An official website of the United States government
Diffusion-weighted magnetic resonance imaging (dMRI) allows for non-invasive, detailed examination of the white matter structures of the brain. White matter tract-specific measures based on either the diffusion tensor model (e.g. FA, ADC, and MD) or tractography (e.g. volume, streamline count or density) are often compared between groups of subjects to localize differences within the white matter. Less commonly examined is the shape of the individual white matter tracts. In this paper, we propose to use the Laplace-Beltrami (LB) spectrum as a descriptor of the shape of white matter tracts. We provide an open, automated pipeline for the computation of the LB spectrum on segmented white matter tracts and demonstrate its efficacy through machine learning classification experiments. We show that the LB spectrum allows for distinguishing subjects diagnosed with bipolar disorder from age and sex-matched healthy controls, with classification accuracy reaching 95%. We further demonstrate that the results cannot be explained by traditional measures, such as tract volume, streamline count or mean and total length. The results indicate that there is valuable information in the anatomical shape of the human white matter tracts.
more »
« less
Implementation considerations for deep learning with diffusion MRI streamline tractography
One area of medical imaging that has recently experienced innovative deep learning advances is diffusion MRI (dMRI) streamline tractography with recurrent neural networks (RNNs). Unlike traditional imaging studies which utilize voxel-based learning, these studies model dMRI features at points in continuous space off the voxel grid in order to propagate streamlines, or virtual estimates of axons. However, implementing such models is nontrivial, and an open-source implementation is not yet widely available. Here, we describe a series of considerations for implementing tractography with RNNs and demonstrate they allow one to approximate a deterministic streamline propagator with comparable performance to existing algorithms. We release this trained model and the associated implementations leveraging popular deep learning libraries. We hope the availability of these resources will lower the barrier of entry into this field, spurring further innovation.
more »
« less
- Award ID(s):
- 2040462
- PAR ID:
- 10447853
- Date Published:
- Journal Name:
- Medical Imaging with Deep Learning (MIDL)
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
We use a multidimensional signal representation that inte- grates diffusion Magnetic Resonance Imaging (dMRI) and tractography (brain connections) using sparse tensor decomposition. The representa- tion encodes brain connections (fibers) into a very-large, but sparse, core tensor and allows to predict dMRI measurements based on a dictionary of diffusion signals. We propose an algorithm to learn the constituent parts of the model from a dataset. The algorithm assumes a tractography model (support of core tensor) and iteratively minimizes the Frobenius norm of the error as a function of the dictionary atoms, the values of nonzero entries in the sparse core tensor and the fiber weights. We use a nonparametric dictionary learning (DL) approach to estimate signal atoms. Moreover, the algorithm is able to learn multiple dictionaries associated to different brain locations (voxels) allowing for mapping distinctive tissue types. We illustrate the algorithm through results obtained on a large in-vivo high-resolution dataset.more » « less
-
Recently, linear formulations and convex optimization methods have been proposed to predict diffusion-weighted Magnetic Resonance Imaging (dMRI) data given estimates of brain connections generated using tractography algorithms. The size of the linear models comprising such methods grows with both dMRI data and connectome resolution, and can become very large when applied to modern data. In this paper, we introduce a method to encode dMRI signals and large connectomes, i.e., those that range from hundreds of thousands to millions of fascicles (bundles of neuronal axons), by using a sparse tensor decomposition. We show that this tensor decomposition accurately approximates the Linear Fascicle Evaluation (LiFE) model, one of the recently developed linear models. We provide a theoretical analysis of the accuracy of the sparse decomposed model, LiFESD, and demonstrate that it can reduce the size of the model significantly. Also, we develop algorithms to implement the optimization solver using the tensor representation in an efficient way.more » « less
-
The Human Connectome Project (HCP) has become a keystone dataset in human neuroscience, with a plethora of important applications in advancing brain imaging methods and an understanding of the human brain. We focused on tractometry of HCP diffusion-weighted MRI (dMRI) data. We used an open-source software library (pyAFQ;https://yeatmanlab.github.io/pyAFQ) to perform probabilistic tractography and delineate the major white matter pathways in the HCP subjects that have a complete dMRI acquisition (n = 1,041). We used diffusion kurtosis imaging (DKI) to model white matter microstructure in each voxel of the white matter, and extracted tract profiles of DKI-derived tissue properties along the length of the tracts. We explored the empirical properties of the data: first, we assessed the heritability of DKI tissue properties using the known genetic linkage of the large number of twin pairs sampled in HCP. Second, we tested the ability of tractometry to serve as the basis for predictive models of individual characteristics (e.g., age, crystallized/fluid intelligence, reading ability, etc.), compared to local connectome features. To facilitate the exploration of the dataset we created a new web-based visualization tool and use this tool to visualize the data in the HCP tractometry dataset. Finally, we used the HCP dataset as a test-bed for a new technological innovation: the TRX file-format for representation of dMRI-based streamlines. We released the processing outputs and tract profiles as a publicly available data resource through the AWS Open Data program's Open Neurodata repository. We found heritability as high as 0.9 for DKI-based metrics in some brain pathways. We also found that tractometry extracts as much useful information about individual differences as the local connectome method. We released a new web-based visualization tool for tractometry --- “Tractoscope” (https://nrdg.github.io/tractoscope). We found that the TRX files require considerably less disk space - a crucial attribute for large datasets like HCP. In addition, TRX incorporates a specification for grouping streamlines, further simplifying tractometry analysis.more » « less
-
Abstract There are a growing number of neuroimaging studies motivating joint structural and functional brain connectivity. Brain connectivity of different modalities provides insight into brain functional organization by leveraging complementary information, especially for brain disorders such as schizophrenia. In this paper, we propose a multi-modal independent component analysis (ICA) model that utilizes information from both structural and functional brain connectivity guided by spatial maps to estimate intrinsic connectivity networks (ICNs). Structural connectivity is estimated through whole-brain tractography on diffusion-weighted MRI (dMRI), while functional connectivity is derived from resting-state functional MRI (rs-fMRI). The proposed structural-functional connectivity and spatially constrained ICA (sfCICA) model estimates ICNs at the subject level using a multi-objective optimization framework. We evaluated our model using synthetic and real datasets (including dMRI and rs-fMRI from 149 schizophrenia patients and 162 controls). Multi-modal ICNs revealed enhanced functional coupling between ICNs with higher structural connectivity, improved modularity, and network distinction, particularly in schizophrenia. Statistical analysis of group differences showed more significant differences in the proposed model compared to the unimodal model. In summary, the sfCICA model showed benefits from being jointly informed by structural and functional connectivity. These findings suggest advantages in simultaneously learning effectively and enhancing connectivity estimates using structural connectivity.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Conference Paper:
- The DOI is not currently available.
