Dear Migueel Ángel,

Which is the problematic subregion?

Also: would you be able / willing to share a problematic case?

Cheers,

/Eugenio

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.com>
Date: Thursday, March 6, 2025 at 11:52 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hypothalamic subunits segmentation: volumes = 0

        External Email - Use Caution        

Dear FreeSurfer devs,

I have tried to use the hypothalamic segmentation tool on my T1w data (voxel size = 1mm), but in in some subjects, one of the volume measurements of the structures is equal to 0. I have used the following command:

mri_segment_hypothalamic_subunits --i /home/user1/data/scans/ --o /home/user1/data/segmentations/ --vol /home/user1/data/hypothalamic_volumes.csv

I am using FreeSurfer version 8.0.0. Am I forgetting any important flag in the command? Any help to solve this issue would be appreciated.

Thank you very much for your time.

Best,

--

Miguel Ángel Rivas Fernández