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