I would argue that, if you manually edit the region, there’s no need to rerun anything downstream since the surfaces won’t be affected, no? All you’d need to do is recomputing the ventricular volume.
Independently: I would quickly run the images (T1 and/of FLAIR) through SynthSeg and see if the ventricles look better. If they do, you can simply take the ventricular masks & volumes from there, right?
From: Betz, Anja Katharina <Anja.Betz@med.uni-muenchen.de>
Date: Monday, August 3, 2026 at 11:40 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon-all-clinical pediatric ventricle segmentation
External Email - Use Caution
Good afternoon,
we have acquired a number of pediatric scans (ages 6-18y) on a 3T research MRI scanner. Most likely due to motion artifacts, the regular recon-all pipeline produces (amongst other problems) severe undersegmentation of the gray matter. Instead, we have started
using the
recon-all-clinical
pipeline, which on average seems to produce more accurate results. Our FS version is 8.0.0.
Unfortunately, a reoccurring problem is that the recon-all-clinical workflow often undersegments the ventricles and classifies them as white matter. Two images from two different subjects are attached to show the issue.
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Is there a way to remedy this on a pipeline level? I could not find an option to, for example, add an axial FLAIR image to the pipeline.
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Alternatively, if we manually edit the region, how can the downstream steps be re-run with recon-all-clinical? I am looking for a pipeline similar to adding control points in the regular recon-all.
Thank you and best wishes!
Anja