Image corruption detection in diffusion tensor imaging for post-processing and real-time monitoring

Brain multi-contrast, multi-atlas segmentation of diffusion tensor imaging and ensemble learning automatically diagnose late-life depression

We investigated the potential of machine learning for diagnostic classification in late-life major depression based on an advanced whole brain white matter segmentation framework. Twenty-six late-life depression and 12 never depressed individuals aged > 55 years, matched for age, MMSE, and education underwent brain diffusion tensor imaging and a multi-contrast, multi-atlas segmentation in MRIcloud. Fractional anisotropy volume, mean fractional anisotropy, trace, axial and radial diffusivity (RD) extracted from 146 white matter parcels for each subject were used to train and test the AdaBoost classifier using stratified 12-fold cross validation. Performance was evaluated using various measures. The statistical power of the classifier was assessed using label permutation test. Statistical analysis did not yield significant differences in DTI measures between the groups. The classifier achieved a balanced accuracy of 71% and an Area Under the Receiver Operator Characteristic Curve (ROC-AUC) of 0.81 by trace, and a balanced accuracy of 70% and a ROC-AUC of 0.80 by RD, in limbic, cortico-basal ganglia-thalamo-cortical loop, brainstem, external and internal capsules, callosal and cerebellar structures. Both indices shared important structures for classification, while fornix was the most important structure for classification by both indices. The classifier proved statistically significant, as trace and RD ROC-AUC scores after permutation were lower than those obtained with the actual data (P = 0.022 and P = 0.024, respectively). Similar results were obtained with the Gradient Boosting classifier, whereas the RBF-kernel Support Vector Machine with k-best feature selection did not exceed the chance level. Finally, AdaBoost significantly predicted the class using all features together. Limitations are discussed. The results encourage further investigation of the implemented methods for computer aided diagnostics and anatomically informed therapeutics.

Multivariate associations between behavioural dimensions and white matter across children and adolescents with and without attention-deficit/hyperactivity disorder

BACKGROUND

Attention deficit/hyperactivity disorder (ADHD) is a heterogeneous neurodevelopmental disorder. Integrity of white matter microstructure plays a key role in the neural mechanism of ADHD presentations. However, the relationships between specific behavioural dimensions and white matter microstructure are less well known. This study aimed to identify associations between white matter and a broad set of clinical features across children and adolescent with and without ADHD using a data-driven multivariate approach.

METHOD

We recruited a total of 130 children (62 controls and 68 ADHD) and employed regularized generalized canonical correlation analysis to characterize the associations between white matter and a comprehensive set of clinical measures covering three domains, including symptom, cognition and behaviour. We further applied linear discriminant analysis to integrate these associations to explore potential developmental effects.

RESULTS

We delineated two brain-behaviour dimensional associations in each domain resulting a total of six multivariate patterns of white matter microstructural alterations linked to hyperactivity-impulsivity and mild affected; executive functions and working memory; externalizing behaviour and social withdrawal, respectively. Apart from executive function and externalizing behaviour sharing similar white matter patterns, all other dimensions linked to a specific pattern of white matter microstructural alterations. The multivariate dimensional association scores showed an overall increase and normalization with age in ADHD group while remained stable in controls.

CONCLUSIONS

We found multivariate neurobehavioral associations exist across ADHD and controls, which suggested that multiple white matter patterns underlie ADHD heterogeneity and provided neural bases for more precise diagnosis and individualized treatment.

Microstructural Neurodegeneration of the Entorhinal-Hippocampus Pathway along the Alzheimer's Disease Continuum

BACKGROUND

Conventional neuroimaging biomarkers for the neurodegeneration of Alzheimer's disease (AD) are not sensitive enough to detect neurodegenerative alterations during the preclinical stage of AD individuals.

OBJECTIVE

We examined whether neurodegeneration of the entorhinal-hippocampal pathway could be detected along the AD continuum using ultra-high-field diffusion tensor imaging and tractography for ex vivo brain tissues.

METHODS

Postmortem brain specimens from a cognitively unimpaired individual without AD pathological changes (non-AD), a cognitively unimpaired individual with AD pathological changes (preclinical AD), and a demented individual with AD pathological changes (AD dementia) were scanned with an 11.7T diffusion magnetic resonance imaging. Fractional anisotropy (FA) values of the entorhinal layer II and number of perforant path fibers counted by tractography were compared among the AD continuum. Following the imaging analyses, the status of myelinated fibers and neuronal cells were verified by subsequent serial histological examinations.

RESULTS

At 250μm (zipped to 125μm) isotropic resolution, the entorhinal layer II islands and the perforant path fibers could be identified in non-AD and preclinical AD, but not in AD dementia, followed by histological verification. The FA value of the entorhinal layer II was the highest among the entorhinal laminae in non-AD and preclinical AD, whereas the FA values in the entorhinal laminae were homogeneously low in AD dementia. The FA values and number of perforant path fibers decreased along the AD continuum (non-AD>preclinical AD > AD dementia).

CONCLUSION

We successfully detected neurodegenerative alterations of the entorhinal-hippocampal pathway at the preclinical stage of the AD continuum.

