Greetings Aylin,
If you have made edits to both the brainmask.mgz and wm.mgz files, I would recommend running recon-all with the -autorecon2 and -autorecon3 flags.
Each step in the FreeSurfer recon-all process draws on files generated in previous steps. So, if you have made edits to the wm.mgz volume, you will need to re-run the portion of the recon-all pipeline to incoperate you wm.mgz edits before you run the edits you made to brainmask.mgz through recon-all. This is because the pial surface processing happens after the white matter segmentation.
Below is a link to the FreeSurfer wiki page about recon-all. The section "Manual Intervention Workflow Directives" gives a breakdown of the steps in the recon-all pipeline.
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Manual-InterventionWorkf... recon-all - Free Surfer Wikihttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Manual-InterventionWorkflowDirectives Description. Performs all, or any part of, the FreeSurfer cortical reconstruction process. This help only gives some simple information. See also ReconAllDevTable.. Basic usages: 1. Subject dir does not exist: surfer.nmr.mgh.harvard.edu
Best, Jackson
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Dincer, Aylin aylin.dincer@wustl.edu Sent: Wednesday, January 6, 2021 1:05 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] freesurfer flag for multiple edited volumes
External Email - Use Caution
Hello FreeSurfer Experts,
If I need to manually edit both the brainmask.mgz and the wm.mgz in a FreeSurfer, what are the recommended flags when rerunning recon-all with the edits (-all, -autorecon2, etc)? Or is it recommended to run an edited volume through recon-all one at a time (i.e. editing the brainmask.mgz first, running recon-all using autorecon2-pial flag, editing the wm.mgz afterwards, then running recon-all again with autorecon2-wm)?
Thank you for the help!
Aylin
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