[FieldTrip] fieldtrip Digest, Vol 77, Issue 9
Laxmi Shaw
laxmi.shaw22 at gmail.com
Thu Apr 13 08:07:37 CEST 2017
Dear Fieldtrip user,
Can anybody have EEG 64 channel head model or anyother web source where i
can get the 64 channel head model then please share with me .
On Wed, Apr 12, 2017 at 3:30 PM, <fieldtrip-request at science.ru.nl> wrote:
> Send fieldtrip mailing list submissions to
> fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
> fieldtrip-owner at science.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
> 1. Need help with cluster-based permutation test with 3 groups
> of subjects (Jos? Antonio Uriguen Garaizabal)
> 2. Error when running ft_sourceanalysis with stats across two
> conditions (Maris Skujevskis)
> 3. Re: cluster-based statistics with one covariate
> (Stephen Politzer-Ahles)
> 4. Installing gui_streamer (Robin K?mpe)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 11 Apr 2017 12:08:44 +0200
> From: Jos? Antonio Uriguen Garaizabal <jose.uriguen at deusto.es>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Need help with cluster-based permutation test
> with 3 groups of subjects
> Message-ID:
> <CAMMf7X15byC6p3gqaie6wEuKekV2krZ0++keLLUPZ3pn2h-PAA at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all
>
>
> My name is Toni and I am working on EEG signal processing at University of
> Deusto, Bilbao, Spain. More specifically, right now trying to
> apply cluster-based permutation testing to determine whether there exist
> differences among 3 groups of subjects.
>
>
> So, for my testing, subject groups are E, EN and N, the 2 former being
> different types of patients and the latter being a control group. I am
> forming clusters based on proximity (in space) and each subject is
> characterized by a matrix of values that vary in 2D (per channel and
> another variable related but not equal to frequency).
>
> By means of a T-statistic (indepsamplesT) I can find differences in between
> E and EN, but I find no clusters/differences in between E and N or EN and
> N, even though hypothetically (I think) they should exist. By means of an
> F-statistic (indepsamplesF) I can find differences among the 3 groups at
> the same time, then also between E and EN and no differences between E and
> N or EN and N...
>
> Am I missing something? I do not understand why the might exist a
> significant cluster when comparing all 3 groups that does not exist in the
> 1vs1 comparisons, even though the cluster is not the same I obtain when I
> compare E vs EN...
>
>
> For additional information, I attach how I run the test:
>
> cfg.method = 'distance';
> cfg.neighbourdist = 1;
> cfg.elec = ft_datatype_sens(subjEN{1}.elec);
> neighbours = ft_prepare_neighbours(cfg);
>
> cfg = [];
> cfg.channel = {'EEG'};
> cfg.latency = 'all';
> cfg.method = 'montecarlo';
> cfg.statistic = 'indepsamplesT';
> cfg.correctm = 'cluster';
> cfg.clusteralpha = 0.05;
> cfg.clusterstatistic = 'maxsum';
>
> cfg.minnbchan = 2;
>
> cfg.neighbours = neighbours; % same as defined for the
> between-trials experiment
> cfg.tail = 0;
> cfg.clustertail = 0;
> cfg.alpha = 0.025;
> cfg.numrandomization = 5000;
>
> nsubj = size(subjE,2)+size(subjEN,2);
> design = zeros(2,nsubj);
> design(1,:) = [1:nsubj/2 1:nsubj/2];
> design(2,1:size(subjE,2)) = 1;
> design(2,size(subjE,2)+1:nsubj) = 2;
>
> cfg.design = design;
> cfg.ivar = 2;
>
> [stat] = ft_timelockstatistics(cfg, subjEN{:}, subjE{:});
>
>
> When I compare the 3 groups
>
> cfg.method = 'distance';
> cfg.neighbourdist = 1;
> cfg.elec = ft_datatype_sens(subjEN{1}.elec);
> neighbours = ft_prepare_neighbours(cfg);
>
> cfg = [];
> cfg.channel = {'EEG'};
> cfg.latency = 'all';
> cfg.method = 'montecarlo';
> cfg.statistic = 'indepsamplesF'; %F-statistic
> cfg.correctm = 'cluster';
> cfg.clusteralpha = 0.05;
> cfg.clusterstatistic = 'maxsum';
