Publications

In this paper we generalize the Log-Euclidean polyaffine registration framework of Arsigny et al. to deal with articulated structures. This framework has very useful properties as it guarantees the invertibility of smooth geometric transformations. In articulated registration a skeleton model is defined for rigid structures such as bones. The final transformation is affine for the bones and elastic for other tissues in the image. We extend the Arsigny el al.’s method to deal with locally-affine registration of pairs of wires. This enables the possibility of using this registration framework to deal with articulated structures. In this context, the design of the weighting functions, which merge the affine transformations defined for each pair of wires, has a great impact not only on the final result of the registration algorithm, but also on the invertibility of the global elastic transformation. Several experiments, using both synthetic images and hand radiographs, are also presented.

Experimental and imaging studies in monkeys have outlined various long association fiber bundles within the temporoparietal region. In the present study the trajectory of the middle longitudinal fascicle (MdLF) has been delineated in 4 human subjects using diffusion tensor magnetic resonance imaging segmentation and tractography. The MdLF seems to extend from the inferior parietal lobule (IPL), specifically the angular gyrus, to the temporal pole remaining within the white matter of the superior temporal gyrus (STG). Comparison of the superior longitudinal fascicle II-arcuate fascicle (SLF II-AF) with the MdLF in the same subjects revealed that MdLF is located in a medial and caudal position relative to SLF II-AF and that it extends more rostrally. Given the location of MdLF between the IPL (angular gyrus) and the STG, it is suggested that MdLF could have a role in language and attention functions.

In this paper we deal with the problem of quantification of diffusion tensor (DT) data sets. A set of measures and a 2D tract mapping technique are proposed to analyze the fiber structures in brain white matter and to allow for comparisons between different subjects, either patients or controls. Features such as integrity, discontinuity and connectivity of the fiber bundles are proposed and analyzed, taking into account longitudinal and transverse information of the fiber bundle under study. The performance of the proposed characterization framework is shown analyzing the corticospinal tracts of control data sets and pathological cases, comparing the measures between controls and patients and also between the right and left hemispheres. A reproducibility study is also performed to show the robustness of the proposed measures.

The aim of this work was to study the diffusion-related signal attenuation curves (signal-vs.-b curves) measured perpendicular and parallel to the neuronal fibers of the corticospinal tract in vivo and to determine whether effects of restricted diffusion could be observed when varying the diffusion time (T(D)). A biexponential model and a two-compartment model including exchange according to the Kärger formalism were employed to analyze the signal-vs.-b curves. To validate the two-compartment model, restricted diffusion with exchange was simulated for uniformly sized cylinders, using different diameters and exchange times. The model was shown to retrieve the simulated parameters well, also when the short gradient pulse approximation was not met. The in vivo measurements performed perpendicular to the tracts, using b values up to 28000 s/mm(2) and T(D) values between 64 and 256 ms, did not show the effects of restricted diffusion as expected from previous ex vivo studies. The applied two-compartment model yielded an average axonal diameter of about 4 mum and an intracellular exchange time of about 300 ms, but did not fit statistically well to the data. In conclusion, this study indicates that if the diffusion is modeled as two compartments, of which one is restricted, exchange must be included in the model.

It has been shown that the tensor calculation is very sensitive to the presence of noise in the acquired images, yielding to very low quality Diffusion Tensor Images (DTI) data. Recent investigations have shown that the noise present in the Diffusion Weighted Images (DWI) causes bias effects on the DTI data which cannot be corrected if the noise characteristic is not taken into account. One possible solution is to increase the minimum number of acquired measurements (which is 7) to several tens (or even several hundreds). This has the disadvantage of increasing the acquisition time by one (or two) orders of magnitude, making the process inconvenient for a clinical setting. We here proposed a turn-around procedure for which the number of acquisitions is maintained but, the DWI data are filtered prior to determining the DTI. We show a significant reduction on the DTI bias by means of a simple and fast procedure which is based on linear filtering; well-known drawbacks of such filters are circumvented by means of anisotropic neighborhoods and sequential application of the filter itself. Information of the first order probability density function of the raw data, namely, the Rice distribution, is also included. Results are shown both for synthetic and real datasets. Some error measurements are determined in the synthetic experiments, showing how the proposed scheme is able to reduce them. It is worth noting a 50% increase in the linear component for real DTI data, meaning that the bias in the DTI is considerably reduced. A novel fiber smoothness measure is defined to evaluate the resulting tractography for real DWI data. Our findings show that after filtering, fibers are considerably smoother on the average. Execution times are very low as compared to other reported approaches which allows for a real-time implementation.

Parallel MRI (pMRI) achieves imaging acceleration by partially substituting gradient-encoding steps with spatial information contained in the component coils of the acquisition array. Variable-density subsampling in pMRI was previously shown to yield improved two-dimensional (2D) imaging in comparison to uniform subsampling, but has yet to be used routinely in clinical practice. In an effort to reduce acquisition time for 3D fast spin-echo (3D-FSE) sequences, this work explores a specific nonuniform sampling scheme for 3D imaging, subsampling along two phase-encoding (PE) directions on a rectilinear grid. We use two reconstruction methods-2D-GRAPPA-Operator and 2D-SPACE RIP-and present a comparison between them. We show that high-quality images can be reconstructed using both techniques. To evaluate the proposed sampling method and reconstruction schemes, results via simulation, phantom study, and in vivo 3D human data are shown. We find that fewer artifacts can be seen in the 2D-SPACE RIP reconstructions than in 2D-GRAPPA-Operator reconstructions, with comparable reconstruction times.

