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Hi

Have you tried running with the -bigventricles flag?

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From: Ran Yan <rachyan@umich.edu>
Sent: Monday, September 1, 2025 6:57 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Fixing Misclassified Ventricles During QC

 

        External Email - Use Caution        

Hi Freesurfer team, 

I am new to FreeSurfer and am currently doing QC using FreeSurfer (v.8). I wanted to check what the best approach is to correcting the following participant (screenshot attached). 

It appears that the participant had very large ventricles (?), which have been misclassified (as indicated by FreeSurfer drawing the white and pial surfaces around them). My initial thought was to add control points or manually fill the ventricles in WM.mgz, but I wanted to check first, since this issue is widespread across the brain volumes. 

Many thanks for your help!

Sincerely,

Rachel 

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Ran (Rachel) Yan

She/her

Ph.D. Candidate in Developmental Psychology

University of Michigan

530 Church St. | East Hall 2048 | Ann Arbor, MI | 48109-1043

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