>
> cfg.minnbchan = 2;
>
> cfg.neighbours = neighbours; % same as defined for the
> between-trials experiment
> cfg.tail = 1; %One sided
> cfg.clustertail = 1;
> cfg.alpha = 0.025;
> cfg.numrandomization = 5000;
>
> nsubj1 = size(subjE,2);
> nsubj2 = size(subjEN,2);
> nsubj3 = size(subjN,2);
> nsubj = nsubj1+nsubj2+nsubj3;
>
> design = zeros(2,nsubj);
> design(1,:) = [1:nsubj1 1:nsubj2 1:nsubj3];
> design(2,1:nsubj1) = 1;
> design(2,nsubj1+1:nsubj1+nsubj2) = 2;
> design(2,nsubj1+nsubj2+1:nsubj) = 3;
>
> cfg.design = design;
> cfg.ivar = 2; %2nd row is independent var
>
> [stat] = ft_timelockstatistics(cfg, subjE{:}, subjEN{:}, subjN{:});
>
>
> Then, subjE, subjN and subjEN are like this:
>
> Eall = subjE{:}
>
> Eall =
>
> struct with fields:
>
> label: {1?18 cell}
> fsample: 200
> elec: [1?1 struct]
> trial: {[18?115 double]}
> time: {[1?115 double]}
> cfg: [1?1 struct]
>
>
> Thanks in advance
>
> --
> *Jose Antonio Urig?en*
> PostDoc at Deustotech-LIFE (eVIDA Research Group)
> [image: Deusto] <http://www.deusto.es/>
> Universidad de Deusto / Deustuko Unibertsitatea / University of Deusto
> Facultad de Ingenier?a, 4? Planta
> Avda. Universidades 24. 48007 Bilbao
> Tel. +34 94 413 90 00 / Mov. +34 656 711 643
> Ext. 2980
> jose.uriguen at deusto.es <sanchez.alain at deusto.es>
> Web: evida.deusto.es
> *www.deusto.es <http://www.deusto.es/>*
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/
> attachments/20170411/7a169976/attachment-0001.html>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 11 Apr 2017 12:13:42 +0200
> From: Maris Skujevskis <icelandhouse at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Error when running ft_sourceanalysis with stats
> across two conditions
> Message-ID:
> <CAKEvDiczSha1zYC0wY7mgNQG9wR9Ge0AYhV0Rrz17qRLipQ7gA at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Fieldtrip developers/source localizing experts,
>
> I get an error when running ft_sourceanalysis on two EEG conditions with
> the statistical testing (permutation) enabled (no issues with single
> condition and no statistics).
> As far as I can see, I am doing everything right (as per ft_sourceanalysis
> reference page; my fieldtrip version: fieldtrip-20161122). Please correct
> me where I am wrong or ask for more information in case what I
> paste/explain below is not sufficient.
>
> CODE INPUT:
>
> cfg = [];
> cfg.method = 'dics';
> cfg.frequency = 10;
> cfg.grid = leadfield;
> cfg.keepleadfield = 'no';
> cfg.headmodel = vol;
> cfg.dics.keepfilter = 'yes';
> cfg.dics.lambda = '5%';
> cfg.dics.fixedori = 'yes';
> cfg.dics.keepmom = 'yes';
> cfg.dics.realfilter = 'yes';
> cfg.grid.filter = source_cmb.avg.filter;
> cfg.permutation = 'yes';
> cfg.numpermutation = 500;
>
> sourceStatsAB = ft_sourceanalysis(cfg, condA, condB);
>
> COMMAND WINDOW OUTPUT:
>
> the input is freq data with 128 channels, 1 frequencybins and no timebins
> the input is freq data with 128 channels, 1 frequencybins and no timebins
> the call to "ft_selectdata" took 0 seconds
> converting the linearly indexed channelcombinations into a square
> CSD-matrix
> using electrodes specified in the data
> converting units from 'cm' to 'mm'
> determining source compartment (3)
> projecting electrodes on skin surface
> combining electrode transfer and system matrix
> creating dipole grid based on user specified dipole positions
> using gradiometers specified in the configuration
> 5124 dipoles inside, 0 dipoles outside brain
> the call to "ft_prepare_sourcemodel" took 0 seconds
> the call to "ft_selectdata" took 0 seconds
> the call to "ft_selectdata" took 0 seconds
> 2 conditions, each with 3 data objects
> averaging 182 replications for one condition
> averaging 182 replications for one condition
> 2 conditions, each with 3 data objects
> <<<<<<<<<<<<<---------- what are the "3 data objects"?
