Hello Freesurfers-
I wondered what the word was on preprocessing before you get into the land of freesurfer and recon-all.
I have some Inversion Recovery-T1s, where bias / field inhomogeneity is a slight issue. The standard N3ing that is done autorecon1 really wasn't cutting it (it was fine, but it required additional time in the back end, e.g., correcting skull-strips, adding control points). And for all non-freesurfing, I have been using either: 1) a combo of N3 and MFAST (b/c we have T2 where the same bias isn't present) or 2) a tweaked MFAST routine.
I however didn't want to "over-correct" my data, so I wanted to get some feedback before I go down either rabbit-hole. Anyone have some feedback / past experiences?
Pics from both routines are at: http://brainimaging.waisman.wisc.edu/~hanson/freesurf1/
Prefix of n3mfast- Combo of N3 and MFAST Prefix of superrestore- Tweaked MFAST routine
The superrestores looked cleaner, but I was worried it might be "too much" preprocessing.
Thoughts? Thanks much, jamie.