Christian Ros

Atlas-Guided Cluster Analysis of Large Tractography Datasets

Diffusion Tensor Imaging (DTI) and fiber tractography are important tools to map the cerebral white matter microstructure in vivo and to model the underlying axonal pathways in the brain with three-dimensional fiber tracts. As the fast and consistent extraction of anatomically correct fiber bundles for multiple datasets is still challenging, we present a novel atlas-guided clustering framework for exploratory data analysis of large tractography datasets. The framework uses an hierarchical cluster analysis approach that exploits the inherent redundancy in large datasets to time-efficiently group fiber tracts. Structural information of a white matter atlas can be incorporated into the clustering to achieve an anatomically correct and reproducible grouping of fiber tracts. This approach facilitates not only the identification of the bundles corresponding to the classes of the atlas; it also enables the extraction of bundles that are not present in the atlas. The new technique was applied to cluster datasets of 46 healthy subjects. Prospects of automatic and anatomically correct as well as reproducible clustering are explored. Reconstructed clusters were well separated and showed good correspondence to anatomical bundles. Using the atlas-guided cluster approach, we observed consistent results across subjects with high reproducibility. In order to investigate the outlier elimination performance of the clustering algorithm, scenarios with varying amounts of noise were simulated and clustered with three different outlier elimination strategies. By exploiting the multithreading capabilities of modern multiprocessor systems in combination with novel algorithms, our toolkit clusters large datasets in a couple of minutes. Experiments were conducted to investigate the achievable speedup and to demonstrate the high performance of the clustering framework in a multiprocessing environment.

Fast low-angle shot diffusion tensor imaging with stimulated echo encoding in the muscle of rabbit shank.

In the past, spin‐echo (SE) echo planar imaging(EPI)‐based diffusion tensor imaging (DTI) has been widely used to study the fiber structure of skeletal muscles in vivo. However, this sequence has several shortcomings when measuring restricted diffusion in small animals, such as its sensitivity to susceptibility‐related distortions and a relatively short applicable diffusion time. To address these limitations, in the current work, a stimulated echo acquisition mode (STEAM) MRI technique, in combination with fast low‐angle shot (FLASH) readout (turbo‐STEAM MRI), was implemented and adjusted for DTI in skeletal muscles. Signal preparation using stimulated echoes enables longer effective diffusion times, and thus the detection of restricted diffusion within muscular tissue with intracellular distances up to 100 µm. Furthermore, it has a reduced penalty for fast T2 muscle signal decay, but at the expense of 50% signal loss compared with a SE preparation. Turbo‐STEAM MRI facilitates high‐resolution DTI of skeletal muscle without introducing susceptibility‐related distortions. To demonstrate its applicability, we carried out rabbit in vivo measurements on a human whole‐body 3 T scanner. DTI parameters of the shank muscles were extracted, including the apparent diffusion coefficient, fractional anisotropy, eigenvalues and eigenvectors. Eigenvectors were used to calculate maps of structural parameters, such as the planar index and the polar coordinates θ and ϕ of the largest eigenvector. These parameters were compared between three muscles. θ and ϕ showed clear differences between the three muscles, reflecting different pennation angles of the underlying fiber structures. Fiber tractography was performed to visualize and analyze the architecture of skeletal pennate muscles. Optimization of tracking parameters and utilization of T2‐weighted images for improved muscle boundary detection enabled the determination of additional parameters, such as the mean fiber length. The presented results support the applicability of turbo‐STEAM MRI as a promising method for quantitative DTI analysis and fiber tractography in skeletal muscles. Copyright

Diffusion weighted inner volume imaging of lumbar disks based on turbo-STEAM acquisition.

