Hello,
I'm trying to register an oblique EPI to a cardinal anat, and I'm getting poor alignment with FLIRT. The EPI I'm dealing with has 27 axial slices and is a slab which partially covers brain. I've run 3dWarp (-oblique2card), motion correction, and field map correction. Before FLIRT, the EPI and anat look relatively aligned; however, FLIRT ends up shifting the EPI along the pitch rotation. I've tried several options including -searchrx -searchry -search-rz and -nosearch but none of these seem to make a difference in the output. Are there any other options you might suggest to improve coregistration?
Thanks,
Angela
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