A PyQt6-based neuroimaging application for localizing implanted electrodes in epilepsy patients. CiCLONE provides automated CT/MRI processing pipelines using FSL and FreeSurfer, with an intuitive graphical interface for electrode marking and coordinate transformation.
- User-Friendly GUI - Intuitive interface for subject management and image processing
- Automated Pipelines - CT and MRI-based workflows for electrode localization
- Image Import - Automatic cropping and registration of medical images
- Built-in Image Viewer - Multi-planar visualization with electrode marking tools
- MNI Transformation - Convert electrode coordinates to standard MNI space
- Python: 3.10, 3.11, 3.12, or 3.13
- Poetry: Package manager (install via
pipx install poetry) - FSL: Medical image analysis toolkit
- FreeSurfer: (optional) For cortical reconstruction
# Clone the repository
git clone <repository-url>
cd CiCLONE
# Create virtual environment with Poetry
poetry env use $(pyenv which python3.12) # or any Python 3.10-3.13
# Install dependencies
poetry installSet up the required environment variables before running CiCLONE:
export FSLDIR=/path/to/fsl
export FREESURFER_HOME=/path/to/freesurfer # optionalLaunch CiCLONE:
poetry run cicloneThe application provides:
- Subject creation and file import
- Interactive pipeline execution
- Built-in image viewer with electrode marking
- Real-time processing feedback
For detailed usage instructions, see the User Guide.
- User Guide - Complete guide for using CiCLONE's GUI and features
- Architecture Documentation - Technical architecture and design patterns
- Developer Guide - Development setup and contribution guidelines
This project has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number 23.00638, as part of the Horizon Europe project "EBRAINS 2.0".