Hi Jiun-Wei

have you looked at the ?h.defect_labels overlaid on the inflated.nofix and orig.nofix surfaces? That will tell you where the defect is that is causing you trouble. If you have lesions they may be the source of the issue. If you can't sort it out you can tar and gzip the entire subject directory and put it on our ftp site for us to have a look
cheers
Bruce
On Mon, 9 Sep 2019, Jiun Wei Chen wrote:


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Dear freesurfer experts,
When executing recon-all in two subjects with brain lesions, the recon-all
process stopped at CORRECTING DEFECT 13 (vertices=49319, convex hull=12973,
v0=65403) and 
CORRECTING DEFECT 6 (vertices=23529, convex hull=6740, v0=16029),
respectively.

After reading the relevant problem from freesufer mailing list, I had
checked the skull and cerebellum not attached to the surface, two
hemispheres are separated using freeview. In addition, I also load
the brain.mgz, wm.mgz, ?h.orig.nofix and ?h.inflated.nofix and separately
overlap the ?h.defect_label onto ?h.orig.nofix  , ?h.inflated.nofix to edit
wm.mgz to solve this problem.

However, after editing wm.mgz in two subjects, the recon-all process still
stopped at CORRECTING DEFECT 0 (vertices=32853, convex hull=7926) and
CORRECTING DEFECT 6 (vertices=16533, convex hull= 4510) , respectively.

Although I try to erase the non-white matter and label voxels as white
matter as much as possible, there are too many voxels I think I need to
label, which may cause the failure. 

I can't figure out how to continue to solve this problem. I use freesurfer
version 6.0.0.

I really appreciate your help. Thanks a lot.

Best regards,

Jiun-Wei





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