Hi Peter and Daniel,
thank you for your helpful suggestions!
Based on your feedback, I finally managed to successfully coregister the b0 image to the hires space via the anat using the align_eip_anat.py, 3dQwarp and 3dNwarpApply commands (cf. attached image top 2 rows vs bottom 3 rows).
For some reason I was under the impression that you have to go through MNI space, which very much complicates the process with more affine transformation matrices and warps to integrate into 3dNwarpApply, which I was not able to do. Thankfully that was not necessary after all.
Bests,
Philipp
Edited 1 time(s). Last edit at 10/03/2022 05:14PM by philippn.
