I used Multi-Band Accelerated EPI Pulse Sequences, so-called CMRR protocol.
TR = 460 ms, voxel size = 2.7 mm
When I used this protocol, additional 4 images for distortion corrections (two for each of polarity, A->P or P->A) were acquired before actual fMRI scanning.
Also, for each run, there were additional reference images.
I heard that I can use FSL function, “topup” for correcting distortion using the four images.
Also, I heard that for each run, I can use the reference image when I perform motion correction.
Is there any AFNI script for this procedure of preprocessing?
I don’t know how to use these additional images in addition to conventional AFNI preprocessing (guided by afni_proc.py)
Thank you in advance.