Installation

We provide installation instructions here.

Setup

Using Docker

The simplest way to use SwinMM is to use our docker image swinmm, which has contained all the needed dependencies. Download the swinmm.tar into the SwinMM directory and try the following scripts:

cd SwinMM
docker import - swinmm < swinmm.tar
docker run --runtime=nvidia --gpus=all -m="800g" --shm-size="32g" -itd -v ./:/volume swinmm /bin/bash
docker exec -it swinmm /bin/bash
conda activate SwinMM

To use docker, make sure you have installed docker and nvidia-docker.

Manual

For fast dataset loading, we required the users to install the Redis database, for example, on Ubuntu: sudo apt-get install redis

We also recommend the users install the PyTorch-based version from the official website.

Two packages are recommended to install manually according to their complicated dependencies: bagua==0.9.2, monai==0.9.0

The others can be installed through pip install -r requirements.txt

Datasets

Our pre-training dataset includes 5833 volumes from 8 public datasets:

• AbdomenCT-1K
• BTCV
• MSD
• TCIACovid19
• WORD
• TCIA-Colon
• LiDC
• HNSCC

We choose two popular datasets to test the downstream segmentation performance:

• WORD (The Whole abdominal Organ Dataset)
• ACDC (Automated Cardiac Diagnosis Challenge)

The dataset is organized as below:

SwinMM
├── WORD    
│   └── dataset
│       └── dataset12_WORD
│           ├── imagesTr
│           ├── imagesTs
│           ├── imagesVal
│           ├── labelsTr
│           ├── labelsTs
│           ├── labelsVal
│           └── dataset12_WORD.json
└── Pretrain
    ├── dataset
    │   ├── dataset00_BTCV
    │   ├── dataset02_Heart
    │   ├── dataset03_Liver
    │   ├── dataset04_Hippocampus
    │   ├── dataset06_Lung
    │   ├── dataset07_Pancreas
    │   ├── dataset08_HepaticVessel
    │   ├── dataset09_Spleen
    │   ├── dataset10_Colon
    │   ├── dataset11_TCIAcovid19
    │   ├── dataset12_WORD
    │   ├── dataset13_AbdomenCT-1K
    │   ├── dataset_HNSCC
    │   ├── dataset_TCIAcolon
    │   └── dataset_LIDC
    └── jsons
        ├── dataset00_BTCV.json
        ├── dataset01_BrainTumour.json
        ├── dataset02_Heart.json
        ├── dataset03_Liver.json
        ├── dataset04_Hippocampus.json
        ├── dataset05_Prostate.json
        ├── dataset06_Lung.json
        ├── dataset07_Pancreas.json
        ├── dataset08_HepaticVessel.json
        ├── dataset09_Spleen.json
        ├── dataset10_Colon.json
        ├── dataset11_TCIAcovid19.json
        ├── dataset12_WORD.json
        ├── dataset13_AbdomenCT-1K.json
        ├── dataset_HNSCC.json
        ├── dataset_TCIAcolon.json
        └── dataset_LIDC.json