Monai Usage

Back to Monai

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!