Marco Reisert

Gibbs‐ringing artifact removal based on local subvoxel‐shifts

To develop a fast and stable method for correcting the gibbs‐ringing artifact.

Single shot whole brain imaging using spherical stack of spirals trajectories.

MR-encephalography allows the observation of functional signal in the brain at a frequency of 10 Hz, permitting filtering of physiological noise and the detection of single event activations. High temporal resolution is achieved by the use of undersampled non-Cartesian trajectories, parallel imaging and regularized image reconstruction. MR-encephalography is based on 3D-encoding, allowing undersampling in two dimensions and providing advantages in terms of signal to noise ratio. Long readout times, which are necessary for single shot whole brain imaging (up to 75 ms), cause off-resonance artifacts. To meet this issue, a spherical stack of spirals trajectory is proposed in this work. By examining the trajectories in local k-space, it is shown that in areas of strong susceptibility gradients spatial information is fundamentally lost, making a meaningful image reconstruction impossible in the affected areas. It is shown that the loss of spatial information is reduced when using a stack of spirals trajectory compared to concentric shells.

Whole-Brain In-vivo Measurements of the Axonal G-Ratio in a Group of 37 Healthy Volunteers.

The g-ratio, quantifying the ratio between the inner and outer diameters of a fiber, is an important microstructural characteristic of fiber pathways and is functionally related to conduction velocity. We introduce a novel method for estimating the MR g-ratio non-invasively across the whole brain using high-fidelity magnetization transfer (MT) imaging and single-shell diffusion MRI. These methods enabled us to map the MR g-ratio in vivo across the brains prominent fiber pathways in a group of 37 healthy volunteers and to estimate the inter-subject variability. Effective correction of susceptibility-related distortion artifacts was essential before combining the MT and diffusion data, in order to reduce partial volume and edge artifacts. The MR g-ratio is in good qualitative agreement with histological findings despite the different resolution and spatial coverage of MRI and histology. The MR g-ratio holds promise as an important non-invasive biomarker due to its microstructural and functional relevance in neurodegeneration.

MesoFT: unifying diffusion modelling and fiber tracking.

One overarching challenge of clinical magnetic resonance imaging (MRI) is to quantify tissue structure at the cellular scale of micrometers, based on an MRI acquisition with a millimeter resolution. Diffusion MRI (dMRI) provides the strongest sensitivity to the cellular structure. However, interpreting dMRI measurements has remained a highly ill-posed inverse problem. Here we propose a framework that resolves the above challenge for human white matter fibers, by unifying intra-voxel mesoscopic modeling with global fiber tractography. Our algorithm is based on a Simulated Annealing approach which simultaneously optimizes diffusion parameters and fiber locations. Each fiber carries its by their individual set of diffusion parameters which allows to link them structural relationships.

Deletion of the mu opioid receptor gene in mice reshapes the reward-aversion connectome.

Significance Mice manipulated by targeted deletion of a specific brain gene show diverse pathological phenotypes, apparent, for example, in behavioral experiments. To explain observed findings, connectome genetics attempts to uncover how brain functional connectivity is affected by genetics. However the causal impact of a single gene on whole-brain networks is still unclear. Here the sole targeted deletion of the mu opioid receptor gene (Oprm1), the main target for morphine, induced widespread remodeling of brain functional connectome in mice. The strongest perturbations occurred within the so-called reward/aversion-circuitry, predominantly influencing the negative affect centers. We present a hypothesis-free analysis of combined structural and functional connectivity data obtained via MRI of the living mouse brain, and identify a specific Oprm1 gene-to-network signature. Connectome genetics seeks to uncover how genetic factors shape brain functional connectivity; however, the causal impact of a single gene’s activity on whole-brain networks remains unknown. We tested whether the sole targeted deletion of the mu opioid receptor gene (Oprm1) alters the brain connectome in living mice. Hypothesis-free analysis of combined resting-state fMRI diffusion tractography showed pronounced modifications of functional connectivity with only minor changes in structural pathways. Fine-grained resting-state fMRI mapping, graph theory, and intergroup comparison revealed Oprm1-specific hubs and captured a unique Oprm1 gene-to-network signature. Strongest perturbations occurred in connectional patterns of pain/aversion-related nodes, including the mu receptor-enriched habenula node. Our data demonstrate that the main receptor for morphine predominantly shapes the so-called reward/aversion circuitry, with major influence on negative affect centers.

