gradunwarp: gradient field inhomogenities unwarping

[bpinsard]

I am starting to investigate the feasibility to implement gradunwarp step in fMRIPrep and list the changes to be made in the different packages.

• niworkflows
  • Create an interface for gradunwarp estimation
  • Implement a single-step interpolation that combines gradunwarp, HMC, and SDC
    • Can the gradunwarp field be applied by AntsApplyTransforms or does it require a conversion (nitransforms)
  • BIDS/automation: detect 'ND' in ImageType of all images to determine if they need offline distortion correction or not
• smriprep:
  • add option to pass Siemens coefficients
  • unwarp T1w/T2w/Flair images prior to robust template creation or longitudinal pipeline
• fmriprep:
  • add option to pass Siemens coefficients
  • unwarp EPIs fmap passed to sdcflows (or should that be included in sdcflows)
  • unwarp bold in the single-step transform implemented in niworkflow.

Am I missing anything?

[effigies]

This looks right to me. Please see also #1550 for comments from those more knowledgeable than myself.