Abstract
This work describes Microstructure Imaging Sequence Simulation Toolbox (MISST), a practical diffusion MRI simulator for development, testing, and optimisation of novel MR pulse sequences for microstructure imaging. Diffusion MRI measures molecular displacement at microscopic level and provides a non-invasive tool for probing tissue microstructure. The measured signal is determined by various cellular features such as size, shape, intracellular volume fraction, orientation, etc., as well as the acquisition parameters of the diffusion sequence. Numerical simulations are a key step in understanding the effect of various parameters on the measured signal, which is important when developing new techniques for characterizing tissue microstructure using diffusion MRI. Here we present MISST - a semi-analytical simulation software, which is based on a matrix method approach and computes diffusion signal for fully general, user specified pulse sequences and tissue models. Its key purpose is to provide a deep understanding of the restricted diffusion MRI signal for a wide range of realistic, fully flexible scanner acquisition protocols, in practical computational time.
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References
Jones, D.K., Diffusion, M.R.I.: Theory, Methods and Application. Oxford University Press, Oxford (2010)
Johansen-Berg, H., Behrens, T.E.J.: MRI: Diffusion from Quantitative Measurement to in Vivo Neuroanatomy. Academic Press, San Diego (2009)
Assaf, Y., Blumenfeld-Katzir, T., Yovel, Y., Basser, P.J.: AxCaliber: a method for measuring axon diameter distribution from diffusion MRI. Magn. Reson. Med. 59(6), 1347–1354 (2008)
Alexander, D.C., Hubbard, P.L., Hall, M.G., Moore, E.A., Ptito, M., Parker, G.J.M., Dyrby, T.B.: Orientationally invariant indices of axon diameter and density from diffusion MRI. NeuroImage 52, 1374–1389 (2010)
Panagiotaki, E., Walker-Samuel, S., Siow, B., Johnson, S.P., Rajkumar, V., Pedley, R.B., Lythgoe, M.F., Alexander, D.C.: Noninvasive quantification of solid tumor microstructure using VERDICT MRI. Cancer Res. 74, 1902–1912 (2014)
Zhang, H., Hubbard, P.L., Parker, G.J.M., Alexander, D.C.: Axon diameter mapping in the presence of orientation dispersion with diffusion MRI. NeuroImage 56, 1301–1315 (2011)
Ianuş, A., Drobnjak, I., Alexander, D.C.: Model-based estimation of microscopic anisotropy using diffusion MRI: a simulation study. NMR Biomed. 29, 627–685 (2016)
Drobnjak, I., Zhang, H., Ianuş, A., Kaden, E., Alexander, D.C.: PGSE, OGSE, and sensitivity to axon diameter in diffusion MRI: Insight from a simulation study. Magn. Reson. Med. 75, 688–700 (2016)
Shemesh, N., Lanuş, A., Alexander, D.C., Drobnjak, I.: Double oscillating diffusion encoding (DODE) augments microscopic anisotropy contrast. In: Proceedings of ISMRM, p. 952, Toronto, Canada (2015)
Stejskal, E.O.: Use of spin echoes in a pulsed magnetic-field gradient to study anisotropic, restricted diffusion and flow. J. Chem. Phys. 43, 3597–3603 (1965)
Neuman, C.H.: Spin echo of spins diffusing in a bounded medium. J. Chem. Phys. 60, 4508–4511 (1974)
Xu, J., Does, M.D., Gore, J.C.: Quantitative characterization of tissue microstructure with temporal diffusion spectroscopy. J. Magn. Reson. 200, 189–197 (2009)
Ianuş, A., Siow, B., Drobnjak, I., Zhang, H., Alexander, D.C.: Gaussian phase distribution approximations for oscillating gradient spin-echo diffusion (MRI). J. Magn. Reson. 227, 25–34 (2013)
Callaghan, P.T.: A simple matrix formalism for spin echo analysis of restricted diffusion under generalized gradient waveforms. J. Magn. Reson. 129, 74–84 (1997)
Grebenkov, D.: Laplacian eigenfunctions in NMR. I. A numerical tool. Concepts Magn. Reson. Part A 32, 277–301 (2008)
Kuder, T.A., Laun, F.B.: NMR-based diffusion pore imaging by double wave vector measurements. Magn. Reson. Med. 70, 836–841 (2013)
Xu, J., Does, M.D., Gore, J.C.: Numerical study of water diffusion in biological tissues using an improved finite difference method. Phys. Med. Biol. 52, N111–N126 (2007)
Li, J.-R., Calhoun, D., Poupon, C., Le Bihan, D.: Numerical simulation of diffusion mri signals using an adaptive time-stepping method. Phys. Med. Biol. 59, 441–454 (2014)
Hall, M.G., Alexander, D.C.: Convergence and parameter choice for Monte-Carlo simulations of diffusion MRI. IEEE Trans. Med. Imaging 28, 1354–1364 (2009)
Yeh, C.H., Schmitt, B., Le Bihan, D., Li-Schlittgen, J.R., Lin, C.P., Poupon, C., Diffusion microscopist simulator: a general monte carlo simulation system for diffusion magnetic resonance imaging. In: PLoS ONE (2013)
Drobnjak, I., Alexander, D.C.: Optimising time-varying gradient orientation for microstructure sensitivity in diffusion-weighted MR. J. Magn. Reson. 212, 344–354 (2011)
Westin, C.-F., Szczepankiewicz, F., Pasternak, O., Özarslan, E., Topgaard, D., Knutsson, H., Nilsson, M.: Measurement tensors in diffusion MRI: generalizing the concept of diffusion encoding. In: Golland, P., Hata, N., Barillot, C., Hornegger, J., Howe, R. (eds.) MICCAI 2014, Part III. LNCS, vol. 8675, pp. 209–216. Springer, Heidelberg (2014)
Callaghan, P.T.: Principles of Magnetic Resonance Microscopy. Oxford Science Publications, Oxford (1991)
Drobnjak, I., Zhang, H., Hall, M.G., Alexander, D.C.: The matrix formalism for generalised gradients with time-varying orientation in diffusion NMR. J. Magn. Reson. 210, 151–157 (2011)
Caprihan, A., Wang, L.Z., Fukushima, E.: A multiple-narrow-pulse approximation for restricted diffusion in a time-varying field gradient. J. Magn. Reson. Ser. A 118, 94–102 (1996)
Panagiotaki, E., Schneider, T., Siow, B., Hall, M.G., Lythgoe, M.F., Alexander, D.C.: Compartment models of the diffuison MR signal in brain white matter: a taxonomy and comparison. NeuroImage 59, 2241–2254 (2012)
Callaghan, P.T., Coy, A., MacGowan, D., Packer, K.J., Zelaya, F.O.: Diffraction-like effects in NMR diffusion studies of fluids in porous solids. Nature 351, 467–469 (1991)
Balinov, B., Jonsson, B., Linse, P., Soderman, O.: The NMR self-diffusion method applied to restricted diffusion. simulation of echo attenuation from molecules in spheres and between planes. J. Magn. Reson. 104, 17–25 (1993)
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Ianuş, A., Alexander, D.C., Drobnjak, I. (2016). Microstructure Imaging Sequence Simulation Toolbox. In: Tsaftaris, S., Gooya, A., Frangi, A., Prince, J. (eds) Simulation and Synthesis in Medical Imaging. SASHIMI 2016. Lecture Notes in Computer Science(), vol 9968. Springer, Cham. https://doi.org/10.1007/978-3-319-46630-9_4
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