Frontiers in Neuroinformatics (May 2012)

PyXNAT: XNAT in Python

  • Yannick eSchwartz,
  • Alexis eBarbot,
  • Benjamin eThyreau,
  • Vincent eFrouin,
  • Gael eVaroquaux,
  • Gael eVaroquaux,
  • Aditya eSiram,
  • Daniel eMarcus,
  • Jean-Baptiste ePoline

DOI
https://doi.org/10.3389/fninf.2012.00012
Journal volume & issue
Vol. 6

Abstract

Read online

As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using high-level languages to automate data management and processing tasks. For this, a structured and programatic access to the data store is necessary. Web services are a first step toward this goal. They however lack in functionality and ease of use because they provide only low level interfaces to databases. We introduce here {PyXNAT}, a Python module that interacts with The Extensible Neuroimaging Archive Toolkit (XNAT) through native Python calls across multiple operating systems. The choice of Python enables {PyXNAT} to expose the XNAT Web Services and unify their features with a higher level and more expressive language. {PyXNAT} provides XNAT users direct access to all the scientific packages in Python. Finally {PyXNAT} aims to be efficient and easy to use, both as a backend library to build XNAT clients and as an alternative frontend from the command line.

Keywords