Hi Emily,

I do believe you need to include the same -seg-wlo <threshold> in the next run of recon-all. Otherwise, the default thresholds will be applied.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Harriott, Emily M
Sent: Wednesday, February 15, 2023 4:33 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] quick question about using the -seg-wlo flag

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Dear FS experts,

If I run recon-all with the -seg-wlo <threshold> flag to include more white matter in the segmentation, and then remove some stray white matter voxels on the output wm.mgz using recon edit, necessitating another run of recon-all, do I again need to include -seg-wlo <threshold> in that next run of recon-all?

Any assistance anyone might be able to provide would be greatly appreciated.

Thank you so very much!
Emily Harriott

(doctoral student, Vanderbilt University)