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 > > _______________________________________________ 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.
