SIMRI
A
versatile
and interactive 3D MRI simulator
H. BENOIT-CATTIN, B. BELAROUSSI, F. BELLET,
C. ODET
Purpose and
Context
MRI simulation
is an important counterpart to MRI acquisitions. Simulation is
naturally suited
to acquire theoretical understanding of the complex MR technology. It
can be
used as an educational tool in medical and technical environments. MRI
simulation permits the investigation of artifact causes and effects.
Likewise
simulation may help in the development and optimization of MR
sequences. Finally,
with the increased interest in computer-aided MRI image analysis
methods
(segmentation, data fusion, quantization ...), an MRI simulator
provides an
interesting assessment tool since it generates 3D realistic images from
medical
virtual objects perfectly known.
In this
context, we develop the SIMRI simulator. Based on the Bloch
equations, it
includes an efficient management of the T2* effect. It takes into
account the main static field value and enables realistic simulations
of the
chemical shift artifact
including off-resonance phenomena. It also simulates
the artifacts linked to the static
field inhomogeneity like those induced by
susceptibility variation within
an object. It is implemented in the C language
and the MRI sequence programming is done using high level C functions
with a
simple programming interface. To manage large simulations, the
magnetization
kernel is implemented in a parallelized
way that enables simulation on PC grid
architecture. Furthermore, this simulator includes a 1D interactive interface
for pedagogic purpose illustrating the magnetization vector motion as
well as
the MRI contrast.
Overview
The
simulator overview is given below. From a 3D virtual object, the static
field
definition and an MRI sequence, the magnetization kernel computes a set
of RF
signals, i.e the k-space. To simulate
realistic
images, noise can be added to the k-space, which can be filtered like
in a real
imager before the reconstruction of the MR image (Modulus and phase)
using Fast
Fourier transform.
At the
moment, SIMRI contains Spin Echo, Gradient Echo sequences for
1D, 2D and
3D images as well as their turbo versions. It contains also FISP,
saturation-recovery as well as inversion-recovery sequences.
The
whole
code of the SIMRI simulator is written in ANSI C language and
separated
in different software modules working identically under Microsoft
Windows and Linux operating systems.
The
whole
simulation package is linked into a dynamic library wrapped for being
used with
the Python scripting
language. Such a
library has been used to develop an interactive portable 1D simulator
for
pedagogic purpose, the SpinPlayer.
Finally,
the magnetization kernel is parallelized using MPI to enable the
simulator to
run on data grid architecture in order to significantly reduce the
simulation
time [2].
Results
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|
|
Simulated 256x256 SE image, B0=1.5 T TE=100
ms TR=2000 ms BW=25.6 kHz |
Simulated 256x256 True-FISP image, B0=1,5T RF = 20°, 0,3 ms – TR=4 ms – BW=256 kHz Parabolic
static field default : 6.10-5 T |
|
|
|
|
Susceptibility artefact :
Simulated 256x256 GE image of an air bubble into water, B0 = 7 T. TE=20 ms ,TR=1000 ms, BW=20 kHz, RF=90° |
Chemical shift artefact
: Simulated 256x256 SE image of cylinder of oil within a
cylinder of water. B0=7T, TE=20 ms, TR=2500 ms. |
References
[1] H.
Benoit-Cattin, G. Collewet,
B. Belaroussi, H. Saint-Jalmes,
C. Odet, « The SIMRI project :
A versatile and interactive MRI simulator », Journal of Magnetic
Resonance, Accepted in Sept.
2004, 30 p.
[2] H. Benoit-Cattin, F. Bellet, J. Montagnat, C. Odet, "Magnetic Resonance Imaging (MRI) simulation on a grid computing architecture", in IEEE CGIGRID'03- BIOGRID'03, Tokyo, pp. 582-587 (2003).
Collaborations
& Acknowledgements
Our main collaborators on the SIMRI development are G.
Collewet (CEMAGREF / Food Processes Engineering
Research
Unit,
The SIMRI project has been initiated
thanks to
the work done by G. Soufflet and H. Saint-Jalmes on the initial 1D MRI simulator of J. Bittoun.
We want to thank S. Balac
from the CNRS MAPLY lab for its contribution on the susceptibility
artifact
simulation.
Many thanks to F. Bellet
and
J. Montagnat for their help in the SIMRI
parallelization and grid implementation, to G. Bonnilo
and L. Alexandre for their work on the 1D
interface
and to T. Lamotte for his contribution on
the
chemical shift artifact.
This work is partly supported by the IST
European
Data-Grid Project, the IST European EGEE project and the French ministry for
research
ACI-GRID project.
This work has been also funded
by the
INSA Lyon.
Download the
SIMRI code
-
Version 1.0 (8 Nov. 2005)
SIMRI mailing list
Simri has its mailing list : simri@creatis.insa-lyon.fr
If you are interested, subscribe to the simri mailing list.
http://www.creatis.insa-lyon.fr/mailman/listinfo/simri