hi sean,

i think i ran those in june 2013 at ohbm. however, my recollection of how it failed is encoded in that mail thread.

it may be worthwhile to just run through those images with freesurfer 6.0.

since it's only 6 brains, we can try running it through again.

cheers,

satra

On Thu, Oct 19, 2017 at 3:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Seán

I'm not sure. I think Satra posted the original issue, so maybe he knows. Satra?

cheers Bruce On Thu, 19 Oct 2017, Seán Froudist Walsh wrote:

...

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-J uly/031482.html

Best wishes, Mike

On 19 October 2017 at 15:05, Seán Froudist Walsh froudiss@tcd.ie wrote: Hi, Was the following issue ever solved?

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