External Email - Use Caution

Hello FreeSurfer Developers,

I need to compute volumes of different brain regions using T1 MPRAGE MRIs, and the standard approach of running `recon-all`, followed by `asegstats2table` is working fine for most regions. However, in some cases, the volumes are either zeroed out (e.g., for choroid plexus) or missing altogether (e.g., for habenula), and I am wondering what is the recommended approach to calculate volumes in these cases.

Should I create a new segmentation volume manually on top of fsaverage​ that is aligned to my subject MRIs and run `mri_segstats`, or should I use `mri_synthseg`?

Adding FreeSurfer and computer info in case it is helpful:

* FreeSurfer version: `freesurfer-linux-centos7_x86_64-8.2.0-20260314-d932c45` * Platform: CentOS Linux 7 (Core)

Thank you in advance, Robin

Parth Chholak, Ph.D. Clinical NeuroImaging Research Core National Institute on Alcohol Abuse and Alcoholism National Institutes of Health Phone: +1 (301) 594-7416