It looks more likely that it is a problem with the skull stripping. If you clone the brain voxels back in and rerun do things work?
On Aug 11, 2014, at 4:11 PM, "Makaretz, Sara Johanna" SMAKARETZ@mgh.harvard.edu wrote:
I am having trouble getting a usable brainmask for one of my subjects - a screenshot of the initial brainmask.mgz is attached as image_1. The talairach transformation looks fine, so I tried running recon-all -multistrip with raised watershed heights to no avail - see image_2.
Does this mean the problem is with the mri_em_register step / lta output? How can I check this, and what can I try changing?
Thank you! <image_1.jpg> <image_2.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer