157 bug bet deface masks are not saved #159
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Pull Request Overview
This PR adds functionality to save bet (brain extraction) and defacing masks to specified output paths, addressing the issue where these masks were not being persisted. The changes enable users to specify output paths for both bet and defacing masks in preprocessing workflows.
Key changes:
- Added bet_mask_output_path and defacing_mask_output_path parameters to CenterModality initialization
- Implemented mask saving functionality in extract_brain_region and deface methods
- Added proper type hints and default parameters for better code maintainability
Reviewed Changes
Copilot reviewed 8 out of 8 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| example/example_native_space_preprocessor.py | Added bet_mask_output_path and defacing_mask_output_path parameters to CenterModality initialization |
| example/example_atlas_centric_preprocessor.py | Added mask output paths and save_dir_transformations parameter |
| brainles_preprocessing/registration/registrator.py | Added default value for interpolator parameter |
| brainles_preprocessing/preprocessor/atlas_centric_preprocessor.py | Added null check for atlas_mask and improved logging |
| brainles_preprocessing/normalization/*.py | Added proper return type hints using NDArray |
| brainles_preprocessing/modality.py | Implemented mask saving functionality and improved type annotations |
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neuronflow
approved these changes
Sep 4, 2025
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