3D-CNN Segmentation

Visualize 3D Input and Mask of Kidney MRI

Data	Mask

Output

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• Quick start
• Description
  • Files
  • Network
• Usage
  • Training
  • Prediction
• Data
• Reference

Quick start

1. Clone this repository

git clone https://github.com/joewong00/3D-CNN-Segmentation.git

2. Initialize local configuration and fetch data from submodule project (surface distance)

git submodule update --init

3. Install CUDA
4. Install PyTorch
5. Install dependencies

pip install -r requirements.txt

6. Start with main.ipynb using Jupyter notebook or Google Colab

Description

This model was trained from scratch with 50 3D kidney MRI and scored a Dice coefficient of 0.929516 on over 50 test MRI.

Files:

• main.ipynb: Contains the main elements for data visualization, single data predicting and evaluation
• train.py: Script for model training
• test.py: Script for model testing
• dataloader.py: Custom dataset dataloading class
• predict.py: Script for predicting single image data and evaluation

Network

Reference: wolny/pytorch-3dunet

3D Residual UNet

Implementation based on https://arxiv.org/pdf/1706.00120.pdf

3D UNet

Implementation based on 3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation

Recurrent Residual 3D UNet (R2U3D)

Implementation based on R2U3D: Recurrent Residual 3D U-Net for Lung Segmentation

• Architecture

• Recurrent Residual Convolutional Unit (RRCU)

Usage

Note : Use Python 3.6 or newer

Training

> python train.py -h
usage: train.py [-h] [--network NETWORK] [--batch-size N] [--epochs N]
                [--lr LR] [--gamma M] [--no-cuda] [--dry-run] [--seed S]
                [--log-interval N] [--save-model] [--checkpoint FILE]

PyTorch 3D Segmentation

optional arguments:
  -h, --help            show this help message and exit
  --network NETWORK, -u NETWORK
                        Specify the network (Unet3D / ResidualUnet3D)
  --batch-size N        input batch size for training (default: 1)
  --epochs N            number of epochs to train (default: 10)
  --lr LR               learning rate (default: 2.5e-4)
  --gamma M             Learning rate step gamma (default: 0.1)
  --no-cuda             disables CUDA training
  --dry-run             quickly check a single pass
  --seed S              random seed (default: 1)
  --log-interval N      how many batches to wait before logging training
                        status
  --save-model          For Saving the current Model
  --checkpoint FILE, -c FILE
                        Specify the path to the model

If a checkpoint exist, then use --checkpoint to specify the path to the checkpoint to continue training

Prediction

• For test dataset, use test.py
• For single image testing, use predict.py or main.ipynb

After training your model and saving it to checkpoints/model.pt, you can easily test the output masks on your images via the CLI or main.ipynb

To predict a single image and compare result with its mask: python predict.py --network "ResidualUnet3D" --model 'checkpoints/model.pt' --input "./MRI1_T2.nii.gz" --mask "./MRI1_T2mask.nii.gz"

> python predict.py -h
usage: predict.py [-h] [--network NETWORK] [--model FILE] --input INPUT
                  [--mask INPUT] [--viz] [--no-save] [--no-cuda]
                  [--mask-threshold MASK_THRESHOLD]

Predict masks from input images

optional arguments:
  -h, --help            show this help message and exit
  --network NETWORK, -u NETWORK
                        Specify the network (Unet3D / ResidualUnet3D)
  --model FILE, -m FILE
                        Specify the path to the file in which the model is
                        stored (default:model.pt)
  --input INPUT, -i INPUT
                        Path to the image file (format: nii.gz)
  --mask INPUT, -l INPUT
                        Path to the ground truth of the input image
                        (if_available) (default:None)
  --viz, -v             Visualize the output (default:True)
  --no-save, -n         Do not save the output masks
  --no-cuda             disables CUDA testing (default: False)
  --mask-threshold MASK_THRESHOLD, -t MASK_THRESHOLD
                        Minimum probability value to consider a mask pixel
                        white (default: 0.5)

To predict the whole test dataset (with test dataloader): python test.py --network "ResidualUNet3D" --model "checkpoints/model.pt" --batch-size 1

> python test.py -h
usage: test.py [-h] [--network NETWORK] [--model FILE] [--batch-size N]
               [--no-cuda] [--mask-threshold MASK_THRESHOLD]

Evaluate using test loader

optional arguments:
  -h, --help            show this help message and exit
  --network NETWORK, -u NETWORK
                        Specify the network (Unet3D / ResidualUnet3D)
  --model FILE, -m FILE
                        Specify the paht to the file in which the model is
                        stored (model.pt)
  --batch-size N        input batch size for testing (default: 1)
  --no-cuda             disables CUDA testing (default: False)
  --mask-threshold MASK_THRESHOLD, -t MASK_THRESHOLD
                        Minimum probability value to consider a mask pixel
                        white (default: 0.5)

You can specify which model file to use with --model model.pt.

Data

The input images and target masks (for training) should be in the dataset/train/T2/ and dataset/train/T2Masks/ folders respectively. Original dataset have 3D size (W * H * D), they are preprocessed by adding channel dimension and written into the h5 files for dataloading.

You can use your own dataset as long as you make sure it is loaded properly in dataloader.py.

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Reference:

• milesial/Pytorch-UNet
• wolny/pytorch-3dunet