[FieldTrip] Inner matrix mismatch in source interpolate
Russell G Port
russgport at gmail.com
Tue Mar 19 16:56:04 CET 2013
Thanks Jim,
That was exactly what was wrong. Sorry for the delayed response. I
mistakenly thought that the leadfield function would create a grid (which
it can, but I forgot to put in a cfg.resolution).
On Fri, Mar 15, 2013 at 4:01 AM, Herring, J.D. (Jim) <
j.herring at fcdonders.ru.nl> wrote:
> Hi Russ,****
>
> ** **
>
> I ran into a similar error which was avoided by following the steps in the
> *extended* beamformer tutorial (
> http://fieldtrip.fcdonders.nl/tutorial/beamformingextended). The problem
> seems to rather be that ft_sourceinterpolate wrongly detects your
> functional data as being 2 dimensional (if I remember correctly) because a
> .dim field is not present. I did not have the time yet to find-out if it is
> a problem with the other beamformer tutorial or an actual bug.****
>
> ** **
>
> In any case, if I compare the steps in the extended beamformer tutorial
> with the steps you took I noticed that in the extended beamformer tutorial
> a sourcemodel (ft_prepare_sourcemodel) is calculated after calculating the
> headmodel, which is then used to calculate the leadfield
> (ft_prepare_leadfield), followed by using this leadfield in
> ft_sourceanalysis. Could you try and see if that works? ****
>
> ** **
>
> Best,****
>
> ** **
>
> Jim****
>
> ** **
>
> *From:* fieldtrip-bounces at science.ru.nl [mailto:
> fieldtrip-bounces at science.ru.nl] *On Behalf Of *Russell G Port
> *Sent:* vrijdag 15 maart 2013 0:18
> *To:* FieldTrip discussion list
> *Subject:* [FieldTrip] Inner matrix mismatch in source interpolate****
>
> ** **
>
> Hi Fieldtrippers,****
>
> ** **
>
> When running ft source interpolate on my CTF MEG data, I get an error
> where it reaches line 237; tmp = interpmat*tmp. The error is an inner
> matrix dimension mismatch. Here interpmat is a 16777216(256x256x256) x642
> matrix, (mri voxels X leaderfield interpolation matrix). tmp is a 1 * 642
> matrix of power at the leaderfield coordinates. If this is just matrix
> math, then I assume the problem is just that the matrix have to be mxn and
> nxp. Is there any reason I cannot just use tmp=tmp' to make the inner
> dimensions match?****
>
> ** **
>
> Cheers Russ****
>
> ** **
>
> ---------- Forwarded message ----------
> From: *Russell G Port* <russgport at gmail.com>
> Date: Sat, Mar 9, 2013 at 8:38 PM
> Subject: source interpolate - tmp = interpmat*tmp; inner matrix must agree
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
>
>
> Hi Fieldtrippers,
>
> I have a slight issue that I was hoping someone can help with. I have some
> CTF data, that I was trying to perform DICS beamforming and then source
> interpolation on. I am trying to beamform to the source of gamma frequency
> in the right hemisphere, comparing pre and post stimuli. Heres the basic
> script:
>
> *People can skip the first part of code, I included it as possibly useful
> information for this plead
> *
> %%%%% Data has already been preprocessed and timelocked%%%%%%
>
> load('processed_data_500Hz.mat')
> load('timelock_data_500Hz.mat')
>
> %%%% following the beamforming tutorial %%%%%%%
>
> %%%%%%%%%%%%%split and combine%%%%%%%%%%%%%
>
> cfg = [];
> cfg.toilim = baseline;
> cfg.channel=channel
> total_bsl = ft_redefinetrial(cfg, data);
>
>
> cfg = [];
> cfg.toilim = interest;
> cfg.channel=channel
> total_interest = ft_redefinetrial(cfg, data);
>
> cfg = [];
> total_cmb = ft_appenddata(cfg, total_bsl, total_interest);
>
> total_cmb.trialinfo = [zeros(length(total_bsl.trial), 1);
> ones(length(total_interest.trial), 1)];
>
>
> %%%%%%%%%%%%%cross spectrial density for dics and tf for common
> filter%%%%%%%%%%%%%%
>
> cfg = [];
> cfg.method = 'mtmfft';
> cfg.output = 'powandcsd';
> cfg.tapsmofrq = 25;
> cfg.foilim = 55;
> freqPre_total = ft_freqanalysis(cfg, total_bsl);
>
> cfg = [];
> cfg.method = 'mtmfft';
> cfg.output = 'powandcsd';
> cfg.tapsmofrq = 25;
> cfg.foilim = 55;
> freqPost_total = ft_freqanalysis(cfg, total_interest);
>
> cfg = [];
> cfg.method = 'mtmfft';
> cfg.output = 'powandcsd';
> cfg.tapsmofrq = 25;
> cfg.foilim = 55;
> freqALL_total = ft_freqanalysis(cfg, total_cmb);
>
>
> %%%%%%%%%%%%%%%%%%%%%%%% calc leadfield %%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> %
> T=ft_read_mri('R128_V2.mri')
>
> cfg.fiducial.nas = T.hdr.fiducial.mri.nas
> cfg.fiducial.lpa = T.hdr.fiducial.mri.lpa
> cfg.fiducial.rpa = T.hdr.fiducial.mri.rpa
> cfg.method = 'fiducial'
> cfg.coordsys = 'ctf'
>
> [mri] = ft_volumerealign(cfg, T)
>
> cfg = [];
> cfg.coordsys = 'ctf'; % the MRI is expressed in the CTF coordinate system,
> see below
> segmentedmri = ft_volumesegment(cfg, mri);
>
> cfg = [];
> cfg.method = 'singleshell';
> hdm = ft_prepare_headmodel(cfg, segmentedmri);
>
> vol = ft_convert_units(hdm, 'cm');
>
> %%%%%%%%%%%%%%%
>
>
> cfg = [];
> cfg.grad = freqPost_total.grad;
> cfg.vol = vol;
> cfg.reducerank = 2;
> cfg.channel = 'MR'
> [grid] = ft_prepare_leadfield(cfg);
>
>
>
> *Upto this point everything works. My volume conduction model, grads, and
> grid looks good when verified visually...
