rvignav / contour2dso

Creation of a DICOM Segmentation Object from an AIM file storing the contours of a DICOM image series. Integrated into Stanford's ePAD platform as a plugin.

contour2DSO

Creation of a DICOM Segmentation Object (DSO) from an AIM file storing the contours of a DICOM image series. Integrated into Stanford University's ePAD Imaging Platform as a plugin. View full documentation on the ePAD website.

Available on Docker Hub here.

Table of Contents

• Usage
• Errors

Usage

To test the contour to DSO algorithm, run the following commands:

git clone https://github.com/rvignav/contour2DSO.git
cd contour2DSO
docker build -t run .
docker run -it -v "local/aims:/home/series/files" -v "local/patient/series:/home/series/PatientSeries" run

A possible command satisfying the bind and argument requirements is:

docker run -it -v "$(pwd)/aims:/home/series/files" -v "$(pwd)/SamplePatient:/home/series/PatientSeries" run

Note that the AIM file must be stored in the aims folder.

The generated DSO is now stored in the /output folder of the Docker container and can be accessed by ePAD.

Errors

To fix the error Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?, run:

Windows:

systemctl start docker

MacOS:

brew cask install docker virtualbox
brew install docker-machine
docker-machine create --driver virtualbox default
docker-machine restart
eval "$(docker-machine env default)"

To fix the error docker: Error response from daemon: Conflict. The container name <container-name> is already in use, run:

docker ps -q -a | xargs docker rm