > >> > >> Dear Hamza, > >> > >> I think this message appears when you specify a specific buffer server > >> to connect to. The biosemi2ft.exe can be run in two modes, 1) it > >> starts an baked-in buffer server (default), or 2) it can can use a > >> buffer server that is run in a separate process. > >> > >> The default mode is probably a good choice. You can select the default > >> mode *by not specifying a server of port*. > >> > >> Best regards, > >> > >> Boris > >> > >> On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) > >> wrote: > >> > Hello, > >> > > >> > I'd tried to use the biosemi2ft function for realtime acquiring. But the > >> > following message appears: > >> > > >> > "Could not connect to buffer server at localhost: 1972". > >> > > >> > Should I change the Hostname and the Port, if yes what should they be? > >> > > >> > Best, > >> > > >> > > >> > -- > >> > Hamza Fawzi Altakroury > >> > Graduate student - MA > >> > Faculty of Engineering and Natural Sciences > >> > Sabancı University > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > fieldtrip at donders.ru.nl > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From s.bogels at psy.gla.ac.uk Thu Dec 22 10:26:57 2011 From: s.bogels at psy.gla.ac.uk (Sara =?iso-8859-1?b?QvZnZWxz?=) Date: Thu, 22 Dec 2011 09:26:57 +0000 Subject: [FieldTrip] problems with ft_multiplotTFR Message-ID: <20111222092657.846462fkkxbzywgx@horde.psy.gla.ac.uk> Hi all, I have performed a cluster-based permutation test on time-frequency data and I am trying to plot the significant clusters. Since I used multiple frequencies I cannot use ft_clusterplot but I should use ft_multiplotTFR if I understand correctly. I also did not average over time and I used all channels. The analysis resulted in 1 significant positive cluster and 1 significant negative cluster. I have tried ft_multiplotTFR with the following settings (plus a correct cfg.layout): cfg = []: cfg.maskparameter = 'mask'; cfg.parameter = 'stat'; cfg.maskalpha = 0.025; figure, ft_multiplotTFR(cfg,stats) This gives me plots on the head for all channels but they are all black. If I outcomment cfg.maskparameter I do get nicely coloured plots (of the teststatistic I assume) but of course without the significant cluster(s). Any help is appreciated. Thank you, Sara ---------------------------------------------------------------- This message was sent using the Web mail system for The University of Glasgow School of Psychology ------------------------------------------------------------------ From r.vandermeij at donders.ru.nl Thu Dec 22 10:37:43 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Thu, 22 Dec 2011 10:37:43 +0100 Subject: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? In-Reply-To: References: Message-ID: <4EF2FA67.8010108@donders.ru.nl> Hi Johann, If you update to the newest fieldtrip version, you can use the option cfg.highlightsymbol or cfg.markersymbol to pick a marker that is filled, like '.'. Best, Roemer On 21-12-11 16:50, Johann Heinz Martínez Huartos wrote: > Hello dear fieldtripers > > Currently im using ft_topoplotER() function in order to visualize a > cluster of channels in the head. But i cant fill the marker im using > to highlight those channels. I know that the commend to chage this > opction in matlab is markerfacecolor = 'k'. > if i want to fill it up with black color, but this option does not > makes anything happend and the markers are not filled. So, anyone > knows how to fill the marker in ft_topoplotER() funtion? > > Thanks > > -- > Atentamente: > Johann Martínez. M.Sc. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Thu Dec 22 14:36:31 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 22 Dec 2011 15:36:31 +0200 Subject: [FieldTrip] Address of biosemi device In-Reply-To: <28B62884-7633-4554-A460-31E1BF711582@donders.ru.nl> References: <28B62884-7633-4554-A460-31E1BF711582@donders.ru.nl> Message-ID: Dear Mr Robert Thanks a lot for your help. It works. Best On Wed, Dec 21, 2011 at 9:58 PM, Robert Oostenveld < r.oostenveld at donders.ru.nl> wrote: > Dear Hamza > > According to the documentation on > http://fieldtrip.fcdonders.nl/development/realtime/biosemi the full > command line is > biosemi2ft > and "The first argument must be the name of a configuration file (see > below). The second argument determines the base name of a GDF file that > data is written to. The .gdf will be added automatically, as