Dear Nima,

We never included the CP in SynthSeg because we didn’t manage to segment it reliably from images of any resolution and contrast. I am CCing the first author Benjamin Billot who can further clarify (or correct me).

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 Taghizadeh Mortezaei, Nima <ntaghizadehmortezaei@mgh.harvard.edu>
Date: Monday, January 13, 2025 at 10:24 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Missing Choroid Plexus Segmentation in final output

Dear FreeSurfer Developers and Community,

I recently ran recon-all-clinical using FreeSurfer version freesurfer-macOS-darwin_x86_64-8.0.0-beta-20241103-b8aacdc on a T1-weighted axial post-contrast MRI. However, I noticed that the choroid plexus is neither segmented nor labeled in the aseg.mgz or synthseg.mgz files in the final output.

I would greatly appreciate it if anyone could help me understand or resolve this issue. I have attached the log file for reference.

Thank you for your assistance.

Best regards,

Nima Taghizadeh Mortezaei, M.D.

Radiation Oncology Research Fellow, MGH