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P J Basser

Publications and source records attributed to P J Basser.

At least 19 recordsLinked to original sources
PubMed2004

Comprehensive approach for correction of motion and distortion in diffusion-weighted MRI.

Patient motion and image distortion induced by eddy currents cause artifacts in maps of diffusion parameters computed from diffusion-weighted (DW) images. A novel and comprehensive approach to correct for spatial misalignment of DW imaging (DWI) volumes acquired with different strengths and orientations of the diffusion sensitizing gradients is presented. This approach uses a mutual information-based registration technique and a spatial transformation model containing parameters that correct for eddy current-induced image distortion and rigid body motion in three dimensions. All parameters are optimized simultaneously for an accurate and fast solution to the registration problem. The images can also be registered to a normalized template with a single interpolation step without additional computational cost. Following registration, the signal amplitude of each DWI volume is corrected to account for size variations of the object produced by the distortion correction, and the b-matrices are properly recalculated to account for any rotation applied during registration. Both qualitative and quantitative results show that this approach produces a significant improvement of diffusion tensor imaging (DTI) data acquired in the human brain.

Algorithms↗
PubMed2002

Cartilage calcification studied by proton nuclear magnetic resonance microscopy.

A three-dimensional (3D) mineralizing culture system using hollow fiber bioreactors has been developed to study the early stages of endochondral ossification by proton nuclear magnetic resonance (NMR) microscopy. Chondrocytes harvested from the cephalic half of the sterna from 17-day-old chick embryos were terminally differentiated with 33 nM of retinoic acid for 1 week and mineralization was initiated by the addition of 1% beta-glycerophosphate to the culture medium. Histological sections taken after 6 weeks of development in culture confirmed calcification of the cartilage matrix formed in bioreactors. Calcium to phosphorus ratios (1.62-1.68) from X-ray microanalysis supported electron diffraction of thin tissue sections showing the presence of a poorly crystalline hydroxyapatite mineral phase in the cultures. After 4 weeks of culture, quantitative proton NMR images showed water proton magnetization transfer rate constants (km) were higher in premineralized cartilage compared with uncalcified cartilage, a result suggesting collagen enrichment of the matrix. Notably after 5 weeks mineral deposits formed in bioreactors principally in the collagen-enriched zones of the cartilage with increased km values. This caused marked reductions in water proton longitudinal (T1) and transverse (T2) relaxation times and water diffusion coefficients (D). These results support the hypothesis that mineralization proceeds in association with a collagen template. After 6 weeks of culture development, the water proton T2 values decreased by 13% and D increased by 7% in uncalcified areas, compared with the same regions of tissue examined 1 week earlier. These changes could be attributed to the formation of small mineral inclusions in the cartilage, possibly mediated by matrix vesicles, which may play an important role in cartilage calcification. In summary, NMR images acquired before and after the onset of mineralization of the same tissue provide unique insights into the matrix events leading to endochondral mineral formation.

Animals↗
PubMed2001

Analytical computation of the eigenvalues and eigenvectors in DT-MRI.

In this paper a noniterative algorithm to be used for the analytical determination of the sorted eigenvalues and corresponding orthonormalized eigenvectors obtained by diffusion tensor magnetic resonance imaging (DT-MRI) is described. The algorithm uses the three invariants of the raw water spin self-diffusion tensor represented by a 3 x 3 positive definite matrix and certain math functions that do not require iteration. The implementation requires a positive definite mask to preserve the physical meaning of the eigenvalues. This algorithm can increase the speed of eigenvalue/eigenvector calculations by a factor of 5-40 over standard iterative Jacobi or singular-value decomposition techniques. This approach may accelerate the computation of eigenvalues, eigenvalue-dependent metrics, and eigenvectors especially when having high-resolution measurements with large numbers of slices and large fields of view.

Algorithms↗
PubMed2001

Effect of monovalent-divalent cation exchange on the swelling of polyacrylate hydrogels in physiological salt solutions.

