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Porting Matlab Applications to High-Performance C++ Codes: CPU/GPU-Accelerated Spherical Deconvolution of Diffusion MRI Data

  • Javier Garcia Blas
  • Manuel F. Dolz
  • J. Daniel Garcia
  • Jesus Carretero
  • Alessandro Daducci
  • Yasser Aleman
  • Erick Jorge Canales-Rodriguez
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10048)

Abstract

In many scientific research fields, Matlab has been established as de facto tool for application design. This approach offers multiple advantages such as rapid deployment prototyping and the use of high performance linear algebra, among others. However, the applications developed are highly dependent of the Matlab runtime, limiting the deployment in heterogeneous platforms. In this paper we present the migration of a Matlab-implemented application to the C++ programming language, allowing the parallelization in GPUs. In particular, we have chosen RUMBA-SD, a spherical deconvolution algorithm, which estimates the intravoxel white-matter fiber orientations from diffusion MRI data. We describe the methodology used along with the tools and libraries leveraged during the translation task of such application. To demonstrate the benefits of the migration process, we perform a series of experiments using different high performance computing heterogeneous platforms and linear algebra libraries. This work aims to be a guide for future developments that are implemented out of Matlab. The results show that the C++ version attains, on average, a speedup of 8\(\times \) over the Matlab one.

Keywords

Matlab Magnetic resonance imaging Linear algebra 

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Copyright information

© Springer International Publishing AG 2016

Authors and Affiliations

  • Javier Garcia Blas
    • 1
  • Manuel F. Dolz
    • 1
  • J. Daniel Garcia
    • 1
  • Jesus Carretero
    • 1
  • Alessandro Daducci
    • 2
  • Yasser Aleman
    • 3
    • 4
  • Erick Jorge Canales-Rodriguez
    • 4
    • 5
  1. 1.Dpto. de InformáticaUniversidad Carlos III de MadridLeganésSpain
  2. 2.Signal Processing LabÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
  3. 3.Instituto de Investigación Sanitaria Gregorio MarañónMadridSpain
  4. 4.Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM)OviedoSpain
  5. 5.FIDMAG Germanes HospitalàriesBarcelonaSpain

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