Performance of image matching in the computational anatomy gateway: CPU and GPU implementations in opencl

Tward, DJ, Lee, B, Mitra, P, Miller, MI (July 2017) Performance of image matching in the computational anatomy gateway: CPU and GPU implementations in opencl. In: PEARC17: Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact.

DOI: 10.1145/3093338.3093361


The Computational Anatomy Gateway is a software as a service tool that provides tools for analysis of structural MRI to the neuroimaging community by calculating diffeomorphic mappings between a user's data and well characterized atlas images. These tools include automatic parcellation of brain images into labeled regions, described by dense 3D arrays; and shape analysis of regions described by triangulated sur-faces, for hypothesis testing in specific populations. We have developed mapping techniques that combine the benefits of working with triangulated surfaces with those of working with dense images, and have been working toward uniting these two tools: To automatically perform shape analysis on each segmented subcortical structure simultaneously. In this work we investigate the performance of our algo-rithm across a wide range of input data, examining the effect of number of voxels in 3D images, number of vertices in tri-Angulated surfaces, and number of structures being mapped onto simultaneously. Further, we investigate the performance of our OpenCL code implemented in two different environ-ments: The Intel OpenCL environment on a CPU, and the CUDA OpenCL environment on a GPU. We identify a range of inputs, generally smaller datasets, for which the CPU out performs the GPU. Finally we show the feasibility of mapping onto all the human gray matter sub-cortical structures simultaneously, and discuss our strategy.

Item Type: Conference or Workshop Item (Paper)
Subjects: bioinformatics > computational biology
bioinformatics > genomics and proteomics > computers > computer hardware
neurobiology > neuroanatomy
CSHL Authors:
Communities: CSHL labs > Mitra lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 9 July 2017
Date Deposited: 24 May 2021 15:46
Last Modified: 24 May 2021 15:46

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