The volume transition induced by monovalent-divalent cation exchange of fully neutralized polyacrylate hydrogels was investigated in aqueous NaCl solutions. The variation of the osmotic swelling pressure, shear modulus, and mixing pressure was measured when Na(+) ions were substituted by divalent or trivalent cations. Alkali metal salts move freely throughout the entirely network, and alkaline earth metal salts (CaCl(2), SrCl(2)) promote aggregation of polyacrylate chains, but these aggregates are relatively weak. Transition metal salts (CoCl(2), NiCl(2)) form stronger interchain associates. Rare earth cations (La(3+) and Ce(3+)) bind practically irreversibly to the polymer. Experimental data indicate that transition metal cations modify both the elastic and mixing components of the free energy, while alkaline earth metal cations affect primarily the mixing term. The behavior of freely swollen gels was compared with similar gels subjected to uniaxial compression. In uniaxially compressed gels, volume transition occurs at lower cation concentrations than in the corresponding undeformed gels. The shift of the transition point increases with the deformation ratio and is larger for Co(2+) than for Ca(2+).

Acrylic Resins↗
PubMed2001

Spatial transformations of diffusion tensor magnetic resonance images.

We address the problem of applying spatial transformations (or "image warps") to diffusion tensor magnetic resonance images. The orientational information that these images contain must be handled appropriately when they are transformed spatially during image registration. We present solutions for global transformations of three-dimensional images up to 12-parameter affine complexity and indicate how our methods can be extended for higher order transformations. Several approaches are presented and tested using synthetic data. One method, the preservation of principal direction algorithm, which takes into account shearing, stretching and rigid rotation, is shown to be the most effective. Additional registration experiments are performed on human brain data obtained from a single subject, whose head was imaged in three different orientations within the scanner. All of our methods improve the consistency between registered and target images over naïve warping algorithms.

Adult↗
PubMed2000

Statistical artifacts in diffusion tensor MRI (DT-MRI) caused by background noise.

This work helps elucidate how background noise introduces statistical artifacts in the distribution of the sorted eigenvalues and eigenvectors in diffusion tensor MRI (DT-MRI) data. Although it was known that sorting eigenvalues (principal diffusivities) by magnitude introduces a bias in their sample mean within a homogeneous region of interest (ROI), here it is shown that magnitude sorting also introduces a significant bias in the variance of the sample mean eigenvalues. New methods are presented to calculate the mean and variance of the eigenvectors of the diffusion tensor, based on a dyadic tensor representation of eigenvalue-eigenvector pairs. Based on their use it is shown that sorting eigenvalues by magnitude also introduces a bias in the mean and the variance of the sample eigenvectors (principal directions). This required the development of new methods to calculate the mean and variance of the eigenvectors of the diffusion tensor, based on a dyadic tensor representation of eigenvalue-eigenvector pairs. Moreover, a new approach is proposed to order these pairs within an ROI. To do this, a correspondence between each principal axis of the diffusion ellipsoid, an eigenvalue-eigenvector pair, and a dyadic tensor constructed from it is exploited. A measure of overlap between principal axes of diffusion ellipsoids in different voxels is defined that employs projections between these dyadic tensors. The optimal eigenvalue assignment within an ROI maximizes this overlap. Bias in the estimate of the mean and of the variance of the eigenvalues and of their corresponding eigenvectors is reduced in DT-MRI experiments and in Monte Carlo simulations of such experiments. Improvement is most significant in isotropic regions, but some is also observed in anisotropic regions. This statistical framework should enhance our ability to characterize microstructure and architecture of healthy tissue, and help to assess its changes in development, disease, and degeneration. Mitigating these artifacts should also improve the characterization of diffusion anisotropy and the elucidation of fiber-tract trajectories in the brain and in other fibrous tissues. Magn Reson Med 44:41-50, 2000. Published 2000 Wiley-Liss, Inc.

Artifacts↗
PubMed2000

In vivo fiber tractography using DT-MRI data.

