The PET image with the ROIs is aligned to the T1 with FLIRT. So all I need to do is to align the FA/MD to the TI using FLIRT as well. It is the same brain so i cannot see any reason to use FNIRT.
Unfortunately the sampling was done without reversing the phase coding so Top up is hard to apply unless one tries the T2 image. I have tried that before, with help from Jesper Andersson, but the distortions were not corrected to any larger degree.
I understand doing the b0 (aligning to the T1) first and then running eddy and the rest of the preprocessing into FA. Or only aligning the final FA. But in the latter case, the B0 will not be aligned to the T1. Or how do you mean?
best
nick
I am wondering, we are going to register FA images to T1 and PET images and I am wondering when in the process this is preferred to be carried out?
We have ROIs outlined in PET where we want to assess FA in the sane areas.
Before the DTI images are processed into FA, MD etc or after?
Best
Nick
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