It says that there is only one time point in that data. Are you sure that run is fMRI? Try mri_info 007/f.nii.gz and see how many time points it has
On 12/20/2019 8:56 AM, Baptista, Paulo wrote:
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Hello FreeSurfer Developers,
I'm helping researchers test Freesurfer 4.5 getting a Matlab error. I'm wondering if this is a Freesurfer or Matlab issue. Any ideas? THANKS IN ADVANCE.
1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 2) Platform: CentOS release 5.11 (Final)
pbaptist@clps-baba:/var/tmp/SNF/epi/SNF01D1/bold_decode$ mcparams2extreg -mcfile 007/fmc.mcdat -northog 6 -extreg 007/mcextreg Logfile is 007/mcparams2extreg.log ----------- Matlab file -------------- mcfile = '007/fmc.mcdat'; extreg = '007/mcextreg'; nkeep = []; northog = [6]; pctorthog = []; monly = 0;
mc = textread(mcfile); mc = mc(:,2:7); ntrs = size(mc,1); if(ntrs < 6) fprintf('ERROR: ntrs = %d < 6\n',ntrs); if(~monly) fprintf('Quiting matlab\n'); quit; fprintf('should not be here\n'); end end
if(~isempty(nkeep)) x = mc(:,1:nkeep); elseif(~isempty(northog)) [u s v] = svd(mc); ds = diag(s); pct = 100*cumsum(ds)/sum(ds); x = u(:,1:northog); nkeep = northog; fprintf('INFO: northog = %d, pct = %g\n',northog,pct(nkeep)); else [u s v] = svd(mc); ds = diag(s); pct = 100*cumsum(ds)/sum(ds); nkeep = min(find(pct > pctorthog)); x = u(:,1:nkeep); fprintf('INFO: pctorthog = %g, nkeep = %d\n',pctorthog,nkeep); end
x2 = zeros(1,1,nkeep,ntrs); x2(1,1,:,:) = x'; %' %fmri_svbvolume(x2,extreg);
mri.vol = permute(x2,[1 3 2 4]); mri.trhttp://mri.tr = 0; mri.flip_angle = 0; mri.te = 0; mri.ti = 0; mri.vox2ras0 = eye(4); mri.xsize = 1; mri.ysize = 1; mri.zsize = 1; mri.volres = [1 1 1]; mri.volsize = [size(mri.vol,1) size(mri.vol,2) size(mri.vol,3)]; fname = sprintf('%s.bhdr',extreg); MRIwrite(mri,fname);
quit;
----------------------------------- ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen.
< M A T L A B (R) > Copyright 1984-2012 The MathWorks, Inc. R2012a (7.14.0.739) 64-bit (glnxa64) February 9, 2012
Warning: Duplicate directory name: /usr/local/MATLAB/R2012a/toolbox/images/images. Warning: Duplicate directory name: /usr/local/MATLAB/R2012a/toolbox/images/images/eml.
To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.comhttp://www.mathworks.com.
>> >> >> >> >> >> >> >> ERROR: ntrs = 1 < 6
Quiting matlab ------------------------------------------ ERROR: output not created pbaptist@clps-baba:/var/tmp/SNF/epi/SNF01D1/bold_decode$
Any ideas? I can start up matlab fine in the environment.
Thanks,
Paulo
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