> creating 100 random permutations from total 6.129982e+54
>
> HERE COMES THE ERROR:
>
> Error using prepare_resampled_data (line 381)
> the dimensions should be the same for every condition
>
> Error in ft_sourceanalysis (line 561)
> [dum, rnd_aCf, rnd_aCr, rnd_aPr, rnd_bCf, rnd_bCr, rnd_bPr] =
> prepare_resampled_data(cfg, aCf, aCr, aPr, bCf, bCr, bPr);
>
>
> When checking the function prepare_resampled_data, it turns out that it
> requires a cell named "datain" to have the same size matrices column-wise
> (whatever the columns may represent) :
>
> datain =
>
> [182x128x128 double] [182x128 double] [182x1 double]
> [182x128x128 double] [ 1x128 double] [ NaN]
>
>
> My input data condA and condB have identical dimensions, so I have no idea
> what has gone wrong here:
>
> condA =
>
> label: {128x1 cell}
> dimord: 'rpt_chan_freq'
> freq: 9.8462
> powspctrm: [182x128 double]
> labelcmb: {8128x2 cell}
> crsspctrm: [182x8128 double]
> cumsumcnt: [182x1 double]
> cumtapcnt: [182x1 double]
> elec: [1x1 struct]
> trialinfo: [182x22 double]
> cfg: [1x1 struct]
>
> condB =
>
> label: {128x1 cell}
> dimord: 'rpt_chan_freq'
> freq: 9.8462
> powspctrm: [182x128 double]
> labelcmb: {8128x2 cell}
> crsspctrm: [182x8128 double]
> cumsumcnt: [182x1 double]
> cumtapcnt: [182x1 double]
> elec: [1x1 struct]
> trialinfo: [182x22 double]
> cfg: [1x1 struct]
>
>
>
>
> Thanks for your input!
>
> Best wishes,
> Maris
>
>
>
>
>
> On Sun, Apr 9, 2017 at 12:00 PM, <fieldtrip-request at science.ru.nl> wrote:
>
> > Send fieldtrip mailing list submissions to
> > fieldtrip at science.ru.nl
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > fieldtrip-request at science.ru.nl
> >
> > You can reach the person managing the list at
> > fieldtrip-owner at science.ru.nl
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
> >
> >
> > Today's Topics:
> >
> > 1. error in source parcellation and source connectivity analysis
> > (velmurugan jayabal)
> > 2. Problem with Matlab system commands in OS X (XTerm, Logout,
> > crash, sleep mode) (Markus Gschwind)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Sat, 8 Apr 2017 17:54:43 -0700
> > From: velmurugan jayabal <velmurugan.nimhans at gmail.com>
> > To: fieldtrip at science.ru.nl
> > Subject: [FieldTrip] error in source parcellation and source
> > connectivity analysis
> > Message-ID:
> > <CAKmRZP1gp6W54S4aKPDXAU_4uZQa1LzWQiobxn7uDpR8MN-Wmw@
> > mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear Field-trip community,
> >
> > I am having the following errors when computing connectivity
> > analysis. Please any help in this regard would be highly appreciated.
> > Thanks in advance.
> >
> > 1. How to compute atlas based source model grid, from MMP atlas?. Since
> MMP
> > atlas doesn't contain the *dim *field, the ft_volumelookup function
> doesn't
> > work prompting me the same error.
> >
> >
> > 2. Alternatively, I had created AAL atlas based source model grid and
> used
> > to compute source connectivity (img.coh) from PCC beamformer source
> output.
