Fixing human atlas script

[viktorpm]

Description

What is this PR?

• Bug fix
• Addition of a new feature
• Other

What does this PR do?

• Fixes humanatlas.py atlas generation script.
• Automates the annotation and reference downloading steps.
• Fixes validate_atlases.py additional_references error #275

How has this PR been tested?

• locally
• on the HPC
• the regenerated atlas was validated

Is this a breaking change?

no

Does this PR require an update to the documentation?

no

Checklist:

• The code has been tested locally
• Tests have been added to cover all new functionality (unit & integration)
• The documentation has been updated to reflect any changes
• The code has been formatted with pre-commit

[viktorpm]

Meshes and image extent don't match. It needs to be fixed.

[viktorpm]

scaling is fixed

[alessandrofelder]

As discussed in person

• it looks like we ignore the nifti header, and the raw array data is oriented in rpi
• we should run again with this, and add this info the header
• it would be useful to provide the whole brain in the script (not just one of the hemispheres)

annotations both hemisphere link: http://download.alleninstitute.org/informatics-archive/allen_human_reference_atlas_3d_2020/version_1/annotation_full.nii.gz

[alessandrofelder]

Looks good. Also sanity check of the packaged atlas looks good. I'll let you upload to GIN and merge this when it's done @viktorpm . Thank you 🎉

[adamltyson]

Thanks @viktorpm!