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 > > _______________________________________________ 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.