| 1. |
- Miri, Maliheh, et al.
(författare)
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Brain fingerprinting using EEG graph inference
- 2023
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Ingår i: 31st European Signal Processing Conference, EUSIPCO 2023 - Proceedings. - 2219-5491. - 9789464593600 ; , s. 1025-1029
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Konferensbidrag (refereegranskat)abstract
- Taking advantage of the human brain functional connectome as an individual's fingerprint has attracted great research in recent years. Conventionally, Pearson correlation between regional time-courses is used as a pairwise measure for each edge weight of the connectome. Building upon recent advances in graph signal processing, we propose here to estimate the graph structure as a whole by considering all time-courses at once. Using data from two publicly available datasets, we show the superior performance of such learned brain graphs over correlation-based functional connectomes in characterizing an individual.
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| 2. |
- Miri, Maliheh, et al.
(författare)
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Spectral representation of EEG data using learned graphs with application to motor imagery decoding
- 2024
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Ingår i: Biomedical Signal Processing and Control. - 1746-8094. ; 87
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Tidskriftsartikel (refereegranskat)abstract
- Electroencephalography (EEG) data entail a complex spatiotemporal structure that reflects ongoing organization of brain activity. Characterization of the spatial patterns is an indispensable step in numerous EEG processing pipelines. We present a novel method for transforming EEG data into a spectral representation. First, we learn subject-specific graphs from each subject's EEG data. Second, by eigendecomposition of the normalized Laplacian matrix of each subject's graph, an orthonormal basis is obtained using which any given EEG map of the subject can be decomposed, providing a spectral representation of the data. We show that energy of EEG maps is strongly associated with low frequency components of the learned basis, reflecting the smooth topography of EEG maps. As a proof-of-concept for this alternative view of EEG data, we consider the task of decoding two-class motor imagery (MI) data. To this aim, the spectral representations are first mapped into a discriminative subspace for differentiating two-class data using a projection matrix obtained by the Fukunaga–Koontz transform (FKT). An SVM classifier is then trained and tested on the resulting features to differentiate MI classes. The method is benchmarked against features extracted from a subject-specific functional connectivity matrix as well as four alternative MI-decoding methods on Dataset IVa of BCI Competition III. Experimental results show the superiority of the proposed method over alternative approaches in differentiating MI classes, reflecting the added benefit of (i) decomposing EEG data using data-driven, subject-specific harmonic bases, and (ii) accounting for class-specific temporal variations in spectral profiles.
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| 3. |
- Abramian, David, 1992-, et al.
(författare)
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Diffusion-Informed Spatial Smoothing of fMRI Data in White Matter Using Spectral Graph Filters
- 2021
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Ingår i: NeuroImage. - : Elsevier. - 1053-8119 .- 1095-9572. ; 237
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Tidskriftsartikel (refereegranskat)abstract
- Brain activation mapping using functional magnetic resonance imaging (fMRI) has been extensively studied in brain gray matter (GM), whereas in large disregarded for probing white matter (WM). This unbalanced treatment has been in part due to controversies in relation to the nature of the blood oxygenation level-dependent (BOLD) contrast in WM and its detachability. However, an accumulating body of studies has provided solid evidence of the functional significance of the BOLD signal in WM and has revealed that it exhibits anisotropic spatio-temporal correlations and structure-specific fluctuations concomitant with those of the cortical BOLD signal. In this work, we present an anisotropic spatial filtering scheme for smoothing fMRI data in WM that accounts for known spatial constraints on the BOLD signal in WM. In particular, the spatial correlation structure of the BOLD signal in WM is highly anisotropic and closely linked to local axonal structure in terms of shape and orientation, suggesting that isotropic Gaussian filters conventionally used for smoothing fMRI data are inadequate for denoising the BOLD signal in WM. The fundamental element in the proposed method is a graph-based description of WM that encodes the underlying anisotropy observed across WM, derived from diffusion-weighted MRI data. Based on this representation, and leveraging graph signal processing principles, we design subject-specific spatial filters that adapt to a subject’s unique WM structure at each position in the WM that they are applied at. We use the proposed filters to spatially smooth fMRI data in WM, as an alternative to the conventional practice of using isotropic Gaussian filters. We test the proposed filtering approach on two sets of simulated phantoms, showcasing its greater sensitivity and specificity for the detection of slender anisotropic activations, compared to that achieved with isotropic Gaussian filters. We also present WM activation mapping results on the Human Connectome Project’s 100-unrelated subject dataset, across seven functional tasks, showing that the proposed method enables the detection of streamline-like activations within axonal bundles.
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| 4. |
- Abramian, David, 1992-, et al.