Development of a composite diffusion tensor imaging score correlating with short-term neurological status in neonatal hypoxic-ischemic encephalopathy

Hypoxic-ischemic encephalopathy (HIE) is the most common cause of neonatal acquired brain injury. Although conventional MRI may predict neurodevelopmental outcomes, accurate prognostication remains difficult. As diffusion tensor imaging (DTI) may provide an additional diagnostic and prognostic value over conventional MRI, we aimed to develop a composite DTI (cDTI) score to relate to short-term neurological function. Sixty prospective neonates treated with therapeutic hypothermia (TH) for HIE were evaluated with DTI, with a voxel size of 1 × 1 × 2 mm. Fractional anisotropy (FA) and mean diffusivity (MD) from 100 neuroanatomical regions (FA/MD *100 = 200 DTI parameters in total) were quantified using an atlas-based image parcellation technique. A least absolute shrinkage and selection operator (LASSO) regression was applied to the DTI parameters to generate the cDTI score. Time to full oral nutrition [short-term oral feeding (STO) score] was used as a measure of short-term neurological function and was correlated with extracted DTI features. Seventeen DTI parameters were selected with LASSO and built into the final unbiased regression model. The selected factors included FA or MD values of the limbic structures, the corticospinal tract, and the frontotemporal cortices. While the cDTI score strongly correlated with the STO score (rho = 0.83, p = 2.8 × 10-16), it only weakly correlated with the Sarnat score (rho = 0.27, p = 0.035) and moderately with the NICHD-NRN neuroimaging score (rho = 0.43, p = 6.6 × 10-04). In contrast to the cDTI score, the NICHD-NRN score only moderately correlated with the STO score (rho = 0.37, p = 0.0037). Using a mixed-model analysis, interleukin-10 at admission to the NICU (p = 1.5 × 10-13) and tau protein at the end of TH/rewarming (p = 0.036) and after rewarming (p = 0.0015) were significantly associated with higher cDTI scores, suggesting that high cDTI scores were related to the intensity of the early inflammatory response and the severity of neuronal impairment after TH. In conclusion, a data-driven unbiased approach was applied to identify anatomical structures associated with some aspects of neurological function of HIE neonates after cooling and to build a cDTI score, which was correlated with the severity of short-term neurological functions.

Preservation of Cerebellar Afferent Pathway May Be Related to Good Hand Function in Patients with Stroke

Many chronic stroke patients suffer from worsened hand function, and functional recovery of the hand does not occur well after six months of stroke. Therefore, predicting final hand function after stroke through acute phase imaging would be an important issue in counseling with the patients or their family. Thus, we investigated the remaining white matter integrity in the corticospinal tract (CST) and cortico-ponto-cerebellar tract (CPCT) at the acute stage of stroke and chronic hand function after stroke, and present the cut-off value of fiber number (FN) and fractional anisotropy (FA) of CST and CPCT at the acute stage for predicting final hand function after the recovery period. This retrospective case-control study included 18 stroke patients who were classified into two groups: poor hand function with stroke (n = 11) and good hand function with stroke (n = 7). DTI was done within two months ± 15 days after onset, and the Jebson’s Hand Function test was conducted 6–12 months after onset. The investigation of white matter was focused on the values of FN and FA for CST and CPCT, which were measured separately. The normalized (affected/non-affected) FA and FN values in the CPCT in the good hand function group were higher than those in the poor hand function group. The normalized FN and FA values in the CST were not significantly different between the poor hand function group and the good hand function group. The normalized cut-off value that distinguished the good hand function group from the poor hand function group was 0.8889 for FA in the CPCT. The integrity of the CPCT in the acute stage was associated with hand function in the chronic stage after a stroke. Ultimately, the integrity of the CPCT in the early stage after onset can be used to predict chronic hand function. Based on these results, cerebellar afferent fiber measurements may be a useful addition to predict hand function and plan specific rehabilitation strategies in stroke patients.

Superficial and deep white matter diffusion abnormalities in focal epilepsies

OBJECTIVE

This study was undertaken to evaluate superficial-white matter (WM) and deep-WM magnetic resonance imaging diffusion tensor imaging (DTI) metrics and identify distinctive patterns of microstructural abnormalities in focal epilepsies of diverse etiology, localization, and response to antiseizure medication (ASM).

METHODS

We examined DTI data for 113 healthy controls and 113 patients with focal epilepsies: 51 patients with temporal lobe epilepsy (TLE) and hippocampal sclerosis (HS) refractory to ASM, 27 with pharmacoresponsive TLE-HS, 15 with temporal lobe focal cortical dysplasia (FCD), and 20 with frontal lobe FCD. To assess WM microstructure, we used a multicontrast multiatlas parcellation of DTI. We evaluated fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD), and axial diffusivity (AD), and assessed within-group differences ipsilateral and contralateral to the epileptogenic lesion, as well as between-group differences, in regions of interest (ROIs).

RESULTS

The TLE-HS groups presented more widespread superficial- and deep-WM diffusion abnormalities than both FCD groups. Concerning superficial WM, TLE-HS groups showed multilobar ipsilateral and contralateral abnormalities, with less extensive distribution in pharmacoresponsive patients. Both the refractory TLE-HS and pharmacoresponsive TLE-HS groups also presented pronounced changes in ipsilateral frontotemporal ROIs (decreased FA and increased MD, RD, and AD). Conversely, FCD patients showed diffusion changes almost exclusively adjacent to epileptogenic areas.

SIGNIFICANCE

Our findings add further evidence of widespread abnormalities in WM diffusion metrics in patients with TLE-HS compared to other focal epilepsies. Notably, superficial-WM microstructural damage in patients with FCD is more restricted around the epileptogenic lesion, whereas TLE-HS groups showed diffuse WM damage with ipsilateral frontotemporal predominance. These findings suggest the potential of superficial-WM analysis for better understanding the biological mechanisms of focal epilepsies, and identifying dysfunctional networks and their relationship with the clinical-pathological phenotype. In addition, lobar superficial-WM abnormalities may aid in the diagnosis of subtle FCDs.

Functional and Structural Brain Connectivity in Children With Bilateral Cerebral Palsy Compared to Age-Related Controls and in Response to Intensive Rapid-Reciprocal Leg Training

Background

Compared to unilateral cerebral palsy (CP), less is known about brain reorganization and plasticity in bilateral CP especially in relation or response to motor training. The few trials that reported brain imaging results alongside functional outcomes include a handful of studies in unilateral CP, and one pilot trial of three children with bilateral CP. This study is the first locomotor training randomized controlled trial (RCT) in bilateral CP to our knowledge reporting brain imaging outcomes.

