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•Subject motion in dMRI leads to a set of scattered slices with unique contrast.•We introduce a slice-to-volume reconstruction framework for multi-shell HARDI data•Based on a data-driven representation as spherical harmonics and radial decomposition (SHARD).•The method is evaluated in test-retest scans and in the neonatal dHCP cohort.•Results show robust reconstruction in severely motion-corrupted scans. Diffusion MRI offers a unique probe into neural microstructure and connectivity in the developing brain. However, analysis of neonatal brain imaging data is complicated by inevitable subject motion, leading to a series of scattered slices that need to be aligned within and across diffusion-weighted contrasts. Here, we develop a reconstruction method for scattered slice multi-shell high angular resolution diffusion imaging (HARDI) data, jointly estimating an uncorrupted data representation and motion parameters at the slice or multiband excitation level. The reconstruction relies on data-driven representation of multi-shell HARDI data using a bespoke spherical harmonics and radial decomposition (SHARD), which avoids imposing model assumptions, thus facilitating to compare various microstructure imaging methods in the reconstructed output. Furthermore, the proposed framework integrates slice-level outlier rejection, distortion correction, and slice profile correction. We evaluate the method in the neonatal cohort of the developing Human Connectome Project (650 scans). Validation experiments demonstrate accurate slice-level motion correction across the age range and across the range of motion in the population. Results in the neonatal data show successful reconstruction even in severely motion-corrupted subjects. In addition, we illustrate how local tissue modelling can extract advanced microstructure features such as orientation distribution functions from the motion-corrected reconstructions.

We propose a method for constructing a spatio-temporal cortical surface atlas of neonatal brains aged between 36 and 44 weeks of post-menstrual age (PMA) at the time of scan. The data were acquired as part of the Developing Human Connectome Project (dHCP), and the constructed surface atlases are publicly available. The method is based on a spherical registration approach: Multimodal Surface Matching (MSM), using cortical folding for driving the alignment. Templates have been generated for the anatomical cortical surface and for the cortical feature maps: sulcal depth, curvature, thickness, T1w/T2w myelin maps and cortical regions. To achieve this, cortical surfaces from 270 infants were first projected onto the sphere. Templates were then generated in two stages: first, a reference space was initialised via affine alignment to a group average adult template. Following this, templates were iteratively refined through repeated alignment of individuals to the template space until the variability of the average feature sets converged. Finally, bias towards the adult reference was removed by applying the inverse of the average affine transformations on the template and de-drifting the template. We used temporal adaptive kernel regression to produce age-dependant atlases for 9 weeks (36–44 weeks PMA). The generated templates capture expected patterns of cortical development including an increase in gyrification as well as an increase in thickness and T1w/T2w myelination with increasing age. •Creation of spatio-temporal cortical surface atlas of the developing brain (36-44 weeks PMA).•Atlas captures patterns of cortical development in the neonatal dHCP population.•Includes surface features: sulcal depth, curvature, thickness, T1w/T2w myelin, cortical labels.

