SIMRI

A versatile and interactive 3D MRI simulator


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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.

It enables the simulation images taking into account B1 map.

 

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

 

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.

 

 

 

 

Images of uniform spherical object without/with B1 accounting at 11.7 T

 

 

 

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).

 

Main authors 

License

The SIMRI software is distributed under the CeCiLL license (http://www.cecill.info/index.en.html). The CeCiLL license is a free-software license, created under the supervision of the three biggest research institutions on computer sciences in France :

Collaborations & Acknowledgements

Our main collaborators on the SIMRI development are G. Collewet (CEMAGREF / Food Processes Engineering Research Unit, Rennes, France.) and H. Saint-Jalmes (LRMN-MIB, UMR CNRS 5012,Lyon France).

Many thanks to A. Amadon (CEA, SHFJ-UNAF, Orsay, France) for his contribution on B1 map integration.

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 and EGEE-2 projects and the French ministry for research ACI-GRID project. This work has been also funded by the INSA Lyon. The SIMRI project is also part of the I3M Région Rhône Alpes cluster project.

 

Download  the SIMRI code

 

- Version 2.0 (20 Déc. 2006)

 

- Version 1.0 (8 Nov. 2005)

 

SIMRI mailing  list

Simri has its mailing list: simri’at’creatis.insa-lyon.fr
If you are interested, subscribe to the simri mailing list.
http://www.creatis.insa-lyon.fr/mailman/listinfo/simri

 

SIMRI funding institutions

   


 

(Last web page update 30/05/2007)