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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Taghizadeh Mortezaei, Nima <ntaghizadehmortez...@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
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