problems with segmentation

[Jan Hirschmann]

Hi there,


I am having trouble segmenting an MRI scan using volumesegment on a realigned scan (obtained by volumerealign). Actually, I think this not really a fieldtrip but a spm problem. It seems there are nans or infs in some covariance matrix calculated by spm_segment, but honestly, I don't really see through this. Strangely, it did work once but then found no gray nor white matter but only CSF. Maybe it depends on how I choose the fiducials... If someone has any experience with this I would be really glad for any clue, as I am completley stuck. Thanks in advance! Here's the code and the error message:


addpath('/data/apps/spm/spm2')
cd('/net/avidya/storage/home/jan/seidel_dicom/S00002/SER00002');
mrifilename = 'I00001';
mri = read_mri(mrifilename);


cfg=[];
cfg.interactive='yes';
seg_mri=volumerealign(cfg,mri);
cd('/net/avidya/storage/home/jan/seidel_dicom/mat_anatomy_files');
save mri_realigned mri


cfg                = [];
cfg.template       = '/data/apps/spm/spm2/templates/T1.mnc';
cfg.coordinates    = 'ctf';
cfg.write          = 'no';
cfg.name           = 'temp';
[segmentedmri]     = volumesegment(cfg, mri);


??? Error using ==> schur
Input to SCHUR must not contain NaN or Inf.

Error in ==> sqrtm at 33
[Q, T] = schur(A,'complex');  % T is complex Schur form.

Error in ==> spm_segment>get_p at 552
	dst       = (cor-ones(size(cor,1),1)*CP.mn(:,i)')/sqrtm(CP.cv(:,:,i));

Error in ==> spm_segment>run_segment at 335
		[P,ll0]   = get_p(cor,msk,s,sums,CP,bf);

Error in ==> spm_segment at 106
[CP,BP,SP] = run_segment(CP,BP,SP,VF,sums,x1,x2,x3);

Error in ==> ft_volumesegment at 176
  spm_segment(Va,cfg.template,flags);

Error in ==> volumesegment at 17
[varargout{1:nargout}] = funhandle(varargin{:});

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