uploading nifty files
Miklos Espak
I would like to upload nifty (*.nii and *.nii.gz) files to XNAT.
Is there a way for that?
Cheers,
Miklos
Herrick, Rick
Miklos,
Funny you should ask. At the demo and workshop in Munich last week, we were harassed endlessly… er, politely requested by many kind users to provide exactly this functionality. As it happens, I literally JUST opened a Python script from Christian that does just this operation. Let me have a look through it and then, with Christian’s review and permission, will post it to the XNAT Marketplace. I’ll let you know when it’s ready to go.
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Miklos Espak
you mean that's a Python script that simply uploads the file through the REST API, right?
That's possible, I know, that was a question at the workshop at the WashU as well.
Or is it a module that adds a web interface?
Herrick, Rick
Correct, it’s a Python script. We don’t have a built-in facility for NIFTI yet. That will probably one of the big things we work on immediately after the 1.6.1 release. We’re also planning on a major refactoring of the upload applet and that will probably go hand-in-hand with supporting NIFTI, NRRD, and probably a couple of other formats. Ideally it will be implemented modularly so that we can then plug format handlers in dynamically, but sometimes that’s easier said than done J
Miklos Espak
However, I have to create a web service this week that processes nifty files. I then I will hack something now. With a new action maybe?
Herrick, Rick
Sure, absolutely. The main issue is that you guys are still on 1.5.4, so the custom REST service support is not in there yet. We need to validate the 1.6 update process and go from there.
Miklos Espak
Miklos Espak
I found a bug / restriction in the current state of Nifty format support.
If I upload a *.nii.gz reconstruction file then no files are shown under the reconstruction on the web. If only *.nii files are uploaded then those are listed well.
Miklos
Mohana Ramaratnam
Miklos Espak
$ curl -u test1:test1 -X PUT https://hipposeg.cs.ucl.ac.uk/data/archive/projects/testproject1/subjects/HippoSeg_S00001/experiments/HippoSeg_E00002/reconstructions/hippocampus
Upload Nifti:
$ curl -u test1:test1 -X PUT --data-binary @mdeft.1.nii "https://hipposeg.cs.ucl.ac.uk/data/archive/projects/testproject1/subjects/HippoSeg_S00001/experiments/HippoSeg_E00002/reconstructions/hippocampus/files/scan-2-right-hippocampus.nii?format=NIFTI&inbody=true"
The image appears well on the web.
Then upload the compressed Nifti:
$ curl -u test1:test1 -X PUT --data-binary @mdeft.1.nii.gz "https://hipposeg.cs.ucl.ac.uk/data/archive/projects/testproject1/subjects/HippoSeg_S00001/experiments/HippoSeg_E00002/reconstructions/hippocampus/files/scan-2-right-hippocampus.nii.gz?format=NIFTI&inbody=true"
They appear, however in the file manager:
|
| scans |
| reconstructions |
| hippocampus |
NO LABEL 2 files, 29.60 Mb NIFTI  |
| scan-2-right-hippocampus.nii NIFTI 19.25 Mb |
|
| scan-2-right-hippocampus.nii.gz NIFTI 10.35 Mb |