Reinvent dmriprep?

[dPys]

Okay everybody ( @akeshavan, @richford, @arokem, @josephmje, @nrajamani3 )

I've overhauled nearly everything. Feel free to accept whatever elements of this PR that you deem useful and agreeable. I'm very flexible about how we go about this from here.

*Stripped of everything freesurfer (at least for now since it was weighing down the package and is not necessary for dmri preprocessing).
*BIDS bindings still need to be updated (I'm working off of a homemade API-- get_bids_layout)
*metadata from raw .json's are used to automatically generate any arbitrary configuration of acqparameters and index.txt files
*Eddy options have been extended, and no need for a second workflow for non-reverse phase encoded acquisitions. The present workflow works for single phase-encodings as well.
*Regarding qc, dwi (and corresponding bvecs) are forced to RAS+ and isotropic voxels (either 1mm or 2mm) using a slightly more robust set of routine that I've also been implementing in PyNets and NDMG.
*Order of operations has changed-- use ART to remove gross motion artifact first, then run topup/eddy, then remove outliers detected from the susceptibility correction
*I'm working on an API for handling multishell data. Shouldn't take too much longer.
*added gibbs noise ringing and denoising routines (various strategies available) to the end of the workflow.
*Still need to connect to the viewer @akeshavan , and to the eddy qc report. save_json/load_json from nipype were giving me issues -- most likely a version issue -- so I commented out for now.

Please let me know if you have any thoughts, questions, critiques, etc. and I'll respond when I can.

@dPys

[pep8speaks]

Hello @dPys! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file dmriprep/cli.py:

Line 30:80: E501 line too long (99 > 79 characters)
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• In the file dmriprep/core.py:

Line 15:80: E501 line too long (88 > 79 characters)
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Line 81:53: E712 comparison to True should be 'if cond is True:' or 'if cond:'
Line 88:80: E501 line too long (85 > 79 characters)
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• In the file dmriprep/interfaces.py:

Line 13:80: E501 line too long (83 > 79 characters)
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Line 112:80: E501 line too long (88 > 79 characters)

• In the file dmriprep/io.py:

Line 12:80: E501 line too long (116 > 79 characters)
Line 13:80: E501 line too long (85 > 79 characters)
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• In the file dmriprep/qc.py:

Line 230:80: E501 line too long (92 > 79 characters)
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Line 386:80: E501 line too long (81 > 79 characters)

• In the file dmriprep/run.py:

Line 97:80: E501 line too long (84 > 79 characters)
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Line 320:80: E501 line too long (98 > 79 characters)
Line 321:80: E501 line too long (81 > 79 characters)
Line 322:80: E501 line too long (94 > 79 characters)
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Line 379:80: E501 line too long (108 > 79 characters)
Line 380:80: E501 line too long (86 > 79 characters)
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Line 419:5: E722 do not use bare 'except'

Comment last updated at 2019-09-08 07:57:18 UTC

[dPys]

And if anyone wishes to experiment, a quick and dirty run can be accomplished as follows:

from dmriprep.run import init_single_subject_wf
from dmriprep.io import get_bids_layout

bdir = '/Users/derekpisner/Downloads/HNU1'
sub='0025427'
ses=1
out_dir = '/Users/derekpisner/Downloads/HNU1_output'
sub_dict = get_bids_layout(bdir, sub, ses)
dwi = sub_dict[ses]['dwi']
fbvec = sub_dict[ses]['bvec']
fbval = sub_dict[ses]['bval']
metadata = sub_dict[ses]['metadata']

wf = init_single_subject_wf(sub, ses, dwi, fbval, fbvec, metadata, out_dir)

out = wf.run()

[josephmje]

Hi @dPys . Thanks for this! dmriprep is actually being moved to nipreps. I've made a PR for some of my dwi workflow changes. Do you want to connect your changes to my fork? Or wait till I'm done?

[dPys]

Hi @josephmje , I might just make a direct PR there then, but will sync to your changes as applicable. Thanks for the heads up!