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:
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<http://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<http://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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