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Making FinalSurf edits - base

If preferred, one can use the edited cross sectional data to create a new base. However, edits made to the brain.finalsurfs volume of the cross sectional data sets will not transfer to the base since the base creation takes off from the norm.mgz of the cross data sets.

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

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 make a copy of the edited brain.finalsurfs.mgz file to one called brain.finalsurfs.manedit.mgz in the base:

cp OAS2_0002/mri/brain.finalsurfs.mgz OAS2_0002/mri/brain.finalsurfs.manedit.mgz 

Next, run the following to have edits take effect:

recon-all -base OAS2_0002 -autorecon3-pial

Results will look as follows:

Here is zoomed in version of above:

Now that the base and cross sectionals are fixed, you must re-create the longitudinal data sets for each time point. Return to the Longitudina Tutorial to read that section.