Nifti file upload

[Camilla Scapicchio]

Hi,

is it possible to upload a nifti file/image so that it could be searchable like a dicom session and not a resource file?

If yes, how? Does a specific plugin have to be used or an easier way exist?

Thank you,

Camilla Scapicchio

[Rick Herrick]

Not really or at least not directly.

Part of the reason is that NIFTI data doesn't include any metadata, so there wouldn't be anything to search on, but also because, technically speaking, you're not searching the DICOM when you're searching through sessions, you're searching through the XFT data object representing the session, i.e. you are searching in the database. The DICOM itself is actually just a resource stored in a location associated with the DICOM session.

This is where the "at least not directly" part comes in. NIFTI is often associated with a DICOM session, where the NIFTI is generated from the original incoming DICOM. But there are also XNAT deployments where there is no DICOM associated with some imaging sessions, only NIFTI. The problem is that the NIFTI itself can't be the source for the metadata stored in the image session object since there's no metadata in the NIFTI from which the session metadata can be generated, so the session and its scans need to be "manually" generated (I put "manually" in quotes because you don't necessarily need to do it by hand–you could have a script that creates the session and scan(s) from metadata stored in a CSV file, for instance–but XNAT itself can't do it), then the NIFTI can be added to a resource on the appropriate scan.

So suppose you have 20 sessions with one scan each. You'd create a session with the appropriate modality for the source (e.g. NIFTI from an MRI would use xnat:mrSessionData), create a scan within that session, set values for whatever attributes you have on the session and scan level, create a NIFTI resource associated with the scan, then finally upload the NIFTI to that resource. Once completed, you'd have 20 searchable sessions containing nothing but NIFTI scans.

Any plugin for this would need to provide a way to import the NIFTI data and allow you to provide the session- and scan-level metadata, either through manual entry, a CSV file, or something similar. There's an XNAT BIDS importer project that may be of help if your NIFTI was generated as part of a BIDS conversion, but I'm not sure what state that's in.

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[James Dickson]

Also, see https://wiki.xnat.org/xnat-api/upload-image-session-files-with-rest-api for a general example. You can also use xnatpy or any other tool to make those rest calls.

james

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