When I run recon-all with the -autorecon2-wm flag, my white matter edits get
overwritten, presumably by aseg, even if I use the -keepwmedits flag. Is
that the correct behavior or is this a bug?
If instead of -autorecon2-wm I use -stage2, then the wm is untouched (as
desired). For some reason though, it was then unable to find the pons and I
had to use the -pons-xyz option to get it to work. Any idea why using
-stage2 would produce this problem with finding the pons?
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