Hi Mark,
Thanks so much for the great answer! As far as the answers to the first two questions I asked, I completely understand. I am just using BET to extract the brain, no need for betsurf, hence no need for T2-weighted scans.
As far as the proper non-brain-to-brain ratio after BET, here are some thoughts and more questions...and I apologize for the long email:
1. I just want to explicitly state that I’m performing a functional MRI experiment, and I took a T1 structural as well as a B0 fieldmap. I’m using the FEAT GUI to analyze functional MRI data, so I’m doing my registration there. If I understood things at the FSL course correctly, I’m registering my functional data to my BET’ed T1 with an affine transformation (6 DOF, FLIRT within FEAT), and I’m registering my BET’ed T1 to the MNI152 brain with a non-liner transformation (12 DOF, FNIRT within FEAT). Oh, and I’ll also be use the B0 fieldmap in FUGUE within FEAT to correct for bias. Is this correct?
2. Just clarify the problem; it’s my concern over the non-brain-to-brain ratio after BET. It’s not localized to one specific area (like the frontal cortex), but rather wherever there is a dura-to-brain transition. For example, depending on the parameters I’ve entered, after BET’ing I am never left with a 90% dura-free brain without having parts of cortex removed as well. So I need to settle for a 65-70% dura-free brain in order for the cortex to appear 98% intact. I’m just trying to find the right non-brain-to-brain ratio. Am I to understand that you think this ratio is relatively unimportant when doing FLIRT or FNIRT (in FEAT as I am doing it)? I mean, a little extra dura here, a little more brain over there...doesn't make a big difference because of the way the brain is transformed?
3. Also, do the above-mentioned problems with BET (the non-brain-to-brain ratio when just looking at a brain post-BET, not checking registration, etc) imply that I have a field bias? My T1 structural scan looks uniformly bright, but how do I know? To note, I’m consistently having to provide a slightly negative value for the “threshold gradient” (around -0.1) in order to get the neck area (what is left after ROI’ing) removed. Does this mean my field has a bias? If so, you mentioned to use FAST, but I’m not sure how to use this, and also, if I’m not mistaken, I thought this was something that was done in FUGUE (or FUGUE within FEAT) using a B0 field map after I BET. Am I correct? Sorry, just got a little confused because I am unfamiliar with FAST :)
4. Final question…you mentioned that FNIRT uses the whole head structural scan for the last few passes…does FEAT know to do this? I don’t see where in the FEAT GUI I can enter the whole head T1 scan. If this is a problem, should I be doing all my registration outside of FEAT?
Thanks so much! I really appreciate your time and effort.
Have a great day,
Dar
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