Methods

Objective was to compare MRI brain volumes, resting state connectivity and white matter integrity using DTI in children with bilateral CP with PVL and preterm birth history (<34 weeks), to age-related controls, and from an RCT of intensive 12 week rapid-reciprocal locomotor training using an elliptical or motor-assisted cycle. We hypothesized that connectivity in CP compared to controls would be greater across sensorimotor-related brain regions and that functional (resting state) and structural (fractional anisotropy) connectivity would improve post intervention. We further anticipated that baseline and post-intervention imaging and functional measures would correlate.

Results

Images were acquired with a 3T MRI scanner for 16/27 children with CP in the trial, and 18 controls. No conclusive evidence of training-induced neuroplastic effects were seen. However, analysis of shared variance revealed that greater increases in precentral gyrus connectivity with the thalamus and pons may be associated with larger improvements in the trained device speed. Exploratory analyses also revealed interesting potential relationships between brain integrity and multiple functional outcomes in CP, with functional connectivity between the motor cortex and midbrain showing the strongest potential relationship with mobility. Decreased posterior white matter, corpus callosum and thalamic volumes, and FA in the posterior thalamic radiation were the most prominent group differences with corticospinal tract differences notably not found.

Conclusions

Results reinforce the involvement of sensory-related brain areas in bilateral CP. Given the wide individual variability in imaging results and clinical responses to training, a greater focus on neural and other mechanisms related to better or worse outcomes is recommended to enhance rehabilitation results on a patient vs. group level.

What's New and What's Next in Diffusion MRI Preprocessing

Diffusion MRI (dMRI) provides invaluable information for the study of tissue microstructure and brain connectivity, but suffers from a range of imaging artifacts that greatly challenge the analysis of results and their interpretability if not appropriately accounted for. This review will cover dMRI artifacts and preprocessing steps, some of which have not typically been considered in existing pipelines or reviews, or have only gained attention in recent years: brain/skull extraction, B-matrix incompatibilities w.r.t the imaging data, signal drift, Gibbs ringing, noise distribution bias, denoising, between- and within-volumes motion, eddy currents, outliers, susceptibility distortions, EPI Nyquist ghosts, gradient deviations, B₁ bias fields, and spatial normalization. The focus will be on “what’s new” since the notable advances prior to and brought by the Human Connectome Project (HCP), as presented in the predecessing issue on “Mapping the Connectome” in 2013. In addition to the development of novel strategies for dMRI preprocessing, exciting progress has been made in the availability of open source tools and reproducible pipelines, databases and simulation tools for the evaluation of preprocessing steps, and automated quality control frameworks, amongst others. Finally, this review will consider practical considerations and our view on “what’s next” in dMRI preprocessing.

Motion-insensitive diffusion imaging of the brain using optical tracking and dynamic sequence updates

PURPOSE

Diffusion-weighted imaging (DWI) is sensitive to head movements, which may cause signal losses because of motion-induced gradient imbalances. Prospective motion correction using fast optical tracking can attenuate these artifacts. Approaches include quasicontinuous updates of gradients and radiofrequency (RF) pulses or dynamically applying a rebalancing gradient to restore the gradient balance, but these prior methods used bipolar diffusion gradients. The goal of this project was to develop and evaluate a motion-insensitive implementation for the more common monopolar diffusion sequence.

METHODS

A monopolar diffusion sequence was developed with motion updates before each RF pulse and each diffusion-weighting gradient. The sequence was tested in a phantom and human brain at b = 1000 s/mm² and rotational velocities up to 20°/s. Motion sensitivity, signal losses, and in vivo image profiles were compared between scans with and without intrasequence motion updates.

RESULTS

With typical motion parameters, intrasequence motion updates with optimal parameters reduced the motion sensitivity of DWI (motion-induced gradient moment imbalance) sevenfold. Optimal results were achieved by matching the echo time of the pulse sequence to an even multiple of the tracking system frame-to-frame period. Average signal losses and the frequency of signal dropouts in phantom and in vivo measurements were reduced when intrasequence updates were enabled, and quality measures of DTI analyses were improved.

CONCLUSION

A correction scheme for the monopolar DWI sequence can reduce the motion sensitivity of brain DWI up to sevenfold compared with an implementation without intrasequence updates.

Developmental score of the infant brain: characterizing diffusion MRI in term- and preterm-born infants

Large-scale longitudinal neuroimaging studies of the infant brain allow us to map the spatiotemporal development of the brain in its early phase. While the postmenstrual age (PMA) is commonly used as a time index to analyze longitudinal MRI data, the nonlinear relationship between PMA and MRI data imposes challenges for downstream analyses. We propose a mathematical model that provides a Developmental Score (DevS) as a data-driven time index to characterize the brain development based on MRI features. 319 diffusion tensor imaging (DTI) datasets were collected from 87 term-born and 66 preterm-born infants at multiple visits, which were automatically segmented based on the JHU neonatal atlas. The mean diffusivity (MD) and fractional anisotropy (FA) in 126 brain parcels were used in the model to derive DevS. We demonstrate that transforming the time index from PMA to DevS improves the linearity of the longitudinal changes in MD and FA in both gray and white matter structures. More importantly, regional developmental differences in DTI metrics between preterm- and term-born infants were identified more clearly using DevS, e.g. 79 structures showed significantly different regression patterns in MD between preterm- and term-born infants, compared to only 27 structures that showed group differences using PMA as the index. Therefore, the DevS model facilitates linear analyses of DTI metrics in the infant brain, and provides a useful tool to characterize altered brain development due to preterm-birth.

