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Clara CT Image Reconstruction

This asset requires the Clara Deploy SDK. Follow the instructions on the Clara Ansible page to install the Clara Deploy SDK.

Overview

CT reconstruction pipeline is defined using the Pipeline definition language (that Clara supports). The content is shown below,

api-version: 0.4.0
name: ct-recon-example
operators:
- name: recon-operator
  description: CT reconstruction algorithm on 3D cone beam projections
  container:
    image: clara/recon-operator
    tag: latest
  # Change the variables for the payload that is being used to run the pipeline
  variables:
    nvrtkalgo: fdk
    nvrtkhardware: gpu
    nvrtkhann: 0.95
    nvrtkdimension: 512,512,163
    nvrtkspacing: 0.75,0.75,3
    nvrtkorigin: -192,-192,-244.5
    nvrtkproj: 1024
    nvrtkindir: in
    nvrtkoutdir: out
    nvrtkgeomdir: geom
    nvrtklogs: logs
    nvrtksubset: 16
  requests:
    gpu: 1
    memory: 16384
  input:
  - path: /app/in
  output:
  - name: out
    path: /app/out
  - name: logs
    path: /app/logs
  - name: geom
    path: /app/geom

Data

Sample lung dataset in mhd format is available. Sample dataset (recon_raw_proj_mhd_0.0.1.zip) is available. If using the sample dataset, unzip it before using.

Operators

Recon pipeline definition consists of 1 operator, recon-operator.

recon-operator: Recon operators takes the result from the Clara pipeline payload and mounts it to /app/in folder. Recon-operator has 3 output folders. 'out' folder gets the actual reconstructed volume. 'logs' folder gets all logs from recon-operator. 'geom' folder contains the geometry file created by recon-operator. Recon-operator defines the reconstruction parameters under 'variables'. All parameters are defined in detail in recon operator definition. These variables are passed by platform as environment variables to the recon-operator at runtime. Reconstruction is GPU accelerated, and the need for GPU is specified with 'request' under recon-operator definition.

Execution of Reconstruction docker

All parameters within the reconstruction operator can be used by the user. Users can run reconstruction operator using the pipeline definition files and sample datasets.

Before executing the reconstruction pipeline, ensure that all environment variables are correctly set and appropriate data folders are mounted. This can be done in the "variables" section of recon-operator within the pipeline definition file.

Get the data: Have projection data ready for execution. If sample dataset (recon_raw_proj_mhd_0.0.1.zip) is desired, it can be extracted. If using the sample dataset, unzip it before using.

License

An End User License Agreement is included with the product. By pulling and using the Clara Deploy asset on NGC, you accept the terms and conditions of these licenses.

Clara Deploy CT Image Reconstruction Pipeline [Deprecated]