AUTHOR=Gherman Adrian , Muschelli John , Caffo Brian , Crainiceanu Ciprian 

TITLE=Rxnat: An Open-Source R Package for XNAT-Based Repositories

JOURNAL=Frontiers in Neuroinformatics

VOLUME=14

YEAR=2020

URL=https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2020.572068

DOI=10.3389/fninf.2020.572068

ISSN=1662-5196

ABSTRACT=<p>The extensible neuroimaging archive toolkit (XNAT) is a common platform for storing and distributing neuroimaging data and is used by many key repositories of public neuroimaging data. Some examples include the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC, <ext-link ext-link-type="uri" xlink:href="https://nitrc.org/" xmlns:xlink="http://www.w3.org/1999/xlink">https://nitrc.org/</ext-link>), the ConnectomeDB for the Human Connectome Project (<ext-link ext-link-type="uri" xlink:href="https://db.humanconnectome.org/" xmlns:xlink="http://www.w3.org/1999/xlink">https://db.humanconnectome.org/</ext-link>), and XNAT Central (<ext-link ext-link-type="uri" xlink:href="https://central.xnat.org/" xmlns:xlink="http://www.w3.org/1999/xlink">https://central.xnat.org/</ext-link>). We introduce Rxnat (<ext-link ext-link-type="uri" xlink:href="https://github.com/adigherman/Rxnat" xmlns:xlink="http://www.w3.org/1999/xlink">https://github.com/adigherman/Rxnat</ext-link>), an open-source R package designed to interact with any XNAT-based repository. The program has similar capabilities with PyXNAT and XNATpy, which were developed for Python users. Rxnat was developed to address the increased popularity of R among neuroimaging researchers. The Rxnat package can query multiple XNAT repositories and download all or a specific subset of images for further processing. This provides a lingua franca for the large community of R analysts to interface with multiple XNAT-based publicly available neuroimaging repositories. The potential of Rxnat is illustrated using an example of neuroimaging data normalization from two neuroimaging repositories, NITRC and HCP.</p>