Fiber-Flux Diffusion Density for White Matter Tracts Analysis: Application to Mild Anomalies Localization in Contact Sports Players

We present the concept of fiber-flux density for locally quantifying white matter (WM) fiber bundles. By combining scalar diffusivity measures (e.g., fractional anisotropy) with fiber-flux measurements, we define new local descriptors called Fiber-Flux Diffusion Density (FFDD) vectors. Applying each descriptor throughout fiber bundles allows along-tract coupling of a specific diffusion measure with geometrical properties, such as fiber orientation and coherence. A key step in the proposed framework is the construction of an FFDD dissimilarity measure for sub-voxel alignment of fiber bundles, based on the fast marching method (FMM). The obtained aligned WM tract-profiles enable meaningful inter-subject comparisons and group-wise statistical analysis. We demonstrate our method using two different datasets of contact sports players. Along-tract pairwise comparison as well as group-wise analysis, with respect to non-player healthy controls, reveal significant and spatially-consistent FFDD anomalies. Comparing our method with along-tract FA analysis shows improved sensitivity to subtle structural anomalies in football players over standard FA measurements

Learning-based Ensemble Average Propagator Estimation

By capturing the anisotropic water diffusion in tissue, diffusion magnetic resonance imaging (dMRI) provides a unique tool for noninvasively probing the tissue microstructure and orientation in the human brain. The diffusion profile can be described by the ensemble average propagator (EAP), which is inferred from observed diffusion signals. However, accurate EAP estimation using the number of diffusion gradients that is clinically practical can be challenging. In this work, we propose a deep learning algorithm for EAP estimation, which is named learning-based ensemble average propagator estimation (LEAPE). The EAP is commonly represented by a basis and its associated coefficients, and here we choose the SHORE basis and design a deep network to estimate the coefficients. The network comprises two cascaded components. The first component is a multiple layer perceptron (MLP) that simultaneously predicts the unknown coefficients. However, typical training loss functions, such as mean squared errors, may not properly represent the geometry of the possibly non-Euclidean space of the coefficients, which in particular causes problems for the extraction of directional information from the EAP. Therefore, to regularize the training, in the second component we compute an auxiliary output of approximated fiber orientation (FO) errors with the aid of a second MLP that is trained separately. We performed experiments using dMRI data that resemble clinically achievable $q$-space sampling, and observed promising results compared with the conventional EAP estimation method.Comment: Accepted by MICCAI 201

Evaluating 35 Methods to Generate Structural Connectomes Using Pairwise Classification

There is no consensus on how to construct structural brain networks from diffusion MRI. How variations in pre-processing steps affect network reliability and its ability to distinguish subjects remains opaque. In this work, we address this issue by comparing 35 structural connectome-building pipelines. We vary diffusion reconstruction models, tractography algorithms and parcellations. Next, we classify structural connectome pairs as either belonging to the same individual or not. Connectome weights and eight topological derivative measures form our feature set. For experiments, we use three test-retest datasets from the Consortium for Reliability and Reproducibility (CoRR) comprised of a total of 105 individuals. We also compare pairwise classification results to a commonly used parametric test-retest measure, Intraclass Correlation Coefficient (ICC).Comment: Accepted for MICCAI 2017, 8 pages, 3 figure

Multi-view fusion of diffusion MRI microstructural models: a preterm birth study

Objective High Angular Resolution Diffusion Imaging (HARDI) models have emerged as a valuable tool for investigating microstructure with a higher degree of detail than standard diffusion Magnetic Resonance Imaging (dMRI). In this study, we explored the potential of multiple advanced microstructural diffusion models for investigating preterm birth in order to identify non-invasive markers of altered white matter development.Approach Rather than focusing on a single MRI modality, we studied on a compound of HARDI techniques in 46 preterm babies studied on a 3T scanner at term-equivalent age and in 23 control neonates born at term. Furthermore, we investigated discriminative patterns of preterm birth using multiple analysis methods, drawn from two only seemingly divergent modeling goals, namely inference and prediction. We thus resorted to (i) a traditional univariate voxel-wise inferential method, as the Tract-Based Spatial Statistics (TBSS) approach; (ii) a univariate predictive approach, as the Support Vector Machine (SVM) classification; and (iii) a multivariate predictive Canonical Correlation Analysis (CCA).Main results The TBSS analysis revealed significant differences between preterm and term cohorts in several white matter areas for multiple HARDI features. SVM classification on skeletonized HARDI measures yielded satisfactory accuracy, particularly for highly informative parameters about fiber directionality. Assessment of the degree of overlap between the two methods in voting for the most discriminating features exhibited a good, though parameter-dependent, rate of agreement. Finally, CCA identified joint changes precisely for those measures exhibiting less correspondence between TBSS and SVM.Significance Our results suggest that a data-driven intramodal imaging approach is crucial for gathering deep and complementary information. The main contribution of this methodological outline is to thoroughly investigate prematurity-related white matter changes through different inquiry focuses, with a view to addressing this issue, both aiming toward mechanistic insight and optimizing predictive accuracy

