[FieldTrip] source localization only at the edges
RICHARDS, JOHN
RICHARDS at mailbox.sc.edu
Wed Feb 25 14:22:30 CET 2015
I would like to see an answer to this also. I am in the middle of
Œbeginning¹ to use FT for mne and eloreta. I had the same issue, and then
used ³depth normalization², since mne tends to have only surface results.
I read on the www (google mne depth normalization) that this might be an
issue, and tried:
cfg.normalizeparam=5;
cfg.normalize='yes';
I got Œdepth¹ results to my mne¹s and eloreta solutions, though I am not
sure if I have accurate results.
I can¹t find any use of these in the examples.
John
***********************************************
John E. Richards Carolina Distinguished Professor
Department of Psychology
University of South Carolina
Columbia, SC 29208
Dept Phone: 803 777 2079
Fax: 803 777 9558
Email: richards-john at sc.edu
HTTP: jerlab.psych.sc.edu
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On 2/25/15, 6:00 AM, "fieldtrip-request at science.ru.nl"
<fieldtrip-request at science.ru.nl> wrote:
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>Today's Topics:
>
> 1. Re: source localization only at the edges (Eelke Spaak)
> 2. source localization only at the edges (Saurabh Kumar)
> 3. Re: ft_clusterstat OUT OF MEMORY - DICS (Martin Winkels)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Tue, 24 Feb 2015 15:41:30 +0100
>From: Eelke Spaak <eelke.spaak at donders.ru.nl>
>To: FieldTrip discussion list <fieldtrip at science.ru.nl>
>Subject: Re: [FieldTrip] source localization only at the edges
>Message-ID:
> <CABPNLUoooTCxE6Nx+RB6DsNouptomnbFsNej3aMDgYxkV2qG8w at mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Dear Saurabh,
>
>Without having gone through the details of your code, my hunch is that
>this has something to do with the units (m/cm/mm) of your geometrical
>objects (electrode/gradiometer description, volume conduction model,
>source model). You could explicitly convert them all to the same using
>ft_convert_units([data.grad|vol|source], 'm') and then try again,
>perhaps that helps?
>
>Best,
>Eelke
>
>On 24 February 2015 at 15:33, Saurabh Kumar <kumar at cbs.mpg.de> wrote:
>> Hello fieldtrippers,
>>
>> I have a question which I could not find has been answered.
>> I am doing source localization for my data and the problem is that no
>>matter the data, (even random numbers) the source always comes out at
>>the edges of the mri. (Figure attached)
>>
>> I am using mne to localize the source.
>> The code in short is attached below which I use. Please have a look and
>>lemme know if you find something that can be changed.
>>
>> Code:
>>
>> %% load MRI data %%%%%%%%
>> mri = ft_read_mri('Subject01.mri');
>> % convert the coordinate system
>> mri = ft_convert_coordsys(mri,'mni'); %% convert the coordinate system
>>from the ctf into the mni
>> mri.coordsys = 'mni';
>>
>>
>> %% Volume segmentation %%%%%%%%
>> cfg = [];
>> cfg.output = {'brain','skull','scalp'};
>> seg = ft_volumesegment(cfg, mri); % it takes some time.
