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Hi,
I am trying to create a surface of a macaque brain, but I am running into issues with white matter. I segmented the white matter and manually edit wm.mgz, however the surf/?h.white output of recon all is not outlining everything in wm.mgz, creating problems with the surface. I attached an image demonstrating the problem. The red is wm.mgz and the yellow outline is lh.white. Why would regions identified as white matter in the left hemisphere of wm.mgz not be recognized as white matter in surf/lh.white, and what could I do to fix this issue?
Also, when I run recon-all with the -autorecon2-wm flag, it seems that all my edits are reversed in wm.mgz. wm.seg.mgz is created by mri_segment, and then during mri_pretess, wm.mgz reverts back to what it was before my manual edits. Is there something wrong? Here's how I call recon-all:
recon-all -autorecon2-wm \ -subjid ${subj} \ -cc-crs ${CC_string} \ -pons-crs ${PONS_string} \ -noaseg \ -xopts-use
Thanks, Shridhar Singh
