DICOMinator is an open-source Python script for sorting images from common 4D Flow pulse sequences.

• 📂 Recursively traverses the input directory to find all DICOM files.
• 📂 Sorts the DICOM files into a specified output directory based on encoding direction.
• 💾 Provides options to save the sorted data in various formats:
  • 📦 NIfTI: The NIfTI files are split along the time dimension, allowing them to be imported as a Sequence (or MultiVolume) in 3D Slicer.
  • 📦 h5: The h5 format should be compatible with Edward Ferdian's 4DFlowNet.
  • 📦 mat: The mat format should be compatible with Julio Sotelo's 4D-Flow-Matlab-Toolbox.

1. Clone the repository:

   git clone https://github.com/fyrdahl/dicominator.git
   cd dicominator

2. Install the required dependencies:

   pip install -r requirements.txt

• Python 3.6 or higher
• Required Python libraries (listed in requirements.txt)

• input_root: The root folder where DICOMs are stored.
• output_root: The root folder where DICOMs will be stored (will be created if it does not exist).
• -d, --desc: Optional 'SeriesDescription' to search for.
• -p, --purge: Purge the output folder before processing.
• --nii: Save as NIfTI.
• --h5: Save as h5.
• --mat: Save as mat.
• -l, --list: List all unique Series Descriptions in the dataset without further processing.
• -f, --force: Force process files thay may or may not be flow datasets.

python dicominator.py /path/to/input /path/to/output --desc "4D Flow" --nii --h5 --mat

For support, please contact [email protected] or open an issue.

• Edward Ferdian for 4DFlowNet
• Julio Sotelo for 4D-Flow-Matlab-Toolbox
• Pia Callmer for contributing code

Contributions are welcome! Is your 4D Flow sequence not supported? Please feel free to open an issue or submit a pull request.

This project uses Ruff for code formatting.

This project is licensed under the MIT License.