Making Pial Surfaces Edits
To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names.
Toward the anterior region of the brain, notice that there's a lot of dura remain from the skullstrip making the pial surface extend further out from the grey matter. In these cases, manual edits will be the quickest way to fix the problem. You also notice that this problem exists in all three stages: cross, base, and long. If you are not looking to use the cross-sectional data, it is easiest and quickest to just make the edit on the base, and then rerun the longitudinal data from there. If you prefer to correct the cross-sectionals, you can also do that.
The following are images from the base OAS2_0057_before coronal slices 175 and 205, respectively.
After deleting the extra dura from brainmask.mgz, rerun the base with the following command:
recon-all -autorecon-pial -autorecon3 -base OAS2_0057_before
To rerun the longitudinal, use the following commands (note - it is better if you delete the existing longitudinal directories for this subject or rename them to something else and delete them. Or you can delete the brainmask.mgz in the mri directories if you don't want to delete the whole subjectdir. If the brainmask.mgz exists, it won't copy the pial edits that were done on the base.)
recon-all -long OAS2_0057_MR1 OAS2_0057_before* -all recon-all -long OAS2_0057_MR2 OAS2_0057_before* -all
*note: here we use OAS2_0057_before as the base name to keep it consistent with the file you are using for the edits, but note that in your actual data, the base name cannot be renamed to something else (e.g. _before, _edit) unless it's after it's already ran/reran. So if you want a copy of the before version, rename that to baseid_before and edit the baseid version.
Here is the final output of the base:
and the longitudinals, OAS2_0057_MR1.long.OAS2_0057 and OAS2_0057_MR2.long.OAS2_0057 respectively:
<insert image> <insert image>
You can compare these results with the before-edit versions in tkmedit.
tkmedit OAS2_0057_MR1.long.OAS2_0057_before -brainmask.mgz -aux T1.mgz -surfs tkmedit OAS2_0057_MR1.long.OAS2_0057 -brainmask.mgz -aux T1.mgz -surfs