MR diffusion-based inference of a fiber bundle model from a population of subjects

A systematic review of automated methods to perform white matter tract segmentation

White matter tract segmentation is a pivotal research area that leverages diffusion-weighted magnetic resonance imaging (dMRI) for the identification and mapping of individual white matter tracts and their trajectories. This study aims to provide a comprehensive systematic literature review on automated methods for white matter tract segmentation in brain dMRI scans. Articles on PubMed, ScienceDirect [NeuroImage, NeuroImage (Clinical), Medical Image Analysis], Scopus and IEEEXplore databases and Conference proceedings of Medical Imaging Computing and Computer Assisted Intervention Society (MICCAI) and International Symposium on Biomedical Imaging (ISBI), were searched in the range from January 2013 until September 2023. This systematic search and review identified 619 articles. Adhering to the specified search criteria using the query, "white matter tract segmentation OR fiber tract identification OR fiber bundle segmentation OR tractography dissection OR white matter parcellation OR tract segmentation," 59 published studies were selected. Among these, 27% employed direct voxel-based methods, 25% applied streamline-based clustering methods, 20% used streamline-based classification methods, 14% implemented atlas-based methods, and 14% utilized hybrid approaches. The paper delves into the research gaps and challenges associated with each of these categories. Additionally, this review paper illuminates the most frequently utilized public datasets for tract segmentation along with their specific characteristics. Furthermore, it presents evaluation strategies and their key attributes. The review concludes with a detailed discussion of the challenges and future directions in this field.

System for integrated neuroimaging analysis and processing of structure

Mapping brain structure in relation to neurological development, function, plasticity, and disease is widely considered to be one of the most essential challenges for opening new lines of neuro-scientific inquiry. Recent developments with MRI analysis of structural connectivity, anatomical brain segmentation, cortical surface parcellation, and functional imaging have yielded fantastic advances in our ability to probe the neurological structure-function relationship in vivo. To date, the image analysis efforts in each of these areas have typically focused on a single modality. Here, we extend the cortical reconstruction using implicit surface evolution (CRUISE) methodology to perform efficient, consistent, and topologically correct analyses in a natively multi-parametric manner. This effort combines and extends state-of-the-art techniques to simultaneously consider and analyze structural and diffusion information alongside quantitative and functional imaging data. Robust and consistent estimates of the cortical surface extraction, cortical labeling, diffusion-inferred contrasts, diffusion tractography, and subcortical parcellation are demonstrated in a scan-rescan paradigm. Accompanying this demonstration, we present a fully automated software system complete with validation data.

QuickBundles, a Method for Tractography Simplification

Diffusion MR data sets produce large numbers of streamlines which are hard to visualize, interact with, and interpret in a clinically acceptable time scale, despite numerous proposed approaches. As a solution we present a simple, compact, tailor-made clustering algorithm, QuickBundles (QB), that overcomes the complexity of these large data sets and provides informative clusters in seconds. Each QB cluster can be represented by a single centroid streamline; collectively these centroid streamlines can be taken as an effective representation of the tractography. We provide a number of tests to show how the QB reduction has good consistency and robustness. We show how the QB reduction can help in the search for similarities across several subjects.

Direct segmentation of the major white matter tracts in diffusion tensor images

Diffusion-weighted images of the human brain are acquired more and more routinely in clinical research settings, yet segmenting and labeling white matter tracts in these images is still challenging. We present in this paper a fully automated method to extract many anatomical tracts at once on diffusion tensor images, based on a Markov random field model and anatomical priors. The approach provides a direct voxel labeling, models explicitly fiber crossings and can handle white matter lesions. Experiments on simulations and repeatability studies show robustness to noise and reproducibility of the algorithm, which has been made publicly available.

A Hough transform global probabilistic approach to multiple-subject diffusion MRI tractography

A global probabilistic fiber tracking approach based on the voting process provided by the Hough transform is introduced in this work. The proposed framework tests candidate 3D curves in the volume, assigning to each one a score computed from the diffusion images, and then selects the curves with the highest scores as the potential anatomical connections. The algorithm avoids local minima by performing an exhaustive search at the desired resolution. The technique is easily extended to multiple subjects, considering a single representative volume where the registered high-angular resolution diffusion images (HARDI) from all the subjects are non-linearly combined, thereby obtaining population-representative tracts. The tractography algorithm is run only once for the multiple subjects, and no tract alignment is necessary. We present experimental results on HARDI volumes, ranging from simulated and 1.5T physical phantoms to 7T and 4T human brain and 7T monkey brain datasets.

A statistical model of white matter fiber bundles based on currents

The purpose of this paper is to measure the variability of a population of white matter fiber bundles without imposing unrealistic geometrical priors. In this respect, modeling fiber bundles as currents seems particularly relevant, as it gives a metric between bundles which relies neither on point nor on fiber correspondences and which is robust to fiber interruption. First, this metric is included in a diffeomorphic registration scheme which consistently aligns sets of fiber bundles. In particular, we show that aligning directly fiber bundles may solve the aperture problem which appears when fiber mappings are constrained by tensors only. Second, the measure of variability of a population of fiber bundles is based on a statistical model which considers every bundle as a random diffeomorphic deformation of a common template plus a random non-diffeomorphic perturbation. Thus, the variability is decomposed into a geometrical part and a "texture" part. Our results on real data show that both parts may contain interesting anatomical features.

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. We determine the fibre point correspondences and impact factors of individual fibres, upon which we estimate average HARDI models along the tract mean lines. This way we obtain a compact tract representation that exploits all the available information, and is at the same time free of the outlier influence and undesired tract edge effects.