2014 Winter Project Week:XNATSlicerLink

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Key Investigators

  • Erwin Vast, ErasmusMC, The Netherlands
  • Nicole Aucoin, BWH
  • Andrey Fedorov, BWH

Project Description


  • Radiologist sometimes would like to make an annotation on an existing CT/MRI/US image. 3D Slicer contains a module to create different kind of annotations.
  • The focus of this project is to store annotations created in 3D Slicer in XNAT. XNAT (http://xnat.org) is a framework for storing image (derived) data.
  • The annotations should be downloadable in the XNAT webinterface.
  • It should be possible to store a description accompanied with the annotation.
  • The annotations should be downloadable and viewable in 3D Slicer.
  • The interface should not only support DICOM, but also NIFTI and other relevant image filetypes.

Approach, Plan

  • Extend or build a module upon the existing XNATSlicer module (https://github.com/skumar221/XNATSlicer) of Sunil Kumar.
  • Use custom variables in XNAT to store the description (and possibly other relevant information).


  • Approach 1: Store annotation files only.
  • Approach 2: Store mrb file without image included (but next to original image data). Advantages: 1) more generic as is can include other meta-data, 2) all in one file, 3) prevents duplicate image data.
  • Almost implemented approach 2) but encountered some small problems which have to be discussed with the XNATSlicer developer.
  • Propose code to XNATSlicer developer.