Fiber tract trajectories in coherently organized brain white matter pathways were computed from in vivo diffusion tensor magnetic resonance imaging (DT-MRI) data. First, a continuous diffusion tensor field is constructed from this discrete, noisy, measured DT-MRI data. Then a Frenet equation, describing the evolution of a fiber tract, was solved. This approach was validated using synthesized, noisy DT-MRI data. Corpus callosum and pyramidal tract trajectories were constructed and found to be consistent with known anatomy. The method's reliability, however, degrades where the distribution of fiber tract directions is nonuniform. Moreover, background noise in diffusion-weighted MRIs can cause a computed trajectory to hop from tract to tract. Still, this method can provide quantitative information with which to visualize and study connectivity and continuity of neural pathways in the central and peripheral nervous systems in vivo, and holds promise for elucidating architectural features in other fibrous tissues and ordered media.

Artifacts↗
PubMed2000

Osmotic swelling of polyacrylate hydrogels in physiological salt solutions.

The swelling behavior of fully neutralized sodium polyacrylate gels was investigated in aqueous solutions of alkali metal (LiCl, NaCl, KCl, CsCl) and alkaline earth metal salts (CaCl2, SrCl2, BaCl2). The total salt concentration and the ratio of monovalent to divalent cations were varied in the biologically significant range. It is found that the concentrations of both monovalent and divalent cations vary continuously and smoothly in the gel despite the abrupt change in the gel volume. The individual elastic, mixing, and ionic contributions to the free energy of the gel were separately determined as a function of the degree of network swelling to elucidate the thermodynamics of swelling. Shear modulus measurements performed at different Ca2+ concentrations suggest that Ca2+ does not form stable cross-links between the polymer chains. At low and moderate swelling ratios the concentration dependence of the shear modulus follows a power law behavior, G variation of phi n, with n = 0.34 +/- 0.03. At high swelling degrees, however, the shear modulus increases with increasing swelling. The value of the Flory-Huggins interaction parameter, chi, determined from osmotic swelling pressure and shear modulus measurements, strongly depends on the ionic composition of the equilibrium solution and increases with increasing Ca2+ concentration.

Acrylates↗
PubMed2000

New currents in electrical stimulation of excitable tissues.

Electric fields can stimulate excitable tissue by a number of mechanisms. A uniform long, straight peripheral axon is activated by the gradient of the electric field that is oriented parallel to the fiber axis. Cortical neurons in the brain are excited when the electric field, which is applied along the axon-dendrite axis, reaches a particular threshold value. Cardiac tissue is thought to be depolarized in a uniform electric field by the curved trajectories of its fiber tracts. The bidomain model provides a coherent conceptual framework for analyzing and understanding these apparently disparate phenomena. Concepts such as the activating function and virtual anode and cathode, as well as anode and cathode break and make stimulation, are presented to help explain these excitation events in a unified manner. This modeling approach can also be used to describe the response of excitable tissues to electric fields that arise from charge redistribution (electrical stimulation) and from time-varying magnetic fields (magnetic stimulation) in a self-consistent manner. It has also proved useful to predict the behavior of excitable tissues, to test hypotheses about possible excitation mechanisms, to design novel electrophysiological experiments, and to interpret their findings.

Animals↗
PubMed1998

Mechanical properties of the collagen network in human articular cartilage as measured by osmotic stress technique.

We have used an isotropic osmotic stress technique to assess the swelling pressures of human articular cartilage over a wide range of hydrations in order to determine from these measurements, for the first time, the tensile stress in the collagen network, Pc, as a function of hydration. Osmotic stress was applied by means of calibrated solutions of polyethylene glycol. Calculations of osmotic stress were based on the balance, at equilibrium, between the applied stress, the collagen stress, and the proteoglycan osmotic pressure, piPG, acting within the extrafibrillar matrix compartment. Pc vs hydration was determined for several normal human samples, both native and trypsin-treated, and for cartilage from one osteoarthritic (OA) joint. We found that for normal cartilage the collagen network does not become "limp" until the volume of cartilage has decreased by 20-25% of its initial value and that its contribution to the balance of forces in cartilage therefore must be taken into account over a much wider range of hydrations than was previously thought. For normal cartilage, the Pc vs hydration curves exhibit a steep increase with increasing hydration; trypsin treatment does not change their slope, showing that PG concentration does not influence the inherent stiffness of the collagen network. By contrast, the curves for OA specimens are considerably shallower and displaced to higher hydrations. Our findings thus highlight the role of the stiffness of the collagen network in limiting hydration in normal cartilage and ensuring a high PG concentration in the matrix, which is essential for effective load-bearing and is lost in OA.

