Hi folks,
My main question is: how much does the registration to T1 matter when applying the TOPUP field map (w/ Hz-to-rads) to a same-session fMRI dataset?
My topup-derived fieldmaps are making things worse regarding OFC geometric distortion, and I'm pretty sure that my choice of timing parameters is ok.
When I check the Registration/Unwarp HTML output, the registration for "fieldmap_to_hires" (at home, don't have access to precise filenames) is definitely off, especially in the z-direction. I read a post on the FSL forum about this today regarding what registrations to check, which I then lost (GRRR!). Could anyone remind me what files to check, or a link to THAT post if you recall?
My secret suspicion is that (if a registration to T1 issue) our T1s are collected sagittally (although I used 'fslreorient2std' on this volume). This gives a lot of extra neck. I then used SPM for skull stripping, which may have screwed things up further re: origin/sform/qform). Our scanner (GE 750 3T) produces axial volumes for the sagittal acquisition, and I wonder if I should be trying with those?
Thanks in advance,
Conrad
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