>>
>>
>> %% creating the head model %%%%%%%%
>> cfg = [];
>> cfg.method ='bemcp';
>> vol = ft_prepare_headmodel(cfg, seg);
>>
>>
>> %% setting the electrodes (have checked the electrodes are in correct
>>positions) %%%%%%%%
>> %load elec_new
>> cfg = [];
>> cfg.method = 'interactive';
>> cfg.elec = elec_new;
>> cfg.headshape = vol.bnd(3);
>> elec_aligned = ft_electroderealign(cfg);
>>
>> %% make grid %%%%%%%%
>> cfg = [];
>> cfg.vol = vol;
>> cfg.elec = elec_aligned; % sa_new_elec; % elec_aligned;
>> cfg.grid.resolution = 0.8; % a 3D grid with a part of cm resolution
>> cfg.grid.unit = 'cm';
>> grid = ft_prepare_leadfield(cfg);
>>
>>
>>
>> % %%%%%%%% Check the full model %%%%%%%
>> % grid.pos = grid.pos * 10;
>> % elec_aligned.chanpos = elec_aligned.chanpos*100;
>> % ft_plot_mesh(grid.pos(grid.inside,:));hold
>>on;ft_plot_mesh(vol.bnd(1),'edgecolor','none', 'facealpha',0.5); hold
>>on; ft_plot_sens(elec_aligned);
>> % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>>
>>
>>
>> %% source analysis %%%%%%%%
>> cfg = [];
>> cfg.method = 'mne';
>> cfg.vol = vol;
>> cfg.elec = elec_aligned; % elec_aligned; % sa_new_elec;
>> cfg.grid = grid;
>> cfg.mne.lambda = 3;
>> cfg.mne.prewhiten = 'yes';
>> cfg.mne.scalesourcecov = 'yes';
>> source = ft_sourceanalysis(cfg,avg_data); % the data is in avg_data
>>
>> %% Interpolation of the localized source with the mri %%%%%%%%
>> mri_reslice = ft_volumereslice([],mri);
>> cfg=[];
>> cfg.parameter = 'pow';
>> source_int = ft_sourceinterpolate(cfg, source, mri_reslice);
>>
>> %% Visualization (Orthogonal plot) %%%%%%%%
>> cfg = [];
>> cfg.method = 'ortho';
>> cfg.funparameter = 'pow';
>> cfg.funcolormap = 'jet';
>> cfg.maskparameter = cfg.funparameter;
>> ft_sourceplot(cfg, source_int_admit); % (figure attached)
>>
>>
>>
>>
>> ----------------------------------------------------
>> Thanks for your time,
>> Saurabh Kumar
>>
>> Cognitive Neurology
>> Max Planck Institute
>> for Human Cognitive and Brain Sciences
>> Stephanstr. 1a
>> 04103 Leipzig
>
>
>------------------------------
>
>Message: 2
>Date: Tue, 24 Feb 2015 16:13:10 +0100 (CET)
>From: Saurabh Kumar <kumar at cbs.mpg.de>
>To: fieldtrip <fieldtrip at science.ru.nl>
>Subject: [FieldTrip] source localization only at the edges
>Message-ID:
> <1761066429.1447014.1424790790305.JavaMail.zimbra at cbs.mpg.de>
>Content-Type: text/plain; charset=utf-8
>
>Dear Eelke
>
>I checked again the units of mri, leadfield, electrode positions and the
>volume and all seem to be in harmony.
>I also think that even though you dont specify them explicitely they are
>adjusted to a common one as the results remain exactly the same as I just
>checked.
>
>Do you have any idea what else could be the problem?
>
>----------------------------------------------------
>Saurabh Kumar
>
>Cognitive Neurology
>Max Planck Institute
>for Human Cognitive and Brain Sciences
>Stephanstr. 1a
>04103 Leipzig
>
>
>------------------------------
>
>Message: 3
>Date: Tue, 24 Feb 2015 22:57:00 +0100
>From: Martin Winkels <m_wink10 at uni-muenster.de>
>To: FieldTrip discussion list <fieldtrip at science.ru.nl>
>Subject: Re: [FieldTrip] ft_clusterstat OUT OF MEMORY - DICS
>Message-ID:
> <CAHDG_rX205OCdcLmzoRb3b4b3JYqfGOLG8TPaP2qFs2pEuqEUA at mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>Hey Julian,
>
>thanks for the answer.
>
>We are using some sort of an Intel iCore i7 with 16 GB of RAM as well as
>40
>GB of swap and Fedora 16.
>
>We do interpolate the data on an MRI. In fact I'm not sure if that is the
>source of the problem. We downsampled the data and it did not change
>anything. The problem seems to be that there is a number generated that is
>too big for MATLAB to process it with the zeros(x) instruction.
