[ENH] Respect SliceEncodingDirection metadata

[fliem]

Changes proposed in this pull request

closes #1345
adds slice encoding direction to stc

depends on nipype PR#2753

Documentation that should be reviewed

Not sure...

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[fliem]

@effigies thanks for merging the nipype PR. I can't figure out how to get the newest nipype version into fmriprep. Via niworkflows?

[effigies]

Once the new nipype is released, we'll incorporate the fix here. We're waiting on one fix in nipype before release (scheduled for Monday anyway).

[effigies]

Although, you can pin to the latest nipype commit in requirements.txt, for testing purposes:

git+https://github.com/nipy/nipype.git@d83b06d7f8ddb76d4e1033c149eecc966eddb514#egg=nipype

[effigies]

If you update the nipype dependency to >=1.1.4, I think this should be nearly ready.

https://github.com/poldracklab/fmriprep/blob/92786d1456c4098197f6a61e46fde7275f891777/fmriprep/__about__.py#L87-L108

[fliem]

Thanks. I am still running some tests. I'll get back to you when they are done.

[effigies]

Maybe we could be as clear (and not hit line length limits) by just adding slice_encoding_direction=metadata.get('SliceEncodingDirection', 'k') to the TShift() call.

[fliem]

OK. I have tested the previous version and this looks good

• same list order, different direction gives different results (as expected)
• flipped list, flipped direction gives same results (as expected)
• no direction vs "k" gives same results (as expected)

[effigies]

LGTM. I merged master in, as there've been some updates to the tests and CI config. If this tests clean, I'll merge right away.

[effigies]

Thanks!