Thanks Bruce, will try that!

Yann


On 16 Mar 2017, at 10:39 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

if you edit the aseg to make them thalamus and rerun autorecon2-wm and autorecon3 it should fix it. Not sure why the aseg failed there though - it usually does better
cheers
Bruce
On Thu, 16 Mar 2017, Yann Quidé wrote:

Hi Bruce,

Thanks for your reply. Most of the voxels are not labelled as thalamus on the aseg, only few partially cross the wm/pial lines (see screenshot attached).
Any recommendation?

Thanks.

Yann


On 16 Mar 2017, at 1:24 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Yann

are those voxels labeled thalamus in the aseg?

cheers
Bruce
On Wed, 15 Mar 2017, Yann Quidé wrote:

Dear all,

We have this issue around the thalamus that is recurring in several of our scans and there does not seem to be a problem with the white matter mask in that area.

Is it a problem? Does anyone have an idea how to fix this? We are using Freesurfer v5.3.

Thanks.

Yann

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