Cartilage, Articular↗
PubMed1998

A simplified method to measure the diffusion tensor from seven MR images.

Analytical expressions of the diffusion tensor of water, D, and of scalar invariants derived from it, are given in terms of the intensities of seven diffusion-weighted images (DWIs). These formulas simplify the post-processing steps required in diffusion tensor imaging, including estimating D in each voxel (from the set of b-matrices and their corresponding DWIs), and then computing its eigenvalues, eigenvectors, and scalar invariants. In a study conducted using artifact-free DWIs with high diffusion weighting (bmax approximately 900 s/mm2, maps of Trace(D) and the Relative and Lattice Anisotropy indices calculated analytically and by multivariate linear regression showed excellent agreement in brain parenchyma of a healthy living cat. However, the quality of the analytically computed maps degraded markedly as diffusion weighting was reduced. Although diffusion tensor MRI with seven DWIs may be useful for clinical applications where rapid scanning and data processing are required, it does not provide estimates of the uncertainty of the measured imaging parameters, rendering it susceptible to noise and systematic artifacts. Therefore, care should be taken when using this technique in radiological applications.

Animals↗
PubMed1998

Anisotropically weighted MRI.

The intensity of an isotropically weighted MR image is proportional to a rotationally invariant measure of bulk diffusion, Trace(D) (where D is the effective diffusion tensor). Such images can be acquired from as few as two diffusion-weighted images (DWIs). Analogously, the intensity of an anisotropically weighted MR image is proportional to a rotationally invariant measure of diffusion anisotropy derived from D, such as the variance of the principal diffusivities of D. By using linear algebra, we show that to produce an anisotropically weighted MR image requires acquiring at least seven DWIs, which is also the minimum number of DWIs sufficient to estimate the entire diffusion tensor, as well as the T2-weighted amplitude image, A(b = 0), in each voxel. A general mathematical framework for constructing isotropically weighted and anisotropically weighted MR images is also provided.

Anisotropy↗
PubMed1997

The b matrix in diffusion tensor echo-planar imaging.

In diffusion tensor imaging (DTI) an effective diffusion tensor in each voxel is measured by using a set of diffusion-weighted images (DWIs) in which diffusion gradients are applied in a multiplicity of oblique directions. However, to estimate the diffusion tensor accurately, one must account for the effects of all imaging and diffusion gradient pulses on each signal echo, which are embodied in the b matrix. For DTI to be practical clinically, one must also acquire DWIs rapidly and free of motion artifacts, which is now possible with diffusion-weighted echo-planar imaging (DW-EPI). An analytical expression for the b matrix of a general DW-EPI pulse sequence is presented and then validated experimentally by measuring the diffusion tensor in an isotropic phantom whose diffusivity is already known. The b matrix is written in a convenient tabular form as a sum of individual pair-wise contributions arising from gradient pulses applied along parallel and perpendicular directions. While the contributions from readout and phase-encode gradient pulse trains are predicted to have a negligible effect on the echo, the contributions from other imaging and diffusion gradient pulses applied in both parallel and orthogonal directions are shown to be significant in our sequence. In general, one must understand and account for the multiplicity of interactions between gradient pulses and the echo signal to ensure that diffusion tensor imaging is quantitative.

Algorithms↗
PubMed1996

Toward a quantitative assessment of diffusion anisotropy.

