Thank you Rob for this detailed explanation. I understand the complexity of acquisition related to three image axis. This is one of my struggle too when I am automating my pipeline, as phase encoding may differ in terms of numerous factors.
If the phase encoding direction is tracked within the image header, there’s no need to provide such to dwipreproc explicitly: just use the -rpe_header option.
- If I use this option, will not dwipreproc default it to topup for distortion correction? Unfortunately, ADNI only acquires (that too in my understanding only for Siemen’s data) fieldmap scan in the form of phase/mag image. This was the key reason for me to use epi_reg outside of MRtrix3 to correct for distortion correction using phase/map acquired fieldmap.
- Besides, if you see the screenshot I attached in earlier email, distortion correction is better in “+j” (which is fsl’s y+) direction which is opposite to the one saved in the DWI.mif’s header ("-j" direction). In that case, would it matter if I use “+j” for distortion correction, and “-j” for eddy correction?
The outcome of dwipreproc would (I think) be identical regardless of which direction you provide. Since eddy current correction is based on registration, all that matters is the axis. Even for -rpe_pair and -rpe_all , all that negating the phase encoding direction does is correspondingly negate the values of the estimated field offsets; in the correction of geometric distortions arising from such, the negation cancels itself out.
- Seeing the o/p of unwrapped images, I might not be sure of we may see identical o/p from dwipreproc. I would understand that we may see some percent of error in our metric calculations, also see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4845159/ for reference, which is one of my concern.
Thanks again,
Sneha