Skip to content

CHANGELOG.md

Latest commit

 

History

History
103 lines (82 loc) · 3.93 KB

CHANGELOG.md

File metadata and controls

103 lines (82 loc) · 3.93 KB

Changelog

All notable changes to the CAT12 BIDS Pipeline project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.0.0] - 2025-10-09

Added

  • Core Pipeline Features

    • BIDS-compatible longitudinal neuroimaging data processing using CAT12 standalone
    • Automated identification of longitudinal and cross-sectional subjects
    • Pilot/cross-sectional and full longitudinal processing modes
    • Session validation and robust error handling
    • Parallel processing with auto-calculation of jobs based on available RAM
    • Background processing mode with nohup support

  • CLI Interface

    • Comprehensive Click-based command-line interface
    • Support for participant filtering and session selection
    • Options for preprocessing, smoothing, and quality assessment
    • Customizable configuration via YAML files
    • Dry-run mode for validation before execution

  • Processing Components

    • Automatic CAT12 MATLAB script generation for longitudinal analysis
    • Surface and volume processing with configurable smoothing kernels
    • Quality assessment with NCR and IQR metrics extraction
    • TIV estimation and ROI value extraction (placeholder)
    • Real-time progress monitoring with TQDM

  • Reproducibility & Documentation

    • Automated boilerplate generation for publication methods sections
    • Comprehensive HTML and Markdown boilerplate with processing details
    • Log parsing and software version tracking
    • BIDS derivatives output with dataset_description.json

  • Environment Management

    • UV-based virtual environment setup
    • Reproducible dependency management
    • Environment activation scripts for CAT12 and Python
    • No global package installation (isolated environments)

  • Utilities & Validation

    • BIDS dataset validation with bids-validator integration
    • Session management and longitudinal data identification
    • Robust error handling with detailed logging
    • File existence checks and output organization

Code Quality

  • All critical linting issues resolved (unused imports, variables, f-strings)
  • Blank line and whitespace consistency enforced
  • Block comment formatting standardized
  • Flake8 configuration for consistent code style (120 char line length)
  • Comprehensive type hints and docstrings

Documentation

  • README with installation, usage, and examples
  • Quick start guide for common workflows
  • BIDS App usage documentation
  • CAT12 commands reference
  • Project summary and architecture overview
  • Instruction files for repository standards

Configuration

  • Default processing configuration with sensible defaults
  • Support for custom YAML configuration files
  • Environment variables for CAT12 paths and settings
  • Configurable parallelization and resource limits

Dependencies

  • Python 3.8+ support
  • Core: nibabel, pybids, pandas, numpy, pyyaml, click, tqdm, colorlog, psutil
  • Dev: black, flake8, pytest, mypy
  • CAT12 standalone (external dependency)

Known Limitations

  • CAT12 standalone must be installed separately
  • Linux-only support (CAT12 standalone limitation)
  • MATLAB Runtime (MCR) required for CAT12 execution

[Unreleased]

Added

  • OpenNeuro input support for preprocessing via --openneuro (downloads public datasets, then runs CAT12).
  • End-to-end OpenNeuro demo launcher ./run_demo_openneuro_ds003138.sh (download + preprocessing + stats).

Changed

  • Documentation and CLI help examples for --participant-label / --session-label now use repeated flags (Click multiple=True).

Planned Features

  • Extended quality assessment metrics
  • Additional smoothing options for surfaces
  • ROI extraction implementation
  • More comprehensive test suite
  • Docker/Singularity container support

Note: This is the first official release of the CAT12 BIDS Pipeline. For installation instructions and usage examples, see the README.md.