2010 Winter Project Week catalyst

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Key Investigators

  • Yong Gao
  • Randy Gollub
  • John Paulett
  • Tim Olsen
  • Dan Marcus

Objective

Provide support to the Harvard Catalyst as they work to stand up XNAT throughout their user community. Investigate the possibility that the Harvard Catalyst use case could be a model for additional CTSC sites that are also using the i2b2 framework, such as Emory University.

Approach, Plan

Specific open issues:

  1. Review data modeling requirement for XNAT from a MGH PI
  2. Contributing SubjectHandler Yong wrote into DicomServer release.
  3. Scan Level search capabilities for queries like "find all mr sessions with a usable MPRAGE scan". According to Tim, this is not an out-of-the-box thing offered by the REST API.
  4. Processing and loading images in NRRD format.

Progress

  1. Most of the data should have a close map to XNAT schema. Extensions to XNAT are needed to cover Testing session and Clinic Visit. XNAT will add a new field for "site".
  2. The SubjectHandler code was sent to Kevin Archie for consideration.
  3. This is now supported in xnat 1.4 rc3. Tim's example request would get a list of sessions with at least one usable MPRAGE from XNAT central: http://central.xnat.org/REST/experiments?xsiType=xnat:mrSessionData&format=xml&columns=ID,label,project&xnat:mrSessionData/scans/scan/quality=usable&xnat:mrSessionData/scans/scan/type=MPRAGE
  4. NRRD files can be loaded just as any other files. New parser is needed to be written if it's is desired to get header information from the NRRD files.


References