SIMULATION D'IRM ANGIOGRAPHIQUE PAR EXTENSION DU LOGICIEL JEMRIS
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1 SIMULATION D'IRM ANGIOGRAPHIQUE PAR EXTENSION DU LOGICIEL JEMRIS Alexandre FORTIN Supervised by Emmanuel DURAND and Stéphanie SALMON Laboratoire de Mathématiques de Reims Model : clipart-fr.com
2 VIVABRAIN PROJECT
3 PHYSICAL BASIS OF MRI Schematically : MRI machine = a magnet + radio antennas
4 PHYSICAL BASIS OF MRI # A magnet : to generate macroscopic magnetization in tissues
5 PHYSICAL BASIS OF MRI # Radio antennas : to excite protons with RF pulses and to collect MR signal RF pulse
6 PHYSICAL BASIS OF MRI Building image from MR signal Sample MR signal Fourier plane Image (after 2D Fourier transform)
7 WHY MRI SIMULATION? Motivations : Education, understanding MRI physics Optimization of MRI sequences Validation of physic models (CFD models for us) Conducting experiments difficult in reality (because of time, ethic, cost...)
8 WHY MRI SIMULATION? Motivations : Education, understanding MRI physics Optimization of MRI sequences Validation of physic models (CFD models for us) Conducting experiments difficult in reality (because of time, ethic, cost...)
9 WHY MRI SIMULATION? Motivations : Education, understanding MRI physics Optimization of MRI sequences Validation of physic models (CFD models for us) Conducting experiments difficult in reality (because of time, ethic, cost...)
10 WHY MRI SIMULATION? Motivations : Education, understanding MRI physics Optimization of MRI sequences Validation of physic models (CFD models for us) Conducting experiments impossible in vivo (because of time, ethic, cost...)
11 MRI SIMULATORS Some advanced MRI simulators (mostly open-source) JEMRIS, ODIN, SIMRI, POSSUM...
12 POSITION OF THE PROBLEM What simulators can do (static What we expect tissues) (angiographic images)
13 POSITION OF THE PROBLEM Necessity to simulate complex blood movements What we expect (angiographic images)
14 POSITION OF THE PROBLEM Necessity to simulate complex blood movements Not implemented in advanced softwares What we expect (angiographic images)
15 FLOW MOTION IN JEMRIS JEMRIS Version 2.7 Copyright (C) Tony Stöcker, Kaveh Vahedipour, Daniel Pflugfelder Forschungszentrum Jülich, Deutschland
16 FLOW MOTION IN JEMRIS Limit of motions in Jemris Only rigid motion of the whole sample (eg to simulate a movement of the patient). Oscillating sphere (from Stöcker T, Vahedipour K, Pflugfelder D, Shah NJ. High-performance computing MRI simulations. Magn Reson Med Jul,64(1):186-93)
17 HOW TO SIMULATE FLOW MOTION? Simulate MRI = Simulate evolution of macroscopic magnetization of tissues, ie solve an ODE (Bloch equation) in every point of the sample. dm xb =γ M dt ( plus a relaxation term)
18 HOW TO SIMULATE FLOW MOTION? Isochromat Summation
19 HOW TO SIMULATE FLOW MOTION? And for flow motion? M )M. =γ M xb +( V t ( plus relaxation term) We could express Bloch equation considering velocity in each point. But resolution becomes more complex (PDE). Eulerian approach
20 HOW TO SIMULATE FLOW MOTION? And for flow motion? dm xb =γ M dt ( plus relaxation term) Otherwise, keep the same equation but make evolve the position of each flow particle over time. Lagrangian approach
21 HOW TO SIMULATE FLOW MOTION? And for flow motion? dm xb =γ M dt r = ri(t) B(t) = Bo + G(t).ri(t) Lagrangian approach ( plus relaxation term)
22 HOW TO SIMULATE FLOW MOTION? And for flow motion? dm xb =γ M dt ( plus relaxation term) Advantages : Easy to solve, flexible, possibility to simulate contrast agent injection. Lagrangian approach
23 FLOW MOTION IN JEMRIS Limit of motions in Jemris One unique trajectory can be specified for the whole sample in Jemris... but...
24 FLOW MOTION IN JEMRIS Limit of motions in Jemris Only rigid motion of the whole sample (eg to simulate a movement of the patient). Oscillating sphere (from Stöcker T, Vahedipour K, Pflugfelder D, Shah NJ. High-performance computing MRI simulations. Magn Reson Med Jul,64(1):186-93)
25 FLOW MOTION IN JEMRIS Limit of motions in Jemris One unique trajectory can be specified for the whole sample in Jemris... but... Simulating flow motion suppose to know the individual trajectory of each particle.
26 FLOW MOTION IN JEMRIS Limit of motions in Jemris => Necessity to modify Jemris code in order to take multiple trajectories as input Simulating flow motion suppose to know the individual trajectory of each particle.
27 HOW TO SIMULATE FLOW MOTION? And for flow motion? dm xb =γ M dt r = ri(t) B(t) = Bo + G(t).ri(t) Lagrangian approach ( plus relaxation term)
28 FIRST RESULTS Simple test : 4 spins with 4 different trajectories
29 FIRST RESULTS Simulation of phase contrast MRI Input data : Synthetic trajectories of Poiseuille. zi (t) = zi (0) + Vmax. ( 1 ( ri/r )² ). t
30 FIRST RESULTS Simulation of phase contrast MRI Input data : Synthetic trajectories of Poiseuille. zi (t) = zi (0) + Vmax. ( 1 ( ri/r )² ). t Trajectories JEMRIS
31 FIRST RESULTS Simulation of phase contrast MRI Input data : Synthetic trajectories of Poiseuille. zi (t) = zi (0) + Vmax. ( 1 ( ri/r )² ). t MRI sequence (phase contrast) Trajectories JEMRIS
32 FIRST RESULTS Simulation of phase contrast MRI Input data : Synthetic trajectories of Poiseuille. zi (t) = zi (0) + Vmax. ( 1 ( ri/r )² ). t MRI sequence (phase contrast) Trajectories JEMRIS Image
33 FIRST RESULTS Simulation of phase contrast MRI Velocity map
34 EXPERIENCES Comparison to experimental images Hydrodynamic pulsed bench.
35 COMPARISON SIMULATION HYDRO BENCH
36 OTHER SIMULATIONS : FLOW ARTIFACTS «Normal» image with flow compensation Misregistration artifact with uncompensated sequence
37 PROSPECT Simulate images of cerebral vasculature with velocities obtained by Computational Fluid Dynamic (numerical solving of Navier-Stokes equations)
38 PROSPECT
39 PROSPECT Use Jemris to study errors in PC concerning flow rate and vessels diameter measurement Eventually couple this measures with other well-known source of errors, such as concomitant fields or non uniform gradients
40 PROSPECT THANK YOU! AND THANKS TO JEMRIS DEVELOPERS... Jemris website:
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