Can I use 'nil' format?

Hi, I want to use .nil files which is anonymized.

Can I enter nil files? Or should I convert it to DICOM file and input it through an adpater?

Hi Alex
Thanks for you interest in Clara Deploy. I am not familiar with nil, Google didn’t help. did you mean nii as nifti file format?
In all cases you can write your own adapter to read in files however it would require some work. However, you should figure out first how and who will be passing images to clara deploy ? if you are to trigger it from command line and pass in folders. If so then this capability is including in the Clara CLI. You would then only need to write a simple operator to read the nil file and convert to to numpy for the next operator/ inference. if the format is nii or nii.gz then our app base inferences can already read then and run inference

Hope that helps

Hello @aharouni

Is there some way to adapt the clara_ai_covid19_pipeline to read NIfTI file? Or should I create a new pipeline for it?

Hi Ilan,

Thanks for your interest in Deploy. Yes, the COVID 19 operators take nii as input, so you can modify the pipeline definition to remove the dicom reader and replace any operators that take input from dicom-reader

  input:
  - from: dicom-reader
    path: /input

to take the input payload directly:

  input:
  - path: /input

An example of this updated pipeline is attached.

You can use this to create the pipeline and start the job as usual,

clara create pipeline -p COVID-19-pipeline-nii.yaml
clara create job -p <pipeline ID> -n <job name> -f /path/to/input/nii
clara start job -j <job ID>

where /path/to/nii is the directory that contains your input nii file.

Let me know if you run into any issues.

Thanks,
Kris

COVID-19-pipeline-nii.yaml (12.5 KB)