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Release Notes

0.1.2 [2025-06-10]

Enhancements:

  • Added brain lobe labels documentation file with detailed region mappings
  • Added classification metadata to manifest.json for function, modality, organ, species, and therapeutic area
  • Added input file type validation requiring nifti format
  • Added requirements-dev.txt to Docker build context via .dockerignore

Fixes:

  • Fixed multiprocessing configuration by setting threads to 1 to resolve std::bad_alloc errors
  • Removed unused variable combined_subcortical_indices in fw_gear_brain_lobe_segmentation/utils.py:200

Maintenance:

  • Migrated CI configuration from sse-qa-ci to qa-ci project with updated reference and file paths
  • Updated CI to use .gitlab-runner-large runner with 3h timeout for test:gear job
  • Updated .pre-commit-config.yaml hooks to sse reference and reorganized hook execution order
  • Switched to ruff_format and simplified ruff hook arguments to use pyproject.toml configuration
  • Updated Dockerfile build stages to use uppercase AS syntax for stage naming
  • Added dev layer to Dockerfile for pytest dependencies
  • Removed reprozip dependency from pyproject.toml
  • Improved manifest descriptions with proper punctuation
  • Swapped source and url fields in manifest.json to correct their purposes
  • Added PYTHON_SHA256 environment variable to manifest.json
  • Added tests/__init__.py file
  • Reorganized import statements across test files for consistency
  • Reduced nested context managers in tests/test_utils.py:204

Documentation:

  • Fixed broken hyperlink formatting in CONTRIBUTING.md:50
  • Removed trailing whitespace in CONTRIBUTING.md:76
  • Added reference to brain lobe labels documentation in README.md

0.1.1 [2023-12-13]

Maintenance:

  • Updated Docker image name from flywheel/fw-brain-lobe-segmentation to flywheel/brain-lobe-segmentation

0.1.0 [2023-12-13]

Enhancements:

  • Added brain lobe segmentation functionality using FreeSurfer SynthSeg for segmenting brain MRI images into cortical lobes
  • Added support for including white matter in lobe segmentation using nearest neighbor approach
  • Added optional output of individual mask files for each brain lobe (frontal, parietal, temporal, occipital)
  • Added volume computation for segmented brain regions with CSV output
  • Added QC validation to ensure segmentation quality meets threshold requirements
  • Added ability to output original SynthSeg parcellation alongside lobe segmentation
  • Added resampling to match original image resolution after processing
  • Added automatic upload of segmentation results to Flywheel parent container

Documentation:

  • Added comprehensive README with usage instructions, workflow diagrams, and gear configuration details
  • Added CONTRIBUTING guide with development setup, dependency management, and testing instructions
  • Added citations for FreeSurfer and SynthSeg publications

Maintenance:

  • Added CI/CD pipeline configuration with pre-commit hooks for code quality
  • Added Apache 2.0 license
  • Added project structure with pyproject.toml for dependency management
  • Added test suite with coverage for main functionality, parser, and utility functions
  • Added Docker multi-stage build to optimize image size by extracting only required FreeSurfer components
  • Added python 3.10 runtime environment with required dependencies (nibabel, numpy, scipy, nilearn, pandas, pyyaml)