ProbaStem, a pipeline towards the first high-resolution probabilistic atlas of the whole human brainstem.

The brainstem plays an essential role in many vital functions, such as autonomic control, consciousness and sleep, motricity, somatic afferent function, and cognition. Its involvement in several neurological diseases and the definition of brainstem targets for deep brain stimulation (DBS) explain the need for brainstem atlases describing its structural organization and connectivity from several modalities, from histology to ultrahigh field ex vivo MRI. Nonetheless, these atlases are often limited to a subpart of the brainstem or only include a single subject, the brainstem variability being considered low.

A novel male Japanese quail structural connectivity atlas using ultra-high field diffusion MRI at 11.7 T.

The structural connectivity of animal brains can be revealed using post-mortem diffusion-weighted magnetic resonance imaging (MRI). Despite the existence of several structural atlases of avian brains, few of them address the bird's structural connectivity. In this study, a novel atlas of the structural connectivity is proposed for the male Japanese quail (Coturnix japonica), aiming at investigating two lines divergent on their emotionality trait: the short tonic immobility (STI) and the long tonic immobility (LTI) lines.

WIKIBrainStem: An online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field MRI.

The brainstem is one of the most densely packed areas of the central nervous system in terms of gray, but also white, matter structures and, therefore, is a highly functional hub. It has mainly been studied by the means of histological techniques, which requires several hundreds of slices with a loss of the 3D coherence of the whole specimen. Access to the inner structure of the brainstem is possible using Magnetic Resonance Imaging (MRI), but this method has a limited spatial resolution and contrast in vivo.

MEDUSA: A GPU-based tool to create realistic phantoms of the brain microstructure using tiny spheres.

A GPU-based tool to generate realistic phantoms of the brain microstructure is presented. Using a spherical meshing technique which decomposes each microstructural item into a set of overlapping spheres, the phantom construction is made very fast while reliably avoiding the collisions between items in the scene. This novel method is applied to the construction of human brain white matter microstructural components, namely axonal fibers, oligodendrocytes and astrocytes.

Fronto-Subcortical Circuits for Cognition and Motivation: Dissociated Recovery in a Case of Loss of Psychic Self-Activation.

In humans and non-humans primates, extensive evidence supports the existence of subcortico-cortical circuits for cognition and behavior. Lesions studies are critical to understand the clinical significance of these functionally segregated circuits. Mapping these circuits from lesion studies is difficult given the heterogeneous etiology of the lesions, the lack of long-term and systematic testing of cognitive and behavioral disturbances, as well as the scarcity of neuroimaging data for identifying the precise location and extent of subcortical lesions.

A framework based on sulcal constraints to align preterm, infant and adult human brain images acquired in vivo and post mortem.

Robust spatial alignment of post mortem data and in vivo MRI acquisitions from different ages, especially from the early developmental stages, into standard spaces is still a bottleneck hampering easy comparison with the mainstream neuroimaging results. In this paper, we test a landmark-based spatial normalization strategy as a framework for the seamless integration of any macroscopic dataset in the context of the Human Brain Project (HBP). This strategy stems from an approach called DISCO embedding sulcal constraints in a registration framework used to initialize DARTEL, the widely used spatial normalization approach proposed in the SPM software.

Post-mortem inference of the human hippocampal connectivity and microstructure using ultra-high field diffusion MRI at 11.7 T.

The human hippocampus plays a key role in memory management and is one of the first structures affected by Alzheimer's disease. Ultra-high magnetic resonance imaging provides access to its inner structure in vivo. However, gradient limitations on clinical systems hinder access to its inner connectivity and microstructure.

High nigral iron deposition in LRRK2 and Parkin mutation carriers using R2* relaxometry.

Objectives: The goal of this work was to investigate iron deposition in the basal ganglia and thalamus in symptomatic and asymptomatic leucine-rich repeat kinase 2 (LRRK2) and Parkin-associated Parkinson's disease (PD), using R2* relaxometry rate.

