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Add --skip-brain-extraction flag #1829
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Thank your for raising your pull request. Some of the fMRIPRep maintainers will review your changes as soon as time permits. ## PR Review
*Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide*
- [ ] As the reviewer I confirm that there are no conflicts of interest for me to review this work.
Please check what applies in the following aspects of the PR:
#### Code documentation
- [ ] New functions and modules are documented following the guidelines.
- [ ] Existing code required amendments in documentation and has been updated.
- [ ] Sufficient inline comments ensure readability by other contributors in the long term.
#### Documentation site
- [ ] The modifications to *fMRIPrep* in this PR **do not require extra documentation**. This is a common situation when a bug fix that does not change the code base substantially is submitted.
- [ ] This PR requires documentation. The corresponding documentation will be submitted as an additional PR in the future.
- [ ] This PR requires extra documentation, and will be included within this PR. Please check the boxes that apply best:
- [ ] An existing feature is substantially modified, changing the interface and/or logic of a module.
- [ ] A new feature is being added, therefore full documentation of it will be included
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- [ ] Yes, all expected sections of documentation were generated by the CI build, and look as expected
#### Tests
- [ ] The new functionalities in this PR are covered by the existing tests
- [ ] New test batteries have been included with this PR
#### Data
- [ ] This PR does not require any additional data to be uploaded to OSF.
- [ ] This PR requires additional data for tests.
#### Dependencies: smriprep
- [ ] This PR does not require any update on `smriprep`; or
- [ ] `smriprep` has correctly been pinned.
#### Dependencies: niworkflows
- [ ] This PR does not require any update on `niworkflows`; or
- [ ] `niworkflows` has correctly been pinned.
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- [ ] This PR does not require any update on `sdcflows`; or
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#### Dependencies: Nipype
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- [ ] `nipype` has correctly been pinned.
#### Dependencies: other
- [ ] This PR does not require any update on other dependencies; or
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#### Reports generated within CI tests
- [ ] Yes, I have checked the reports of ds005 and they are not modified or the changes are as expected
- [ ] Yes, I have checked the reports of ds054 and they are not modified or the changes are as expected
- [ ] Yes, I have checked the reports of ds010 and they are not modified or the changes are as expected
### Review Comments (other than those left inline with the code)
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adelavega
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oesteban
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In particular, nipreps#167 introduces a few changes that need to be considered before nipreps#1829 is merged.
oesteban
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Mar 17, 2020
Please follow up conversations on #2039 |
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This PR depends on nipreps/smriprep#116
I also merged #1827 into this so I can test it.
Let me know if you rather implement brain extraction detection instead of a flag (or in addition, could change flag to
--force-skip-brain-extraction
I also added a fix for #1828 so I could test this