Skip to content

Conversation

@rciric
Copy link
Contributor

@rciric rciric commented Apr 17, 2020

Changes proposed in this pull request

Future work should consider adding the option to flag outliers on the basis of RMS (Jenkinson) FD.

Documentation that should be reviewed

  • Brief descriptions have been added to the confounds documentation and to the boilerplate.

@auto-comment
Copy link

auto-comment bot commented Apr 17, 2020

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 check off during the
review.

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

@oesteban oesteban changed the title Add root mean square (RMS) framewise displacement following Jenkinson et al. (2002) ENH: Add RMS framewise displacement following Jenkinson et al. (2002) Apr 18, 2020
Copy link
Member

@oesteban oesteban left a comment

Choose a reason for hiding this comment

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

LGTM

Co-Authored-By: Oscar Esteban <code@oscaresteban.es>
Copy link
Member

@oesteban oesteban left a comment

Choose a reason for hiding this comment

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

A few new nitpicks

@oesteban oesteban linked an issue Apr 20, 2020 that may be closed by this pull request
4 tasks
@oesteban oesteban requested a review from mgxd April 20, 2020 17:03
@oesteban
Copy link
Member

@mgxd anything jumping out into your eye?

Copy link
Collaborator

@mgxd mgxd left a comment

Choose a reason for hiding this comment

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

LGTM

Co-Authored-By: Oscar Esteban <code@oscaresteban.es>
@oesteban oesteban merged commit d358ad9 into nipreps:master Apr 28, 2020
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.

Write FD calculated with fsl_motion_outliers to confounds file.

3 participants