Enabling Grids for E-scienc. E SIMRI@Grid: An MRI Simulation Web Portal on EGEE Grid Architecture F. Bellet, I. Nistoreanu, C. Pera, H. Benoit-Cattin CREATIS, UMR CNRS #5515, U 630 Inserm, FRANCE www. eu-egee. org INFSO-RI-508833
SIMRI@Grid Enabling Grids for E-scienc. E • 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 – 1 D MRI simulation [Bittoun-81] – 2 D MRI simulation [Olsson-95] – Simulation with a distributed implementation [Brenner-97] – 3 D brain MRI simulation [Kwan-99] – Susceptibility and MRI simulation [Yoder-02 -04] INFSO-RI-508833 EGEE User Forum, March 2006 2
SIMRI@Grid Enabling Grids for E-scienc. E • SIMRI Overview Acquisition noise model Virtual object (i, ρ, T 1, T 2) K-space Magnetization process kernel RF signals Bo + ∆B map FFT based MRI sequence - RF Pulse - Gradient Precession Acquisition reconstruction - • Kernel implements Bloch’s electromagnetism equation • Huge computation time (5122 = 12 h, 5123 > 100 years !) • Parallel implementation > MPI INFSO-RI-508833 Filtering MRI Image EGEE User Forum, March 2006 3
SIMRI@Grid Enabling Grids for E-scienc. E • SIMRI Milestones • June 2002 : Parallelisation of the magnetization kernel • Dec. 2002 : Cluster deployment • June 2003: Spin. Player : 1 D 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 • EGEE June 2001 : SIMRI Project start • DATAGRID • Nov: 2005 : SIMRI distribution under CECILL public licence INFSO-RI-508833 EGEE User Forum, March 2006 4
SIMRI@Grid Enabling Grids for E-scienc. E • 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 3 D 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. INFSO-RI-508833 EGEE User Forum, March 2006 5
SIMRI@Grid Enabling Grids for E-scienc. E • SIMRI@Grid Web portal • Functionalities – Full simulation access (all simulation parameters) – Two simulation targets : EGEE grid (LCG 2), 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 INFSO-RI-508833 EGEE User Forum, March 2006 6
SIMRI@Grid Enabling Grids for E-scienc. E • SIMRI@Grid Web portal • Technical context – Serveur Web Apache v. 2. 0. 54 – Module PHP 5 (libssh 2. so et mysql. so) – My. Sql v. 4 – Java 1. 4. 2 (jsch. jar, mysql-connector-java-3. jar) – MPI and batch managers (LCG 2, PBS) Web server • Architecture – Three layers architecture § Presentation layer (PHP) Targeted platform Job submission Client JAVA § Process Layer • User management (Apache) Thread Job add • Job management (Java. Thread) § Data Layer (My. Sql) : user and job data Simri Job. Server INFSO-RI-508833 EGEE User Forum, March 2006 7
SIMRI@Grid Enabling Grids for E-scienc. E • SIMRI@Grid illustration INFSO-RI-508833 EGEE User Forum, March 2006 8
SIMRI@Grid Enabling Grids for E-scienc. E • SIMRI Facts • Software – The most advanced available MRI simulator : 1 D, 2 D, 3 D, field default, Chemical shift, T 2* 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 Data. Grid 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. INFSO-RI-508833 EGEE User Forum, March 2006 9
SIMRI@Grid Enabling Grids for E-scienc. E • 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. INFSO-RI-508833 EGEE User Forum, March 2006 10
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