Hi Marco, the aparc+aseg.mgz is probably going to be the best one (it is what I use:). When you binarize it, you can dilate it by a voxel as well with:
mri_binarize --i aparc+aseg.mgz --min 0.5 --dilate 1 --o yourmask.mgz
doug
On 04/11/2013 03:31 PM, Marco Loggia, PhD wrote:
Dear all,
what is the 'best' skull stripped file produced by freesurfer? From what I see, it would seem to be 'brainmask'. However this file -if I understand correctly- is produced in the very first stages of recon-all, and therefore does not take advantage of the detailed reconstruction of the brain 'borders' which is achieved in the subsequent stages of recon-all. For this reason, I have been masking my brainmask.mgz file with a binary file created using the aparc+aseg file (which labels only the brain), slightly smoothed to be conservative in the stripping.
Or is there already a file skull-stripped this way?
Thanks,
Marco
Marco L. Loggia, PhD Instructor in Radiology Harvard Medical School
Massachusetts General Hospital 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 726-7422 marco@nmr.mgh.harvard.edu mailto:marco@nmr.mgh.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer