Tool to download the data from the Erasmus Glioma Database

This tool can be used to download the data from the Erasmus Glioma Database that is hosted on the BMIA XNAT. This data is described in the accompanying publication: https://doi.org/10.1016/j.dib.2021.107191. Please cite this publication when using this data.

The data is hosted on XNAT, and can be interacted with using the XNAT API or one of the python packages that can interact with XNAT such as xnatpy or pyxnat.

This tool was designed to obviate the need for interacting with XNAT, instead directly downloading the data to a local directory.

This tool requires the installation of Docker. Installation instructions can be found on the docker website.

Once Docker has been installed, run the following command to install the data locally:

docker run  --mount type=bind,source=/PATH/TO/YOUR/OUTPUT/FOLDER,target=/output --rm svdvoort/egd-downloader:1.1 --user <YOUR_USERNAME> --password <YOUR_PASSWORD>

In this command three items have to be set by the user:

• /PATH/TO/YOUR/OUTPUT/FOLDER needs to be replaced by your desired output folder (folder should exist)
• <YOUR_USERNAME> needs to be replaced by the user's username for the BMIA XNAT.
• <YOUR_PASSWORD> needs to be replaced by the user's password for the BMIA XNAT.

Some scans might have a poor image quality or errors due to registration issues. We have marked this scans as 'unacceptable' scan quality in the XNAT database.

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 952103