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
>
>
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