xnat_downloader

xnat_downloader downloads dicom data from an xnat server, converts the dicoms to niftis using dcm2niix, and saves the output in BIDS format. See the documentation for details and usage.

Requirements

• Python 3.9 or newer (tested up through Python 3.13)
• Access to an XNAT instance with the appropriate credentials
• Optional: integration tests require a populated XNAT project that mirrors the historical xnatDownload dataset. The public central.xnat.org instance referenced in older versions has been decommissioned.

Installation (development)

git clone https://github.com/NeuroimagingUIowa/xnat_downloader.git
cd xnat_downloader
python -m pip install --upgrade pip
python -m pip install -e ".[test]"

After installation you can use the CLI:

xnat_downloader -i /path/to/config.json