------------------------------------------
mcparams2extreg $Id: mcparams2extreg,v 1.4.2.1 2008/04/01 20:26:25 greve Exp $
Comments or questions: analysis-bugs@nmr.mgh.harvard.edu
Darwin dhcp-0020469059-ee-5e.client.fas.harvard.edu 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
dhcp-0020469059-ee-5e.client.fas.harvard.edu
Mon Apr 25 03:56:08 EDT 2011
/Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold
/Applications/freesurfer/fsfast/bin/mcparams2extreg
-mcfile 006/fmc.mcdat -northog 6 -extreg 006/mcextreg
----------- Matlab file --------------
  mcfile = '006/fmc.mcdat';
  extreg = '006/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 1984-2009 The MathWorks, Inc.
                 Version 7.9.0.529 (R2009b) 64-bit (maci64)
                              August 12, 2009

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