9.1. Clara DICOM Reader

The DICOM Reader is a pre-processor that converts DICOM files into MHD files.

Each DICOM series is converted into a single MHD file. DICOM files are associated with a DICOM series using the Series Instance UID header.

9.1.1. Requirements

Docker

9.1.2. Running the DICOM Reader

Before running the container, use docker pull to ensure an up-to-date image is installed. Once the pull is complete, you can run the container image as part of a pipeline.

  1. In the Tags section, locate the container image release that you want to run.

  2. In the PULL TAG column in the table, click the icon to copy the docker pull command.

  3. Open a command prompt and paste the pull command. Ensure the pull completes successfully before proceeding to the next step.

  4. Create input and output folders for mounting to the container with the following command:

    mkdir -p input output
    
  5. Copy DICOM files to the input folder with the following command:

    cp -r /path/to/dicom/files input
    
  6. Run the DICOM Reader using the input and output directories with the following command:

    docker run -it --rm \
    -e NVIDIA_CLARA_NOSYNCLOCK=TRUE \
    -e NVIDIA_CLARA_JOBID="692f5d9e2c974e4b87e87dc9bfacf5b2" \
    -e NVIDIA_CLARA_JOBNAME="test-dicom-read" \
    -e NVIDIA_CLARA_STAGENAME="io" \
    -e NVIDIA_CLARA_INPUT="/payload/input" \
    -e NVIDIA_CLARA_OUTPUT="/payload/output" \
    -v `pwd`/input:/payload/input \
    -v `pwd`/output:/payload/output \
    dicom-reader:latest
    

Note

The above image tag is set to latest. Replace latest with the image tag used in step 1.