namhoangle / dlia

Paper "A clinically applicable deep-learning model for detecting intracranial aneurysm in computed tomography angiography images"

DLIA

create time: 2020.08.26

Introduction

This repository contains the source code and the trained model for our work Deep Learning for Intracranial Aneurysm Detection in Computed Tomography Angiography Images.

Prerequisites

• Ubuntu: 16.04 lts
• Python 3.6.5
• Pytorch 1.0.1.post2
• NVIDIA GPU + CUDA_10.0 CuDNN_7.5

This repository has been tested on NVIDIA RTX2080Ti. Configurations (e.g batch size, image patch size) may need to be changed on different platforms.

Installation

Other packages are as follows:

• yacs
• nibabel
• scipy
• joblib
• opencv-python
• SimpleITK
• scikit-image
• numpy

Install dependencies:

pip install -r requirements.txt

Usage

We mainly use main.py (under the project) to train/val/test our models.

The following is one example:

python main.py --gpu 0 1 2 3  --train --config tasks/configs/aneurysm_seg.daresunet.yaml

The main parameters are following:

• --train: used to train the model.
• --test: used to test(val) the model.
• --config: the path to the configuration file(*.yaml).
• --resume(optional): the path to the checkpoint pth(resume the model).
• --gpu(default 0): decide to which gpu to select. Format: one or multiple integers(separated by space keys), such as
• --gpu 0 1 2 3
• --check_point(optional): the path to save the trained model, we usually specify the parameter in the config file, if you specify this parameter here, it will override this parameter in the config file.

Train

Run command as below.

python main.py --gpu 0 1 2 3  --train --config tasks/configs/aneurysm_seg.daresunet.yaml

Inference

the weight of the model: raws/weight/da_resunet.pth.tar

configuration file: tasks/configs/aneurysm_seg.daresunet.yaml

• TEST.DATA.NII_FOLDER: directory of input files
• TEST.DATA.TEST_FILE: list of file names
• TEST.SAVE_DIR: the directory to save results If you want to use your custom data, you need modify the yaml file to set the path and file names of the test data.

Run command as below.

python main.py --gpu 0 1 2 3  --test --config tasks/configs/aneurysm_seg.daresunet.yaml --check_point raws/weight/da_resunet.pth.tar

qucik start

you can quick start inference and visualization using vis_demo.ipynb

• the example image data: raws/image/example.nii.gz
• the ground truth : raws/image/example_mask.nii.gz
• the expected output: raws/example_seg.nii.gz

other

in the ./raws directory, we supply an example dataset

raws
├── image  # directory of image files
├── mask   # directory of ground truth
├── lesion_bbox.txt  # lesion bbox info 
├── part_train.txt  # train list
├── part_val.txt    # validation list
├── part_test.txt   # test list