Methods: Twenty subjects with genetic PD (four symptomatic and two asymptomatic Parkin subjects, nine symptomatic and five asymptomatic LRRK2 subjects) were compared with 20 patients with idiopathic PD (IPD) and 20 healthy subjects. Images were obtained at 3 teslas, using multi-echo T2 and T2* sequences.

Altered structural connectivity of cortico-striato-pallido-thalamic networks in Gilles de la Tourette syndrome.

Gilles de la Tourette syndrome is a childhood-onset syndrome characterized by the presence and persistence of motor and vocal tics. A dysfunction of cortico-striato-pallido-thalamo-cortical networks in this syndrome has been supported by convergent data from neuro-pathological, electrophysiological as well as structural and functional neuroimaging studies. Here, we addressed the question of structural integration of cortico-striato-pallido-thalamo-cortical networks in Gilles de la Tourette syndrome.

Noise correction for HARDI and HYDI data obtained with multi-channel coils and sum of squares reconstruction: an anisotropic extension of the LMMSE.

Parallel magnetic resonance imaging (MRI) yields noisy magnitude data, described in most cases as following a noncentral χ distribution when the signals received by the coils are combined as the sum of their squares. One well-known case of this noncentral χ noise model is the Rician model, but it is only valid in the case of single-channel acquisition. Although the use of parallel MRI is increasingly common, most of the correction methods still perform Rician noise removal, yielding an erroneous result due to an incorrect noise model.

Mapping cortico-striatal connectivity onto the cortical surface: a new tractography-based approach to study Huntington disease.

Huntington disease (HD) is associated with early and severe damage to the basal ganglia and particularly the striatum. We investigated cortico-striatal connectivity modifications occurring in HD patients using a novel approach which focuses on the projection of the connectivity profile of the basal ganglia onto the cortex. This approach consists in computing, for each subcortical structure, surface connectivity measures representing its strength of connections to the cortex and comparing these measures across groups.

Parallel MRI noise correction: an extension of the LMMSE to non central chi distributions.

Parallel MRI leads to magnitude data corrupted by noise described in most cases as following a Rician or a non central chi distribution. And yet, very few correction methods perform a non central chi noise removal. However, this correction step, adapted to the correct noise model, is of very much importance, especially when working with Diffusion Weighted MR data yielding a low SNR.

Analysis of the striato-thalamo-cortical connectivity on the cortical surface to infer biomarkers of Huntington's disease.

The deep brain nuclei play an important role in many brain functions and particularly motor control. Damage to these structures result in movement disorders such as in Parkinson's disease or Huntington's disease, or behavioural disorders such as Tourette syndrome. In this paper, we propose to study the connectivity profile of the deep nuclei to the motor, associative or limbic areas and we introduce a novel tool to build a probabilistic atlas of these connections to the cortex directly on the surface of the cortical mantel, as it corresponds to the space of functional interest.

Spherical wavelet transform for ODF sharpening.

The choice of local HARDI reconstruction technique is crucial for discerning multiple fiber orientations, which is itself of substantial importance for tractography, and reliable and accurate assessment of white matter fiber geometry. Due to the complexity of the diffusion process and its milieu, distinct diffusion compartments can have different frequency signatures, making the HARDI signal spread over multiple frequency bands. Therefore, we put forth the idea of multiscale analysis with localized basis functions, ensuring that different frequency ranges are probed.

New diffusion phantoms dedicated to the study and validation of high-angular-resolution diffusion imaging (HARDI) models.

We present new diffusion phantoms dedicated to the study and validation of high-angular-resolution diffusion imaging (HARDI) models. The phantom design permits the application of imaging parameters that are typically employed in studies of the human brain. The phantoms were made of small-diameter acrylic fibers, chosen for their high hydrophobicity and flexibility that ensured good control of the phantom geometry.

Mean q-ball strings obtained by constrained procrustes analysis with point sliding.

The idea underpinning the work we present herein is to design robust and objective tools for brain white matter (WM) morphometry. We focus on WM tracts, and propose to represent them by their mean lines, to which we associate the attributes derived from high-angular resolution diffusion imaging (HARDI). The definition of the tract mean line derives directly from the geometry of the tract fibres.

