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To view the topological defects and how they were fixed, first run

  defect-seg --s subject

This will take a few min to run. Next, run defect-seg --help to get commands for viewing on the volume or surface. You can replace "tkmedit" and "tksurfer" with "tkmeditfv" and "tksurferfv" to use freeview instead of tkmedit/tksurfer.

Surfaces

Viewing Surface Defects

To view the defects without using defect-seg, first, load the ?h.orig.nofix surface, then load the ?h.defect_labels as an overlay. Clicking "use surface color" will color the surface regions that have defects, which is very useful for fixing topological errors.