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$

Thanks,

Paulo