Dear Mohamad,
The brainstem module uses different anatomical definitions than aseg/wmparc, and yes, the largest discrepancy is in the midbrain.
For the midbrain, I like the segmentation from the brainstem module better, since it is based on manual annotations made by UCSF collaborators working explicitly on the brainstem regions. But Bruce's opinion might be different?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Mohamad J. Alshikho" <MALSHIKHO@mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Tuesday, January 26, 2016 4:05:24 PM
Subject: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}
Dear Freesurfers,
After segmenting the brain stem using FS6 tools. I used Free view to visualize the final images. In Free view I opened "orig.mgz", "wmparc.mgz" and "brainstemSsLabels.v10.mgz" Then I tried to check the segmented structures by flipping the images.
I noticed an overlap between Ventral DC ( left and right) and mid brain ( as an output of brain stem segmentation).
I "wmparc.mgz" atlas: Ventral DC and brain stem are totally different segments. Now After segmenting the brain stem. I see that the Ventral DC belongs to the mid brain.
Is this natural?
Thanks in advance for any suggestion!
Mohamad
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