Dear Francesca, Our method cannot reliably segment these thin/faint structures from clinical scans of arbitrary resolution and contrast, which is why they don’t get segmented. If you want to segment the choroid plexus, you could take then intensities under the ventricles and split them into cerebrospinal fluid and choroid eg with optimal thresholding. 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 Biondo, Francesca f.biondo@ucl.ac.uk Date: Friday, January 5, 2024 at 2:59 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all vs. recon-all-clinical: missing ROIs

External Email - Use Caution Hi, recon-all generates these volumes, amongst others: “Left-vessel”, “Left-choroid-plexus”, “Right-vessel”, “Right-choroid-plexus” recon-all-clinical does not generate these volumes. Or at least that I am able to detect. Any ideas how to extract or calculate them?

Regarding the choroid plexus, would it be correct to use this formula? Estimated choroid plexus volume (both left and right) = “VentricleChoroidVol” – “left lateral ventricle” – “right lateral ventricle”

Thank you very much for your support - Francesca