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.
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Clone the repository:
git clone https://github.com/fyrdahl/dicominator.git cd dicominator -
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.--pcmra: Save PCMRA image in NIfTI format-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 --matFor support, please contact alexander.fyrdahl@ki.se 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.