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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

The CT reconstruction operator within the Clara Deploy SDK uses the reconstruction toolkit (RTK). RTK is open-source and cross-platform software based on the Insight Toolkit (ITK). RTK performs fast circular cone-beam CT reconstruction.

CT reconstruction design in Clara uses pre-compiled binaries and applications from RTK and ITK, and a wrapper is provided with several options to the user. Output from the reconstruction operator is generated in the mounted folder.

Data Input

The Reconstruction Operator runs on raw CT projections from a cone-beam geometry. A geometry file is created by the reconstruction container and is fed into the reconstruction algorithm.

Projections are fed into reconstruction algorithm as a MHD volume. MHD format of dataset (recon_raw_proj_mhd_0.0.1.zip) is available.

Data Output

The pipeline outputs a reconstructed volume in MHD format.

Parameters

The following reconstruction parameters are supported:

• Number of projections: Number of projections for creation of cone beam geometry. This is created internally by reconstruction container and is used in reconstruction process. Range [1,1024]
• Recon Algorithms: Clara R3 supports two reconstruction algorithms. FDK (Feldkemp, David and Kress) and Iterative FDK.
• Input projections: Input projection data in MHD format. User must provide the projection volume (coming from a cone beam geometry) and in sync with the number of projection parameters provided.
• Spacing of reconstructed volume: (X,Y,Z) spacing information of the volume to be reconstructed.
• Origin of reconstructed volume:/ (X,Y,Z) origin information of the volume to be reconstructed.
• Dimensions of reconstructed volume:/ (X,Y,Z) dimension information of the volume to be reconstructed.
• Use GPU: Hardware to perform the reconstruction. Options are CPU or GPU.
• Number of iterations: Applicable only for Iterative FDK.
• Pre processing filter parameters: If the user wants to process the input projections before starting the reconstruction, Hanning filter is supported. Filter smoothing parameters can be specified from a value between 0 and 1.

Dependencies

The algorithms depend on the ITK libraries. All required libraries are pre-built and part of the Docker container.

Prerequisites

Download the input dataset from the MODEL SCRIPTS section for this container on NGC, following the steps in the Setup section.

Execution of Reconstruction operator

Following command can be executed to run reconstruction operator. Populate the input, output, logs folder and the container image tag before executing.

docker run -it --rm -v :/app/in \
 -v :/app/out \
 -v :/app/logs \
 -e nvrtkindir=in/data/ \
 -e nvrtkoutdir=out \
 -e nvrtkgeomdir=out \
 -e nvrtkspacing=0.976562,0.976562,2 \
 -e nvrtkorigin=-250,-250,-164.5 \
 -e nvrtkdimension=512,512,141 \
 -e nvrtkhann=0.95 \
 -e nvrtkhardware=gpu \
 -e nvrtklogs=logs/reconlogs \
 -e NVIDIA_CLARA_NOSYNCLOCK=TRUE \
 nvcr.io/nvstaging/clara/recon-operator:

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.