adding SliceEncodingDirection to afni.TShift

[fliem]

Summary

BIDS allows to specify SliceEncodingDirection. How about adding a parameter to afni.TShift to use this information and SliceTiming from BIDS sidecar files directly.

This comes via fmriprep. @effigies suggested to add this here.

BIDS allows to declare SliceEncodingDirection to specify the direction of SliceTiming. What do you think about adding a SliceEncodingDirection input ({k, k-}) to afni.TShift. If this is k-, reverse the slice timing list before running the correction.

Does it make sense to also add i, j, i-, j-? Or does it make sense to always assume that slices have been acquired along the third axis?

What do you think?

[effigies]

I'll review, so I'd say full speed ahead. :-)

SliceTiming is passed to the slice_timing input, defined here:

nipype/nipype/interfaces/afni/preprocess.py

Lines 2615 to 2620 in 39675df

	slice_timing = traits.Either(
	File(exists=True),
	traits.List(traits.Float),
	desc='time offsets from the volume acquisition onset for each slice',
	argstr='-tpattern @%s',
	xor=['tpattern'])

I would start with {k, k-} as you suggest, as that will cover the majority of the cases, and we can think about i and j in a separate PR.