List of valid modalities supported by Xnat
James Allsopp
Herrick, Rick
Not directly really. The main thing you can look at is the data types administration page in your XNAT installation, which will tell you which data types are installed and configured for use. You can also configure other data types that may be installed but not set up through that page. Finally, many people have created custom data types that may be able to handle additional modalities (although most custom data types are usually for subject or experiment assessors, e.g. subject data collections instruments or processed data from imaging sessions).
The REST API can help you in one way if you’re on XNAT 1.7. You can call the schemas XAPI function to get a list of the data-type schemas on your deployment:
$ http --session=admin --verify no --body https://xnatdev.xnat.org/xapi/schemas
[
"security",
"xnat",
"assessments",
"screening/screeningAssessment",
"pipeline/build",
"pipeline/repository",
"pipeline/workflow",
"birn/birnprov",
"catalog",
"project",
"validation/protocolValidation",
"xdat/display",
"xdat",
"xdat/instance",
"xdat/PlexiViewer"
]
You can then get a specific schema with any of the strings returned, so e.g.:
https://xnatdev.xnat.org/xapi/schemas/xnat
https://xnatdev.xnat.org/xapi/schemas/birn/birnprov
Those will return the XSD for the data type, which you can look through to find supported data types and then possibly modalities.
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
Phone: +1 (314) 273-1645
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Moore, Charlie
To take this question from a different angle, I believe that if you want to import DICOM into XNAT in a “nice” way and have it build a session object directly for you according to that modality, XNAT needs to have a “session builder” for the corresponding modality. Based on lines 81-121 of this file: https://bitbucket.org/xnatdcm/dicom-xnat/src/6527cfc2f05edd0ca7929d2bbab02e9edc8bfb0a/dicom-xnat-mx/src/main/java/org/nrg/dcm/xnat/DICOMSessionBuilder.java?at=master&fileviewer=file-view-default, I believe the full list of modalities that XNAT will make a session out of would be:
- MR
- PT
- CT
- XA
- US
- CR
- OPT
- MG
- DX
- NM
- OT
- SR
- RT [this is weird, because “RT” doesn’t actually even seem to be a valid modality code at all according to the DICOM standard]
For what it’s worth, this lines up closely with my own experience in trying to import many different types of modalities into XNAT: I’ve made sessions out of all of the modalities listed above, except:
- SR: doing this at all would be really strange. That is, wanting to have an “SR Session” instead of SR scans under a different type of session would be very unusual.
- RT (see the note above)
On the flip side, I have tried with various other modalities not on this list and never been able to create a session out of them.
Now, that’s not to say that XNAT can’t import DICOM with modalities outside this list at all. For example, if you have a study with MR modality DICOM and SEG modality DICOM, when importing it with REST, XNAT should make an “MR Session” out of the DICOM just fine. This session will contain both MR and SEG scans (the scans will be of type xnat:mrScanData and xnat:segScanData). The issue would be if you wanted to just import the SEG modality data; that wouldn’t work.
Thanks,
Charlie