Until the freesurfer gurus can weigh in, I consider this wiki page relevant:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview
There are regions where the surfaces are not intended to be accurate that you should be aware of:
Areas around the hippocampus and amygdala. The surfaces will not completely include or exclude certain subcortical regions. These inaccuracies can be ignored as subcortical regions are excluded from the
cortical measures and subcortical volume is measured by the aseg, not the surfaces.
For an example of this, scroll to coronal slice 128 (slice numbers appear in the upper right hand corner of the viewing window).
From:
Mahta Abbaspour <mahtaabbaspour96@gmail.com>
Date: Wednesday, June 25, 2025 at 12:13 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] QC recon- all and manual editing
External Email - Use Caution
Hi,
I recently attended your FreeSurfer course in June and found it incredibly helpful—thank you! I’m currently working on a research project on AD patients and have been performing quality control on my FreeSurfer
outputs using version 8.0.0.
I’d really appreciate your input on a few slices I came across, as I wasn’t sure whether they require manual correction.
In this image, do you think the pial surface (red line) near both hippocampus (light blue) are undersegmented?
This is also another screenshot of the same brain. The pial surface on the left placed inside the WM surface. It's just 1-2 slices but I was wondering what's the best approach to these types of error.
Thank you for your time.
Best