Mapping tracts in the human subthalamic area by 11.7T ex vivo diffusion tensor imaging

The cortico-basal ganglia-thalamo-cortical feedback loops that consist of distinct white matter pathways are important for understanding in vivo imaging studies of functional and anatomical connectivity, and for localizing subthalamic white matter structures in surgical approaches for movement disorders, such as Parkinson's disease. Connectomic analysis in animals has identified fiber connections between the basal ganglia and thalamus, which pass through the fields of Forel, where other fiber pathways related to motor, sensory, and cognitive functions co-exist. We now report these pathways in the human brain on ex vivo mesoscopic (250 μm) diffusion tensor imaging and on tractography. The locations of the tracts were identified relative to the adjacent gray matter structures, such as the internal and external segments of the globus pallidus; the zona incerta; the subthalamic nucleus; the substantia nigra pars reticulata and compacta; and the thalamus. The connectome atlas of the human subthalamic region may serve as a resource for imaging studies and for neurosurgical planning.

The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data

Quantifying, controlling, and monitoring image quality is an essential prerequisite for ensuring the validity and reproducibility of many types of neuroimaging data analyses. Implementation of quality control (QC) procedures is the key to ensuring that neuroimaging data are of high-quality and their validity in the subsequent analyses. We introduce the QC system of the Laboratory of Neuro Imaging (LONI): a web-based system featuring a workflow for the assessment of various modality and contrast brain imaging data. The design allows users to anonymously upload imaging data to the LONI-QC system. It then computes an exhaustive set of QC metrics which aids users to perform a standardized QC by generating a range of scalar and vector statistics. These procedures are performed in parallel using a large compute cluster. Finally, the system offers an automated QC procedure for structural MRI, which can flag each QC metric as being 'good' or 'bad.' Validation using various sets of data acquired from a single scanner and from multiple sites demonstrated the reproducibility of our QC metrics, and the sensitivity and specificity of the proposed Auto QC to 'bad' quality images in comparison to visual inspection. To the best of our knowledge, LONI-QC is the first online QC system that uniquely supports the variety of functionality where we compute numerous QC metrics and perform visual/automated image QC of multi-contrast and multi-modal brain imaging data. The LONI-QC system has been used to assess the quality of large neuroimaging datasets acquired as part of various multi-site studies such as the Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Study and the Alzheimer's Disease Neuroimaging Initiative (ADNI). LONI-QC's functionality is freely available to users worldwide and its adoption by imaging researchers is likely to contribute substantially to upholding high standards of brain image data quality and to implementing these standards across the neuroimaging community.

Extended multimodal whole-brain anatomical covariance analysis: detection of disrupted correlation networks related to amyloid deposition

Background

An anatomical covariance analysis (ACA) enables to elucidate inter-regional connections on a group basis, but little is known about the connections among white matter structures or among gray and white matter structures. Effect of including multiple magnetic resonance imaging (MRI) modalities into ACA framework in detecting white-to-white or gray-to-white connections is yet to be investigated.

New method

Proposed extended anatomical covariance analysis (eACA), analyzes correlations among gray and white matter structures (multi-structural) in various types of imaging modalities (T1-weighted images, T2 maps obtained from dual-echo sequences, and diffusion tensor images (DTI)). To demonstrate the capability to detect a disruption of the correlation network affected by pathology, we applied the eACA to two groups of cognitively-normal elderly individuals, one with (PiB+) and one without (PiB-) amyloid deposition in their brains.

Results

The volume of each anatomical structure was symmetric and functionally related structures formed a cluster. The pseudo-T2 value was highly homogeneous across the entire cortex in the PiB- group, while a number of physiological correlations were altered in the PiB + group. The DTI demonstrated unique correlation network among structures within the same phylogenetic portions of the brain that were altered in the PiB + group.

Comparison with Existing Method

The proposed eACA expands the concept of existing ACA to the connections among the white matter structures. The extension to other image modalities expands the way in which connectivity may be detected.

Conclusion

The eACA has potential to evaluate alterations of the anatomical network related to pathological processes.

Cloud-Based Brain Magnetic Resonance Image Segmentation and Parcellation System for Individualized Prediction of Cognitive Worsening

For patients with cognitive disorders and dementia, accurate prognosis of cognitive worsening is critical to their ability to prepare for the future, in collaboration with health-care providers. Despite multiple efforts to apply computational brain magnetic resonance image (MRI) analysis in predicting cognitive worsening, with several successes, brain MRI is not routinely quantified in clinical settings to guide prognosis and clinical decision-making. To encourage the clinical use of a cutting-edge image segmentation method, we developed a prediction model as part of an established web-based cloud platform, MRICloud. The model was built in a training dataset from Alzheimer's Disease Neuroimaging Initiative (ADNI) where baseline MRI scans were combined with clinical data over time. Each MRI was parcellated into 265 anatomical units based on the MRICloud fully automated image segmentation function, to measure the volume of each parcel. The Mini Mental State Examination (MMSE) was used as a measure of cognitive function. The normalized volume of 265 parcels, combined with baseline MMSE score, age, and sex were input variables for a Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis, with MMSE change in the subsequent two years as the target for prediction. A leave-one-out analysis performed on the training dataset estimated a correlation coefficient of 0.64 between true and predicted MMSE change. A receiver operating characteristic (ROC) analysis estimated a sensitivity of 0.88 and a specificity of 0.76 in predicting substantial cognitive worsening after two years, defined as MMSE decline of ≥4 points. This MRICloud prediction model was then applied to a test dataset of clinically acquired MRIs from the Johns Hopkins Memory and Alzheimer's Treatment Center (MATC), a clinical care setting. In the latter setting, the model had both sensitivity and specificity of 1.0 in predicting substantial cognitive worsening. While the MRICloud prediction model demonstrated promise as a platform on which computational MRI findings can easily be extended to clinical use, further study with a larger number of patients is needed for validation.

