Therefore, in order to fix the base, one must edit the brain.finalsurfs volume of the base as follows:

A. Below is a visualization of the problem area in the base: brain.finalsurfs.mgz, slice 89 at coordinates 98, 172, 89 in right hemi. The problem area extends through slices 85 - 94.

And here is the area zoomed in:

Next, edit the affected slices by removing the appropriate voxels, and save the changes to the aux volume. Then, cd into the mri directory of the base data set, and make a copy of the edited brain.finalsurfs.mgz file to one called brain.finalsurfs.manedit.mgz.: 1. cd OAS2_0002/mri 2. cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz

Next, run the following to have edits take effect: {{{recon-all -autorecon3-pial -base OAS2_0002 }}}

Results will look as follows: {{