Updated version of MMIT-DDPM
The classic BraTS 2021 dataset can be downloaded from Kaggle using the following command:
!curl -L -o /content/brats-2021-task1.zip https://www.kaggle.com/api/v1/datasets/download/dschettler8845/brats-2021-task1
!unzip -q /content/brats-2021-task1.zip
Then after the unzip, untar the training data BraTS2021_Training_Data.tar
To download ISBI 2015 and MICCAI 2016 run the following script:
./download_datasets.sh <path/to/target/directory>
change then the paths in the train_test.sh script with the correct dataset locations
To create a new environment and install all the required packages run the script
source ./setup.sh
it will create a new virtual environment with venv called test_env (name can be changed in the script), and after activation the script will install all the necessary packages to run the code.
To delete the test_env simply run
./delete_env.sh
The generated outputs will be stored in the results folder. A visualization of the sampling process is done using Visdom.
To run the visdom local server, open a new shell/terminal and run visdom, a local server will start giving a localhost address where the output is displayed.