Hi Robert, it might be that the brainmask.mgz is a little to tight given the inaccuracies of talairach registration. You can expand the mask with mri_binarize --i brainmask.mgz --dilate 2 --o output.mgz This will dilate the mask by 2 voxels. doug
Robert Boldt wrote:
Thank you for a beautiful program.
I'm using freesurfer to preprocess fMRI images (using a command similar to that in your manual):
preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
I want my preprocessed fMRI data to be sampled into 'Common space', but need the data as volume files, not surface file. I solved this by simply deleting fsaverage/mri.2mm/subcort.mask.mgz, and renaming the fsaverage/mri.2mm/brainmask.mgz as subcort.mask.mgz. This resulted in
fmcpr.up.sm5.mni305.2mm.nii.gz
containing the whole volume instead of only subcortical structures. I made the assumption that the whole brain is sampled to 'Common space', but that all cortical structure are masked out, so that information contained in the surface files would not be replicated.
My results are fine, but I'm afraid that I violated some assumption done for the volume files.
I'm very grateful for your program, as I would be for an answer
Best regards
Robert Boldt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer