Note that each of those set commands should be a single line. The file to change is $FREESURFER_HOME/fsfast/bin/rawfunc2tal-sess
doug On 11/27/2012 01:23 PM, Douglas N Greve wrote: > Yep, that's a bug. I've fixed it in my version. To fix it in yours, do > the following two steps: > > Step 1: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/subcort.mask.1mm.mgz > cp subcort.mask.1mm.mgz $SUBJECTS_DIR/fsaverage/mri > > Step 2: In rawfunc2tal-sess, change: > > set subcortmask = > $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz > > To > > if($res == 2) then > set subcortmask = > $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz > else > set subcortmask = > $FREESURFER_HOME/subjects/fsaverage/mri/subcort.mask.1mm.mgz > endif > > doug > > On 11/27/2012 04:48 AM, Jörg Pfannmöller wrote: >> Hi, >> >> if I apply the following command: >> >> preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh -mni305-1mm >> -fwhm 0 -per-run -nosmooth -force >> >> The preprocessing runs into trouble at the following point >> >> mri_vol2vol done >> >> mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii >> /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz >> /...path.../bold/001/masks/brain.mni305.1mm.nii >> freadFloat: fread failed >> ERROR: dimension mismatch between source and mask >> >> As far as I can see freesurfer uses a 2mm mask for a 1mm brain, which >> results in the dimension mismatch. How can I get rid of this problem? >> >> Cheers Joerg >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
