Brain Tumor Segmentation with Clara Deploy Pipeline

We will use the installed Clara deploy SDK (refer to previous posts to install Clara Deploy in AWS) to run a brain tumor segmentation pipeline. We will use the clara ngc segmentation model for this purpose (ref - https://ngc.nvidia.com/catalog/resources/nvidia:clara:clara_ai_brain_tumor_pipeline)

Create a pipeline folder and pull the pipeline from ngc

clara pull pipeline clara_ai_brain_tumor_pipeline

Unzip the input dicom series

Unzip the model

Register the model

clara create model -p segmentation_mri_brain_tumors_br16_t1c2tc_v1/ -t tensorflow

Create the pipeline

clara create pipeline -p brain-tumor-pipeline-model-repo.yaml

Create and start the job

clara create jobs -n brain-test -p b8703c88407848a48a58496ef411daee -f ~/.clara/pipelines/clara_ai_brain_tumor_pipeline/dcm

Check the Clara Console in localhost:32002 and take the output download of the job.

View the output in 3d-slicer-segmented tumor

Location of the tumor through rendering