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Quickstart ✌

Not ready

This feature is in alpha and not ready for use.

Gingerbread comes with medquery and the certificates to access the database already installed.

Here is an example code for downloading data.

python
import data_download as dd

mqd = dd.MedqueryDataDownloader()
mqd.download_data(
                project_id="booby",
                get_affines=True,
                get_all=True,
                include_mask=False,
                batch_size=20
                )

This will download the data into ./data and add it to a hdf5 file. hdf5 files are storage files that simulates a harddrive. This makes it easier to store and lazy load during training. Check out the documentation here: https://docs.h5py.org/en/stable/

We have also included two functions to convert the hdf5 files to nifti. This is useful if you want to use the data in other software. The functions are hdf5_to_nifti_all and hdf5_to_nifti_single. The first one will convert all the data in the hdf5 file to nifti. The second one will convert a single image.

For more information check out the reference api in the documentation.