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.
9.1.2. 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.
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.
outputfolders for mounting to the container with the following command:
mkdir -p input output
Copy DICOM files to the
inputfolder with the following command:
cp -r /path/to/dicom/files input
Run the DICOM Reader using the
outputdirectories 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
The above image tag is set to
latest with the image tag used in step 1.