Abstract
Non-invasive estimation of cell size and shape is a key challenge in diffusion MRI. Changes in cell size and shape discriminate functional areas in the brain and can highlight different degrees of malignancy in cancer tumours. Consequently various methods have emerged recently that aim to measure the microscopic anisotropy of porous media such as biological tissue and aim to reflect pore eccentricity, the simplest shape feature. However, current methods assume a substrate of identical pores, and are strongly influenced by non-trivial size distribution. This paper presents a model-based approach that provides estimates of pore size and shape from diffusion MRI data. The technique uses a geometric model of randomly oriented finite cylinders with gamma distributed radii. We use Monte Carlo simulation to generate synthetic data in substrates consisting of randomly oriented cuboids with various size distributions and eccentricities. We compare the sensitivity of single and double pulsed field gradient (sPFG and dPFG) sequences to the size distribution and eccentricity and further compare different protocols of dPFG sequences with parallel and/or perpendicular pairs of gradients. The key result demonstrates that this model-based approach can provide features of pore shape (specifically eccentricity) that are independent of the size distribution unlike previous attempts to characterise microscopic anisotropy. We show further that explicitly accounting for size distribution is necessary for accurate estimates of average size and eccentricity, and a model that assumes a single size fails to recover the ground truth values. We find the most accurate parameter estimates for dPFG sequences with mixed parallel and perpendicular gradients, nevertheless all other sequences, including sPFG, show sensitivity as well.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
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)
Savadiev, P., Campbell, J.S.W., Descoteaux, M., Deriche, R., Pike, G.B., Siddiqi, K.: Labeling of ambiguous subvoxel fibre bundle configurations in high angular resolution diffusion MRI. NeuroImage 41, 58–68 (2008)
Nilsson, M., Latt, J., Stahlberg, F., van Westen, D., Hagslätt, H.: The importance of axonal undulation in diffusion MR measurements: a monte carlo simulation study. NMR Biomed. 25, 795–805 (2012)
Kleinnijenhuis, M., Zerbi, V., Küsters, B., Slump, C.H., Barth, M., van Cappellen van Walsum, A.: Layer-specific diffusion weighted imaging in human primary visual cortex in vitro. Cortex 49, 2569–2582 (2013)
Novikov, M., Jensen, J.H., Helpern, J.A., Fieremans, E.: Revealing mesoscopic structural universality with diffusion. Proc. Nat. Acad. Sci. 11, 5088–5093 (2014)
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, 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)
Ferizi, U., Schneider, T., Panagiotaki, E., Nedjati-Gilani, G., Zhang, H., Wheeler-Kingshott, C., Alexander, D.C.: A ranking of diffusion MRI compartment models with in vivo human brain data. Magn. Reson. Med. 72, 1785–92 (2014)
Cory, D.G., Garroway, A.N., Miller, J.B.: Applications of spin transport as a probe of local geometry. Polym. Prepr. 31, 149–150 (1990)
Mitra, P.P.: Multiple wave-vector extensions of the NMR pulsed-field-gradient spin-echo diffusion measurement. Phys. Rev. B 51(21), 15074–15078 (1995)
Lawrenz, M., Koch, M.A., Finsterbusch, J.: A tensor model and measures of microscopic anisotropy for double-wave-vector diffusion-weighting experiments with long mixing times. J. Magn. Reson. 202, 43–56 (2010)
Jespersen, S.N., Lundell, H., Sonderby, C.K., Dyrby, T.B.: Orientationally invariant metrics of apparent compartment eccentricity from double pulsed field gradient diffusion experiments. NMR Biomed. 26, 1647–1662 (2013)
Lasic, S., Szczepankiewicz, F., Eriksson, S., Nilsson, M., Topgaard, D.: Microanisotropy imaging: quantification of microscopic diffusion anisotropy and orientational order parameter by diffusion MRI with magic-angle spinning of the q-vector. Front. Phys. 2 (2014)
Ozarslan, E.: Compartment shape anisotropy (CSA) revealed by double pulsed field gradient MR. J. Magn. Reson. 199, 56–67 (2009)
Shemesh, N., Ozarslan, E., Basser, P.J., Cohen, Y.: Accurate noninvasive measurement of cell size and compartment shape anisotropy in yeast cells using double-pulsed field gradient MR. NMR Biomed. 25, 236–246 (2012)
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)
Komlosh, M.E., Ozarslan, E., Lizak, M.J., Horkay, F., Schram, V., Shemesh, N., Cohen, Y., Basser, P.J.: Pore diameter mapping using double pulsed-field gradient MRI and its validation using a novel glass capillary array phantom. J. Magn. Reson. 208, 128–135 (2011)
Hall, M., Alexander, D.C.: Convergence and parameter choice for Monte-Carlo simulations of diffusion MRI. IEEE Trans. Med. Imaging 28, 1354–1364 (2009)
Neuman, C.H.: Spin echo of spins diffusing in a bounded medium. J. Chem. Phys. 60, 4508–4511 (1974)
Assaf, Y., Freidlin, R.Z., Rohde, G.K., Basser, P.J.: New modeling and experimental framework to characterize hindered and restricted water diffusion in brain white matter. Magn. Reson. Med. 52, 965–978 (2004)
Stepisnik, J.: Time-dependent self-diffusion by NMR spin echo. Phys. B 183, 343–350 (1993)
Dyrby, T.B., Søgaard, L.V., Hall, M.G., Ptito, M., Alexander, D.C.: Contrast and stability of the axon diameter index from microstructure imaging with diffusion MRI. Magn. Reson. Med. 70, 711–721 (2013)
Alexander, D.C.: A general framework for experiment design in diffusion MRI and its application in measuring direct tissue-microstructure features. Magn. Reson. Med. 60, 439–448 (2008)
Acknowledgements
The EPSRC support this work through the following grants: EP/G007748, EP/H046410/01, EP/K020439/1, EP/M020533/1.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
Ianuş, A., Drobnjak, I., Alexander, D.C. (2015). Model-Based Estimation of Microscopic Anisotropy in Macroscopically Isotropic Substrates Using Diffusion MRI. In: Ourselin, S., Alexander, D., Westin, CF., Cardoso, M. (eds) Information Processing in Medical Imaging. IPMI 2015. Lecture Notes in Computer Science(), vol 9123. Springer, Cham. https://doi.org/10.1007/978-3-319-19992-4_55
Download citation
DOI: https://doi.org/10.1007/978-3-319-19992-4_55
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-19991-7
Online ISBN: 978-3-319-19992-4
eBook Packages: Computer ScienceComputer Science (R0)