Bruce- I only plan on using it for cortical surface models... So do you think it is ok to erode away, use the super-restore images, and save a fair amount of time?
Any additional check to make sure I am not "over-correcting" or is that not as much of an issue if you are just shooting for cortical surface modeling? Could I shoot you over a volume or two to look at? Thanks much, jamie. > 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. > > > > > > > > > -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53706 Phone: (608) 262-5148 ***Please note my new email: [EMAIL PROTECTED] _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
