7 Nov
2005
7 Nov
'05
3:58 p.m.
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?