INFSO-RI-508833
Enabling Grids for E-sciencE
www.eu-egee.org
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
2/10
Enabling Grids for E-sciencE
INFSO-RI-508833
SIMRI@Grid
EGEE User Forum, March 2006
• 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]
3/10
Enabling Grids for E-sciencE
INFSO-RI-508833
SIMRI@Grid
EGEE User Forum, March 2006
Virtual object
(i,ρ,T1,T2)
MRI
Image
FFT based
reconstruction
Magnetizationprocess kernel
K-space
RF signals
MRI sequence - RF Pulse - Gradient - Precession - Acquisition
Bo + ∆B map
Filtering
Acquisition noise model
• Kernel implements Bloch’s electromagnetism equation• Huge computation time (5122 = 12h, 5123 > 100 years !)
• Parallel implementation > MPI
• SIMRI Overview
4/10
Enabling Grids for E-sciencE
INFSO-RI-508833
SIMRI@Grid
EGEE User Forum, March 2006
• 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
DA
TA
GR
IDE
GE
E
• SIMRI Milestones
5/10
Enabling Grids for E-sciencE
INFSO-RI-508833
SIMRI@Grid
EGEE User Forum, March 2006
• 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 : A grid experience
6/10
Enabling Grids for E-sciencE
INFSO-RI-508833
SIMRI@Grid
EGEE User Forum, March 2006
• 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
• SIMRI@Grid Web portal
7/10
Enabling Grids for E-sciencE
INFSO-RI-508833
SIMRI@Grid
EGEE User Forum, March 2006
• 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
Client
Job submission
Web server
Simri JobServer
Job add
Targeted
platform
JAVA
Thread
8/10
Enabling Grids for E-sciencE
INFSO-RI-508833
SIMRI@Grid
EGEE User Forum, March 2006
• SIMRI@Grid illustration
9/10
Enabling Grids for E-sciencE
INFSO-RI-508833
SIMRI@Grid
EGEE User Forum, March 2006
• 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.
10/10
Enabling Grids for E-sciencE
INFSO-RI-508833
SIMRI@Grid
EGEE User Forum, March 2006
• 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.