Monai Usage

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MONAI core

NGC container usage:

ml purge
ml ngc-monai/<version>
python <your__python_script>

MONAI label

NGC container usage:

  1. Server: to start the server as a slurm job:
    • ml purge
    • ml ngc-monailabel/<version>
    • Copy to your directory the file:
      • /apps/nvidia/containers/monai/start_monai_server_readonly.sh
    • Copy these directories to a place you own, e.g.
      • cp -r /apps/nvidia/containers/monai/apps/deepedit <my_place>
      • cp -r /apps/nvidia/containers/monai/datasets/Task09_Spleen <my_place>
    • Modify the start_monai_server_readonly.sh line to read:
      • singularity exec -B /apps/nvidia/containers/monai /apps/nvidia/containers/monai/monailabel/ monailabel start_server --app <my_place>/deepedit --studies <my_place>/Task09_Spleen/imagesTr
    • sbatch start_monai_server_readonly.sh
    • Note server address from job output: used in next step
  2. 3DSlicer client
    • Start Open On Demand (OOD) session
    • Start Console in hwgui with 1 GPU: gpu:geforce:1
    • In console: load & start Slicer
      • ml qt/5.15.4 slicer/4.13.0
      • vglrun -d :0.$CUDA_VISIBLE_DEVICES Slicer
    • In Slicer GUI:
      • Select module: Active Learning -> MONAILabel
      • Fill in server address, e.g.: http://c1007a-s17:8000/
      • Click on refresh button next to server address
      • Load Next Sample
    • You are good to go! Enjoy!