Adding to this question, I'm wondering whether it's appropriate to do both wm & aseg.presurf edits at the same time, and (if yes) whether there is a difference between reprocessing
the recon with -autorecon2-noaseg or -autorecon2-wm
ie.
Hypothetically, a subject with big ventricles is processed in FS v6.0 stable with the flag -bigventricles. The initial recon has wm surfs that dip into the posterior horn of the lateral ventricle.
1st edits: fill ventricle on wm.mgz (and other wm edits in other regions); reprocess w -autorecon2-wm -autorecon3
wm surfs around posterior horn of ventricle not corrected
2nd edits: in aseg.presurf.mgz, relabel problem voxels from cortex -> wm; if just these edits, reprocess w -autorecon2-noaseg -autorecon3
But if the subject has wm.mgz errors in other regions, can those edits be be made together? And would it matter whether the recon is reprocessed with -autorecon2-wm or -autorecon2-noaseg?
Thanks for any advice!
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Makaretz, Sara Johanna [SMAKARETZ@mgh.harvard.edu]
Sent: Tuesday, May 23, 2017 14:31
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Difference between -autorecon2-wm and -autorecon2-noaseg ?