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.
