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

External Email - Use Caution 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)