Cerebrovascular and Aneurysm Segmentation in 3DRA images via a Deep Multi-Task Network
Weights can be download here:
fmnet5.hdf5 for inference_AneuristNet.py https://drive.google.com/file/d/1XZZY_H-Nt6mOZ3E9aFDAVvmYezxWJROi/view?usp=sharing
fmnet84.hdf5 for inference_Transformer.py https://drive.google.com/file/d/1bIBnfGVuFZY_Ggye_vSUF41bdUfeR-tC/view?usp=sharing
Folder structure:
vessel-aneurysm-segmentation/
├── data
│ └── step0 (**put the data you want to do inference here**)
│ │ └── ANSYS_UNIGE_09_image.nii.gz
│ │ ├── ANSYS_UNIGE_28_image.nii.gz
│ │ └── ...
│ ├── step1 (pre-processed data, generate automatically)
│ │ └── ANSYS_UNIGE_09_image.nii.gz
│ │ ├── ANSYS_UNIGE_28_image.nii.gz
│ │ └── ...
├── inference
│ └── inference.ipynb (**use this to do inference**)
│ ├── inference.py
├── results
│ └── aneurysm (aneurysm prediction)
│ │ └── ANSYS_UNIGE_09_image-[360, 633].nii.gz
│ │ ├── ANSYS_UNIGE_28_image-[1540].nii.gz
│ │ └── ...
│ ├── vessel (vessel prediction)
│ │ └── ANSYS_UNIGE_09_image_vessel_59969.nii.gz
│ │ ├── ANSYS_UNIGE_28_image_vessel_68437.nii.gz
│ │ └── ...
├── weights
│ └── fmnet5.hdf5
└── requirements.txt
How to use the code:
cd vessel-aneurysm-segmentation
pip install -r requirements.txt
cd inference
python inference_AneuristNet.py