Hi,
Was the following issue ever solved? (sorry hit send too early!) 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50297.html

I tried and, like the previous two people it fails on mri_watershed.

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50297.html

Best wishes,

Sean

Hi Mike

it's hard to say without looking at the data. if you upload the subject dir we will take a look

Bruce
On Thu, 24 Nov 2016, Michael Craig wrote:

Hi All,
I am trying to run recon-all on the Allen Brain Institute T1 images. It works
without any issue on all but one subject (H0351.1009). 

I saw this post from a few years ago describing the exact problem I’m having,
but don’t see a solution. Has anyone figured out how to get this subject to run
in recon-all? Or is it simply a matter of there not being enough contrast
between grey and white matter? Thanks for the help!

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-July/031482.html

Best wishes,
Mike