well as > session counters (see below) and additional file name parts _1, _2 and so > on for splitting the data over multiple files (to avoid 2 GB limits). The > optional third and fourth argument are the hostname and port of the > FieldTrip buffer. Defaults are localhost and 1972. Replacinghostname by a > minus (-) tells the software to spawn its own buffer server on the given > port." > > If you did not start buffer.exe prior to biosemi2ft.exe, you don't have a > buffer server running and the error message makes sense because the buffer > cannot be found. > > If you specify "-" as 3rd argument then biosemi2ft.exe will spawn its own > buffer server in a separate thread and will connect to that. See > http://fieldtrip.fcdonders.nl/development/realtime/biosemi and > http://fieldtrip.fcdonders.nl/development/realtime/buffer. Note that you > should name the output file "ex", not "ex.gdf". > > best > Robert > > > On 21 Dec 2011, at 17:50, Hamza Fawzi Altakroury (Student) wrote: > > > The directory: fieldtrip-20111211\realtime\acquisition\biosemi > > > > The command: biosemi2ft config.txt ex.gdf > > > > Output : could not connect to buffer server at localhost:1972. > > > > Thank a lot > > > > > > > > On Wed, Dec 21, 2011 at 5:48 PM, Boris Reuderink < > b.reuderink at donders.ru.nl> wrote: > > Could you perhaps send me the exact command you executed? Tomorrow > > I'll have access to a windows machine --- maybe I can find out what > > went wrong. > > > > Best regards, > > > > Boris > > > > 2011/12/21 Hamza Fawzi Altakroury (Student) : > > > Thank you Boris. > > > > > > Well, I tried the default mode (just by specifying the configuration > file > > > and the gdf file in the cmd). But this message appeared. > > > Could you or anyone just tell me exactly what should I do or modify. > > > > > > Thanks a lot > > > > > > > > > On Wed, Dec 21, 2011 at 12:56 PM, Boris Reuderink > > > wrote: > > >> > > >> Dear Hamza, > > >> > > >> I think this message appears when you specify a specific buffer server > > >> to connect to. The biosemi2ft.exe can be run in two modes, 1) it > > >> starts an baked-in buffer server (default), or 2) it can can use a > > >> buffer server that is run in a separate process. > > >> > > >> The default mode is probably a good choice. You can select the default > > >> mode *by not specifying a server of port*. > > >> > > >> Best regards, > > >> > > >> Boris > > >> > > >> On Mon, Dec 19, 2011 at 10:03 AM, Hamza Fawzi Altakroury (Student) > > >> wrote: > > >> > Hello, > > >> > > > >> > I'd tried to use the biosemi2ft function for realtime acquiring. > But the > > >> > following message appears: > > >> > > > >> > "Could not connect to buffer server at localhost: 1972". > > >> > > > >> > Should I change the Hostname and the Port, if yes what should they > be? > > >> > > > >> > Best, > > >> > > > >> > > > >> > -- > > >> > Hamza Fawzi Altakroury > > >> > Graduate student - MA > > >> > Faculty of Engineering and Natural Sciences > > >> > Sabancı University > > >> > > > >> > _______________________________________________ > > >> > fieldtrip mailing list > > >> > fieldtrip at donders.ru.nl > > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > >> > > >> _______________________________________________ > > >> fieldtrip mailing list > > >> fieldtrip at donders.ru.nl > > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > -- > > > Hamza Fawzi Altakroury > > > Graduate student - MA > > > Faculty of Engineering and Natural Sciences > > > Sabancı University > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Thu Dec 22 19:47:56 2011 From: lihqih at gmail.com (qi li) Date: Thu, 22 Dec 2011 13:47:56 -0500 Subject: [FieldTrip] artifact removal Message-ID: Hi, I am following the automatic_artifact_rejection tutorial but the interactive graphic window doesn't show. I am using fieldtrip 1014 version. