External Email - Use Caution
Hello FreeSurfer Developers,
I'm helping researchers test Freesurfer 4.5 and Freesurfer 6. Running same code on Freesurfer4.5 environment produces no image with tksurfer. It says "No colortable found." See attached.
1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 2) Platform: CentOS release 5.11 (Final)
We're are running this in a Singularity container. It's getting close to working properly. It would be nice to have a way to run old code on newer Linux systems.
Thanks,
Paulo
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.
- FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0
- 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, 2012Warning: 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
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.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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Baptista, Paulo -
Greve, Douglas N.,Ph.D.