Selective sensory deafferentation induces structural and functional brain plasticity

Sensory-motor integration models have been proposed aiming to explain how the brain uses sensory information to guide and check the planning and execution of movements. Sensory neuronopathy (SN) is a peculiar disease characterized by exclusive, severe and widespread sensory loss. It is a valuable condition to investigate how sensory deafferentation impacts brain organization. We thus recruited patients with clinical and electrophysiological criteria for SN to perform structural and functional MRI analyses. We investigated volumetric changes in gray matter (GM) using anatomical images; the microstructure of WM within segmented regions of interest (ROI), via diffusion images; and brain activation related to a finger tapping task. All significant results were related to the long disease duration subgroup of patients. Structural analysis showed hypertrophy of the caudate nucleus, whereas the diffusion study identified reduction of fractional anisotropy values in ROIs located around the thalamus and the striatum. We also found differences regarding finger-tapping activation in the posterior parietal regions and in the medial areas of the cerebellum. Our results stress the role of the caudate nucleus over the other basal ganglia in the sensory-motor integration models, and suggest an inhibitory function of a recently discovered tract between the thalamus and the striatum. Overall, our findings confirm plasticity in the adult brain and open new avenues to design neurorehabilitation strategies.

Motion-robust diffusion compartment imaging using simultaneous multi-slice acquisition

PURPOSE

To achieve motion-robust diffusion compartment imaging (DCI) in near continuously moving subjects based on simultaneous multi-slice, diffusion-weighted brain MRI.

METHODS

Simultaneous multi-slice (SMS) acquisition enables fast and dense sampling of k- and q-space. We propose to achieve motion-robust DCI via slice-level motion correction by exploiting the rigid coupling between simultaneously acquired slices. This coupling provides 3D coverage of the anatomy that substantially constraints the slice-to-volume alignment problem. This is incorporated into an explicit model of motion dynamics that handles continuous and large subject motion in robust DCI reconstruction.

RESULTS

We applied the proposed technique, called Motion Tracking based on Simultanous Multislice Registration (MT-SMR) to multi b-value SMS diffusion-weighted brain MRI of healthy volunteers and motion-corrupted scans of 20 pediatric subjects. Quantitative and qualitative evaluation based on fractional anisotropy in unidirectional fiber regions, and DCI in crossing-fiber regions show robust reconstruction in the presence of motion.

CONCLUSION

The proposed approach has the potential to extend routine use of SMS DCI in very challenging populations, such as young children, newborns, and non-cooperative patients.

Fast and accurate Slicewise OutLIer Detection (SOLID) with informed model estimation for diffusion MRI data

The accurate characterization of the diffusion process in tissue using diffusion MRI is greatly challenged by the presence of artefacts. Subject motion causes not only spatial misalignments between diffusion weighted images, but often also slicewise signal intensity errors. Voxelwise robust model estimation is commonly used to exclude intensity errors as outliers. Slicewise outliers, however, become distributed over multiple adjacent slices after image registration and transformation. This challenges outlier detection with voxelwise procedures due to partial volume effects. Detecting the outlier slices before any transformations are applied to diffusion weighted images is therefore required. In this work, we present i) an automated tool coined SOLID for slicewise outlier detection prior to geometrical image transformation, and ii) a framework to naturally interpret data uncertainty information from SOLID and include it as such in model estimators. SOLID uses a straightforward intensity metric, is independent of the choice of the diffusion MRI model, and can handle datasets with a few or irregularly distributed gradient directions. The SOLID-informed estimation framework prevents the need to completely reject diffusion weighted images or individual voxel measurements by downweighting measurements with their degree of uncertainty, thereby supporting convergence and well-conditioning of iterative estimation algorithms. In comprehensive simulation experiments, SOLID detects outliers with a high sensitivity and specificity, and can achieve higher or at least similar sensitivity and specificity compared to other tools that are based on more complex and time-consuming procedures for the scenarios investigated. SOLID was further validated on data from 54 neonatal subjects which were visually inspected for outlier slices with the interactive tool developed as part of this study, showing its potential to quickly highlight problematic volumes and slices in large population studies. The informed model estimation framework was evaluated both in simulations and in vivo human data.

Diffusion MRI of white matter microstructure development in childhood and adolescence: Methods, challenges and progress

Diffusion magnetic resonance imaging (dMRI) continues to grow in popularity as a useful neuroimaging method to study brain development, and longitudinal studies that track the same individuals over time are emerging. Over the last decade, seminal work using dMRI has provided new insights into the development of brain white matter (WM) microstructure, connections and networks throughout childhood and adolescence. This review provides an introduction to dMRI, both diffusion tensor imaging (DTI) and other dMRI models, as well as common acquisition and analysis approaches. We highlight the difficulties associated with ascribing these imaging measurements and their changes over time to specific underlying cellular and molecular events. We also discuss selected methodological challenges that are of particular relevance for studies of development, including critical choices related to image acquisition, image analysis, quality control assessment, and the within-subject and longitudinal reliability of dMRI measurements. Next, we review the exciting progress in the characterization and understanding of brain development that has resulted from dMRI studies in childhood and adolescence, including brief overviews and discussions of studies focusing on sex and individual differences. Finally, we outline future directions that will be beneficial to the field.

