Hi,
I am trying to fix the few subjects in my study ( 3 of 64 ) that need manual fixes resulting from skull strip erros ( 2 of 3 cerebelem was left out ). This is the first study since my student who was doing this for me left ...
So the note he left said do tkmedit practice/subjectname/ brainmask.auto.mgz -aux orig.mgz then config brush, etc. i.e. make the edits and save changes in brainmask.auto.mgz with input from orig.mgz
In the frresufer wiki tutorial it has tkmedit 091_watershed_before brainmask.mgz -aux T1.mgz
i.e. make the edits and save changes brainmask.mgz with input from T1.mgz
the study is with version freesurfer-v3.0 so the difference may be with version.
I was unsure what to do after saving the edits, I tried copying brainmask.auto.mgz to brainmask.mgz, i.e. overwrote the file with cp. recon-all -autorecon2 -subjid <subject name> and it finished with errors. I could find no error message in the logs. I deleted the surfaces in the surface directory and reran and it again finished with errors and only 5 of the surfaces ( on the right side) had been produced. a bit mysterious since the left and right side was involved in the edits ??
anyhow see an obvious change in procedure I need to make ?
thanks again
Greg.