FIX: orientation of visualisations when `species == "rat"`

nipreps / mriqc

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain

http://mriqc.readthedocs.io

Apache License 2.0

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FIX: orientation of visualisations when `species == "rat"` #1027

Closed eilidhmacnicol closed 1 year ago

eilidhmacnicol commented 2 years ago

Usually, rodent brains are viewed in the coronal orientation, as is the convention from physical atlases.

This updates the mosaic viz functions to change the orientation when species == rat: coronal becomes the primary axis (instead of axial), while axial becomes the secondary axis (instead of sagittal)

pep8speaks commented 2 years ago

Hello @eilidhmacnicol, Thank you for updating!

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

Comment last updated at 2022-08-29 16:17:15 UTC

eilidhmacnicol commented 2 years ago

Tested in docker container and seems to work nicely for example data (n = 1):

oesteban commented 1 year ago

Let's keep mriqc/workflows/{anatomical,functional}.py in this PR and move the other two files over to nireports. I've just done the porting of those two.