Dear FreeSurfer Developers,

We are using FreeSurfer v6.0 and our operating system is OS X El Capitan version 10.11.6.

We are going through the manual editing process and are checking the brainmask by following these instructions:

http://freesurfer.net/fswiki/FsTutorial/SkullStripFixV6.0

We have two subjects who appear to have brainmasks that are shifted up considerably (see attached image). The recon-all.log file indicates that it finished without errors:

reading volume /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/mri/wm.mgz...
reading input surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white...
reading input pial surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.pial...
reading input white surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white...
INFO: assuming MGZ format for volumes.

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name

277 173 970 3.493 0.659 0.107 0.039 3 0.4 ./rh.entorhinal_exvivo.label

#------------------------------------------

Started at Thu Jun 8 10:50:24 CDT 2017
Ended at Fri Jun 9 00:06:58 CDT 2017
#@#%# recon-all-run-time-hours 13.276
recon-all -s 2083_base finished without error at Fri Jun 9 00:06:58 CDT 2017

Could you please advise me on how to correct this issue? We have run all of these subjects the same way, but only two have had this problem.

Thank you!

Kaley

Associate Research Specialist

Center for Healthy Minds

Waisman Center for Brain Imaging and Behavior

University of Wisconsin-Madison