Tensor Splines for Interpolation and Approximation of DT-MRI With Applications to Segmentation of Isolated Rat Hippocampi

Barmpoutis, Angelos; Vemuri, Baba C.; Shepherd, Timothy M.; Forder, John R.

doi:10.1109/tmi.2007.903195

Cited by 70 publications

(56 citation statements)

References 31 publications

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“…It is also important to note that, despite the fact that simulation domain is two dimensional (2D), Q conserves its five degrees of freedom. The Q tensor field is visualized using the MATLAB function plotDTI developed by Barmpoutis et al [48]. …”

Section: Computational Domainmentioning

confidence: 99%

“…Figure 4. The Q tensor field is visualized using the MATLAB function plotDTI developed by Barmpoutis et al [48]. Disclination lines of τ type and splitting disclination cores into different pairs of disclinations: Figure 4 shows computed Q-tensor visualization of classical disclinations and disclination pairs arising in chiral nematics.…”

Section: Classification Of Defects In Chiral Nematic Lcsmentioning

confidence: 99%

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Modeling Textural Processes during Self-Assembly of Plant-Based Chiral-Nematic Liquid Crystals

Murugesan

Rey

2010

Polymers

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Biological liquid crystalline polymers are found in cellulosic, chitin, and DNA based natural materials. Chiral nematic liquid crystalline orientational order is observed frozen-in in the solid state in plant cell walls and is known as a liquid crystal analogue characterized by a helicoidal plywood architecture. The emergence of the plywood architecture by directed chiral nematic liquid crystalline self assembly has been postulated as the mechanism that leads to optimal cellulose fibril organization. In natural systems, tissue growth and development takes place in the presence of inclusions and secondary phases leaving behind characteristic defects and textures, which provide a unique testing ground for the validity of the liquid crystal self-assembly postulate. In this work, a mathematical model, based on the Landau-de Gennes theory of liquid crystals, is used to simulate defect textures arising in the domain of self assembly, due to presence of secondary phases representing plant cells, lumens and pit canals. It is shown that the obtained defect patterns observed in some plant cell walls are those expected from a truly liquid crystalline phase. The analysis reveals the nature and magnitude of the viscoelastic material parameters that lead to observed patterns in plant-based helicoids through directed self-assembly. In addition, the results provide new guidance to develop biomimetic plywoods for structural and functional applications.

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Section: Computational Domainmentioning

confidence: 99%

Section: Classification Of Defects In Chiral Nematic Lcsmentioning

confidence: 99%

Modeling Textural Processes during Self-Assembly of Plant-Based Chiral-Nematic Liquid Crystals

Murugesan

Rey

2010

Polymers

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“…For the visualization, we used a modified version of the fanDTasia ToolBox by Angelos Barmpoutis [62].…”

Section: Methodsmentioning

confidence: 99%

Combined Tensor Fitting and TV Regularization in Diffusion Tensor Imaging Based on a Riemannian Manifold Approach

Baust

Weinmann

Wieczorek

et al. 2016

IEEE Trans. Med. Imaging

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In this paper, we consider combined TV denoising and diffusion tensor fitting in DTI using the affine-invariant Riemannian metric on the space of diffusion tensors. Instead of first fitting the diffusion tensors, and then denoising them, we define a suitable TV type energy functional which incorporates the measured DWIs (using an inverse problem setup) and which measures the nearness of neighboring tensors in the manifold. To approach this functional, we propose generalized forward- backward splitting algorithms which combine an explicit and several implicit steps performed on a decomposition of the functional. We validate the performance of the derived algorithms on synthetic and real DTI data. In particular, we work on real 3D data. To our knowledge, the present paper describes the first approach to TV regularization in a combined manifold and inverse problem setup.

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“…Perpendicular fibre sections were traced in three different regions (stratum radiatum, stratum lacunosum-moleculare and stratum oriens) of rat hippocampus. The acquisition protocol included 21 diffusion-weighted image sets with a b-value of approximately 1250 s/mm 2 (Barmpoutis et al, 2007). A diffusion tensor field was estimated from the DW-MRI data set using the method of Barmpoutis et al (2012).…”

Section: Real Data Experimentsmentioning

confidence: 99%

Perpendicular fibre tracking for neural fibre bundle analysis using diffusion MRI

Ray

O’Dell

Barmpoutis

2014

IJBRA

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Information on the directionality and structure of axonal fibres in neural tissue can be obtained by analysing diffusion-weighted MRI data sets. Several fibre tracking algorithms have been presented in the literature that trace the underlying field of principal orientations of water diffusion, which correspond to the local primary eigenvectors of the diffusion tensor field. However, the majority of the existing techniques ignore the secondary and tertiary orientations of diffusion, which contain significant information on the local patterns of diffusion. In this paper, we introduce the idea of perpendicular fibre tracking and present a novel dynamic programming method that traces surfaces, which are locally perpendicular to the axonal fibres. This is achieved by using a cost function, with geometric and fibre orientation constraints, that is evaluated dynamically for every voxel in the image domain starting from a given seed point. The proposed method is tested using synthetic and real DW-MRI data sets. The results conclusively demonstrate the accuracy and effectiveness of our method.

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Tensor Splines for Interpolation and Approximation of DT-MRI With Applications to Segmentation of Isolated Rat Hippocampi

Cited by 70 publications

References 31 publications

Modeling Textural Processes during Self-Assembly of Plant-Based Chiral-Nematic Liquid Crystals

Modeling Textural Processes during Self-Assembly of Plant-Based Chiral-Nematic Liquid Crystals

Combined Tensor Fitting and TV Regularization in Diffusion Tensor Imaging Based on a Riemannian Manifold Approach

Perpendicular fibre tracking for neural fibre bundle analysis using diffusion MRI

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