>
> I then compute the common filter and apply it to the beamforming of each
> condition*
>
>
> %%%%%%%%%%%%%%%%%%%%% computer common filter%%%%%%%%%%%
>
> cfg = [];
> cfg.method = 'dics';
> cfg.grad = freqALL_total.grad;
> cfg.keeptrials = 'yes';
> cfg.frequency = freqALL_total.freq;
> cfg.grid = grid;
> cfg.vol = vol;
> cfg.dics.projectnoise = 'yes';
> cfg.dics.lambda = '5%';
> cfg.dics.keepfilter = 'yes';
> cfg.dics.realfilter = 'yes';
> cfg.channel = 'MR'
> sourceAll = ft_sourceanalysis(cfg, freqALL_total);
>
> %%%%%%%%%%%%%%%%%% source for bsl + interest %%%%%%%%%%%%%
>
> cfg.grid.filter = sourceAll.avg.filter;
> cfg.grid = grid;
> sourcePre_con = ft_sourceanalysis(cfg, freqPre_total );
> sourcePost_con = ft_sourceanalysis(cfg, freqPost_total);
>
>
> %%%%%%%%%% Calc difference %%%%%%%%%%%%%%%%%
>
> sourceDiff = sourcePost_con;
> sourceDiff.avg.pow = (sourcePost_con.avg.pow - sourcePre_con.avg.pow) ./
> sourcePre_con.avg.pow;
>
>
>
> *Heres where it falls apart, because I try to source interpolate*
>
>
> %%%%%%%%%%%%%%%%%%%%% graph time %%%%%%%%%%%%%%%%%%
>
> % slicemri = ft_volumereslice([], mri);
> % % mri = ft_volumereslice([],segmentedmri) %%* didnt appear to help with
> the current problem
> *
> cfg = [];
> cfg.downsample = 2;
> cfg.parameter = 'avg.pow';
> cfg.coordsys = 'ctf';
> cfg.channel = 'MR'
> source_diffInt = ft_sourceinterpolate(cfg, sourceDiff , mri); &&& I also
> tried segmentedmri, but no difference
>
> It works until it reachs line 237; tmp = interpmat*tmp; where there is
> the matrixs are mismatch (interpmat is a 16777216(256x256x256) x642
> matrix, and tmp is a 1 * 642 matrix. From my basic skills I gather that tmp
> is sourceDiff.avg.pow (the power difference for each leadfield point).
> interpmat is the interpolation matrix return by
>
> interpmat = interp_ungridded(functional.pos *(position of the leadfield
> locations)*, pos (mri voxels), 'projmethod', cfg.interpmethod (*nearest*),
> 'sphereradius', cfg.sphereradius) (0.*05*);
>
> what I get out of this is a 16777216(*256x256x256* voxels) x642 *(leadfield
> position)* matrix*. *it then undergoes interpmat(~anatomical.inside(:),
> :) = 0. My *anatomical.inside is all voxels (all of the 256 x 256 x 256
> matrix= 1), as a result of the defaults in ft_checkdata*.
>
> When I try to find the minimum value in this matrix I get (via
> min(interpmat) = All zero sparse: 1-by-642
>
> I think what is supposed to happen is that the interpmat is a matrix that
> relates meg to mri space, and as such then mutlipling with a vector that
> represents the power in meg space, I can see how that would get points of
> power in mri space. Though this must be wrong since the math is not
> allowed.... I cannot see where I went off the beaten track. It seems as if
> other people have not had this problem.
>
> Sorry for the bother,
>
> Russ Port
>
> Graduate Student @ Upenn
>
>
> P.S. thanks to anyone who tries to help in advance...
>
>
>
>
>
>
>
> ****
>
> ** **
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130319/49aba34f/attachment.html>
More information about the fieldtrip
mailing list