-
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)
- ensure correctly configured corporate proxy server
- make sure docker and docker-compose are installed and configured correctly
- CUDA-enabled environment strongly recommended
- 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
$IMAGE_MOUNT
: path to a directory where Orthanc stores its images- i.e.
/mnt/data/ORTHANC/anatomy-db
- i.e.
- bring up Orthanc, OHIF and MONAILabel:
docker-compose up
- if no GPU available use
docker-compose -f docker-compose.cpu.yml up
- Orthanc will be availabel via Web
http://$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
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.