Hi Skyler
after adding control points one usually runs:
recon-all -subjid <subject> -autorecon2-cp -autorecon3
cheers Bruce On Thu, 28 Jun 2012, Skyler Gabriel Shollenbarger wrote:
To whom it may concern,
After running autorecon2 (recon-all -subjid xxxxxxxx -autorecon2) there were areas that required correcting for both the pial and WM boundaries. I added control points to correct the WM boundaries and saved them using File > Save Control Points. I also used the select voxels tool to extend the boundaries in areas where the pial surface was not generous enough resulting in excluded GM and saved them using File > Save Volume.
After adding these voxels and control points I ran (recon-all -autorecon-pial -subjid xxxxxxxx) however received an error that '-autorecon-pial' was not recognized.
Then, in attempt to regenerate the boundaries with the new voxels and control points saved, I ran (recon-all -subjid xxxxxxxx -autorecon2-cp). When reloading the image to inspect the new boundaries using command (tkmedit xxxxxxxx brainmask.mgz -surfs -segmentation wm.mgz $FREESURFER_HOME/ASegStatsLUT.txt), I found that the errors were not fixed.
If anyone has insight into what I'm doing incorrectly it would be much appreciated! Skyler