Spectral Characterization of functional MRI data on voxel-resolution cortical graphs

The human cortical layer exhibits a convoluted morphology that is unique to each individual. Conventional volumetric fMRI processing schemes take for granted the rich information provided by the underlying anatomy. We present a method to study fMRI data on subject-specific cerebral hemisphere cortex (CHC) graphs, which encode the cortical morphology at the resolution of voxels in 3-D. We study graph spectral energy metrics associated to fMRI data of 100 subjects from the Human Connectome Project database, across seven tasks. Experimental results signify the strength of CHC graphs' Laplacian eigenvector bases in capturing subtle spatial patterns specific to different functional loads as well as experimental conditions within each task.Comment: Fixed two typos in the equations; (1) definition of L in section 2.1, paragraph 1. (2) signal de-meaning and normalization in section 2.4, paragraph

Toolbox for enhanced fMRI activation mapping using anatomically adapted graph wavelets

In fMRI studies with evoked activity, brain activity is detected by voxel-wise GLM tting, followed by statistical hypothesis testing. Statistical parametric mapping (SPM), one of the most popular classical methods, relies upon Gaussian smoothing to deal with the multiple-comparison correction. As an alternative, we have recently introduced a graph-based framework for fMRI brain activation mapping (Behjat, et al., 2015). The graph is designed such that it encodes the topological structure of the gray matter (GM). The approach exploits the spectral graph wavelet transform for the purpose of defining an advanced multi-scale spatial transformation for fMRI data. The use of spatial wavelet transforms has the benefit of providing a compact representation of activation patterns. The framework extends wavelet-based SPM (WSPM), which is a framework that combines wavelet processing of non-smoothed data with voxel-wise statistical testing while guaranteeing strong FP control. Here, we present an implementation of the proposed framework as a user-friendly, SPM-compatible toolbox that deals with multi-subject studies

Diffusion-adapted spatial filtering of fMRI data for improved activation mapping in white matter

Brain activation mapping using fMRI data has been mostly focused on finding detections in gray matter. Activations in white matter are harder to detect due to anatomical differences between both tissue types, which are rarely acknowledged in experimental design. However, recent publications have started to show evidence for the possibility of detecting meaningful activations in white matter. The shape of the activations arising from the BOLD signal is fundamentally different between white matter and gray matter, a fact which is not taken into account when applying isotropic Gaussian filtering in the preprocessing of fMRI data. We explore a graph-based description of the white matter developed from diffusion MRI data, which is capable of encoding the anisotropic domain. Based on this representation, two approaches to white matter filtering are tested, and their performance is evaluated on both semi-synthetic phantoms and real fMRI data. The first approach relies on heat kernel filtering in the graph spectral domain, and produced a clear increase in both sensitivity and specificity over isotropic Gaussian filtering. The second approach is based on spectral decomposition for the denosing of the signal, and showed increased specificity at the cost of a lower sensitivity.Novel approach to white matter filtering We introduced new advanced methods for filtering brain scans. Using them, we managed to improve the detection of activity in the white matter of the brain

Combining spatial priors and anatomical information for fMRI detection

In this paper, we analyze Markov Random Field (MRF) as a spatial regularizer in fMRI detection. The low signal-to-noise ratio (SNR) in fMRI images presents a serious challenge for detection algorithms, making regularization necessary to achieve good detection accuracy. Gaussian smoothing, traditionally employed to boost SNR, often produces over-smoothed activation maps. Recently, the use of MRF priors has been suggested as an alternative regularization approach. However, solving for an optimal configuration of the MRF is NP-hard in general. In this work, we investigate fast inference algorithms based on the Mean Field approximation in application to MRF priors for fMRI detection. Furthermore, we propose a novel way to incorporate anatomical information into the MRF-based detection framework and into the traditional smoothing methods. Intuitively speaking, the anatomical evidence increases the likelihood of activation in the gray matter and improves spatial coherency of the resulting activation maps within each tissue type. Validation using the receiver operating characteristic (ROC) analysis and the confusion matrix analysis on simulated data illustrates substantial improvement in detection accuracy using the anatomically guided MRF spatial regularizer. We further demonstrate the potential benefits of the proposed method in real fMRI signals of reduced length. The anatomically guided MRF regularizer enables significant reduction of the scan length while maintaining the quality of the resulting activation maps.National Institutes of Health (U.S.) (National Institute for Biomedical Imaging and Bioengineering (U.S.)/National Alliance for Medical Image Computing (U.S.) Grant U54-EB005149)National Science Foundation (U.S.) (Grant IIS 9610249)National Institutes of Health (U.S.) (National Center for Research Resources (U.S.)/Biomedical Informatics Research Network Grant U24-RR021382)National Institutes of Health (U.S.) (National Center for Research Resources (U.S.)/Neuroimaging Analysis Center (U.S.) Grant P41-RR13218)National Institutes of Health (U.S.) (National Institute of Neurological Disorders and Stroke (U.S.) Grant R01-NS051826)National Science Foundation (U.S.) (CAREER Grant 0642971)National Science Foundation (U.S.). Graduate Research FellowshipNational Center for Research Resources (U.S.) (FIRST-BIRN Grant)Neuroimaging Analysis Center (U.S.