Step #1: Setting Up a MONAI Label Environment

Annotate and Adapt Medical Imaging Models with MONAI (Latest Version)

First, we need to set up the viewer and server environment. To run the server, we need to start our environment by opening the System Console start the MONAI Label docker container:

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docker run --gpus all --rm -ti --ipc=host --net=host -v /home/nvidia/datasets:/opt/monai/datasets projectmonai/monailabel:latest bash

Note

Skip this step if you’ve already started the container for a previous app. There’s no need to start a new container if you already started one for another app. Stop previous server by pressing Ctrl+C and go to the next step.


After starting the docker container the next step is to download the Bundle and start the server using a sample dataset (MSD Task07 Pancreas dataset).

Download the Bundle:

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monailabel apps --download --name monaibundle --output apps


To start the server, the MONAI Label Bundle app requires access to the MODEL Zoo. This means a GitHub authentication token has to be set. Please set the token as follows:

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export MONAI_ZOO_AUTH_TOKEN=<Your github auth token>


If you don’t have a token, please check how to get one from here: https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token

Once we set the authentication token, we should be able to start the MONAI Label server using the following command:

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monailabel start_server --app apps/monaibundle --studies datasets/Task07_Pancreas/imagesTr --conf models pancreas_ct_dints_segmentation_v0.3.5


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