External Email - Use Caution
> 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.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.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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