Container service, Event Subscritpion and triggering after dcm2niix

[Daniel Beasley]

Hi all,

I have a new facemasking container that requires niftis, and I have also installed the dcm2niix container. However I'm having trouble setting it so the facemnasking container runs after the dcm2nii container - at the moment they start simultaneously. I have tried setting it to "xnat:resourceCatalog" under contexts, but that doesn't trigger it when I use event subscription and select 'resource created' as the trigger....

I could, as a fix, merge the two - which might be the easiest route.

Many thanks,

Dan

[kel...@wustl.edu]

Hi Dan,

  Some of the pieces to orchestrate containers in the way you describe are missing from the current release of Container Service, namely, the ability to launch a container on "xnat:resourceCatalog" contexts - deriving parent scans/sessions/etc.  I hope to get those features added to an imminent release.

If you are not concerned with storing the intermediate NIFTI files, you might try using a setup command, similar to this one:

dcm2niix.setup.json

{

"name": "dcm2niix-setup",
"description": "Converts DICOM to NIFTI",
"version": "1.0",
"type": "docker-setup",
"image": "xnat/dcm2niix:dev",
"command-line": "dcm2niix -o /output /input"
}

which can convert DICOM input resources to NIFTI on-the-fly.

Of course, your suggestion of merging the functionality of both containers will work as well.

Best,

Matt

[Daniel Beasley]

Hi Matt,

Many thanks, that's super useful. Once we've tested it, we will share it.  It uses niftyreg for facemasking,

Cheers,

Dan