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.
1.2.8184.108.40.20680043.2.1125.1.30521143073416610365663301213782755.mhd). The output directory is subsequently consumed by the Clara DICOM Adapter.
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.
Tagssection, locate the container image release that you want to run.
PULL TAGcolumn in the table, click the icon to copy the
Open a command prompt and paste the pull command. Ensure the pull completes successfully before proceeding to the next step.
Use the following command to create
outputfolders for mounting the container:
mkdir -p dicom mhd output
Copy DICOM files to the
dicomfolder and MHD files to the
mhdfolder 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
mhdfolder to DICOM files in the
outputfolder using headers from the DICOM files in the
Use the the following commands to run the DICOM Writer with the
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
The above image tag is set to
latest with the image tag used in step 1.