Hi,

according to this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview , there is a separate protocol to correct cerebellar errors with rois such as the lingual gyrus, fusiform and etc specially the creation of the brain.finalsurfs.manedit file. I have a few questions about this step:

I'm assuming that the recon-2, if it detects a brain.finalsurfs.manedit, it makes a mask out of it, and applies it to brain.finalsurfs? The potential conflict I see here if that's not the case is this scenario: I'm doing all the manual edits for the brainmask, re-run recon23, then I create the brain.finalsurfs.manedit and correct the cerebellum, running the recon-all -autorecon-pial. Then I realize that there are still recon errors, and I edit the brainmask again. Would this second instance of editing the brainmask be negated by the fact that the brain.finalsurfs.manedit file doesn't have these edits?

Also, generally, is it okay to do other sort of edits (e.g removing the blood vessel between the cerebral cortex and the cerebellum) @ the brain.finalsurfs.manedit, rather than the brainmask.mgz?

best

Victor Zeng

Beth Israel Deaconess Medical Center

Keshavan Lab

ph: 617 754 1237

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