Arterial input function measurements for bolus tracking perfusion imaging in the brain

Imaging of cerebral perfusion by tracking the first passage of an exogenous paramagnetic contrast agent (termed dynamic susceptibility contrast, MRI) has been used in the clinical practice for about a decade. However, the primary goal of dynamic susceptibility contrast MRI to directly quantify the local cerebral blood flow remains elusive. The major challenge of dynamic susceptibility contrast MRI is to measure the contrast inflow to the brain, i.e., the arterial input function. The measurement is complicated by the limited dynamic range of MRI pulse sequences that are optimized for a good contrast in brain tissue but are suboptimal for a much higher tracer concentration in arterial blood. In this work, we suggest a novel method for direct arterial input function quantification. The arterial input function is measured in the carotid arteries with a dedicated plug‐in to the conventional pulse sequence to enable resolution of T2 on the order of a millisecond. The new technique is compatible with the clinical measurement protocols. Applied to the pig model (N = 13), the method demonstrates robustness of the arterial input function measurement. The cardiac output and cerebral blood volume, obtained without adjustable parameters, agree well with positron emission tomography measurements and values found in the literature. Magn Reson Med, 2013.

Predicting Planning Performance from Structural Connectivity Between Left and Right Mid-Dorsolateral Prefrontal Cortex: Moderating Effects of Age During Postadolescence and Midadulthood

Complex cognitive abilities such as planning are known to critically rely on activity of bilateral mid-dorsolateral prefrontal cortex (mid-dlPFC). However, the functional relevance of the structural connectivity between left and right mid-dlPFC is yet unknown. Here, we applied global tractography to derive streamline counts as estimates of the structural connectivity between mid-dlPFC homologs and related it to planning performance in the Tower of London task across early to midadulthood, assuming a moderating effect of age. Multiple regression analyses with interaction effects revealed that streamline counts between left and right mid-dlPFC were negatively associated with planning performance specifically in early postadolescence. From the fourth life decade on, there was a trend for a reversed, positive association. These differential findings were corroborated by converging results from fractional anisotropy and white-matter density estimates in the genu of the corpus callosum where fibers connecting mid-dlPFC homologs traversed. Moreover, the results for streamline counts were regionally specific, marking the strength of mid-dlPFC connectivity as critical in predicting interindividual differences in planning performance across different stages of adulthood. Taken together, present findings provide first evidence for nonadditive effects of age on the relation between complex cognitive abilities and the structural connectivity of mid-dlPFC homologs.

SHOG: spherical HOG descriptors for rotation invariant 3D object detection

We present a method for densely computing local spherical histograms of oriented gradients (SHOG) in volumetric images. The descriptors are based on the continuous representation of the orientation histograms in the harmonic domain, which we compute very efficiently via spherical tensor products and the Fast Fourier Transformation. Building upon these local spherical histogram representations, we utilize the Harmonic Filter to create a generic rotation invariant object detection system that benefits from both the highly discriminative representation of local image patches in terms of histograms of oriented gradients and an adaptable trainable voting scheme that forms the filter. We exemplarily demonstrate the effectiveness of such dense spherical 3D descriptors in a detection task on biological 3D images. In a direct comparison to existing approaches, our new filter reveals superior performance.

Circular Fourier-HOG features for rotation invariant object detection in biomedical images

In this paper we present a new system for generic rotation invariant 2D object detection based on circular Fourier HOG features. Our system combines the advantages of a dense voting scheme as it is used in the Holomorphic Filter framework with features based on local orientation statistics. Experiments on two different biological datasets show superior detection performance over four state-of-the-art reference approaches.

MR image reconstruction from generalized projections.

Currently, the time required for image reconstruction is prohibitively long if data are acquired using multidimensional imaging trajectories that make use of multichannel systems equipped with nonlinear gradients. Methods are presented that reduce the computational complexity of the iterative time‐domain reconstruction algorithm down from O(N4) to O(N3).