Convert GE pepolar diffusion scan to BIDS format

We are using dcm2bids to convert a GE pepolar diffusion scan to BIDS format. The forward and reverse phase encoding scans are integrated with the dwi scan. Specifically, the series starts with two b0 volumes (first is reverse encoding, the second is forward encoding) followed by forward encoding diffusion volumes. When converting with dcm2bids or dcm2niix directly, a single nii/json pair are created containing the b0 and diffusion scans, and “j” is listed as the phase encoding direction. I have a couple questions:

  1. Can multiple phase encoding directions be contained in the same series, or should the two b0 images be split off separately (perhaps into an fmap folder)?
  2. Assuming the two images should be split, is there are way for dcm2niix to automatically handle this?

It looks like this is similar to an issue previously raised with pepolar rsfmri sequences. Has a similar fix been implemented for diffusion scans?

We have tried using dcm2bids v2.1.7 (wrapping dcm2niix v1.0.20201102) as well as dcm2niix v1.0.20220720. Please let me know if additional details would help.

Any advice is much appreciated, thanks in advance for your help.

Upgrade to the current stable release of dcm2niix (v1.0.20230411. For a validation dataset of this sequence, see dcm_qa_polar. We do not have GE hardware at my center, if this fails to resolve your issue, you can send an exemplar dataset to my institutional email.