Hi Jamie,
it's hard to tell from the pics. The superrestore might be erodeing the
borders of the thalmus and the pallidum. Can you flip back and forth
between the uncorrected and corrected to see if that is the case. Also,
check the gray/white junction in primary motor cortex. Basically you want
as much correction as you can get as long as it doesn't cause these borders
to shift position. Note that our T1.mgz *does* erode the pallidum and
thalamus borders intentionlly, as we only use it for cortical surface
models.
cheers,
Bruce
On Mon, 27 Aug 2007, Jamie Hanson
wrote:
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.
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