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Hello,

The regions you have denoted with the cursor are not part of the cortex, and as such are not included in the pial/wm segmentation.

The 'un-segmented' areas are part of the medial wall. This is not a completly exhaustive list, but these structures are not classified as cortex and are not included in the pial/wm segmentation:
Best,
Jackson

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fatima Abboud <fatme.abboud@mail.mcgill.ca>
Sent: Thursday, July 27, 2023 2:36 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Grey Matter Under Segmentation
 

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Hello,

I have run FreeSurfer v7.1.1 on the CBRAIN platform and I'm performing QC on the output using the information at the following page: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeviewV6.0

It seems though that for almost all of my output, a large portion of the grey matter is not being segmented (please see attached example). 

I'm not sure if there is a solution to this or if the images will just need to be manually edited to fix this under segmentation. I would greatly appreciate any help or insight.

Thank you for your time and help,

Fatima