Usage Overview

This package installs the following executables which constitute the main way that users will interface with xnat-tools

• xnat2bids : xnat_tools/xnat2bids.py
• xnat-dicom-export: xnat_tools/dicom_export.py
• xnat-heudiconv: xnat_tools/run_heudiconv.py
• bids-postprocess: xnat_tools/bids_postprocess.py

xnat2bids exports an XNAT experiment (or MRI session) to the BIDS format in one run. This executable under the hood is performing two operations:

1. Export to a Heudiconv friendly directory structure. We follow the structure suggested by the ReproIn guide, enabling us to use their heuristic file. This step is encapsulated in xnat_tools/dicom_export.py
2. We run Heudiconv using ReproIn heuristic. This step is encapsulated in xnat_tools/run_heudiconv.py

In general, users will be interacting only with xnat2bids. However, in cases where troubleshooting is necessary, it may be convenient to run the two steps separately. The first step, dicom_export, is time consuming as all the data needs to be downloaded form the server. If the user can verify that the export looks correct, and the errors happen only when executing run_heudiconv, then running the two steps separately can save significant time.

At the moment bids-postprocess is used to insert the IntendedFor field to JSON sidecart for fieldmap data.