Hi Octavian
If you upload the subject we will take a look
Cheers
Bruce

> On Nov 9, 2014, at 10:40 PM, Octavian Lie <octavian.lie@gmail.com> wrote:
>
> Dear all,
>
> 1. in the attached there is a gyrus that does not incorporated into surfaces, whatever I do (wm edits/topological defects-cloning voxels from brainmask.mgz or T1.mgz into wm.mgz, save volume then run recon-all autorecon2-wm autorecon 3), or control points addition to wm in brainmask.mgz, then run the -cp flag. Is there any other solution left to clone the white matter (and pial voxels) left out? is brain.finalsurfs.manedit.mgz a solution?
>
> 2. Unrelated, after manual pial edits and reruning the recon-all autorecon-pial command, the pial surface generated is mostly OK, however where there have been heavy dura editing the surface looks granular. Is there a workaround (along with better hands), such as smoothing the final pia a bit more (preferably in the recon-all pipeline as to be convergent with other segmentation results).
>
> I appreciate your help,
>
> Octavian

> <rightgyrusfailure.png>
> <rightgyrusfailurewm.png>
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