9.2. Clara DICOM Writer

The DICOM Writer is a post-processor that converts an MHD file into DICOM files.

Each MHD file is converted into a series of DICOM files, which are output to a specified directory. Each DICOM file is named with an auto-generated UID. Each MHD file should be named after the Series Instance UID associated with its original DICOM series (e.g. 1.2.826.0.1.3680043.2.1125.1.30521143073416610365663301213782755.mhd). The output directory is subsequently consumed by the Clara DICOM Adapter.

9.2.1. Requirements

Docker

9.2.2. Running the DICOM Writer

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. Use the following command to create dicom, mhd, and output folders for mounting the container:

    mkdir -p dicom mhd output
    
  5. Copy DICOM files to the dicom folder and MHD files to the mhd folder with the following commands:

    # Copy DICOM files to the DICOM folder
    cp -r /path/to/dicom/files dicom
    
    # Copy mhd files to the mhd folder
    cp -r /path/to/mhd/files mhd
    

    The DICOM Writer will convert MHD files in the mhd folder to DICOM files in the output folder using headers from the DICOM files in the dicom folder.

  6. Use the the following commands to run the DICOM Writer with the dicom, mhd and output directories:

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

Note

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