Welcome @jxc!
Unless you’re using an exotic Siemens DWI WIP, if there’s a single DICOM folder containing DWIs, there’s a single phase encoding direction. Modification of the phase encoding direction during a single sequence execution isn’t possible with the commonly used sequences.
You should also be able to tell based on simply the number of files generated by dcm2niix. Each JSON file can only encode one phase encoding direction (currently), so if all of the DWI data are stored in a single NIfTI 4D series, then you have only one phase encoding direction.
Do however check the raw data in case there is an additional DWI or spin-echo EPI sequence where only b=0 volumes were acquired for the purpose of susceptibility field estimation. Depending on the sequence used, these may not be reported as DWIs, even if they’re intended to be utilised alongside the DWIs.
… if you’re going to use the
-rpe_noneoption, I’m pretty sure you don’t need to know that information …
No, it’s still compulsory for dwifslpreproc even for -rpe_none. From memory the eddy current correction can be off if your phase encoding axis is wrong.
Alternatively you can do an mrconvert -json_import to convert to .mif, then run dwifslpreproc with -rpe_header, and it will figure out what to do.