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nipreps / dmriprep

dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://www.nipreps.org/dmriprep
Apache License 2.0
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ENH: Use *NiWorkflows*' EPI-reference workflow #169

Closed oesteban closed 3 years ago

oesteban commented 3 years ago

Replaces our workflows under dmriprep.workflows.dwi.util.

josephmje commented 3 years ago

Thanks for this @oesteban! It looks like it should also fix the issues I had with some oblique datasets. Is the old init_enhance_and_skullstrip_dwi_wf also meant to be replaced with init_brainextraction_wf from sdcflows?

oesteban commented 3 years ago

Is the old init_enhance_and_skullstrip_dwi_wf also meant to be replaced with init_brainextraction_wf from sdcflows?

I think we should give it a try, at the very least.

oesteban commented 3 years ago

This looks good to me! It's going to fail because the eddy nodes are no longer corrected properly.

I'll fix the connections tomorrow (my time). No need to break master for this.

josephmje commented 3 years ago

I'll fix the connections tomorrow (my time). No need to break master for this.

Thanks @oesteban. I checked out the reference epi and I don't think it looks like its supposed to.

oesteban commented 3 years ago

ugh - I had fixed that already. I'll double-check that the pinned versions of sdcflows and niworkflows are being used.

josephmje commented 3 years ago

This is looking better. The JHU1 epiref still looks a little weird but I tested it locally and it was fine there. For the masking reportlet, we are currently showing the unwarped epiref and mask. But should we instead show the epiref and mask before unwarping? The warped mask would be the input to head motion correction.

pep8speaks commented 3 years ago

Hello @oesteban, Thank you for updating!

Cheers! There are no style issues detected in this Pull Request. :beers: To test for issues locally, pip install flake8 and then run flake8 dmriprep.

Comment last updated at 2021-05-18 21:35:00 UTC