Hello,
I want to use fMRIPrep to apply the susceptibility distortion correction (SDC) to my fMRI scan. In our project they acquired “reverse fMRI” (rfMRI), which would be an extra fMRI scan with opposite phase-encoding direction (PE) than that of the fMRI scan. Both images are GR scans, but the fMRI has PE=AP, and the rfMRI has PE=PA.
In this thread, a clear distinction is made on how to use GR and SE scans for SDC. However, as I do not have any phasediff nor magnitude.nii files, I tried to use the SE Field Maps approach with two GR scans (only first time volume) with opposite PE. My questions are: 1. What are the risks of doing this? 2. Is there a way to derive the phasediff and magnitude.nii files from the rfMRI?
The results I got seem good from the side of the geometrical deformation i.e. the fMRI scan with SDC seems to be more aligned with the T1w, but I want to be sure that the process is not affecting the intensities of the fMRI. Can someone with more experience give me advice on this?
Thanks a lot,
Giada