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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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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.