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

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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]

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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

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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

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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

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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

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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

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Enabling Grids for E-sciencE

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SIMRI@Grid

EGEE User Forum, March 2006

• SIMRI@Grid illustration

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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.

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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.