Hi Jacky
the first step is to look at the output of the processing (if it finished) and see if it looks good. If so, you don't have to worry about it. The very large defects are difficult to correct (or take prohibitively long), so should be checked, but they certainly can be corrected accurately. The one you have below with 14K vertices and 3K in the convex hull is big, but not extreme (some can be 1/4-1/2 of the surface. This is only around 1/10).
cheers Bruce
On Sun, 20 Mar 2016, Jacky Lee wrote:
Dear freesurfer experts,
I have encountered problems running recon-all on some subjects where the processes were stuck at "CORRECTING DEFECT 5 (vertices=14049, convex hull=3020) XL defect detected...".
I have read from the mailing list that this is a large defect to be manually corrected or control points. So does that mean the recon-all cannot correct this? If that is the case, what are the steps for manual correction or control points and how should I re-run the recon-all afterwards with incorporation of this correction?
Regards,
Jacky Lee