Dynamic Changes in White Matter Abnormalities Correlate With Late Improvement and Deterioration Following TBI: A Diffusion Tensor Imaging Study.

OBJECTIVE: Traumatic brain injury (TBI) is not a single insult with monophasic resolution, but a chronic disease, with dynamic processes that remain active for years. We aimed to assess patient trajectories over the entire disease narrative, from ictus to late outcome. METHODS: Twelve patients with moderate-to-severe TBI underwent magnetic resonance imaging in the acute phase (within 1 week of injury) and twice in the chronic phase of injury (median 7 and 21 months), with some undergoing imaging at up to 2 additional time points. Longitudinal imaging changes were assessed using structural volumetry, deterministic tractography, voxel-based diffusion tensor analysis, and region of interest analyses (including corpus callosum, parasagittal white matter, and thalamus). Imaging changes were related to behavior. RESULTS: Changes in structural volumes, fractional anisotropy, and mean diffusivity continued for months to years postictus. Changes in diffusion tensor imaging were driven by increases in both axial and radial diffusivity except for the earliest time point, and were associated with changes in reaction time and performance in a visual memory and learning task (paired associates learning). Dynamic structural changes after TBI can be detected using diffusion tensor imaging and could explain changes in behavior. CONCLUSIONS: These data can provide further insight into early and late pathophysiology, and begin to provide a framework that allows magnetic resonance imaging to be used as an imaging biomarker of therapy response. Knowledge of the temporal pattern of changes in TBI patient populations also provides a contextual framework for assessing imaging changes in individuals at any given time point

brainlife.io: a decentralized and open-source cloud platform to support neuroscience research

Neuroscience is advancing standardization and tool development to support rigor and transparency. Consequently, data pipeline complexity has increased, hindering FAIR (findable, accessible, interoperable and reusable) access. brainlife.io was developed to democratize neuroimaging research. The platform provides data standardization, management, visualization and processing and automatically tracks the provenance history of thousands of data objects. Here, brainlife.io is described and evaluated for validity, reliability, reproducibility, replicability and scientific utility using four data modalities and 3,200 participants.The brainlife.io project development and operations were supported by awards to F.P.: grant nos. NIH NIBIB 01EB029272, R01EB030896NSF and R01EB030896; NSF BCS 1734853 and 1636893; ACI 1916518, IIS 1912270; a gift from the Kavli Foundation; Wellcome Trust grant no. 226486/Z/22/Z and a Microsoft Investigator Fellowship. Additional funding was provided to support data collection used by the team, research that used brainlife.io or infrastructure that supported the platform: grant no. NIMH UM1NS132207 BRAIN CONNECTS: Center for Mesoscale Connectomics (Principal Investigator K. Ugurbil), grant no. NIMH R01MH133701 (C.R.). NSF grant award nos. 2004877 (S.V.-B.),1541335 and 2232628 (S.M.), 1445604 and 2005506 (D.Y.H.),1341698 and 1928224 (M. Norman), 1445606 (S.T.B.), 1928147 (S.Sanalevici). NIH grant award nos. 1U54MH091657 (HCP data, Principal Investigators D. Van Essen and K. Ugurbil), U01DA041048, U01DA050989, U01DA051016, U01DA041022, U01DA051018, U01DA051037, U01DA050987, U01DA041174, 01DA041106, U01DA041117, U01DA041028, U01DA041134, U01DA050988, U01DA051039, U01DA041156, 01DA041025, U01DA041120, U01DA051038, U01DA041148, U01DA041093, U01DA041089, U24DA041123, 24DA041147 (ABCD Study, multiple Principal Investigators), P41EB017183 (J.V.), NIH NIBIB R01EB030896 (A.P.) and ANR-20-NEUC-0004-01 (mulitple Principal Investigators). Multiple philanthropic contributions to the HBN (M. Milham)

