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

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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

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