Dear freesurfer community,
My question is directed to those who have experience with editing brain.finalsurfs.mgz.
According to the tutorials, after making edits on brainmask.finalsurfs.mgz (which is normally done when the pial surface is not accurate), we can run, recon-all -autorecon-pial -subjid subj"
However, I found an anomaly when I looked at the steps that -autorecon-pial flag goes through. The very first step of autorecon-pial flag is "mri_mask" command. This takes brain.mgz and brainmask.mgz as inputs and gives brain.finalsurfs.mgz as output.
Now, if we have made edits on brain.finalsurfs.mgz, it will be overwritten by the new one and hence our edits won't take an effect.
I ran few experiments too. First, I made edits on brain.finalsurfs.mgz and ran recon-all with autorecon-pial flag. I ended up with a new brain.finalsurfs.mgz and my edits did not make any changes. Second, I made edits on brain.finalsurfs.mgz and ran with white, smooth2, inflate2, autorecon3 flag (basically starting from mri_make_surfaces command). On doing so, the edits made desirable changes and brain.finalsurfs.mgz remained intact.
Third, I made changes on brainmask.mgz and brain.mgz (inputs for mri_mask). It also works as expected.
Finally, I also followed the recommended steps from the tutorial by creating brainmask.finalsurfs.manedit.mgz, however, the edits from "manedit" were not carried on to brainmask.finalsurfs.mgz
Could anyone please shed some light on this? What would be the best strategy to follow?
Thank you, Sankalpa