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Downloading and converting the Stanford MRI datasets

Follow these instructions to batch download the Stanford 2D FSE and Stanford Fullysampled 3D FSE Knees datasets. These datasets can be found here, however batch download is currently not supported on the website.

Here I describe how to download the datasets using the mridata Python command line tool. The MRAugment repository uses the fastMRI codebase to handle MRI datasets, therefore we need to convert the downloaded datasets to have a format similar to fastMRI data. This is done through tools from mridata-recon repository.

The size of the datasets is shown in the following table.

Original Converted
Stanford 2D FSE 40G 37G
Stanford 3D FSE 32G 34G

Requirements

  • Python3

Instructions

  1. In order to install mridata first you need to install requests, tqdm, and boto using

    pip install requests boto3 tqdm

  2. Next, install mridata using

    pip install mridata

  3. Download the dataset. Navigate to the directory where you want to download the dataset and make sure that the correct UUID text file (Stanford_2D_TSE_uuid.txt or Stanford_3D_FSE_knee_uuid.txt) is saved in the same folder. You can find both of these text files in this repository. To dowload the datasets run the command

    mridata batch_download Stanford_2D_FSE_uuid.txt

    or

    mridata batch_download Stanford_3D_FSE_knee_uuid.txt

    depending on which dataset you would like to download.

  4. Convert the datasets using the scripts in this repository. Run python convert_stanford2d.py --input_dir --output_dir

    or

    python convert_stanford3d.py --input_dir --output_dir

    and replace the input and output directories with the desired path on your machine.

References

Both of these datasets can be downloaded directly from http://mridata.org/