Typical resting state sequences use a Gradient Echo (GE) sequence: the BOLD signal is a T2* artifact that would not be seen in a Spin Echo (SE) T2 sequence. In contrast, FSL’s TOPUP is designed to be used for SE sequences. Both GE and SE sequences show EPI-based spatial distortion. However, for SE images the signal is moved in regions of distortion (it becomes compressed in some areas and rarefied in others). In contrast, with GE images the distorted signal vanishes. TOPUP works by comparing two reversed phase encoding images where the signal has been moved in equal distance but opposite direction. This does not work if the signal has vanished.
Assuming your resting state fMRI data uses a GE sequence, you have two choices:
- Acquire two additional series of SE EPI data with identical angulation, center, resolution, etc. as your GE dataset and use TOPUP.
- Acquire a Gradient Echo fieldmap sequence and use FSL’s FUGUE.
The method you describe of acquiring two series with reversed phase encoding works with diffusion-weighted images, as DWI uses SE sequences.
For the data you describe, I would use the conventional GE field map you describe with FUGUE to independently undistort the AP and PA GE resting state data. So your field map is intended for each of the two fMRI sessions.