A magnetic resonance imaging (MRI) technique for diffusion weighted imaging (DWI) is described which, in contrast to echo planar imaging (EPI), is insensitive to off-resonance effects caused by tissue susceptibility differences, magnetic field inhomogeneities, or chemical shifts. The sequence combines a diffusion weighted (DW) spin-echo preparation and a stimulated echo acquisition mode (STEAM) module. Inner volume imaging (IVI) allows reduced rectangular field-of-view (FoV) in the phase encode direction, while suppressing aliasing artifacts that are usually the consequence of reduced FoVs. Sagittal turbo-STEAM images of the lumbar spine were acquired at 3.0T with 2.0 × 2.0 mm² in-plane resolution and 7 mm slice thickness with acquisition times of 407 ms per image. To calculate the apparent diffusion coefficient (ADC) in lumbar intervertebral disks (IVDs), the DW gradients were applied in three orthogonal gradient directions with b-values of 0 and 300 s/mm². For initial assessment of the ADC of normal and abnormal IVDs a pilot study with 8 subjects was performed. Mean ADC values of all normal IVDs were (2.27±0.40)×10⁻³ mm²/s and (1.89±0.34)×10⁻³ mm²/s for turbo-STEAM IVI and SE-EPI acquisition, respectively. Corresponding mean ADC values, averaged over all abnormal disks, were (1.93±0.39)×10⁻³ mm²/s and (1.51±0.46)×10⁻³ mm²/s, respectively, indicating a substantial ADC decrease (p<0.001).

Reconstruction of phase images for GRAPPA accelerated Magnetic Resonance Imaging

In this work we present a method to combine complex-valued phased array MR data based on a uniform sensitivity approach, which incorporates sensitivity profiles calculated from afore acquired data. The algorithm was implemented on a clinical 3T whole-body MR-Scanner and embedded into the vendor-specific standard reconstruction chain.

Vergleich von Long-Axis- und Short-Axis-PROPELLER-EPI für die diffusionsgewichtete Magnetresonanztomographie

Echo planar imaging (EPI) in combination with PROPELLER allows high-resolution diffusion-weighted imaging. In this study, the image quality of short-axis and long-axis PROPELLER was compared and optimized using phantom and in vivo data. Furthermore, diffusion-weighted measurements using both sequences were compared with those of a reference sequence. It was found that the long-axis sequence provided better image quality, whereas the results of the diffusion weighted measurements were more accurate with the short-axis variant. and that the results of the diffusion weighted measurements of both sequences agreed well with those of the reference sequence.

Quantitative fiber bundle-based analysis of diffusion-weighted MRI data

We presented a new method for the analysis of diffusion tensor imaging data sets that uses fiber bundles to enhance the quantitative analysis. By utilizing bundles the occurrence of adverse interpolation effects at the boundaries of white matter structures as a result of the non-linear spatial normalization is prevented. The method was used to assess hemispheric differences in selected fiber bundles using Fractional Anisotropy (FA) maps of 46 healthy volunteers. A statistical analysis was performed and adequate correction methods were employed to deal with statistical errors. In various bundles, statically significant differences were observed that are in line with the literature.

Diffusion Weighted ZOOM Imaging in the Lumbar Spine Based on Single-Shot STEAM

A magnetic resonance imaging (MRI) technique for diffusion weighted imaging (DWI) is described which is, in contrast to echo-planar imaging (EPI), insensitive to offresonances, due to tissue susceptibility differences, magnetic field inhomogeneities or chemical shifts. The sequence combines a diffusion weighted (DW) spin-echo preparation and a single-shot stimulated echo acquisition mode (STEAM) module. The application of an inner-volume excitation by the ZOOM imaging technique allows a reduced rectangular fieldof- view (FOV) in PE direction, but suppresses aliasing artifacts which are usually the consequence of too small FOVs. Sagittal single-shot images of the lumbar spine were acquired at 3.0 T with 2.34 × 2.34 mm2 in-plane resolution and 7 mm slice thickness. For the calculation of the apparent diffusion coefficient (ADC) and to determine the diffusibility of water in lumbar intervertebral disks (IVDs) the DW gradients were applied in orthogonal gradient orientations with b = 100 sec/mm2, b = 150 sec/mm2 and b = 250 sec/mm2.

Visualization of Orientation Distribution Functions (ODFs) with MATLAB

In this work we present a MATLAB based toolkit for the visualization of Orientation Distribution Functions (ODFs), reconstructed from multi-directional diffusion weighted MRI data. The toolkit enables software developers to visualize ODFs interactively during the evaluation and the creation of new algorithms and techniques directly in MATLAB. The MATLAB integration facilitates the alteration of the visualized data by employing user developed routines or MATLAB specific features.