Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ENH: Upgrade SDCFlows to new API (1.0.0rc1) #1886

Merged
merged 3 commits into from
Dec 3, 2019

Conversation

oesteban
Copy link
Member

Closes #1884.

Changes proposed in this pull request

Documentation that should be reviewed

@auto-comment
Copy link

auto-comment bot commented Nov 26, 2019

Thank your for raising your pull request.

Some of the fMRIPRep maintainers will review your changes as soon as time permits.
I'm attaching below a Review Checklist for the reviewers, to copy and paste
it in their review comment.

## 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
  - [ ] This PR addresses an error in existing documentation.
- [ ] 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.

#### Dependencies: sdcflows

- [ ] This PR does not require any update on `sdcflows`; or
- [ ] `sdcflows` has correctly been pinned.

#### Dependencies: Nipype

- [ ] This PR does not require any update on `nipype`; or
- [ ] `nipype` has correctly been pinned.

#### Dependencies: other

- [ ] This PR does not require any update on other dependencies; or
- [ ] other dependencies have correctly been pinned.

#### 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)

@oesteban oesteban force-pushed the rf/new-sdcflows-api branch 2 times, most recently from 5f01a9a to b21a93e Compare November 27, 2019 07:09
@oesteban oesteban requested review from effigies and mgxd November 27, 2019 17:11
@oesteban
Copy link
Member Author

Please note the new condensed view for phase1/2-phasediff-fieldmap kind of fieldmaps (ds054). This PR merges together the magnitude segmentation view, the magnitude registration view and the fieldmap registration view (hopefully you like the new one better).

I think we still need to add a colorbar in Hz to the fieldmap overlay, and make it symmetric bc right now it is a bit confusing. But overall I believe it is much better.

@oesteban
Copy link
Member Author

Another focus point (esp. for @effigies) is nipreps/sdcflows#63, which is necessary for this PR to work.

@oesteban
Copy link
Member Author

Last comment - this PR should be then followed by addressing #1892, ensuring we add MNI152NLin2009cAsym to the standard spaces list if SyN is to run.

@oesteban
Copy link
Member Author

Should also fix #1665.

@kimsin98
Copy link

kimsin98 commented Nov 29, 2019

The actual fieldmaps are fine, but the fieldmap report figures have these values spilling over the y-axis.

yspill

Actually, probably an issue on sdcflows.

@oesteban
Copy link
Member Author

oesteban commented Dec 2, 2019

That extrapolation is added by FUGUE. I agree we should open an issue in SDCFlows about it, to double-check that the extrapolation is done once the fieldmap has been mapped into the target EPI.

The alternative to this, once again, is implementing nipreps/sdcflows#14 so that extrapolation is less of a blanket across the PE-axis solution.

@effigies
Copy link
Member

effigies commented Dec 2, 2019

Sorry, missed this in a flood of notifications... I'll review now.

Copy link
Member

@effigies effigies left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This looks reasonable. I assume you've figured out why the builds are failing?

setup.cfg Show resolved Hide resolved
…0][skip tests]

We need to start looking into intersphinx and how we are going to
coordinate fMRIPrep's documentation and helper packages' documentation.
@oesteban oesteban force-pushed the rf/new-sdcflows-api branch from 434c947 to 9f14aba Compare December 2, 2019 22:21
@oesteban
Copy link
Member Author

oesteban commented Dec 2, 2019

Okay, updated the pin to a released version since the patch is already in SDCFlows/master. That was breaking builds.

@oesteban oesteban merged commit 0fa8ef1 into nipreps:master Dec 3, 2019
@oesteban oesteban deleted the rf/new-sdcflows-api branch December 3, 2019 00:16
oesteban added a commit to oesteban/fmriprep that referenced this pull request Dec 5, 2019
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

PIN: SDCFlows 1.0.0rc1 / compatibility with refactored API
3 participants