[DOC] Add Optic tract example#143
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Pull request overview
This PR adds documentation and functionality for tracking the optic tract and posterior optic nerve in pyAFQ. The example demonstrates how to customize pyAFQ for tracking relatively small bundles using custom ROIs, specialized tractography parameters, and custom PVE maps.
Changes:
- Added a comprehensive example script showing optic tract tracking workflow
- Modified multi-axial model to apply brain mask to predictions
- Enhanced template loading to support tractography (.trk) files
- Added new optic tract/nerve template fetching and loading functions
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 4 comments.
| File | Description |
|---|---|
| examples/howto_examples/optic_tract.py | New example demonstrating optic tract tracking with custom parameters and PVE maps |
| AFQ/tasks/structural.py | Updated mx_model to mask predictions and accept unmasked T1 input |
| AFQ/data/fetch.py | Added support for .trk files in template loading and new optic tract template fetchers |
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@arokem this is ready for review/merge |
arokem
reviewed
Jan 15, 2026
Co-authored-by: Ariel Rokem <arokem@gmail.com>
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