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sat Dec 24 20:37:27 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sat, 24 Dec 2011 21:37:27 +0200 Subject: [FieldTrip] offset2time function Message-ID: Hello I tried to run the "ft_realtime_synchronous" function but, the following error appeared. ??? Undefined function or method 'offset2time' for input arguments of type 'double'. How can I get the offset2time function. Note: I read the "resampledata/offset2time" email and updated the folder but I same problem appeared. Best -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sun Dec 25 18:48:24 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sun, 25 Dec 2011 19:48:24 +0200 Subject: [FieldTrip] Reading online-data from a file Message-ID: Hello, I am using biosemi2ft for saving data into a gdf file online. I want to process the data as the acquiring is taking place. The "ft_read_event" function give me an easy way to get the triggers values. But as I think it reads the file each time from the beginning. Unfortunately the sread function which keep track of the file, does not extract the triggers' values. Any suggestions. -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sun Dec 25 20:46:33 2011 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sun, 25 Dec 2011 21:46:33 +0200 Subject: [FieldTrip] Trigger values in data matrix Message-ID: Hello, I can't get the real trigger values if use sopen function (or ft_read_data), even after adding the min value -1.7281e+009 to get a positive values. Note: I plotted the triggers and their proportion is right but I can't get their exact values, what should I do. Best, -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From johemart at gmail.com Wed Dec 28 14:39:14 2011 From: johemart at gmail.com (=?ISO-8859-1?Q?Johann_Heinz_Mart=EDnez_Huartos?=) Date: Wed, 28 Dec 2011 14:39:14 +0100 Subject: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? In-Reply-To: <4EF2FA67.8010108@donders.ru.nl> References: <4EF2FA67.8010108@donders.ru.nl> Message-ID: Hi Roemer. Thnkx 4 ur answer. But Im using the fieldtrip version October 2011 and in this version cfg.highlightsymbol already appear just for ft_topoplotER() and cfg.markersymbol just appear for ft.singleplot() nor in ft_topoplotER(). In fact, I looking for a way to fill whichever marker i want to use for. (i.e. ^ > < o) not neccesarilly with '.' Do you know how to do that? thnx again for ur answer or comments. Johann On 22 December 2011 10:37, Roemer van der Meij wrote: > Hi Johann, > > If you update to the newest fieldtrip version, you can use the option > cfg.highlightsymbol or cfg.markersymbol to pick a marker that is filled, > like '.'. > > Best, > Roemer > > > > On 21-12-11 16:50, Johann Heinz Martínez Huartos wrote: > > Hello dear fieldtripers > > Currently im using ft_topoplotER() function in order to visualize a > cluster of channels in the head. But i cant fill the marker im using to > highlight those channels. I know that the commend to chage this opction in > matlab is markerfacecolor = 'k'. > if i want to fill it up with black color, but this option does not makes > anything happend and the markers are not filled. So, anyone knows how to > fill the marker in ft_topoplotER() funtion? > > Thanks > > -- > Atentamente: > Johann Martínez. M.Sc. > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Atentamente: Johann Martínez. M.Sc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Wed Dec 28 16:43:19 2011 From: lihqih at gmail.com (qi li) Date: Wed, 28 Dec 2011 10:43:19 -0500 Subject: [FieldTrip] combine sessions Message-ID: Hi, I have 3 identical sessions. Each of them has 40 trials. Is there any command to combine the 3 sessions into one 120 trials? Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at mac.com Wed Dec 28 16:48:39 2011 From: nathanweisz at mac.com (Nathan Weisz) Date: Wed, 28 Dec 2011 16:48:39 +0100 Subject: [FieldTrip] combine sessions In-Reply-To: References: Message-ID: hi, ft_appenddata.m is likely what you need. best, nathan On 28.12.2011, at 16:43, qi li wrote: > Hi, > > I have 3 identical sessions. Each of them has 40 trials. Is there any command to combine the 3 sessions into one 120 trials? > > Thanks! > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From adam at adamcsnyder.com Thu Dec 29 13:33:21 2011 From: adam at adamcsnyder.com (Adam C. Snyder) Date: Thu, 29 Dec 2011 07:33:21 -0500 Subject: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? In-Reply-To: References: Message-ID: <4EFC5E11.8090404@adamcsnyder.com> What about just using a command such as the following: set(findobj(gca,'type','hggroup'),'markerfacecolor','k'); -Adam C. Snyder P.s., on another note, I asked for some help some time ago with a problem I was having using triggers from BioSemi to instigate online analysis using ft_realtime_synchronous. Does anyone have any thoughts about that? I can restate the problem, if needed. Your help would be greatly appreciated. On 29-Dec-2011 06:00, fieldtrip-request at donders.ru.nl wrote: > Send fieldtrip mailing list submissions to > fieldtrip at donders.