OK, sorry for spamming the list. I fixed the the faulty skullstrip by using

recon-all -skullstrip -clean-bm -no-wsgcaatlas -subjid <subject name>

Currently redoing the surface reconstructions, but it should be OK now.
Thanks for the nice documentation.

On Fri, 2017-02-24 at 15:30 -0600, Elijah Rockers wrote:

As far as I can tell, everything looks OK up until brainmask.mgz. The
skullstrip step seems to have cropped out the brain and left the neck...

On Fri, 2017-02-24 at 12:58 -0600, Elijah Rockers wrote:
> Hello all,
> I recon-all'd ~40 different subjects. I have been going through all the
> images to make sure they were processed correctly. Most required no no
> editing and recon-all did a very good job.
> But for one scan in particular, it looks like Freesurfer thinks the top
> of the spinal cord is the brain. Several vertebrae are very nicely
> segmented... :P
> Just wondering if you have any suggestions for reprocessing this
> subject? The error is reproducible with default recon-all settings.
> Subject has some pathology in the white matter which might be causing
> the problem?
> Screenshot of T1.mgz + lh.pial at the following link:
> http://imgur.com/a/uwyaq
> Thanks,
> Eli

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