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