A comprehensive Python toolkit for neuroimaging data processing and analysis, specifically designed for working with brain connectivity data, BIDS datasets, and various neuroimaging formats.
- Free software: Apache Software License 2.0
- Documentation: https://clabtoolkit.readthedocs.io
- Source Code: https://github.com/connectomicslab/clabtoolkit
- Python versions: 3.9+
Install from PyPI:
pip install clabtoolkit
For development installation:
git clone https://github.com/connectomicslab/clabtoolkit.git cd clabtoolkit pip install -e .[dev]
- BIDS Tools (
clabtoolkit.bidstools) - BIDS dataset validation and manipulation
- Entity extraction from BIDS filenames
- Conversion between BIDS formats
- Metadata handling for neuroimaging datasets
- Connectivity Tools (
clabtoolkit.connectivitytools) - Brain connectivity matrix analysis
- Network-based statistics
- Graph theory metrics computation
- Connectivity visualization utilities
- FreeSurfer Tools (
clabtoolkit.freesurfertools) - FreeSurfer output parsing and processing
- Surface-based analysis utilities
- Cortical thickness and morphometry tools
- Integration with FreeSurfer workflows
- Image Processing Tools (
clabtoolkit.imagetools) - Neuroimaging data I/O operations
- Image registration and transformation
- Quality control and preprocessing utilities
- Multi-modal image processing
- Parcellation Tools (
clabtoolkit.parcellationtools) - Brain parcellation scheme handling
- Region-of-interest (ROI) extraction
- Atlas-based analysis tools
- Custom parcellation creation
- Surface Tools (
clabtoolkit.surfacetools) - Surface mesh processing and analysis
- Cortical surface manipulation
- Surface-based statistics
- Visualization of surface data
- DWI Tools (
clabtoolkit.dwitools) - Diffusion-weighted imaging analysis
- Tractography processing utilities
- DTI and advanced diffusion modeling
- White matter analysis tools
- Quality Control Tools (
clabtoolkit.qcqatools) - Automated quality assessment
- Image artifact detection
- Quality metrics computation
- Reporting and visualization
- Visualization Tools (
clabtoolkit.visualizationtools) - Brain visualization utilities
- Interactive plotting capabilities
- Publication-ready figures
- Multi-modal data visualization
import clabtoolkit.bidstools as bids
import clabtoolkit.connectivitytools as conn
# Load BIDS configuration
config = bids.load_bids_json()
# Extract entities from BIDS filename
entities = bids.str2entity("sub-01_ses-M00_T1w.nii.gz")
print(entities) # {'sub': '01', 'ses': 'M00', 'suffix': 'T1w', 'extension': 'nii.gz'}
# Process connectivity data
# conn_matrix = conn.load_connectivity_matrix("path/to/connectivity.mat")Contributions are welcome! Please feel free to submit a Pull Request. For major changes, please open an issue first to discuss what you would like to change.
- Fork the repository
- Create your feature branch (
git checkout -b feature/amazing-feature) - Commit your changes (
git commit -m 'Add some amazing feature') - Push to the branch (
git push origin feature/amazing-feature) - Open a Pull Request
Run tests with:
pytest
Run tests with coverage:
pytest --cov=clabtoolkit
See HISTORY.rst for a detailed changelog.
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.