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at donders.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at donders.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: How to fill the markers in FT_TOPOPLOTER?? > (Johann Heinz Mart?nez Huartos) > 2. combine sessions (qi li) > 3. Re: combine sessions (Nathan Weisz) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 28 Dec 2011 14:39:14 +0100 > From: Johann Heinz Mart?nez Huartos > To: r.vandermeij at donders.ru.nl, Email discussion list for the > FieldTrip project > Subject: Re: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Roemer. > > Thnkx 4 ur answer. But Im using the fieldtrip version October 2011 and in > this version cfg.highlightsymbol already appear just for ft_topoplotER() > and cfg.markersymbol just appear for ft.singleplot() nor in > ft_topoplotER(). > In fact, I looking for a way to fill whichever marker i want to use for. > (i.e. ^> < o) not neccesarilly with '.' > > Do you know how to do that? > > thnx again for ur answer or comments. > > Johann > > > On 22 December 2011 10:37, Roemer van der Meij > wrote: > >> Hi Johann, >> >> If you update to the newest fieldtrip version, you can use the option >> cfg.highlightsymbol or cfg.markersymbol to pick a marker that is filled, >> like '.'. >> >> Best, >> Roemer >> >> >> >> On 21-12-11 16:50, Johann Heinz Mart?nez Huartos wrote: >> >> Hello dear fieldtripers >> >> Currently im using ft_topoplotER() function in order to visualize a >> cluster of channels in the head. But i cant fill the marker im using to >> highlight those channels. I know that the commend to chage this opction in >> matlab is markerfacecolor = 'k'. >> if i want to fill it up with black color, but this option does not makes >> anything happend and the markers are not filled. So, anyone knows how to >> fill the marker in ft_topoplotER() funtion? >> >> Thanks >> >> -- >> Atentamente: >> Johann Mart?nez. M.Sc. >> >> >> _______________________________________________ >> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> Roemer van der Meij M.Sc. >> PhD student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> P.O. Box 9104 >> 6500 HE Nijmegen >> The Netherlands >> Tel: +31(0)24 3655932 >> E-mail: r.vandermeij at donders.ru.nl >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > From johemart at gmail.com Thu Dec 29 16:44:03 2011 From: johemart at gmail.com (=?ISO-8859-1?Q?Johann_Heinz_Mart=EDnez_Huartos?=) Date: Thu, 29 Dec 2011 16:44:03 +0100 Subject: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? In-Reply-To: <4EFC5E11.8090404@adamcsnyder.com> References: <4EFC5E11.8090404@adamcsnyder.com> Message-ID: thnkx Adam. I,ll try to use that command. good luck with your question! Johann. On 29 December 2011 13:33, Adam C. Snyder wrote: > What about just using a command such as the following: > > set(findobj(gca,'type','**hggroup'),'markerfacecolor','**k'); > > -Adam C. Snyder > > P.s., on another note, I asked for some help some time ago with a problem > I was having using triggers from BioSemi to instigate online analysis using > ft_realtime_synchronous. Does anyone have any thoughts about that? I can > restate the problem, if needed. Your help would be greatly appreciated. > > On 29-Dec-2011 06:00, fieldtrip-request at donders.ru.**nlwrote: > >> Send fieldtrip mailing list submissions to >> fieldtrip at donders.ru.nl >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >> or, via email, send a message with subject or body 'help' to >> fieldtrip-request at donders.ru.**nl >> >> You can reach the person managing the list at >> fieldtrip-owner at donders.ru.nl >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of fieldtrip digest..." >> >> >> Today's Topics: >> >> 1. Re: How to fill the markers in FT_TOPOPLOTER?? >> (Johann Heinz Mart?nez Huartos) >> 2. combine sessions (qi li) >> 3. Re: combine sessions (Nathan Weisz) >> >> >> ------------------------------**------------------------------** >> ---------- >> >> Message: 1 >> Date: Wed, 28 Dec 2011 14:39:14 +0100 >> From: Johann Heinz Mart?nez Huartos >> To: r.vandermeij at donders.ru.nl, Email discussion list for the >> FieldTrip project >> Subject: Re: [FieldTrip] How to fill the markers in FT_TOPOPLOTER?? >> Message-ID: >> > gmail.com <75UhLSw at