Objectives To evaluate the diagnostic performance and reliability of MRI descriptors used for the detection of Ménière’s disease (MD) on delayed post-gadolinium MRI. To determine which combination of descriptors should be optimally applied and whether analysis of the vestibular aqueduct (VA) contributes to the diagnosis. Materials and methods This retrospective single centre case-control study evaluated delayed post-gadolinium MRI of patients with Ménièriform symptoms examined consecutively between Dec 2017 and March 2023. Two observers evaluated 17 MRI descriptors of MD and quantified perilymphatic enhancement (PLE) in the cochlea. Definite MD ears according to the 2015 Barany Society criteria were compared to control ears. Cohen’s kappa and diagnostic odds ratio (DORs) were calculated for each descriptor. Forward stepwise logistic regression determined which combination of MRI descriptors would best predict MD ears, and the area under the receiver operating characteristic curve for this model was measured. Results A total of 227 patients (mean age 48.3 ± 14.6, 99 men) with 96 definite MD and 78 control ears were evaluated. The presence of saccular abnormality (absent, as large as or confluent with the utricle) performed best with a DOR of 292.6 (95% confidence interval (CI), 38.305–2235.058). All VA descriptors demonstrated excellent reliability and with DORs of 7.761 (95% CI, 3.517–17.125) to 18.1 (95% CI, 8.445–39.170). Combining these saccular abnormalities with asymmetric cochlear PLE and an incompletely visualised VA correctly classified 90.2% of cases (sensitivity 84.4%, specificity 97.4%, AUC 0.938). Conclusion Either absent, enlarged or confluent saccules are the best predictors of MD. Incomplete visualisation of the VA adds value to the diagnosis. Clinical relevance statement A number of different MRI descriptors have been proposed for the diagnosis of Ménière’s disease, but by establishing the optimally performing MRI features and highlighting new useful descriptors, there is an opportunity to improve the diagnostic performance of Ménière’s disease imaging. Key Points • A comprehensive range of existing and novel vestibular aqueduct delayed post-gadolinium MRI descriptors were compared for their diagnostic performance in Ménière’s disease. • Saccular abnormality (absent, confluent with or larger than the utricle) is a reliable descriptor and is the optimal individual MRI predictor of Ménière’s disease. • The presence of this saccule descriptor or asymmetric perilymphatic enhancement and incomplete vestibular aqueduct visualisation will optimise the MRI diagnosis of Ménière’s disease.

Detailed morphometric analysis of the neonatal brain is required to characterise brain development and define neuroimaging biomarkers related to impaired brain growth. Accurate automatic segmentation of neonatal brain MRI is a prerequisite to analyse large datasets. We have previously presented an accurate and robust automatic segmentation technique for parcellating the neonatal brain into multiple cortical and subcortical regions. In this study, we further extend our segmentation method to detect cortical sulci and provide a detailed delineation of the cortical ribbon. These detailed segmentations are used to build a 4-dimensional spatio-temporal structural atlas of the brain for 82 cortical and subcortical structures throughout this developmental period. We employ the algorithm to segment an extensive database of 420 MR images of the developing brain, from 27 to 45weeks post-menstrual age at imaging. Regional volumetric and cortical surface measurements are derived and used to investigate brain growth and development during this critical period and to assess the impact of immaturity at birth. Whole brain volume, the absolute volume of all structures studied, cortical curvature and cortical surface area increased with increasing age at scan. Relative volumes of cortical grey matter, cerebellum and cerebrospinal fluid increased with age at scan, while relative volumes of white matter, ventricles, brainstem and basal ganglia and thalami decreased. Preterm infants at term had smaller whole brain volumes, reduced regional white matter and cortical and subcortical grey matter volumes, and reduced cortical surface area compared with term born controls, while ventricular volume was greater in the preterm group. Increasing prematurity at birth was associated with a reduction in total and regional white matter, cortical and subcortical grey matter volume, an increase in ventricular volume, and reduced cortical surface area. •A novel methodology is proposed for delineating the cortical ribbon.•Regional brain growth is assessed in the developing preterm brain.•We investigate the effect of prematurity on brain growth and cortical development.•A spatio-temporal neonatal atlas is constructed with 82 brain structures.

