Plastimatch tool for use at Medical Lab
225
Converting scans and annotations (RTSTRUCT) to Nifti/Nrrd
# Convert a scan (CT, MRI, etc.) to Nifti
docker run --rm --it --volume "$(pwd):/app" chumharbour/plastimatch convert --input <PATIENT>/<STUDY>/<CT>/ --output-img <CT>.nii.gz
# Convert an RTSTRUCT to a directory containing one Nrrd file per segmentation
docker run --rm --it --volume "$(pwd):/app" chumharbour/plastimatch convert --input <PATIENT>/<STUDY>/<RTSTRUCT>.dcm --referenced-ct <PATIENT>/<STUDY>/<CT>/ --output-prefix <segmentations>/ --prefix-format nrrd
The working directory inside of the container image is
/app, therefore mounting the current directory via--volumeallows I/O.
Dockerfile
FROM debian:bookworm
LABEL version=1.9.4
WORKDIR /app
RUN apt-get update
RUN apt-get install -y plastimatch
ENTRYPOINT ["plastimatch"]
Content type
Image
Digest
sha256:05a4d8bbe…
Size
196.6 MB
Last updated
about 1 year ago
docker pull chumharbour/plastimatch