> > But, I am unable to compute the connectivity value for each parcel using
> > ft_sourceparcellate. I am writing the codes used to derive the same.
> >
> > 3. Is there any acronym or a clear explanation for the parcellation
> label?.
> > I had read Glasser et al 2016 paper and their resource site. But, I
> > couldn't get complete names or explanation for all the ROIs.
> >
> >
> > CODE:
> > %source is the output of pcc beamformer results.
> > cfg = [];
> > cfg.method ='coh';
> > cfg.complex = 'absimag';
> > source_conn_imcoh = ft_connectivityanalysis(cfg, source);
> >
> > atlas =ft_read_atlas ('ROI_MNI_V5.nii');
> > atlas.pos =source_conn_imcoh.pos;
> > cfg =[];
> > cfg.method ='mean'
> > cfg.parameter ='cohspctrm';
> > cfg.parcellation = 'tissue';
> > parc_conn= ft_sourceparcellate(cfg,source_conn, atlas);
> >
> > I had even tried computing source connectivity interpolation on the atlas
> > before parcellation. But, I am getting a huge array > 50 GB, which
> exceeds
> > my MATLAB and system limit.
> >
> >
> > --
> > - sincerely,
> > *Velmurugan Jayabal,*
> > *Magnetoencephalography (MEG) research centre,*
> > *Department of Clinical Neurosciences,*
> >
> > *National Institute of Mental Health and Neurosciences (NIMHANS),*
> > *Bangalore - 560029, Karnataka, India*
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/
> > attachments/20170408/ede3c3c1/attachment-0001.html>
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Sun, 9 Apr 2017 11:18:21 +0200
> > From: Markus Gschwind <Markus.Gschwind at unige.ch>
> > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > Subject: [FieldTrip] Problem with Matlab system commands in OS X
> > (XTerm, Logout, crash, sleep mode)
> > Message-ID:
> > <CABaUQnyQcLUwAyxxyEfaVYw73Ryxct=sLxe_rV++Qr-zdDgz9w at mail.
> > gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear all,
> >
> > I hope to find here an expert who knows an answer to the following
> problem:
> >
> > I am running Matlab on OSX 10.9.5 started from the Xterm, and I am not
> able
> > to run big and lengthy matlab jobs because at each logout (which occurs
> > after 2h), Matlab crashes, all results are gone (if they are not save to
> > the HD and XTerm closes.
> >
> > I start Matlab form the XTerm (and not by clicking the App Icon) in order
> > to be able to run system (unix) commands within Matlab.
> >
> > I guess, this behaviour is proper to XTerm, and in case I could find an
> > other way to run system commands from Matlab, probably this could be
> > resolved.
> >
> > Could it be that the running matlab job is not visible to the system
> which
> > goes to sleep??
> >
> > For info here the power management info:
> >
> > $ pmset -g custom
> > Battery Power:
> > lidwake 1
> > autopoweroff 1
> > autopoweroffdelay 14400
> > standbydelay 18000
> > standby 1
> > ttyskeepawake 0
> > hibernatemode 3
> > gpuswitch 2
> > hibernatefile /var/vm/sleepimage
> > displaysleep 2
> > sleep 0
> > acwake 1
> > halfdim 1
> > sms 1
> > lessbright 1
> > disksleep 10
> > AC Power:
> > lidwake 1
> > autopoweroff 1
> > autopoweroffdelay 14400
> > standbydelay 18000
> > standby 0
> > ttyskeepawake 1
> > hibernatemode 3
> > gpuswitch 2
> > hibernatefile /var/vm/sleepimage
> > womp 1
> > displaysleep 3
> > networkoversleep 0
> > sleep 0
> > acwake 0
> > halfdim 1
> > sms 1
> > disksleep 60
> >
> >
> > Many thanks for help!
