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 -- Skyler G. Shollenbarger Graduate Student Clinical Psychology & Neurospychology University of Wisconsin-Milwaukee _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
