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.