Hi,
I've primarily used afni in the past, but want to take advantage of the
great non-linear registration in fsl. Because I've already run the
first-level stats is afni, I'd like to use fsl for registration alone, if
possible. I couldn't find an answer to my the question online, so I would
really appreciate it if someone could let me know if there are any problems
with my approach. If there is a problem, alternative would be very much
appreciated.
Convert all relevant files to NIFTI
1) Register run1 epi time series (there are 4 runs but all frames are
aligned to first frame of run1) to skull on T1High (with flirt)
2) Register skull stripped T1High brain to MNI (with flirt)
3) Register skull on T1High to MNI (with fnirt)
4) Register output of glm which has been converted to percent signal change
with output of (3) as warp and output of (1) as premat.
Thanks!
Nicole
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