Real-time MR diffusion tensor and Q-ball imaging using Kalman filtering.

Diffusion magnetic resonance imaging (dMRI) has become an established research tool for the investigation of tissue structure and orientation. In this paper, we present a method for real-time processing of diffusion tensor and Q-ball imaging. The basic idea is to use Kalman filtering framework to fit either the linear tensor or Q-ball model.

Automatic inference of sulcus patterns using 3D moment invariants.

The goal of this work is the automatic inference of frequent patterns of the cortical sulci, namely patterns that can be observed only for a subset of the population. The sulci are detected and identified using brainVISA open software. Then, each sulcus is represented by a set of shape descriptors called the 3D moment invariants.

Real-time MR diffusion tensor and Q-ball imaging using Kalman filtering.

Magnetic resonance diffusion imaging (dMRI) has become an established research tool for the investigation of tissue structure and orientation. In this paper, we present a method for real time processing of diffusion tensor and Q-ball imaging. The basic idea is to use Kalman filtering framework to fit either the linear tensor or Q-ball model.

Characterization and correction of distortions in stereotactic magnetic resonance imaging for bilateral subthalamic stimulation in Parkinson disease.

Object: High-frequency stimulation of the subthalamic nucleus (STN) is effective for treating refractory idiopathic Parkinson disease (PD). In stereotactic conditions magnetic resonance (MR) imaging is used by many teams to perform preoperative targeting of the STN. The goal of this study was to analyze and correct the geometrically observed MR imaging acquisitions used for targeting of the STN.

Brain morphometry using 3D moment invariants.

This paper advocates the use of shape descriptors based on moments of 3D coordinates for morphometry of the cortical sulci. These descriptors, which have been introduced more than a decade ago, are invariant relatively to rotations, translations and scale and can be computed for any topology. A rapid insight into the derivation of these invariants is proposed first.

Foot, hand, face and eye representation in the human striatum.

The present study aimed at determining the three-dimensional organization of striatal activation during foot, hand, face and eye movements. Seven right-handed, healthy volunteers were studied at 1.5 T using blood oxygen level dependent (BOLD) contrast.

Monitoring disease progression in CADASIL with diffusion magnetic resonance imaging: a study with whole brain histogram analysis.

Background And Purpose: In cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), a large increase in water diffusion has been found both inside and outside the cerebral lesions as detected on conventional MRI. The aim of the present study was to assess the sensitivity of diffusion tensor imaging for monitoring the progression of cerebral tissue damage during the course of CADASIL.

Methods: With the use of diffusion tensor imaging, whole brain trace of the diffusion tensor [Trace(D)] histograms were obtained in 22 CADASIL patients and 12 age-matched controls at baseline, in 14 patients after a mean delay of 21 months, and in 5 controls after a mean delay of 29 months.

Clinical characteristics and topography of lesions in movement disorders due to thalamic lesions.

Objective: To determine which thalamic subnuclei are involved in symptomatic unilateral movement disorders due to localized thalamic infarction, and the clinical characteristics of these abnormal movements.

Methods: The authors studied 22 patients with thalamic infarcts for their clinical presentation and the topography of the lesions, using three-dimensional T1-weighted MRI sequencing and stereotaxic analysis of the lesions.

Results: Patients were divided into four groups: 1) absence of abnormal involuntary movements (AIM) (nine patients); 2) isolated dystonic posture (two patients); 3) myoclonic dystonia (five patients); and 4) tremor or myoclonus (six patients).

Role of the supplementary motor area in motor deficit following medial frontal lobe surgery.

Objective: Patients undergoing surgical resection of medial frontal lesions may present a transient postoperative deficit that remains largely unpredictable. The authors studied the role of the supplementary motor area (SMA) in the occurrence of this deficit using fMRI.

Methods: Twenty-three patients underwent a preoperative fMRI before resection of medial frontal lesions.