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FIX: Check for valid qform before calculating change #466

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merged 2 commits into from Feb 27, 2020

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effigies
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@effigies effigies commented Feb 26, 2020

This is a follow-up to #365. We were running into the case where valid_qform was False, and thus qform was an unbound variable, but trying to compare the new qform to the old qform.

This bug was introduced in 92e63fe, first released in 0.10.3. As this was included in fMRIPrep as of nipreps/fmriprep@b6d1e51, this bug is expected to affect versions 1.5.0-20.0.0 of fMRIPrep.

Fixes #465.

@effigies effigies added this to the 1.1.8 milestone Feb 26, 2020
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@pull-assistant pull-assistant bot commented Feb 26, 2020

Score: 1.00

Best reviewed: commit by commit


Optimal code review plan

     FIX: Check for valid qform before calculating change

     TEST: Test bad qform and no good affines

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@pep8speaks pep8speaks commented Feb 26, 2020

Hello @effigies, Thank you for updating!

Cheers! There are no style issues detected in this Pull Request. 🍻 To test for issues locally, pip install flake8 and then run flake8 niworkflows.

Comment last updated at 2020-02-26 17:35:11 UTC

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@effigies effigies commented Feb 26, 2020

Hard one to test. I don't know how to create a file that doesn't have a valid qform. I've asked the submitter to send me their header, and maybe we can do something there.

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@effigies effigies commented Feb 26, 2020

Now have full coverage of this interface. See https://codecov.io/gh/poldracklab/niworkflows/pull/466/src/niworkflows/interfaces/images.py?before=niworkflows/interfaces/images.py

This is ready for a review.

@effigies effigies changed the base branch from master to maint/1.1.x Feb 26, 2020
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@oesteban oesteban left a comment

Looks great!

@effigies effigies merged commit 6794a8b into nipreps:maint/1.1.x Feb 27, 2020
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effigies added a commit to nipreps/fmriprep that referenced this issue Feb 27, 2020
20.0.1 (February 27, 2020)

Bug-fix release in 20.0.x series.

This release includes fixes for rare images with invalid qform matrices and some minor
improvements in report readability and inclusion of common templates in the Docker image.

  * FIX: Handle qforms with invalid quaternions (nipreps/niworkflows#466)
  * FIX: update niworkflows location (#2005)
  * ENH: Display errors as summary/details elements in reports (nipreps/niworkflows#464)
  * DOC: Add ``--fs-subjects-dir`` usage to slurm example (#2003)
  * CI: Test that Docker image can run a common set of output spaces without network access (#1997)
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3 participants