viettham1998 / 3d-nii-visualizer

A NIfTI (nii.gz) 3D Visualizer using VTK and Qt5

A NIfTI (nii.gz) 3D Visualizer using VTK and Qt5

Run with Python

1. Create a virtual environment. Mac can use virtualenv or conda. Windows must use conda.
2. Install the dependencies (PyQt5, vtk, and sip) pip install PyQt5 vtk
3. Start the program python ./visualizer/brain_tumor_3d.py -i "./sample_data/10labels_example/T1CE.nii.gz" -m "./sample_data/10labels_example/mask.nii.gz"

Generate PyInstaller Binaries

Note: Must modify the paths in .spec file to match your project directory

• Mac: pyinstaller Theia_Mac.spec
• Windows: pyinstaller Theia_Windows.spec

Test

• python -m pytest

Acknowledgements

[1] S.Bakas et al, "Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features", Nature Scientific Data, 4:170117 (2017) DOI: 10.1038/sdata.2017.117

[2] B.Menze et al, "The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS)", IEEE Transactions on Medical Imaging 34(10), 1993-2024 (2015) DOI: 10.1109/TMI.2014.2377694