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