ENH: Add Hammers atlas support with license consent gate

[mnoergaard]

Summary

Add support for the Hammers adult brain atlas as an atlas-based segmentation option in PETPrep, preferably using tpl-MNI152NLin2009cAsym through TemplateFlow.

Relevant source pages:

• Hammers / brain atlases overview: https://brain-development.org/brain-atlases/
• Individual adult brain atlases terms page: https://brain-development.org/brain-atlases/adult-brain-atlases/individual-adult-brain-atlases-new/

Proposed work

1. Convert the Hammers atlas data from the brain-development.org distribution to a BIDS-compatible atlas layout.
2. Register/transform the Hammers atlas into a TemplateFlow template space, ideally tpl-MNI152NLin2009cAsym at res-01, preserving integer labels with nearest-neighbor interpolation.
3. Add the converted atlas image, label table, metadata/provenance, citation, and license/terms information to the appropriate TemplateFlow/template data location if redistribution is allowed.
4. Add a PETPrep atlas config entry, likely in petprep/data/segmentation/atlases.json, so users can select the atlas with --seg Hammers or another agreed atlas name.
5. Integrate the query through the existing TemplateFlow-backed atlas machinery in petprep/utils/atlas.py and petprep/workflows/pet/segmentation.py.
6. Document the new option in docs/usage.rst, including the atlas source, citation, labels, and license/terms requirements.

License / terms consent requirement

The Hammers atlas terms require explicit user acceptance before use. PETPrep should not silently run the Hammers workflow or pre-cache/distribute restricted files unless the redistribution and downstream use terms clearly permit it.

Suggested implementation:

• Add an explicit non-interactive opt-in, for example --accept-hammers-atlas-terms and/or PETPREP_ACCEPT_HAMMERS_ATLAS_TERMS=1.
• If --seg Hammers is requested and consent has not been provided, fail early with a clear error that links to the terms page.
• Optionally, when PETPrep is run interactively with a TTY, ask the user to answer yes/no after showing the terms URL. In non-interactive runs, require the explicit flag/env var.
• Record the consent state and terms URL in the run configuration/logs for provenance.
• If the terms do not permit redistribution in TemplateFlow or Docker images, avoid adding the data to PETPrep images and instead support consent-gated download or user-provided local paths.

This pattern would be more robust than relying only on an interactive prompt, because PETPrep is often run in Docker, Apptainer/Singularity, and cluster/batch environments where prompts can hang jobs.

Acceptance criteria

• Hammers atlas is available as a documented PETPrep segmentation option.
• Atlas image and labels are BIDS/TemplateFlow compatible and validated.
• The atlas is transformed into anatomical space through the existing atlas workflow.
• PETPrep refuses to execute the Hammers atlas workflow unless the user has explicitly accepted the atlas terms.
• Documentation includes source links, terms/license information, citation guidance, and an example command.
• Tests cover atlas config/query behavior and the consent-gating behavior.

Open questions

• What exact PETPrep option name should be used: Hammers, Hammers95, or another BIDS/TemplateFlow-friendly atlas identifier?
• Are the Hammers terms compatible with redistributing the transformed atlas through TemplateFlow and/or PETPrep Docker images?
• Should consent apply only when downloading/using the atlas, or also when pre-cached TemplateFlow data already exists locally?
• Which Hammers atlas variant/files from brain-development.org should be considered canonical for PETPrep?