Awesome
3D-SkipDenseSeg
Skip-connected 3D DenseNet for volumetric infant brain MRI segmentation
By Toan Duc Bui, Jitae Shin, Taesup Moon
This is the implementation of our method in the MICCAI Grand Challenge on 6-month infant brain MRI segmentation-in conjunction with MICCAI 2017 in Pytorch.
Introduction
6-month infant brain MRI segmentation aims to segment the brain into: White matter, Gray matter, and Cerebrospinal fluid. It is a difficult task due to larger overlapping between tissues, low contrast intensity. We treat the problem by using very deep 3D convolution neural network. Our result achieved the top performance in 6 performance metrics.
Citation
@article{bui2019skip,
title={Skip-connected 3D DenseNet for volumetric infant brain MRI segmentation},
author={Bui, Toan Duc and Shin, Jitae and Moon, Taesup},
journal={Biomedical Signal Processing and Control},
volume={54},
pages={101613},
year={2019},
publisher={Elsevier}
}
Requirements:
- Pytorch >=0.4, python 3.0, Ubuntu 14.04
- TiTan X Pascal 12GB
Installation
- Step 1: Download the source code
https://github.com/tbuikr/3D-SkipDenseSeg.git
cd 3D-SkipDenseSeg
- Step 2: Download dataset at
http://iseg2017.web.unc.edu/download/
and change the path of the datasetdata_path
and saved pathtarget_path
in fileprepare_hdf5_cutedge.py
data_path = '/path/to/your/dataset/'
target_path = '/path/to/your/save/hdf5 folder/'
- Step 3: Generate hdf5 dataset
python prepare_hdf5_cutedge.py
- Step 4: Run training
python train_v2.py
Run evaluation result.
python val.py
We also provide pretrained model. Use the pretrained model, you should achieve the result as the table.
Dice Coefficient (DC) for 9th subject (9 subjects for training and 1 subject for validation)
Pretrained | CSF | GM | WM | Average | |
---|---|---|---|---|---|
3D-SkipDenseSeg | 20000_model_3d_denseseg_v1 | 94.96 | 91.78 | 91.24 | 92.66 |
Run on testing set
python test.py