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Setting up MONAILabel with Orthanc and OHIF

Principles

  • uses a DICOM image storage (Orthanc) for MONAILabel tasks

    • advantage over file based storage: no conversion needed (i.e. to Niftis), original DICOM files can be used directly without any manipulation/wrangling

  • resulting segmentation files are DICOM-SEGs stored in Orthanc

  • uses three docker images:

    • NGINX (serves as reverse proxy)
    • Orthanc (holds image and segmentation DICOM data)
    • MONAILabel (used for active learning, model training, pre-segmentations, includes OHIF)

Installation

Prerequisites

  • ensure correctly configured corporate proxy server
  • make sure docker and docker-compose are installed and configured correctly
  • CUDA-enabled environment strongly recommended

Bring up all relevant containers

  • clone this repo:
git clone https://github.com/jlvahldiek/tutorial-monailabel-orthanc.git
  • adjust parameters in ./.env first:
    • $SERVICE_HOST: machine's hostname, i.e. hostname.domain.com or just ip address
    • $LOCAL_WORKSPACE: local path to a directory that will contain:
      • db-index: Orthanc stores its database index in here (cannot be stored on network mount)
      • anatomy-model: MONAILabel stores its model files in here
    • $IMAGE_MOUNT: path to a directory where Orthanc stores its images
      • i.e. /mnt/data/ORTHANC/anatomy-db
  • bring up Orthanc, OHIF and MONAILabel:
docker-compose up
  • if no GPU available use
docker-compose -f docker-compose.cpu.yml up
  • Orthanc will be availabel via Web http://$SERVICE_HOST:8042 or via DICOM QR $SERVICE_HOST:4242
    • populate Orthanc with images via Web app or using batch upload
  • MONAILabel will be available via http://$SERVICE_HOST:8000
  • all images on Orthanc can be easily visualized using OHIF http://$SERVICE_HOST:8000/ohif
  • MONAILabel plugin in 3D Slicer should point to http://$SERVICE_HOST:8000
  • Also consider to make use of 3D Slicer's Plugin [DICOMWebBrowser] (https://github.com/lassoan/SlicerDICOMwebBrowser), very useful

Usage

First of all populate Orthanc with DICOM images. Make sure that you import DICOM images that are captured by $SEARCH_FILTER of .env file - otherwise MONAILabel will not recognize them.

As an alternative specify paths to an existing Orthanc database: $IMAGE_MOUNT should point to Orthanc's data folder and $LOCAL_WORKSPACE/db-index should point to Orthanc's index folder.

Use 3D Slicer's MONAILabel plugin to segment images and to train new models.