[FIX] Enhance T2 contrast enhance_t2 in reference estimate

[effigies]

Changes proposed in this pull request

Pass enhance_t2 flag from init_bold_reference_wf to init_enhance_and_skullstrip_wf.

This parameter currently does nothing. It appears to have been an oversight in #966.

Documentation that should be reviewed

None.

[effigies]

@ZhifangYe Sorry for how slow things are going over at #1050. I'm wondering if I could trouble you to verify that this doesn't fix the initial mask as well as your PR does.

[effigies]

The masks look very trivially different in the regression tests: https://circleci.com/gh/poldracklab/fmriprep/5048#artifacts/containers/0

[zhifangy]

Sorry for the long radio silence. I’ve been quite busy the last few months.

I believe this change wouldn't fix the initial mask issue. I had applied the _enhance_t2_contrast function manually on my data and it yielded similar bad brain mask.

[zhifangy]

I think maybe we need a new perspective on #1050 since the current implementation gives inferior results on some legacy data.

Also, I found the N4 correction step fails on some of the distortion corrected BOLD image during processing my dataset. As a result, even my PR gives good brain mask for the original reference image, it fails to generate good final mask as output. I had to replace the entire init_enhance_and_skullstrip_wf workflow to a single Bet step when processing my dataset.

I'm not sure whether the problem come from N4BiasFieldCorrection or my specific data since I didn't find any useful information in ANTs discussion forum. @effigies I'm happy to provide an example data to further investigate this problem and spend more time on #1050.

[effigies]

Roping @oesteban into this conversation, since he's back from vacation and has spent a lot more time thinking about the problem than I have.

[oesteban]

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: niworkflows

• This PR does not require any update on niworkflows.
• niworkflows has correctly been pinned.

Dependencies: Nipype

• This PR does not require any update on nipype.
• nipype has correctly been pinned.

Dependencies: other

• This PR does not require any update on other dependencies.
• 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
• Yes, I have checked the reports generated by regression tests.

Review Comments (other than those left inline with the code)

The differences in the masks calculated after this PR are very minimal. Merging it in...