Mapping the critical gestational age at birth that alters brain development in preterm-born infants using multi-modal MRI

Preterm birth adversely affects postnatal brain development. In order to investigate the critical gestational age at birth (GAB) that alters the developmental trajectory of gray and white matter structures in the brain, we investigated diffusion tensor and quantitative T2 mapping data in 43 term-born and 43 preterm-born infants. A novel multivariate linear model-the change point model, was applied to detect change points in fractional anisotropy, mean diffusivity, and T2 relaxation time. Change points captured the "critical" GAB value associated with a change in the linear relation between GAB and MRI measures. The analysis was performed in 126 regions across the whole brain using an atlas-based image quantification approach to investigate the spatial pattern of the critical GAB. Our results demonstrate that the critical GABs are region- and modality-specific, generally following a central-to-peripheral and bottom-to-top order of structural development. This study may offer unique insights into the postnatal neurological development associated with differential degrees of preterm birth.

Surface-based vertexwise analysis of morphometry and microstructural integrity for white matter tracts in diffusion tensor imaging: With application to the corpus callosum in Alzheimer's disease

In this article, we present a unified statistical pipeline for analyzing the white matter (WM) tracts morphometry and microstructural integrity, both globally and locally within the same WM tract, from diffusion tensor imaging. Morphometry is quantified globally by the volumetric measurement and locally by the vertexwise surface areas. Meanwhile, microstructural integrity is quantified globally by the mean fractional anisotropy (FA) and trace values within the specific WM tract and locally by the FA and trace values defined at each vertex of its bounding surface. The proposed pipeline consists of four steps: (1) fully automated segmentation of WM tracts in a multi-contrast multi-atlas framework; (2) generation of the smooth surface representations for the WM tracts of interest; (3) common template surface generation on which the localized morphometric and microstructural statistics are defined and a variety of statistical analyses can be conducted; (4) multiple comparison correction to determine the significance of the statistical analysis results. Detailed herein, this pipeline has been applied to the corpus callosum in Alzheimer's disease (AD) with significantly decreased FA values and increased trace values, both globally and locally, being detected in patients with AD when compared to normal aging populations. A subdivision of the corpus callosum in both hemispheres revealed that the AD pathology primarily affects the body and splenium of the corpus callosum. Validation analyses and two multiple comparison correction strategies are provided. Hum Brain Mapp 38:1875-1893, 2017. © 2017 Wiley Periodicals, Inc.

Sex-Specific Alterations of White Matter Developmental Trajectories in Infants With Prenatal Exposure to Methamphetamine and Tobacco

IMPORTANCE

Methamphetamine is a common illicit drug used worldwide. Methamphetamine and/or tobacco use by pregnant women remains prevalent. However, little is known about the effect of comorbid methamphetamine and tobacco use on human fetal brain development.

OBJECTIVE

To investigate whether microstructural brain abnormalities reported in children with prenatal methamphetamine and/or tobacco exposure are present at birth before childhood environmental influences.

DESIGN, SETTING, AND PARTICIPANTS

A prospective, longitudinal study was conducted between September 17, 2008, and February 28, 2015, at an ambulatory academic medical center. A total of 752 infant-mother dyads were screened and 139 of 195 qualified neonates were evaluated (36 methamphetamine/tobacco exposed, 32 tobacco exposed, and 71 unexposed controls). They were recruited consecutively from the community.

EXPOSURES

Prenatal methamphetamine and/or tobacco exposure.

MAIN OUTCOMES AND MEASURES

Quantitative neurologic examination and diffusion tensor imaging performed 1 to 3 times through age 4 months; diffusivities and fractional anisotropy (FA) assessed in 7 white matter tracts and 4 subcortical brain regions using an automated atlas-based method.

RESULTS

Of the 139 infants evaluated, 72 were female (51.8%); the mean (SE) postmenstrual age at baseline was 41.5 (0.27) weeks. Methamphetamine/tobacco-exposed infants showed delayed developmental trajectories on active muscle tone (group × age, P < .001) and total neurologic scores (group × age, P = .01) that normalized by ages 3 to 4 months. Only methamphetamine/tobacco-exposed boys had lower FA (group × age, P = .02) and higher diffusivities in superior (SCR) and posterior corona radiatae (PCR) (group × age × sex, P = .002; group × age × sex, P = .01) at baseline that normalized by age 3 months. Only methamphetamine/tobacco- and tobacco-exposed girls showed persistently lower FA in anterior corona radiata (ACR) (group, P = .04; group × age × sex, P = .01). Tobacco-exposed infants showed persistently lower axial diffusion in the thalamus and internal capsule across groups (P = .02).

CONCLUSIONS AND RELEVANCE

Prenatal methamphetamine/tobacco exposure may lead to delays in motor development, with less coherent fibers and less myelination in SCR and PCR only in male infants, but these abnormalities may normalize by ages 3 to 4 months after cessation of stimulant exposure. In contrast, persistently less coherent ACR fibers were observed in methamphetamine/tobacco- and tobacco-exposed girls, possibly from increased dendritic branching or spine density due to epigenetic influences. Persistently lower diffusivity in the thalamus and internal capsule of all tobacco-exposed infants suggests aberrant axonal development. Collectively, prenatal methamphetamine and/or tobacco exposure may lead to delayed motor development and white matter maturation in sex- and regional-specific manners.

Motion-Robust Diffusion-Weighted Brain MRI Reconstruction Through Slice-Level Registration-Based Motion Tracking

This work proposes a novel approach for motion-robust diffusion-weighted (DW) brain MRI reconstruction through tracking temporal head motion using slice-to-volume registration. The slice-level motion is estimated through a filtering approach that allows tracking the head motion during the scan and correcting for out-of-plane inconsistency in the acquired images. Diffusion-sensitized image slices are registered to a base volume sequentially over time in the acquisition order where an outlier-robust Kalman filter, coupled with slice-to-volume registration, estimates head motion parameters. Diffusion gradient directions are corrected for the aligned DWI slices based on the computed rotation parameters and the diffusion tensors are directly estimated from the corrected data at each voxel using weighted linear least squares. The method was evaluated in DWI scans of adult volunteers who deliberately moved during scans as well as clinical DWI of 28 neonates and children with different types of motion. Experimental results showed marked improvements in DWI reconstruction using the proposed method compared to the state-of-the-art DWI analysis based on volume-to-volume registration. This approach can be readily used to retrieve information from motion-corrupted DW imaging data.