Characterizing diffusion of gases and liquids within pores is important in understanding numerous transport processes and affects a wide range of practical applications. Previous measurements of the pulsed gradient stimulated echo (PGSTE) signal attenuation, E(q), of water within nerves and impermeable cylindrical microcapillary tubes showed it to be exquisitely sensitive to the orientation of the applied wave vector, q, with respect to the tube axis in the high-q regime. Here, we provide a simple three-dimensional model to explain this angular dependence by decomposing the average propagator, which describes the net displacement of water molecules, into components parallel and perpendicular to the tube wall, in which axial diffusion is free and radial diffusion is restricted. The model faithfully predicts the experimental data, not only the observed diffraction peaks in E(q) when the diffusion gradients are approximately normal to the tube wall, but their sudden disappearance when the gradient orientation possesses a small axial component. The model also successfully predicts the dependence of E(q) on gradient pulse duration and on gradient strength as well as tube inner diameter. To account for the deviation from the narrow pulse approximation in the PGSTE sequence, we use Callaghan’s matrix operator framework, which this study validates experimentally for the first time. We also show how to combine average propagators derived for classical one-dimensional and two-dimensional models of restricted diffusion (e.g. between plates, within cylinders) to construct composite three-dimensional models of diffusion in complex media containing pores (e.g. rectangular prisms and/or capped cylinders) having a distribution of orientations, sizes, and aspect ratios. This three-dimensional modeling framework should aid in describing diffusion in numerous biological systems and in a myriad of materials sciences applications.

Two strategies are widely used in parallel MRI to reconstruct subsampled multicoil image data. SENSE and related methods employ explicit receiver coil spatial response estimates to reconstruct an image. In contrast, coil-by-coil methods such as GRAPPA leverage correlations among the acquired multicoil data to reconstruct missing k-space lines. In self-referenced scenarios, both methods employ Nyquist-rate low-frequency k-space data to identify the reconstruction parameters. Because GRAPPA does not require explicit coil sensitivities estimates, it needs considerably fewer autocalibration signals than SENSE. However, SENSE methods allow greater opportunity to control reconstruction quality though regularization and thus may outperform GRAPPA in some imaging scenarios. Here, we employ GRAPPA to improve self-referenced coil sensitivity estimation in SENSE and related methods using very few auto-calibration signals. This enables one to leverage each methods’ inherent strength and produce high quality self-referenced SENSE reconstructions.

q-Space diffusion MRI (QSI) provides a means of obtaining microstructural information about porous materials and neuronal tissues from diffusion data. However, the accuracy of this structural information depends on experimental parameters used to collect the MR data. q-Space diffusion MR performed on clinical scanners is generally collected with relatively long diffusion gradient pulses, in which the gradient pulse duration, delta, is comparable to the diffusion time, Delta. In this study, we used phantoms, consisting of ensembles of microtubes, and mathematical models to assess the effect of the ratio of the diffusion time and the duration of the diffusion pulse gradient, i.e., Delta/delta, on the MR signal attenuation vs. q, and on the measured structural information extracted therefrom. We found that for Delta/delta approximately 1, the diffraction pattern obtained from q-space MR data are shallower than when the short gradient pulse (SGP) approximation is satisfied. For long delta the estimated compartment size is, as expected, smaller than the real size. Interestingly, for Delta/delta approximately 1 the diffraction peaks are shifted to even higher q-values, even when delta is kept constant, giving the impression that the restricted compartments are even smaller than they are. When phantoms composed of microtubes of different diameters are used, it is more difficult to estimate the diameter distribution in this regime. Excellent agreement is found between the experimental results and simulations that explicitly account for the use of long duration gradient pulses. Using such experimental data and this mathematical framework, one can estimate the true compartment dimensions when long and finite gradient pulses are used even when Delta/delta approximately 1.

We consider a general double pulsed field gradient experiment with arbitrary experimental parameters and calculate an exact expression for the NMR signal attenuation from restricted geometries, which is valid at long wavelengths, i.e., when the product of the gyromagnetic ratio of the spins, the pulsed gradients’ duration, and their magnitude is small compared to the reciprocal of the pore size. It is possible to observe microscopic anisotropy within the pore space induced by the boundaries of the pore, which can be used to differentiate restricted from free or multicompartmental diffusion and to estimate a characteristic pore dimension in the former case. Explicit solutions for diffusion taking place between parallel plates as well as in cylindrical and spherical pores are provided. In coherently packed cylindrical pores, it is possible to measure simultaneously the cylinders’ orientation and diameter using small gradient strengths. The presence of orientational heterogeneity of cylinders is addressed, and a scheme for differentiating microscopic from ensemble anisotropy is proposed.