mail.gmail.com>> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Hi Roemer. >> >> Thnkx 4 ur answer. But Im using the fieldtrip version October 2011 and in >> this version cfg.highlightsymbol already appear just for ft_topoplotER() >> and cfg.markersymbol just appear for ft.singleplot() nor in >> ft_topoplotER(). >> In fact, I looking for a way to fill whichever marker i want to use for. >> (i.e. ^> < o) not neccesarilly with '.' >> >> Do you know how to do that? >> >> thnx again for ur answer or comments. >> >> Johann >> >> >> On 22 December 2011 10:37, Roemer van der Meij >> **wrote: >> >> Hi Johann, >>> >>> If you update to the newest fieldtrip version, you can use the option >>> cfg.highlightsymbol or cfg.markersymbol to pick a marker that is filled, >>> like '.'. >>> >>> Best, >>> Roemer >>> >>> >>> >>> On 21-12-11 16:50, Johann Heinz Mart?nez Huartos wrote: >>> >>> Hello dear fieldtripers >>> >>> Currently im using ft_topoplotER() function in order to visualize a >>> cluster of channels in the head. But i cant fill the marker im using to >>> highlight those channels. I know that the commend to chage this opction >>> in >>> matlab is markerfacecolor = 'k'. >>> if i want to fill it up with black color, but this option does not makes >>> anything happend and the markers are not filled. So, anyone knows how to >>> fill the marker in ft_topoplotER() funtion? >>> >>> Thanks >>> >>> -- >>> Atentamente: >>> Johann Mart?nez. M.Sc. >>> >>> >>> ______________________________**_________________ >>> fieldtrip mailing listfieldtrip at donders.ru.**nlhttp:// >>> mailman.science.ru.**nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> -- >>> Roemer van der Meij M.Sc. >>> PhD student >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognition >>> P.O. Box 9104 >>> 6500 HE Nijmegen >>> The Netherlands >>> Tel: +31(0)24 3655932 >>> E-mail: r.vandermeij at donders.ru.nl >>> >>> ______________________________**_________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >>> >>> >> >> > ______________________________**_________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip > -- Atentamente: Johann Martínez. M.Sc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eva.patai at psy.ox.ac.uk Thu Dec 29 23:22:16 2011 From: eva.patai at psy.ox.ac.uk (Zita Eva Patai) Date: Thu, 29 Dec 2011 22:22:16 +0000 Subject: [FieldTrip] clusterplot not plotting for gradiometeres Message-ID: Dear All (happy holidays) when plotting significant clusters of tf/erf output of permutation test, i can plot sig. clusters for magnetometers but not gradiometers please see attached image...there are indications that there should be highlights...yet not visible...i am using exact same script, everything, difference is the layout file i use (neuromag306mag vs neuromag306cmb) thank you! z -- Zita Patai DPhil Candidate, Experimental Psychology University of Oxford bcl.psy.ox.ac.uk/people/zita-eva-patai/ eva.patai at psy.ox.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: wherearethehighlights Type: application/octet-stream Size: 30527 bytes Desc: not available URL: From marco.rotonda at gmail.com Fri Dec 30 13:07:15 2011 From: marco.rotonda at gmail.com (Marco Rotonda) Date: Fri, 30 Dec 2011 13:07:15 +0100 Subject: [FieldTrip] Strange path problem? Message-ID: Hi fieldtrippers, yesterday I moved to a win7 64bit version, installed latest matlab (2011b) and updated fieldtrip to the latest version (fieldtrip-20111223). After setting up all I tried to run a script I used until yesterday and I get a strange error: Invalid MEX-file 'C:\Program Files\fieldtrip\fileio\private\read_16bit.mexw64': The specified module could not be found. fileio is in the path, so I thought it was about the x86 program and I moved fieldtrip there, but same result: Invalid MEX-file 'C:\Program Files (x86)\fieldtrip\fileio\private\read_16bit.mexw64': The specified module could not be found. I think I miss a stupid thing. Sorry to disturb you, Marco From bibi.raquel at gmail.com Fri Dec 30 15:18:12 2011 From: bibi.raquel at gmail.com (Raquel Bibi) Date: Fri, 30 Dec 2011 09:18:12 -0500 Subject: [FieldTrip] Strange path problem? In-Reply-To: References: Message-ID: Hi, Marco. As a first test I would run "mbuild -setup" at the Matlab command line and select a C/C++ compiler. If this doesn't fix problem see: http://fieldtrip.fcdonders.nl/faq/how_can_i_compile_the_mex_files_on_64_bit_windows. This should fix the problems