Objectives Delayed post-gadolinium magnetic resonance imaging (MRI) detects changes of endolymphatic hydrops (EH) within the inner ear in Meniere’s disease (MD). A systematic review with meta-analysis was conducted to summarise the diagnostic performance of MRI descriptors across the range of MD clinical classifications. Materials and methods Case-controlled studies documenting the diagnostic performance of MRI descriptors in distinguishing MD ears from asymptomatic ears or ears with other audio-vestibular conditions were identified (MEDLINE, EMBASE, Web of Science, Scopus databases: updated 17/2/2022). Methodological quality was evaluated with Quality Assessment of Diagnostic Accuracy Studies version 2. Results were pooled using a bivariate random-effects model for evaluation of sensitivity, specificity and diagnostic odds ratio (DOR). Meta-regression evaluated sources of heterogeneity, and subgroup analysis for individual clinical classifications was performed. Results The meta-analysis included 66 unique studies and 3073 ears with MD (mean age 40.2–67.2 years), evaluating 11 MRI descriptors. The combination of increased perilymphatic enhancement (PLE) and EH (3 studies, 122 MD ears) achieved the highest sensitivity (87% (95% CI: 79.92%)) whilst maintaining high specificity (91% (95% CI: 85.95%)). The diagnostic performance of “high grade cochlear EH” and “any EH” descriptors did not significantly differ between monosymptomatic cochlear MD and the latest reference standard for definite MD ( p  = 0.3; p  = 0.09). Potential sources of bias were case-controlled design, unblinded observers and variable reference standard, whilst differing MRI techniques introduced heterogeneity. Conclusions The combination of increased PLE and EH optimised sensitivity and specificity for MD, whilst some MRI descriptors also performed well in diagnosing monosymptomatic cochlear MD. Key Points • A meta-analysis of delayed post-gadolinium magnetic resonance imaging (MRI) for the diagnosis of Meniere’s disease is reported for the first time and comprised 66 studies (3073 ears). • Increased enhancement of the perilymphatic space of the inner ear is shown to be a key MRI feature for the diagnosis of Meniere’s disease. • MRI diagnosis of Meniere’s disease can be usefully applied across a range of clinical classifications including patients with cochlear symptoms alone.

We propose a novel method for the automatic segmentation of brain MRI images by using discriminative dictionary learning and sparse coding techniques. In the proposed method, dictionaries and classifiers are learned simultaneously from a set of brain atlases, which can then be used for the reconstruction and segmentation of an unseen target image. The proposed segmentation strategy is based on image reconstruction, which is in contrast to most existing atlas-based labeling approaches that rely on comparing image similarities between atlases and target images. In addition, we propose a Fixed Discriminative Dictionary Learning for Segmentation (F-DDLS) strategy, which can learn dictionaries offline and perform segmentations online, enabling a significant speed-up in the segmentation stage. The proposed method has been evaluated for the hippocampus segmentation of 80 healthy ICBM subjects and 202 ADNI images. The robustness of the proposed method, especially of our F-DDLS strategy, was validated by training and testing on different subject groups in the ADNI database. The influence of different parameters was studied and the performance of the proposed method was also compared with that of the nonlocal patch-based approach. The proposed method achieved a median Dice coefficient of 0.879 on 202 ADNI images and 0.890 on 80 ICBM subjects, which is competitive compared with state-of-the-art methods. •Sparse representation technique is applied to segmentations of brain MR images.•Discriminative dictionary learning is used to achieve a fast implementation.•Validation is carried out on hippocampus of 80 ICBM subjects and 202 ADNI images.•Segmentation results demonstrate the accuracy of the proposed method.•The proposed method may provide a potential direction for human brain labeling.

•An automated and robust pipeline to minimally pre-process highly confounded neonatal fMRI data.•Includes integrated dynamic distortion and slice-to-volume motion correction.•A robust multimodal registration approach which includes custom neonatal templates.•Incorporates an automated and self-reporting QC framework to quantify data quality and identify issues for further inspection.•Data analysis of 538 infants imaged at 26–45 weeks post-menstrual age. The developing Human Connectome Project (dHCP) aims to create a detailed 4-dimensional connectome of early life spanning 20–45 weeks post-menstrual age. This is being achieved through the acquisition of multi-modal MRI data from over 1000 in- and ex-utero subjects combined with the development of optimised pre-processing pipelines. In this paper we present an automated and robust pipeline to minimally pre-process highly confounded neonatal resting-state fMRI data, robustly, with low failure rates and high quality-assurance. The pipeline has been designed to specifically address the challenges that neonatal data presents including low and variable contrast and high levels of head motion. We provide a detailed description and evaluation of the pipeline which includes integrated slice-to-volume motion correction and dynamic susceptibility distortion correction, a robust multimodal registration approach, bespoke ICA-based denoising, and an automated QC framework. We assess these components on a large cohort of dHCP subjects and demonstrate that processing refinements integrated into the pipeline provide substantial reduction in movement related distortions, resulting in significant improvements in SNR, and detection of high quality RSNs from neonates.

