Sounds like your acquisition corresponds to point number 3 in the documentation page, which is activated either explicitly in
dwipreproc* using the
-rpe_all option or implicitly by providing all data and using the
-rpe_header option. In either case, a key to usage is that the DWIs need to be concatenated together before feeding to
dwipreproc doesn’t take multiple DWI series at its input.
There are a couple of advantages to this type of acquisition:
Having more than one b=0 image with reversed phase encoding for B0 inhomogeneity estimation should be more robust (albeit slower) and mitigates the risk of large subject motion during the acquisition of such leading to an inability to estimate that field.
While the DWI signal in a distorted image voxel can be appropriately “relocated” to the undistorted spatial area from which the spins in that distorted voxel originated by simply using an inhomogeneity field estimate, it is not possible to recover the spatial contrast in the region of the undistorted image. Here’s a screendump of a crude slide I made trying to demonstrate this (yes I know, I need to improve the documentation surrounding
In contrast, if you have not only acquired b=0 images for estimating the inhomogeneity field, but also have acquired DWIs with the opposing phase encoding direction, that then gives the possibility of estimating, from two image volumes with the same diffusion sensitisation but opposing phase encoding directions, the underlying undistorted image that led to the two distorted images. In
dwipreproc this is done using the method described in Skare et al. in the command reference.
If you are concerned about acquisition duration prospectively, in my own opinion what will be increasingly used is e.g. splitting the direction scheme in two, acquiring half of the directions with one phase encoding direction, and the other half with the opposing phase encoding direction. This means that in regions of sharp field inhomogeneity gradient, where in one phase encoding direction all of the spins get squished together, you’ll still at least have half of your DWIs with the opposing phase encoding direction where those spins are instead spread out and therefore you have some chance of recovering spatial contrast.
*deprecated command with version 3.0.0 in favour of dwifslpreproc