100 likes | 378 Views
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. Why MRI Simulation ? Better understanding of the complexity of MRI imaging Pedagogic purposes
E N D
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
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]
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
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
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.
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
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
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.
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.