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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