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Weakly supervised perivascular spaces segmentation with salient guidance of Frangi filter

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WPSS

The project repository for Weakly supervised perivascular spaces segmentation with salient guidance of Frangi filter (WPSS). WPSS is a weakly supervised convolutional neural network model which focuses on segmenting perivascular spaces (PVS) in the white matter regions.

Acknowledgement

If you use WPSS code, please cite the following paper:

Weakly upervised Perivascular Spaces Segmentation with salient guidance of Frangi filter
Haoyu Lan, Kirsten M. Lynch, Rachel Custer, Nien‐Chu Shih, Patrick Sherlock, Arthur W. Toga, Farshid Sepehrband, Jeiran Choupan

For data inquiries, please contact me and Dr. Choupan by emails in the publication.

Data

Both training and inference datasets should be organized as the following structure:

dataset
│
└───subject 1
|   |    epc.nii.gz
|   |    mask.nii.gz(optional)
|   |    target.nii.gz(not required for the inference dataset)
└───subject 2
|   |    epc.nii.gz
|   |    mask.nii.gz
|   |    target.nii.gz
└───subject 3
|   |    epc.nii.gz
|   |    mask.nii.gz
|   |    target.nii.gz
│   ...

Human Connectome Project (HCP) dataset was used for the WPSS training and evaluation.

The Enhanced PVS Contrast (EPC) modality and training target generations are upon request. Please refer to the original publication for additional information of EPC modality.

Requirements

python 3 is required and python 3.6.4 was used in the study.

Requirements can be found at requirements.txt.

Please use pip install requirements.txt to install the requirements

How to run the code

Use the following command for the model training and inference. Pretrained weights with quality controlled labels for the model inference using either the EPC modality or the T1w modality are upon request.

Training:

Training script is at ./src/training

Use the following command to run the training script:

python training.py --trainig_size= --gpu= --num_iter= --patch_size= --dataset= --modality= --logdir= --output= --val_portion=

configurations meaning default
--training_size the number of training data to use None
--gpu gpu ID for training None
--val_portion percentage of the training dataset used for the validation 0.25
--num_iter the number of iteration 3000
--patch_size input image size (same for three dimensions) 16
--dataset path to the training dataset None
--modality names of the input image and the target image epc_frangi
--logdir path to the saved tensorboard log None
--output path to saved images during training None
--lr learning rate 0.001
--mask if using the mask for the evaluation on validation data (mask should be save as "mask.nii.gz") False

Inference:

Inference script is at ./src/predict. The corresponding PVS segmentation results will be saved under the same directory as the inference dataset.

Use the following command to run the inference script:

python predict.py --gpu= --weights= --dataset= --modality=

configurations meaning default
--gpu gpu ID for inference 0
--weights path of trained model weights to load None
--patch_size patch size for three dimensions 16
--dataset path to the inference dataset None
--modality name of the modality used as the input (could be either "epc" or "t1w") epc

License

If you use this code for your research, please be familiar with the LICENSE and cite our paper.

Citation

@article{lan2023weakly,
  title={Weakly supervised perivascular spaces segmentation with salient guidance of Frangi filter},
  author={Lan, Haoyu and Lynch, Kirsten M and Custer, Rachel and Shih, Nien-Chu and Sherlock, Patrick and Toga, Arthur W and Sepehrband, Farshid and Choupan, Jeiran},
  journal={Magnetic Resonance in Medicine},
  volume={89},
  number={6},
  pages={2419--2431},
  year={2023},
  publisher={Wiley Online Library}
}

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