I’m hoping you can provide some advice on how to best account for image distortions when reverse phase B0 images are not available.
In my data (single shell, 30 directions, b=700, 6 B0 images, P->A aquistion) I see consistent distortion in the frontal lobe as well as hyper intensity in the temporal lobes. Hopefully this is obvious in this fslview screenshot:
There are unfortunately no facilities within MRtrix3 for distortion correction based on field maps. But you should be able to use FSL fugue to do this.
Otherwise, I think there are ways of doing distortion correction based on the T1, but again, not within MRtrix3. I’m not familiar with the packages required for this, or how well they work, but hopefully others will be able to fill in the gaps…
There’s a good quantitative evaluation of the performance of multi-echo gradient echo field-mapping v.s. reversed phase-encoding EPI acquisitions for susceptibility distortion correction here.
I would be curious myself to see a demonstrated example of fugue in use, since theoretically the functionality could be wrapped by dwipreproc (if someone had the time ).
Theoretically, it is possible to use eddy with -field option. I tried it, but there are several pitfalls I encountered:
There is a problem with robustness/precision of registration of fieldmap to DWI. The magnitude image typically does not offer good contrast, resolution and has to be precisely skull-stripped (another problem).
).