> > Markus
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/
> > attachments/20170409/ce9b8000/attachment-0001.html>
> >
> > ------------------------------
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> > End of fieldtrip Digest, Vol 77, Issue 6
> > ****************************************
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/
> attachments/20170411/3d323db9/attachment-0001.html>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 12 Apr 2017 10:35:29 +0800
> From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] cluster-based statistics with one covariate
> Message-ID:
> <CAJT2k_9mVC_jDFnrLco_qS9fGbGYfvCVaQZDJfbOPd6d_LS--
> A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Caroline,
>
> If your conditions are within-subject, then I think the best way to do this
> is to construct a dataset representing the conditionA - conditionB
> difference for each subject, and then using ft_statfun_indepsamplesregrT to
> regress the subject-wise difference on age. See e.g.
> https://mailman.science.ru.nl/pipermail/fieldtrip/2016-May/010528.html for
> a thread discussing a similar approach.
>
> Best,
> Steve
>
>
> ---
> Stephen Politzer-Ahles
> The Hong Kong Polytechnic University
> Department of Chinese and Bilingual Studies
> http://www.mypolyuweb.hk/~sjpolit/
> <http://www.nyu.edu/projects/politzer-ahles/>
>
>
>
> > Message: 3
> > Date: Mon, 10 Apr 2017 14:50:13 +0200 (CEST)
> > From: Caroline Beese <beese at cbs.mpg.de>
> > To: fieldtrip at science.ru.nl
> > Subject: [FieldTrip] cluster-based statistics with one covariate
> > Message-ID:
> > <1329277450.115066.1491828613491.JavaMail.zimbra at cbs.mpg.de>
> > Content-Type: text/plain; charset=utf-8
> >
> > Dear all,
> >
> > I'm trying to take age as a covariate into my cluster-based statistics
> > comparing two dependent measures.
> >
> > I have read about two options:
> >
> > A) to use ft_regressconfound before I do the stats or
> > B) to create a design with a third row using the .cvar field in the
> > 'depsamplesregrT' statfun.
> >
> > I understand that for correcting head motions ft_regressconfound is a
> > great option but for taking age into account as a covariate, it doesn't
> > seem intuitive to me to do this within-subject on a trial-by-trial basis
> > having only one number per person. Or can you use this function
> differently?
> >
> > However, for option B) the subfunction 'unitselvec' is missing and this
> > seems to be an issue for several years. So I was wondering whether anyone
> > has ever tried to fix this problem themselves and wouldn't mind sharing?
> >
> > More generally, if anyone has successfully implemented a cluster-based
> > statistics with one or more covariates, please share your experience, it
> > would be greatly appreciated.
> >
> > Best Regards,
> > Caroline
> >
> > --
> > Caroline Beese
> > PhD student
> >
> > Max-Planck Institute for Human Cognitive and Brain Sciences
> > Department of Neuropsychology
> > Stephanstr. 1a
> > 04103 Leipzig
> >
> > office phone: +49 (0) 341 9940 129
> >
> > www.cbs.mpg.de/staff/beese-11586
> >
> >
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/
> attachments/20170412/af43a0d6/attachment-0001.html>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 12 Apr 2017 09:01:14 +0000
> From: Robin K?mpe <robin.kampe at liu.se>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Installing gui_streamer
> Message-ID:
> <HE1PR06MB1851F7904ECBE4DEE19D9DBA96030 at HE1PR06MB1851.
> eurprd06.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi!
>
> We want to, from scratch, set up a real time fMRI capabilities. Your
> documentation covers this quite well. I do, however, get stuck on point 1
> which is to launch the gui_streamer from the console. How does one
> obtain/install this program on our Siemens Prisma?
>
> Best,
>
>
> Robin K?mpe
> Research Engineer
>
> [Link?ping University]
>
> CSAN, Center for Social and Affective Neuroscience
> Department of Clinical and Experimental Medicine, IKE
> Mobile: +46 (0)73 8005561
> Please visit us at www.liu.se<http://www.liu.se/>
>
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/
> attachments/20170412/cf35fa04/attachment-0001.html>
>
> ------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> End of fieldtrip Digest, Vol 77, Issue 9
> ****************************************
>
--
Laxmi Shaw
Research Scholar(PhD)
IIT Kharagpur
West Bengal
Ph no-08388837821
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20170413/a44875bd/attachment-0001.html>
More information about the fieldtrip
mailing list