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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: Port bbregister T1-to-dwi registration from fmriprep #125

Closed slimnsour closed 3 years ago

slimnsour commented 3 years ago

Hello, this is to address #115 by adding bbregister to dmriprep. As you can see there is a little more work to be done because I wanted feedback on some things. Specifically:

  1. Is there a best place I should put this workflow in? Ex. dmriprep/workflows/dwi/base.py or dmriprep/workflows/dwi/registration.py?
  2. How should I import init_bbreg_wf in this case? I would have just imported init_bbreg_wf from fmriprep but fmriprep is not part of the packages installed in dmriprep. What is the suggested practice here?

Let me know of any feedback and I'll get to them.

welcome[bot] commented 3 years ago

Thanks for opening this pull request! We have detected this is the first time for you to contribute to dMRIPrep. Please check out our contributing guidelines. We invite you to list yourself as a dMRIPrep contributor, so if your name is not already mentioned, please modify the .zenodo.json file and insert your data last in the contributors list. Example:

{
   "name": "Contributor, New dMRIPrep",
   "affiliation": "Department of dMRI prep'ing, Open Science Made-Up University",
   "orcid": "<your id>",
   "type": "Researcher"
}

Of course, if you want to opt-out this time there is no problem at all with adding your name later. You will be always welcome to add it in the future whenever you feel it should be listed.

pep8speaks commented 3 years ago

Hello @slimnsour, 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 2020-12-04 17:26:32 UTC
oesteban commented 3 years ago

@slimnsour please add your info to https://github.com/nipreps/dmriprep/blob/70028695186b5f4822a9328755c7f6791108c40a/.maint/developers.json#L17-L29

(it is ordered alphabetically by lastname)

oesteban commented 3 years ago

Shoot, I've overwritten your changes - assumed I was changing history (and I shouldn't have).

Can you add the lines here as a comment? @slimnsour

slimnsour commented 3 years ago

No worries, here it is.

{
    "affiliation": "The Centre for Addiction and Mental Health",
    "name": "Mansour, Salim",
    "orcid": "0000-0002-1092-1650"
},
oesteban commented 3 years ago

Works locally. I'm going to merge. Thanks for this great work @slimnsour and sorry for my slow response all the time.