Beauchamp:EditingCortSurf
From OpenWetWare
What if I have created a surface model and it looks bad?
Sometimes the cortical surface model created by FreeSurfer contains large errors.
For instance, in this picture, part of the pia-arachnoid-dura has been classified as part of the cortex.
To fix this error, AFNI's "draw dataset" plug-in can be used to try and fix the problem.
Change the {$ec}_anatavg+orig dataset directly. (If something goes wrong, a new one can be made from the original T1s).
Set the drawing value to 0 and pick a paintbrush style.
Identify the offending voxels and paint them in black.
Then, rerun the surface creation routine.
mv graham_tim graham_tim_v0
/Volumes/data9/surfaces/scripts/@prep_dir {$ec} $subj
/Volumes/data9/surfaces/scripts/@recon {$ec} $subj