Motion-Robust Reconstruction based on Simultaneous Multi-Slice Registration for Diffusion-Weighted MRI of Moving Subjects

Simultaneous multi-slice (SMS) echo-planar imaging has had a huge impact on the acceleration and routine use of diffusion-weighted MRI (DWI) in neuroimaging studies in particular the human connectome project; but also holds the potential to facilitate DWI of moving subjects, as proposed by the new technique developed in this paper. We present a novel registration-based motion tracking technique that takes advantage of the multi-plane coverage of the anatomy by simultaneously acquired slices to enable robust reconstruction of neural microstructure from SMS DWI of moving subjects. Our technique constitutes three main components: 1) motion tracking and estimation using SMS registration, 2) detection and rejection of intra-slice motion, and 3) robust reconstruction. Quantitative results from 14 volunteer subject experiments and the analysis of motion-corrupted SMS DWI of 6 children indicate robust reconstruction in the presence of continuous motion and the potential to extend the use of SMS DWI in very challenging populations.

Heads in the Cloud: A Primer on Neuroimaging Applications of High Performance Computing

With larger data sets and more sophisticated analyses, it is becoming increasingly common for neuroimaging researchers to push (or exceed) the limitations of standalone computer workstations. Nonetheless, although high-performance computing platforms such as clusters, grids and clouds are already in routine use by a small handful of neuroimaging researchers to increase their storage and/or computational power, the adoption of such resources by the broader neuroimaging community remains relatively uncommon. Therefore, the goal of the current manuscript is to: 1) inform prospective users about the similarities and differences between computing clusters, grids and clouds; 2) highlight their main advantages; 3) discuss when it may (and may not) be advisable to use them; 4) review some of their potential problems and barriers to access; and finally 5) give a few practical suggestions for how interested new users can start analyzing their neuroimaging data using cloud resources. Although the aim of cloud computing is to hide most of the complexity of the infrastructure management from end-users, we recognize that this can still be an intimidating area for cognitive neuroscientists, psychologists, neurologists, radiologists, and other neuroimaging researchers lacking a strong computational background. Therefore, with this in mind, we have aimed to provide a basic introduction to cloud computing in general (including some of the basic terminology, computer architectures, infrastructure and service models, etc.), a practical overview of the benefits and drawbacks, and a specific focus on how cloud resources can be used for various neuroimaging applications.

Shape and diffusion tensor imaging based integrative analysis of the hippocampus and the amygdala in Alzheimer's disease

We analyzed, in an integrative fashion, the morphometry and structural integrity of the bilateral hippocampi and amygdalas in Alzheimer's disease (AD) using T1-weighted images and diffusion tensor images (DTIs). We detected significant hippocampal and amygdalar volumetric atrophies in AD relative to healthy controls (HCs). Shape analysis revealed significant region-specific atrophies with the hippocampal atrophy mainly being concentrated on the CA1 and CA2 while the amygdalar atrophy was concentrated on the basolateral and basomedial. In all structures, the structural integrity displayed a significantly decreased mean fractional anisotropy (FA) value and an increased mean trace value in AD. In addition to the inter-group comparisons, we systematically evaluated the discriminative power of our three types of features (volume, shape, and DTI), both individually and in their possible combinations, when differentiating between AD and HCs. We found the volume features to be redundant when the more sophisticated shape features were available. A combination of the shape and DTI features of the right hippocampus, with classification automatically performed by support vector machine, yielded the strongest classification result (overall accuracy, 94.6%; sensitivity, 95.5%; specificity, 93.3%).

The impact of quality assurance assessment on diffusion tensor imaging outcomes in a large-scale population-based cohort

BACKGROUND

Diffusion tensor imaging (DTI) is applied in investigation of brain biomarkers for neurodevelopmental and neurodegenerative disorders. However, the quality of DTI measurements, like other neuroimaging techniques, is susceptible to several confounding factors (e.g., motion, eddy currents), which have only recently come under scrutiny. These confounds are especially relevant in adolescent samples where data quality may be compromised in ways that confound interpretation of maturation parameters. The current study aims to leverage DTI data from the Philadelphia Neurodevelopmental Cohort (PNC), a sample of 1601 youths with ages of 8-21 who underwent neuroimaging, to: 1) establish quality assurance (QA) metrics for the automatic identification of poor DTI image quality; 2) examine the performance of these QA measures in an external validation sample; 3) document the influence of data quality on developmental patterns of typical DTI metrics.

METHODS

All diffusion-weighted images were acquired on the same scanner. Visual QA was performed on all subjects completing DTI; images were manually categorized as Poor, Good, or Excellent. Four image quality metrics were automatically computed and used to predict manual QA status: Mean voxel intensity outlier count (MEANVOX), Maximum voxel intensity outlier count (MAXVOX), mean relative motion (MOTION) and temporal signal-to-noise ratio (TSNR). Classification accuracy for each metric was calculated as the area under the receiver-operating characteristic curve (AUC). A threshold was generated for each measure that best differentiated visual QA status and applied in a validation sample. The effects of data quality on sensitivity to expected age effects in this developmental sample were then investigated using the traditional MRI diffusion metrics: fractional anisotropy (FA) and mean diffusivity (MD). Finally, our method of QA is compared with DTIPrep.