Groupwise Structural Parcellation of the Cortex: A Sound Approach Based on Logistic Models

International audienceCurrent theories hold that brain function is highly related with long-range physical connections through axonal bundles, namely extrinsic connectivity. However, obtaining a groupwise cortical parcella-tion based on extrinsic connectivity remains challenging. Current par-cellation methods are computationally expensive; need tuning of several parameters or rely on ad-hoc constraints. Furthermore, none of these methods present a model for the cortical extrinsic connectivity. To tackle these problems, we propose a parsimonious model for the extrinsic con-nectivity and an efficient parcellation technique based on clustering of tractograms. Our technique allows the creation of single subject and groupwise parcellations of the whole cortex. The parcellations obtained with our technique are in agreement with anatomical and functional par-cellations in the literature. In particular, the motor and sensory cortex are subdivided in agreement with the human homunculus of Penfield. We illustrate this by comparing our resulting parcels with an anatomical atlas and the motor strip mapping included in the Human Connectome Project data

Neuro4Neuro: A neural network approach for neural tract segmentation using large-scale population-based diffusion imaging

Subtle changes in white matter (WM) microstructure have been associated with normal aging and neurodegeneration. To study these associations in more detail, it is highly important that the WM tracts can be accurately and reproducibly characterized from brain diffusion MRI. In addition, to enable analysis of WM tracts in large datasets and in clinical practice it is essential to have methodology that is fast and easy to apply. This work therefore presents a new approach for WM tract segmentation: Neuro4Neuro, that is capable of direct extraction of WM tracts from diffusion tensor images using convolutional neural network (CNN). This 3D end-to-end method is trained to segment 25 WM tracts in aging individuals from a large population-based study (N=9752, 1.5T MRI). The proposed method showed good segmentation performance and high reproducibility, i.e., a high spatial agreement (Cohen's kappa, k = 0.72 ~ 0.83) and a low scan-rescan error in tract-specific diffusion measures (e.g., fractional anisotropy: error = 1% ~ 5%). The reproducibility of the proposed method was higher than that of a tractography-based segmentation algorithm, while being orders of magnitude faster (0.5s to segment one tract). In addition, we showed that the method successfully generalizes to diffusion scans from an external dementia dataset (N=58, 3T MRI). In two proof-of-principle experiments, we associated WM microstructure obtained using the proposed method with age in a normal elderly population, and with disease subtypes in a dementia cohort. In concordance with the literature, results showed a widespread reduction of microstructural organization with aging and substantial group-wise microstructure differences between dementia subtypes. In conclusion, we presented a highly reproducible and fast method for WM tract segmentation that has the potential of being used in large-scale studies and clinical practice.Comment: Preprint to be published in NeuroImag

QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data

Diffusion-weighted magnetic resonance imaging (dMRI) is the primary method for noninvasively studying the organization of white matter in the human brain. Here we introduce QSIPrep, an integrative software platform for the processing of diffusion images that is compatible with nearly all dMRI sampling schemes. Drawing on a diverse set of software suites to capitalize on their complementary strengths, QSIPrep facilitates the implementation of best practices for processing of diffusion images

Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset?

White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same intended white matter pathways, which directly affects tractography results, quantification, and interpretation. In this study, we aim to evaluate and quantify the variability that arises from different protocols for bundle segmentation. Through an open call to users of fiber tractography, including anatomists, clinicians, and algorithm developers, 42 independent teams were given processed sets of human whole-brain streamlines and asked to segment 14 white matter fascicles on six subjects. In total, we received 57 different bundle segmentation protocols, which enabled detailed volume-based and streamline-based analyses of agreement and disagreement among protocols for each fiber pathway. Results show that even when given the exact same sets of underlying streamlines, the variability across protocols for bundle segmentation is greater than all other sources of variability in the virtual dissection process, including variability within protocols and variability across subjects. In order to foster the use of tractography bundle dissection in routine clinical settings, and as a fundamental analytical tool, future endeavors must aim to resolve and reduce this heterogeneity. Although external validation is needed to verify the anatomical accuracy of bundle dissections, reducing heterogeneity is a step towards reproducible research and may be achieved through the use of standard nomenclature and definitions of white matter bundles and well-chosen constraints and decisions in the dissection process