Indices of diffusion anisotropy calculated from diffusion coefficients acquired in two or three perpendicular directions are rotationally variant. In living monkey brain, these indices severely underestimate the degree of diffusion anisotropy. New indices calculated from the entire diffusion tensor are rotationally invariant (RI). They show that anisotropy is highly variable in different white matter regions depending on the degree of coherence of fiber tract directions. In structures with a regular, parallel fiber arrangement, water diffusivity in the direction parallel to the fibers (Dparallel approximately 1400-1800 x 10(-6) mm2/s) is almost 10 times higher than the average diffusivity in directions perpendicular to them (D + D)/2 [corrected] approximately 150-300 x 10(-6) mm2/s), and is almost three times higher than previously reported. In structures where the fiber pattern is less coherent (e.g., where fiber bundles merge), diffusion anisotropy is significantly reduced. However, RI anisotropy indices are still susceptible to noise contamination. Monte Carlo simulations show that these indices are statistically biased, particularly those requiring sorting of the eigenvalues of the diffusion tensor based on their magnitude. A new intervoxel anisotropy index is proposed that locally averages inner products between diffusion tensors in neighboring voxels. This "lattice" RI index has an acceptably low error variance and is less susceptible to bias than any other RI anisotropy index proposed to date.

Animals↗
PubMed1996

Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI.

Quantitative-diffusion-tensor MRI consists of deriving and displaying parameters that resemble histological or physiological stains, i.e., that characterize intrinsic features of tissue microstructure and microdynamics. Specifically, these parameters are objective, and insensitive to the choice of laboratory coordinate system. Here, these two properties are used to derive intravoxel measures of diffusion isotropy and the degree of diffusion anisotropy, as well as intervoxel measures of structural similarity, and fiber-tract organization from the effective diffusion tensor, D, which is estimated in each voxel. First, D is decomposed into its isotropic and anisotropic parts, [D] I and D - [D] I, respectively (where [D] = Trace(D)/3 is the mean diffusivity, and I is the identity tensor). Then, the tensor (dot) product operator is used to generate a family of new rotationally and translationally invariant quantities. Finally, maps of these quantitative parameters are produced from high-resolution diffusion tensor images (in which D is estimated in each voxel from a series of 2D-FT spin-echo diffusion-weighted images) in living cat brain. Due to the high inherent sensitivity of these parameters to changes in tissue architecture (i.e., macromolecular, cellular, tissue, and organ structure) and in its physiologic state, their potential applications include monitoring structural changes in development, aging, and disease.

Animals↗
PubMed1996

Diffusion tensor MR imaging of the human brain.

PURPOSE: To assess intrinsic properties of water diffusion in normal human brain by using quantitative parameters derived from the diffusion tensor, D, which are insensitive to patient orientation. MATERIALS AND METHODS: Maps of the principal diffusivities of D, of Trace(D), and of diffusion anisotropy indices were calculated in eight healthy adults from 31 multisection, interleaved echo-planar diffusion-weighted images acquired in about 25 minutes. RESULTS: No statistically significant differences in Trace(D) (approximately 2,100 x 10(-6) mm2/sec) were found within normal brain parenchyma, except in the cortex, where Trace(D) was higher. Diffusion anisotropy varied widely among different white matter regions, reflecting differences in fiber-tract architecture. In the corpus callosum and pyramidal tracts, the ratio of parallel to perpendicular diffusivities was approximately threefold higher than previously reported, and diffusion appeared cylindrically symmetric. However, in other white matter regions, particularly in the centrum semiovale, diffusion anisotropy was low, and cylindrical symmetry was not observed. Maps of parameters derived from D were also used to segment tissues based on their diffusion properties. CONCLUSION: A quantitative characterization of water diffusion in anisotropic, heterogeneously oriented tissues is clinically feasible. This should improve the neuroradiologic assessment of a variety of gray and white matter disorders.

Adult↗
PubMed1994

Estimation of the effective self-diffusion tensor from the NMR spin echo.

The diagonal and off-diagonal elements of the effective self-diffusion tensor, Deff, are related to the echo intensity in an NMR spin-echo experiment. This relationship is used to design experiments from which Deff is estimated. This estimate is validated using isotropic and anisotropic media, i.e., water and skeletal muscle. It is shown that significant errors are made in diffusion NMR spectroscopy and imaging of anisotropic skeletal muscle when off-diagonal elements of Deff are ignored, most notably the loss of information needed to determine fiber orientation. Estimation of Deff provides the theoretical basis for a new MRI modality, diffusion tensor imaging, which provides information about tissue microstructure and its physiologic state not contained in scalar quantities such as T1, T2, proton density, or the scalar apparent diffusion constant.

Animals↗