SIMRI@Grid: An MRI Simulation Web Portal on EGEE Grid Architecture

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SIMRI_at_Grid An MRI Simulation Web Portal on EGEE
Grid Architecture

• F. Bellet, I. Nistoreanu, C. Pera, H.
  Benoit-Cattin
• CREATIS, UMR CNRS 5515, U630 Inserm, FRANCE

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• Why MRI Simulation ?
• Better understanding of the complexity of MRI
  imaging
• Pedagogic purposes
• Conception, calibration and test of MRI
  sequences in-silico.
• Generation of MRI images with a ground truth
• Artefacts impact and correction
• MR Image processing validation (segmentation,
  quantification)
• Previous works
• 1D MRI simulation Bittoun-81
• 2D MRI simulation Olsson-95
• Simulation with a distributed implementation
  Brenner-97
• 3D brain MRI simulation Kwan-99
• Susceptibility and MRI simulation Yoder-02-04

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• SIMRI Overview

• Kernel implements Blochs electromagnetism
  equation
• Huge computation time (5122 12h, 5123 gt 100
  years !)
• Parallel implementation gt MPI

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• SIMRI Milestones

• June 2001 SIMRI Project start
• June 2002 Parallelisation of the magnetization
  kernel
• Dec. 2002 Cluster deployment
• June 2003 SpinPlayer 1D interactive simulation
  interface
• Nov. 2003 Grid deployment
• 2004 Artefacts simulation (Susceptibility,
  Chemical shift, field default)
• Dec 2004 New parallelisation scheme at a
  sequence level
• March 2005 Major publication in J. Magnetic
  Resonance
• June 2005 SIMRI_at_Grid Simulation web portal
• Nov 2005 SIMRI distribution under CECILL
  public licence

DATAGRID
EGEE
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• SIMRI A grid experience

• Grid added value
• Speeds up the simulation time by a factor linked
  to the node number
• Enables simulation of high resolution images
• Enables simultaneous simulation to a wide user
  community
• Grid key issues
• Homogenisation of MPI implementation on the grid
  clusters.
• Enabling job submission to multiple clusters to
  get numerous nodes for 3D simulation.
• Enhancement of scheduling to estimate job
  termination.
• Providing of web portals to mask the middleware
  to final users
• Facilitation of the server certificate usage.

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• SIMRI_at_Grid Web portal

• Functionalities
• Full simulation access (all simulation
  parameters)
• Two simulation targets EGEE grid (LCG2), Local
  Cluster (PBS)
• User authentification
• Enhanced user job history, Enhanced running job
  status
• Simulation results sent by mail
• Status and evolution
• At the moment, only open to the 10 SIMRI
  developers
• Autumn 2006 Version 2
• Web service architecture, associated to Glite
• Enhanced interface
• New simulation target CINES, SGI multiproc
• Progressive simulation service opening to all
  the scientific community

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• SIMRI_at_Grid Web portal

• Technical context
• Serveur Web Apache v. 2.0.54
• Module PHP5 (libssh2.so et mysql.so)
• MySql v.4
• Java 1.4.2 (jsch.jar,mysql-connector-java-3.jar)
• MPI and batch managers (LCG2, PBS)
• Architecture
• Three layers architecture
• Presentation layer (PHP)
• Process Layer
• User management (Apache)
• Job management (JavaThread)
• Data Layer (MySql) user and job data

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• SIMRI_at_Grid illustration

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• SIMRI Facts

• Software
• The most advanced available MRI simulator 1D,
  2D, 3D, field default, Chemical shift, T2
  management
• Distributed under the public CECILL License (gt
  100 download within 30 labs)
• Simulation service proposed through a web portal
  connected to EGEE grid
• Publications
• H. Benoit-Cattin et al. "The SIMRI project A
  versatile and interactive MRI simulator," Journal
  of Magnetic Resonance, vol. 173, pp. 97-115,
  2005.
• J. Montagnat et al. "Medical images simulation,
  storage, and processing on the European DataGrid
  testbed," Journal of Grid Computing, vol. 2, pp.
  387-400, 2004.
• H. Benoit-Cattin et al. "Magnetic Resonance
  Imaging (MRI) simulation on a grid computing
  architecture,"IEEE CGIGRID'03- BIOGRID'03, Tokyo,
  2003.
• B. Belaroussi et al. "Distortion correction for
  susceptibility-induced artifacts in spin echo MR
  images Simulation study at 1.5 T and 7 T.,"Proc.
  ISMRM'04.
• B. Belaroussi et al. "Susceptibility artifact
  correction in GE images,"Proc. ISMRM'06.

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• SIMRI perpectives

• Simulation features
• Take benefit of the code diffusion to enlarge
  the user
• community and to get contributions in
• New anatomical objects
• New MRI sequences
• New simulation model (diffusion, antennas, pulse
  )
• Simulation services
• Open widely the SIMRI grid portal.
• Turn the portal architecture to an evolutive web
  service one.
• Provide a data management service associated to
  the high value simulated images
• Think about a multimodality (MRI, CT, PET, US)
  Medical Image simulation portal.