Belief propagation based segmentation of white matter tracts in DTI

White Matter Segmentation Algorithm for DTI Images Based on Super-Pixel Full Convolutional Network

Diffusion tensor imaging (DTI) is a new imaging method that can be used to non-invasively measure the diffusion coefficient of water molecules in biological tissue structures in recent years. Since the DTI data is a tensor space, its segmentation is different from ordinary MRI images. Based on the existing deep learning model, an improved image semantic segmentation method based on super-pixels and conditional random field is proposed. Firstly, this paper uses the existing feature extraction model based on deep learning to obtain rough semantic segmentation results, including high-level semantic information of the image but lacking details of the image. In addition, the super-pixel segmentation algorithm is implemented to obtain super-pixels that carries more low-level information. Secondly, due to the lack of image details in rough segmentation results, the segmentation of the edge of the image is inaccurate. In this paper, a boundary optimization algorithm is proposed to optimize the edge segmentation accuracy of the rough results. Finally, the use of super-pixels for local boundary optimization can improve the segmentation accuracy. Experiments results show that this segment is a practical and effective method.

3D-SSF: A bio-inspired approach for dynamic multi-subject clustering of white matter tracts

There is growing interest in the study of white matter (WM) variation across subjects, and in particular the analysis of specific WM bundles, to better understand brain development and aging, as well as to improve early detection of some diseases. Several WM multi-subject clustering methods have been proposed to study WM bundles. These methods aim to overcome the complexity of the problem, which includes the huge size of the WM tractography datasets generated from multiple subjects, the existence of various streamlines with different positions, lengths and geometric forms, as well as the presence of outliers. However, the current methods are not sufficiently flexible to address all of these constraints. Here we introduce a novel dynamic multi-subject clustering framework based on a distributed multiagent implementation of the Multiple Species Flocking model, that we name 3D-Streamlines Stream Flocking (3D-SSF). Specifically, we consider streamlines from different subjects as data streams, and each streamline is assigned to a mobile agent. Agents work together following flocking rules in order to form a flock. Thanks to a similarity function, the agents that are associated with similar streamlines form a flock, whereas the agents that are associated with dissimilar streamlines are considered outliers. We use various experiments performed on noisy synthetic and real human brain data to validate 3D-SSF and demonstrate that it is more efficient and robust to outliers compared to other classical approaches. 3D-SSF is able to extract WM bundles at a population level, while considering WM variation across subjects and eliminating outlier streamlines.

Sequential Hierarchical Agglomerative Clustering of White Matter Fiber Pathways

OBJECTIVE

We consider the problem of clustering white matter fiber pathways, extracted from diffusion MRI data via tractography, into bundles that are consistent with the neuroanatomy.

METHODS

We cast this problem as clustering streams of data, and use a sequential framework to process one fiber at a time. Our method, named as sequential hierarchical agglomerative clustering (HAC), represents the clusters with parametric models, performs HAC of relatively small number of fibers only when the parameters need to be initialized and/or updated, and assigns the labels to the following streams of data according to the current models.

RESULTS

Experiments on phantom data evaluate the sensitivity of our method to initialization and parameter tuning, and show its advantages over alternative techniques. Experiments on real data demonstrate its efficacy and speed in clustering white matter fiber pathways into anatomically distinct bundles.

CONCLUSION

Sequential HAC is a fast method that benefits from having a predefined number of clusters, and rapidly assigns labels to incoming data with high accuracy. It can be thought of as a mechanism that does clustering, while simultaneously accepting newly computed fibers; thereby, alleviating the burden of computing the distances between every pair of fibers in a tractogram.

SIGNIFICANCE

Sequential HAC is a practical tool that can interactively cluster fiber pathways and can be integrated into fiber tracking, which will be very useful for clinical researchers and neuroanatomists.

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.

Automated vs. conventional tractography in multiple sclerosis: variability and correlation with disability

Diffusion-tensor-imaging fiber tractography enables interrogation of brain white matter tracts that subserve different functions. However, tract reconstruction can be labor and time intensive and can yield variable results that may reduce the power to link imaging abnormalities with disability. Automated segmentation of these tracts would help make tract-specific imaging clinically useful, but implementation of such segmentation is problematic in the presence of diseases that alter brain structure. In this work, we investigated an automated tract-probability-mapping scheme and applied it to multiple sclerosis, comparing the results to those derived from conventional tractography. We found that the automated method has consistently lower scan-rescan variability (typically 0.7-1.5% vs. up to 3% for conventional tractography) and avoids problems related to tractography failures within and around lesions. In the corpus callosum, optic radiation, and corticospinal tract, tract-specific MRI indices calculated by the two methods were moderately to strongly correlated, though systematic, tract-specific differences were present. In these tracts, the two methods also yielded similar correlation coefficients relating tract-specific MRI indices to clinical disability scores. In the optic tract, the automated method failed. With judicious application, therefore, the automated method may be useful for studies that investigate the relationship between imaging findings and clinical outcomes in disease.