========================
Connectomics Lab Toolkit
========================
.. image:: https://img.shields.io/pypi/v/clabtoolkit.svg
:target: https://pypi.python.org/pypi/clabtoolkit
.. image:: https://github.com/connectomicslab/clabtoolkit/actions/workflows/ci.yml/badge.svg
:target: https://github.com/connectomicslab/clabtoolkit/actions/workflows/ci.yml
.. image:: https://readthedocs.org/projects/clabtoolkit/badge/?version=latest
:target: https://clabtoolkit.readthedocs.io/en/latest/?version=latest
:alt: Documentation Status
.. image:: https://img.shields.io/pypi/pyversions/clabtoolkit.svg
:target: https://pypi.python.org/pypi/clabtoolkit
.. image:: https://codecov.io/gh/connectomicslab/clabtoolkit/branch/main/graph/badge.svg
:target: https://codecov.io/gh/connectomicslab/clabtoolkit
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+
Installation
------------
Install from PyPI::
pip install clabtoolkit
For development installation::
git clone https://github.com/connectomicslab/clabtoolkit.git
cd clabtoolkit
pip install -e .[dev]
Features
--------
**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
Quick Start
-----------
.. code-block:: python
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")
Contributing
------------
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.
1. Fork the repository
2. Create your feature branch (``git checkout -b feature/amazing-feature``)
3. Commit your changes (``git commit -m 'Add some amazing feature'``)
4. Push to the branch (``git push origin feature/amazing-feature``)
5. Open a Pull Request
Testing
-------
Run tests with::
pytest
Run tests with coverage::
pytest --cov=clabtoolkit
Changelog
---------
See `HISTORY.rst <HISTORY.rst>`_ for a detailed changelog.
Credits
-------
This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
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"description": "========================\nConnectomics Lab Toolkit\n========================\n\n\n.. image:: https://img.shields.io/pypi/v/clabtoolkit.svg\n :target: https://pypi.python.org/pypi/clabtoolkit\n\n.. image:: https://github.com/connectomicslab/clabtoolkit/actions/workflows/ci.yml/badge.svg\n :target: https://github.com/connectomicslab/clabtoolkit/actions/workflows/ci.yml\n\n.. image:: https://readthedocs.org/projects/clabtoolkit/badge/?version=latest\n :target: https://clabtoolkit.readthedocs.io/en/latest/?version=latest\n :alt: Documentation Status\n\n.. image:: https://img.shields.io/pypi/pyversions/clabtoolkit.svg\n :target: https://pypi.python.org/pypi/clabtoolkit\n\n.. image:: https://codecov.io/gh/connectomicslab/clabtoolkit/branch/main/graph/badge.svg\n :target: https://codecov.io/gh/connectomicslab/clabtoolkit\n\n\nA comprehensive Python toolkit for neuroimaging data processing and analysis, specifically designed for working with brain connectivity data, BIDS datasets, and various neuroimaging formats.\n\n* **Free software**: Apache Software License 2.0\n* **Documentation**: https://clabtoolkit.readthedocs.io\n* **Source Code**: https://github.com/connectomicslab/clabtoolkit\n* **Python versions**: 3.9+\n\nInstallation\n------------\n\nInstall from PyPI::\n\n pip install clabtoolkit\n\nFor development installation::\n\n git clone https://github.com/connectomicslab/clabtoolkit.git\n cd clabtoolkit\n pip install -e .[dev]\n\nFeatures\n--------\n\n**BIDS Tools** (``clabtoolkit.bidstools``)\n * BIDS dataset validation and manipulation\n * Entity extraction from BIDS filenames\n * Conversion between BIDS formats\n * Metadata handling for neuroimaging datasets\n\n**Connectivity Tools** (``clabtoolkit.connectivitytools``)\n * Brain connectivity matrix analysis\n * Network-based statistics\n * Graph theory metrics computation\n * Connectivity visualization utilities\n\n**FreeSurfer Tools** (``clabtoolkit.freesurfertools``)\n * FreeSurfer output parsing and processing\n * Surface-based analysis utilities\n * Cortical thickness and morphometry tools\n * Integration with FreeSurfer workflows\n\n**Image Processing Tools** (``clabtoolkit.imagetools``)\n * Neuroimaging data I/O operations\n * Image registration and transformation\n * Quality control and preprocessing utilities\n * Multi-modal image processing\n\n**Parcellation Tools** (``clabtoolkit.parcellationtools``)\n * Brain parcellation scheme handling\n * Region-of-interest (ROI) extraction\n * Atlas-based analysis tools\n * Custom parcellation creation\n\n**Surface Tools** (``clabtoolkit.surfacetools``)\n * Surface mesh processing and analysis\n * Cortical surface manipulation\n * Surface-based statistics\n * Visualization of surface data\n\n**DWI Tools** (``clabtoolkit.dwitools``)\n * Diffusion-weighted imaging analysis\n * Tractography processing utilities\n * DTI and advanced diffusion modeling\n * White matter analysis tools\n\n**Quality Control Tools** (``clabtoolkit.qcqatools``)\n * Automated quality assessment\n * Image artifact detection\n * Quality metrics computation\n * Reporting and visualization\n\n**Visualization Tools** (``clabtoolkit.visualizationtools``)\n * Brain visualization utilities\n * Interactive plotting capabilities\n * Publication-ready figures\n * Multi-modal data visualization\n\nQuick Start\n-----------\n\n.. code-block:: python\n\n import clabtoolkit.bidstools as bids\n import clabtoolkit.connectivitytools as conn\n \n # Load BIDS configuration\n config = bids.load_bids_json()\n \n # Extract entities from BIDS filename\n entities = bids.str2entity(\"sub-01_ses-M00_T1w.nii.gz\")\n print(entities) # {'sub': '01', 'ses': 'M00', 'suffix': 'T1w', 'extension': 'nii.gz'}\n \n # Process connectivity data\n # conn_matrix = conn.load_connectivity_matrix(\"path/to/connectivity.mat\")\n\nContributing\n------------\n\nContributions 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.\n\n1. Fork the repository\n2. Create your feature branch (``git checkout -b feature/amazing-feature``)\n3. Commit your changes (``git commit -m 'Add some amazing feature'``)\n4. Push to the branch (``git push origin feature/amazing-feature``)\n5. Open a Pull Request\n\nTesting\n-------\n\nRun tests with::\n\n pytest\n\nRun tests with coverage::\n\n pytest --cov=clabtoolkit\n\nChangelog\n---------\n\nSee `HISTORY.rst <HISTORY.rst>`_ for a detailed changelog.\n\nCredits\n-------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n",
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