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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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