your having. Best, Raquel On Fri, Dec 30, 2011 at 7:07 AM, Marco Rotonda wrote: > Hi fieldtrippers, > yesterday I moved to a win7 64bit version, installed latest matlab > (2011b) and updated fieldtrip to the latest version > (fieldtrip-20111223). > After setting up all I tried to run a script I used until yesterday > and I get a strange error: > > Invalid MEX-file 'C:\Program > Files\fieldtrip\fileio\private\read_16bit.mexw64': The > specified module could not be found. > > fileio is in the path, so I thought it was about the x86 program and I > moved fieldtrip there, but same result: > > Invalid MEX-file 'C:\Program Files > (x86)\fieldtrip\fileio\private\read_16bit.mexw64': The > specified module could not be found. > > I think I miss a stupid thing. > > Sorry to disturb you, > > Marco > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Fri Dec 30 17:04:35 2011 From: lihqih at gmail.com (qi li) Date: Fri, 30 Dec 2011 11:04:35 -0500 Subject: [FieldTrip] question of planar gradient decomposition Message-ID: Hi, We have a axial ctf 1st order gradiometer. So it measures the axial gradient of the the magnetic field-(dB/dr). If I do the planar gradient transformation by 'sincos ,distance,' your codes looks like computing d^2B/d(theta) and d^2B/d(phi) where theta and phi are azimuth angle and polar angle respectively. It is well known in a spherical coordinate, there is no way to derive the tangential components from axial component, so what is the purpose of your linear transformation? Compared to neuromag which does pick up the planar gradient, is there any advantage for you to do so? Thanks a lot! Happy new year! Qi * * -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.rotonda at gmail.com Fri Dec 30 17:20:34 2011 From: marco.rotonda at gmail.com (Marco Rotonda) Date: Fri, 30 Dec 2011 17:20:34 +0100 Subject: [FieldTrip] Strange path problem? In-Reply-To: References: Message-ID: Thanks, I know it was a quite simple problem... sorry to disturb not reading the faq :( 2011/12/30 Raquel Bibi : > Hi, Marco. > > As a first test I would run "mbuild -setup" at the Matlab command line and > select a C/C++ compiler.  If this doesn't fix problem see: > > http://fieldtrip.fcdonders.nl/faq/how_can_i_compile_the_mex_files_on_64_bit_windows. >  This should fix the problems your having. > > Best, > > Raquel > > On Fri, Dec 30, 2011 at 7:07 AM, Marco Rotonda > wrote: >> >> Hi fieldtrippers, >> yesterday I moved to a win7 64bit version, installed latest matlab >> (2011b) and updated fieldtrip to the latest version >> (fieldtrip-20111223). >> After setting up all I tried to run a script I used until yesterday >> and I get a strange error: >> >> Invalid MEX-file 'C:\Program >> Files\fieldtrip\fileio\private\read_16bit.mexw64': The >> specified module could not be found. >> >> fileio is in the path, so I thought it was about the x86 program and I >> moved fieldtrip there, but same result: >> >> Invalid MEX-file 'C:\Program Files >> (x86)\fieldtrip\fileio\private\read_16bit.mexw64': The >> specified module could not be found. >> >> I think I miss a stupid thing. >> >> Sorry to disturb you, >> >> Marco >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Christos.Papadelis at childrens.harvard.edu Sat Dec 31 18:31:18 2011 From: Christos.Papadelis at childrens.harvard.edu (Papadelis, Christos) Date: Sat, 31 Dec 2011 17:31:18 +0000 Subject: [FieldTrip] Special issue in Advances on Human-Computer Interaction In-Reply-To: <876E0E5B34DB6A4DBD0E65B9091B4350027E0A@CHEXMBX2A.CHBOSTON.ORG> References: <876E0E5B34DB6A4DBD0E65B9091B4350027CAD@CHEXMBX2A.CHBOSTON.ORG>, <876E0E5B34DB6A4DBD0E65B9091B4350027E0A@CHEXMBX2A.CHBOSTON.ORG> Message-ID: <876E0E5B34DB6A4DBD0E65B9091B4350027E95@CHEXMBX2A.CHBOSTON.ORG> Dear Collegues, We would like to draw your attention to the following special issue in Advances on Human-Computer Interaction journal, entitled "Using Brain Waves to Control Computers and Machines" (http://www.hindawi.com/journals/ahci/si/ubw/). We invite authors to submit original research and review articles that explore all aspects of Brain Computer Interfaces (BCIs). My best wishes for Happy New Year. On behalf of all the Editors Christos Papadelis, PhD Instructor in Neurology, Harvard Medical School MEG Lab Manager, Children's Hospital Boston 9 Hope Avenue, Waltham, MA 02453, USA christos.papadelis at childrens.harvard.edu Phone: +1-781-216-1128 Fax: +1-781-216-1172