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Making FinalSurf edits

Here we will look at the second time point ( OAS2_0002_MR2).

In the brain.finalsurfs.mgz volume (your aux volume in tkmedit) you can see the pial surface encroaching into the cerebellum in slices 65 - 68: Representative slice 68 shown below, problem at coordinates 111 136 68 in right hemisphere

Zoomed in version is below

Go through and remove the voxels in the cerebellum and surrounding areas that cause the pial surface misplacement.

Once you are finished editing, save the changes to the volume with File – Save Aux volume. Then make a copy of the edited brain.finalsurfs.mgz file to one called brain.finalsurfs.manedit.mgz in this time point:

cp OAS2_0002_MR2/mri/brain.finalsurfs.mgz OAS2_0002_MR2/mri/brain.finalsurfs.manedit.mgz

Next, run the following to have the edits take effect:

recon-all -subjid OAS2_0002_MR2 -autorecon3-pial 

The results will look as follows: Notice how the pial surface is now pulled in based on the deleted voxels

Zoomed in version

Everything described thus far for MR1 should be repeated for MR2 as required. Next, it is time to fix the base for this subject - return to the Longitudinal Tutorial to see how.