I am new to fMRI processing and have run into an interesting issue with my rsfMRI volumes: every other 3D volume is flipped in the A-P direction (around the y-axis) and I think this is how they were encoded in the scan, because the distortion direction also switches with each volume.
Does anyone have any suggestions for how to go about resolving this? Do you know of any fMRI-specific tools that might deal with this?
I considered flipping the volumes myself and using FSL TOPUP to distortion correct but wasn’t sure whether there were other implications to the flipping that needed to be accounted for.
Any help is more than welcome!