Difference between revisions of "2010 Winter Project Week catalyst"
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==Key Investigators== | ==Key Investigators== | ||
* Yong Gao | * Yong Gao | ||
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<h3>Objective</h3> | <h3>Objective</h3> | ||
| − | Provide support to the Harvard Catalyst as they work to stand up XNAT throughout their user community. | + | 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. |
</div> | </div> | ||
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<h3>Approach, Plan</h3> | <h3>Approach, Plan</h3> | ||
Specific open issues: | Specific open issues: | ||
| + | #Review data modeling requirement for XNAT from a MGH PI | ||
#Contributing SubjectHandler Yong wrote into DicomServer release. | #Contributing SubjectHandler Yong wrote into DicomServer release. | ||
#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. | #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. | ||
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<h3>Progress</h3> | <h3>Progress</h3> | ||
| − | + | #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". | |
| + | #The SubjectHandler code was sent to Kevin Archie for consideration. | ||
| + | #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 | ||
| + | #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. | ||
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</div> | </div> | ||
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| + | </div> | ||
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| + | ==References== | ||
| + | <div> | ||
| + | [http://nrg.wikispaces.com/XNAT+Imaging+Data+Strategies http://nrg.wikispaces.com/XNAT+Imaging+Data+Strategies] | ||
</div> | </div> | ||
Latest revision as of 19:10, 6 January 2010
Home < 2010 Winter Project Week catalystKey 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:
- Review data modeling requirement for XNAT from a MGH PI
- Contributing SubjectHandler Yong wrote into DicomServer release.
- 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.
- Processing and loading images in NRRD format.
Progress
- 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".
- The SubjectHandler code was sent to Kevin Archie for consideration.
- 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
- 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.