>
>Around 1-2 years ago I did nearly the same thing in fieldtrip but
>including
>an LCMV-Beamformer, the resulting data structures where much bigger and it
>worked without a problem.
>
>Thanks, Martin
>
>On Mon, Feb 23, 2015 at 5:14 PM, Julian Keil <julian.keil at gmail.com>
>wrote:
>
>> Dear Martin,
>>
>> what kind of machine are you using?
>> Did you interpolate your data to an MRI?
>> What is your grid resolution?
>>
>> You have quite a high number of grid points that you want to compare.
>> So in case you run out of memory, I'd suggest not interpolating to an
>>MRI
>> (in case you have done this) but to stay on the grid-point level for
>>your
>> stats. Otherwise, you could use a less dense grid which obviously
>>results
>> in smaller data structures.
>>
>> Good luck,
>>
>> Julian
>>
>> ********************
>> *Dr. Julian Keil*
>>
>> AG Multisensorische Integration
>> Psychiatrische Universit?tsklinik
>> der Charit? im St. Hedwig-Krankenhaus
>> Gro?e Hamburger Stra?e 5-11, Raum E 307
>> 10115 Berlin
>>
>> Telefon: +49-30-2311-1879
>> Fax: +49-30-2311-2209
>>
>>
>>http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integr
>>ation
>>
>> Am 23.02.2015 um 17:00 schrieb Martin Winkels:
>>
>> Dear Fieldtrippers,
>>
>> we encountered a problem during our DICS Beamformer-Statistics.
>>
>> After calculating a beamformer (DICS), normalisation and building
>> grandaverages across subjects (here exemplarily 3 subjects) we try to
>> calculate cluster based permutation statistic (in this study: between
>> groups - one condition).
>>
>> The code we used is as follows:
>>
>> cfg = [];
>>
>> cfg.method = 'montecarlo';
>> %cfg.statistic = 'depsamplesT';
>> cfg.statistic = 'ft_statfun_indepsamplesT';
>> cfg.correctm = 'cluster';
>> cfg.clusteralpha = 0.05; %ft default 0.05;
>> cfg.clusterstatistic = 'maxsum';
>> cfg.minnbchan = 2;
>> cfg.tail = 0;
>> cfg.clustertail = 0;
>> cfg.alpha = 0.025; %ft hat hier 0,025
>>
>> cfg.parameter = 'pow';
>> cfg.dim = grandavgA.dim;
>>
>> cfg.numrandomization = 1; % number of draws from the
>> permutation distribution
>>
>> design(1,:) = [1 1 1 2 2 2];
>> design(2,:) = [1 1 1 1 1 1];
>>
>> cfg.design = design;
>> cfg.ivar = 1;
>>
>> stat = ft_sourcestatistics(cfg, grandavgA, grandavgB);
>>
>>
>>
>> The input data structure (grandavgA, grandavgB) is as follows:
>>
>> grandavgA =
>>
>> pow: [3x116380 double]
>> dim: [46 55 46]
>> inside: [116380x1 logical]
>> pos: [116380x3 double]
>> cfg: [1x1 struct]
>>
>> grandavgB =
>>
>> pow: [3x116380 double]
>> dim: [46 55 46]
>> inside: [116380x1 logical]
>> pos: [116380x3 double]
>> cfg: [1x1 struct]
>>
>>
>> Fieldtrip version: current (02/23/2015)
>>
>>
>> Thanks, Martin
>>
>> --
>>
>> M.Sc. Martin Winkels
>>
>> Universit?tsklinikum M?nster
>>
>> Institut f?r Biomagnetismus & Biosignalanalyse
>>
>> Malmedyweg 15
>>
>> 48149 M?nster
>>
>> GERMANY
>>
>>
>> Telefon: +49 251 83 56 846
>> Web: http://biomag.uni-muenster.de
>>
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