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

SIMRI@Grid is an advanced MRI simulation web portal that leverages the power of the EGEE grid architecture. It offers a range of simulation functionalities, enabling users to better understand MRI imaging complexity, facilitate pedagogic purposes, validate MR image processing, and more. The web portal connects to the EGEE grid, providing faster simulation times and enabling high-resolution image simulations for a wide user community.

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

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  1. SIMRI@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

  2. 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]

  3. Acquisition noise model Virtual object (i,ρ,T1,T2) K-space RF signals Magnetization process kernel Filtering Bo + ∆B map FFT based reconstruction MRI sequence- RF Pulse - Gradient - Precession - Acquisition MRI Image • SIMRI Overview • Kernel implements Bloch’s electromagnetism equation • Huge computation time (5122 = 12h, 5123 > 100 years !) • Parallel implementation > MPI

  4. 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@Grid : Simulation web portal • Nov: 2005 :SIMRI distribution under CECILL public licence DATAGRID EGEE

  5. 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.

  6. SIMRI@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

  7. Web server Job submission Targeted platform Client JAVA Thread Job add Simri JobServer • SIMRI@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

  8. SIMRI@Grid illustration

  9. SIMRI Facts • Software • The most advanced available MRI simulator : 1D, 2D, 3D, field default, Chemical shift, T2* management … • Distributed under the public CECILL License (> 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.

  10. 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.

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