RESULTS

TSNR (AUC=0.94) best differentiated Poor data from Good and Excellent data. MAXVOX (AUC=0.88) best differentiated Good from Excellent DTI data. At the optimal threshold, 88% of Poor data and 91% Good/Excellent data were correctly identified. Use of these thresholds on a validation dataset (n=374) indicated high accuracy. In the validation sample 83% of Poor data and 94% of Excellent data was identified using thresholds derived from the training sample. Both FA and MD were affected by the inclusion of poor data in an analysis of an age, sex and race matched comparison sample. In addition, we show that the inclusion of poor data results in significant attenuation of the correlation between diffusion metrics (FA and MD) and age during a critical neurodevelopmental period. We find higher correspondence between our QA method and DTIPrep for Poor data, but we find our method to be more robust for apparently high-quality images.

CONCLUSION

Automated QA of DTI can facilitate large-scale, high-throughput quality assurance by reliably identifying both scanner and subject induced imaging artifacts. The results present a practical example of the confounding effects of artifacts on DTI analysis in a large population-based sample, and suggest that estimates of data quality should not only be reported but also accounted for in data analysis, especially in studies of development.

Comparison of quality control software tools for diffusion tensor imaging

Image quality of diffusion tensor imaging (DTI) is critical for image interpretation, diagnostic accuracy and efficiency. However, DTI is susceptible to numerous detrimental artifacts that may impair the reliability and validity of the obtained data. Although many quality control (QC) software tools are being developed and are widely used and each has its different tradeoffs, there is still no general agreement on an image quality control routine for DTIs, and the practical impact of these tradeoffs is not well studied. An objective comparison that identifies the pros and cons of each of the QC tools will be helpful for the users to make the best choice among tools for specific DTI applications. This study aims to quantitatively compare the effectiveness of three popular QC tools including DTI studio (Johns Hopkins University), DTIprep (University of North Carolina at Chapel Hill, University of Iowa and University of Utah) and TORTOISE (National Institute of Health). Both synthetic and in vivo human brain data were used to quantify adverse effects of major DTI artifacts to tensor calculation as well as the effectiveness of different QC tools in identifying and correcting these artifacts. The technical basis of each tool was discussed, and the ways in which particular techniques affect the output of each of the tools were analyzed. The different functions and I/O formats that three QC tools provide for building a general DTI processing pipeline and integration with other popular image processing tools were also discussed.

Increased microstructural white matter correlations in left, but not right, temporal lobe epilepsy

Microstructural white matter tract correlations have been shown to reflect known patterns of phylogenetic development and functional specialization in healthy subjects. The aim of this study was to establish intertract correlations in a group of controls and to examine potential deviations from normality in temporal lobe epilepsy (TLE). We investigated intertract correlations in 28 healthy controls, 21 left TLE (LTLE) and 23 right TLE (RTLE). Nine tracts were investigated, comprising the parahippocampal fasciculi, the uncinate fasciculi, the arcuate fasciculi, the frontoparietal tracts, and the fornix. An abnormal increase in tract correlations was observed in LTLE, while RTLE showed intertract correlations similar to controls. In the control group, tract correlations increased with increasing fractional anisotropy (FA), while in the TLE groups tract correlations increased with decreasing FA. Cluster analyses revealed agglomeration of bilateral pairs of homologous tracts in healthy subjects, with such pairs separated in our LTLE and RTLE groups. Discriminant analyses aimed at distinguishing LTLE from RTLE, revealing that tract correlations produce higher rates of accurate group classification than FA values. Our results confirm and extend previous work by showing that LTLE compared to RTLE patients display not only more extensive losses in microstructural orientation but also more aberrant intertract correlations. Aberrant correlations may be related to pathologic processes (i.e., seizure spread) or to adaptive processes aimed at preserving key cognitive functions. Our data suggest that tract correlations may have predictive value in distinguishing LTLE from RTLE, potentially moving diffusion imaging to a place of greater prominence in clinical practice.

A robust post-processing workflow for datasets with motion artifacts in diffusion kurtosis imaging

PURPOSE

The aim of this study was to develop a robust post-processing workflow for motion-corrupted datasets in diffusion kurtosis imaging (DKI).

MATERIALS AND METHODS

The proposed workflow consisted of brain extraction, rigid registration, distortion correction, artifacts rejection, spatial smoothing and tensor estimation. Rigid registration was utilized to correct misalignments. Motion artifacts were rejected by using local Pearson correlation coefficient (LPCC). The performance of LPCC in characterizing relative differences between artifacts and artifact-free images was compared with that of the conventional correlation coefficient in 10 randomly selected DKI datasets. The influence of rejected artifacts with information of gradient directions and b values for the parameter estimation was investigated by using mean square error (MSE). The variance of noise was used as the criterion for MSEs. The clinical practicality of the proposed workflow was evaluated by the image quality and measurements in regions of interest on 36 DKI datasets, including 18 artifact-free (18 pediatric subjects) and 18 motion-corrupted datasets (15 pediatric subjects and 3 essential tremor patients).

RESULTS

The relative difference between artifacts and artifact-free images calculated by LPCC was larger than that of the conventional correlation coefficient (p<0.05). It indicated that LPCC was more sensitive in detecting motion artifacts. MSEs of all derived parameters from the reserved data after the artifacts rejection were smaller than the variance of the noise. It suggested that influence of rejected artifacts was less than influence of noise on the precision of derived parameters. The proposed workflow improved the image quality and reduced the measurement biases significantly on motion-corrupted datasets (p<0.05).

CONCLUSION

The proposed post-processing workflow was reliable to improve the image quality and the measurement precision of the derived parameters on motion-corrupted DKI datasets. The workflow provided an effective post-processing method for clinical applications of DKI in subjects with involuntary movements.