Cortical maturation was studied in 65 infants between 27 and 46 wk postconception using structural and diffusion magnetic resonance imaging. Alterations in neural structure and complexity were inferred from changes in mean diffusivity and fractional anisotropy, analyzed by sampling regions of interest and also by a unique whole-cortex mapping approach. Mean diffusivity was higher in gyri than sulci and in frontal compared with occipital lobes, decreasing consistently throughout the study period. Fractional anisotropy declined until 38 wk, with initial values and rates of change higher in gyri, frontal and temporal poles, and parietal cortex; and lower in sulcal, perirolandic, and medial occipital cortex. Neuroanatomical studies and experimental diffusion–anatomic correlations strongly suggested the interpretation that cellular and synaptic complexity and density increased steadily throughout the period, whereas elongation and branching of dendrites orthogonal to cortical columns was later and faster in higher-order association cortex, proceeding rapidly before becoming undetectable after 38 wk. The rate of microstructural maturation correlated locally with cortical growth, and predicted higher neurodevelopmental test scores at 2 y of age. Cortical microstructural development was reduced in a dose-dependent fashion by longer premature exposure to the extrauterine environment, and preterm infants at term-corrected age possessed less mature cortex than term-born infants. The results are compatible with predictions of the tension theory of cortical growth and show that rapidly developing cortical microstructure is vulnerable to the effects of premature birth, suggesting a mechanism for the adverse effects of preterm delivery on cognitive function.

The developing Human Connectome Project is set to create and make available to the scientific community a 4-dimensional map of functional and structural cerebral connectivity from 20 to 44 weeks post-menstrual age, to allow exploration of the genetic and environmental influences on brain development, and the relation between connectivity and neurocognitive function. A large set of multi-modal MRI data from fetuses and newborn infants is currently being acquired, along with genetic, clinical and developmental information. In this overview, we describe the neonatal diffusion MRI (dMRI) image processing pipeline and the structural connectivity aspect of the project. Neonatal dMRI data poses specific challenges, and standard analysis techniques used for adult data are not directly applicable. We have developed a processing pipeline that deals directly with neonatal-specific issues, such as severe motion and motion-related artefacts, small brain sizes, high brain water content and reduced anisotropy. This pipeline allows automated analysis of in-vivo dMRI data, probes tissue microstructure, reconstructs a number of major white matter tracts, and includes an automated quality control framework that identifies processing issues or inconsistencies. We here describe the pipeline and present an exemplar analysis of data from 140 infants imaged at 38–44 weeks post-menstrual age. •A comprehensive and automated pipeline to consistently analyse neonatal dMRI data.•Optimised motion and distortions correction to address newborn specific challenges.•The automated QC framework allows to detect issues and to quantify data quality.•Automated white matter segmentation allows to extract tract-specific masks.•Preliminary data analysis of 140 infants imaged at 38–44 weeks post-menstrual age.

We describe a framework for creating a time-resolved group average template of the developing brain using advanced multi-shell high angular resolution diffusion imaging data, for use in group voxel or fixel-wise analysis, atlas-building, and related applications. This relies on the recently proposed multi-shell multi-tissue constrained spherical deconvolution (MSMT-CSD) technique. We decompose the signal into one isotropic component and two anisotropic components, with response functions estimated from cerebrospinal fluid and white matter in the youngest and oldest participant groups, respectively. We build an orientationally-resolved template of those tissue components from data acquired from 113 babies between 33 and 44 weeks postmenstrual age, imaged as part of the Developing Human Connectome Project. These data were split into weekly groups, and registered to the corresponding group average templates using a previously-proposed non-linear diffeomorphic registration framework, designed to align orientation density functions (ODF). This framework was extended to allow the use of the multiple contrasts provided by the multi-tissue decomposition, and shown to provide superior alignment. Finally, the weekly templates were registered to the same common template to facilitate investigations into the evolution of the different components as a function of age. The resulting multi-tissue atlas provides insights into brain development and accompanying changes in microstructure, and forms the basis for future longitudinal investigations into healthy and pathological white matter maturation.