(författare)
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Improved Functional MRI Activation Mapping in White Matter Through Diffusion-Adapted Spatial Filtering
- 2020
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Ingår i: ISBI 2020. - : IEEE. - 1945-8452 .- 1945-7928. - 9781538693308
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Konferensbidrag (refereegranskat)abstract
- Brain activation mapping using functional MRI (fMRI) based on blood oxygenation level-dependent (BOLD) contrast has been conventionally focused on probing gray matter, the BOLD contrast in white matter having been generally disregarded. Recent results have provided evidence of the functional significance of the white matter BOLD signal, showing at the same time that its correlation structure is highly anisotropic, and related to the diffusion tensor in shape and orientation. This evidence suggests that conventional isotropic Gaussian filters are inadequate for denoising white matter fMRI data, since they are incapable of adapting to the complex anisotropic domain of white matter axonal connections. In this paper we explore a graph-based description of the white matter developed from diffusion MRI data, which is capable of encoding the anisotropy of the domain. Based on this representation we design localized spatial filters that adapt to white matter structure by leveraging graph signal processing principles. The performance of the proposed filtering technique is evaluated on semi-synthetic data, where it shows potential for greater sensitivity and specificity in white matter activation mapping, compared to isotropic filtering.
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| 5. |
- Abramian, David, 1992-
(författare)
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Modern multimodal methods in brain MRI
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Magnetic resonance imaging (MRI) is one of the pillars of modern medical imaging, providing a non-invasive means to generate 3D images of the body with high soft-tissue contrast. Furthermore, the possibilities afforded by the design of MRI sequences enable the signal to be sensitized to a multitude of physiological tissue properties, resulting in a wide variety of distinct MRI modalities for clinical and research use. This thesis presents a number of advanced brain MRI applications, which fulfill, to differing extents, two complementary aims. On the one hand, they explore the benefits of a multimodal approach to MRI, combining structural, functional and diffusion MRI, in a variety of contexts. On the other, they emphasize the use of advanced mathematical and computational tools in the analysis of MRI data, such as deep learning, Bayesian statistics, and graph signal processing. Paper I introduces an anatomically-adapted extension to previous work in Bayesian spatial priors for functional MRI data, where anatomical information is introduced from a T1-weighted image to compensate for the low anatomical contrast of functional MRI data. It has been observed that the spatial correlation structure of the BOLD signal in brain white matter follows the orientation of the underlying axonal fibers. Paper II argues about the implications of this fact on the ideal shape of spatial filters for the analysis of white matter functional MRI data. By using axonal orientation information extracted from diffusion MRI, and leveraging the possibilities afforded by graph signal processing, a graph-based description of the white matter structure is introduced, which, in turn, enables the definition of spatial filters whose shape is adapted to the underlying axonal structure, and demonstrates the increased detection power resulting from their use. One of the main clinical applications of functional MRI is functional localization of the eloquent areas of the brain prior to brain surgery. This practice is widespread for various invasive surgeries, but is less common for stereotactic radiosurgery (SRS), a non-invasive surgical procedure wherein tissue is ablated by concentrating several beams of high-energy radiation. Paper III describes an analysis and processing pipeline for functional MRI data that enables its use for functional localization and delineation of organs-at-risk for Elekta GammaKnife SRS procedures. Paper IV presents a deep learning model for super-resolution of diffusion MRI fiber ODFs, which outperforms standard interpolation methods in estimating local axonal fiber orientations in white matter. Finally, Paper V demonstrates that some popular methods for anonymizing facial data in structural MRI volumes can be partially reversed by applying generative deep learning models, highlighting one way in which the enormous power of deep learning models can potentially be put to use for harmful purposes.
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| 6. |
- Behjat, Hamid, et al.
(författare)
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Anatomically-adapted Graph Wavelets for Improved Group-level fMRI Activation Mapping
- 2015
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Ingår i: NeuroImage. - : Elsevier BV. - 1095-9572 .- 1053-8119. ; 123:Online 07 June 2015, s. 185-199
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Tidskriftsartikel (refereegranskat)abstract
- A graph based framework for fMRI brain activation mapping is presented. The approach exploits the spectral graph wavelet transform (SGWT) for the purpose of defining an advanced multi-resolutional spatial transformation for fMRI data. The framework extends wavelet based SPM (WSPM), which is an alternative to the conventional approach of statistical parametric mapping (SPM), and is developed specifically for group-level analysis. We present a novel procedure for constructing brain graphs, with subgraphs that separately encode the structural connectivity of the cerebral and cerebellar grey matter (GM), and address the inter-subject GM variability by the use of template GM representations. Graph wavelets tailored to the convoluted boundaries of GM are then constructed as a means to implement a GM-based spatial transformation on fMRI data. The proposed approach is evaluated using real as well as semi-synthetic multi-subject data. Compared to SPM and WSPM using classical wavelets, the proposed approach shows superior type-I error control. The results on real data suggest a higher detection sensitivity as well as the capability to capture subtle, connected patterns of brain activity.
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| 7. |
- Behjat, Hamid, et al.
(författare)
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Canonical cerebellar graph wavelets and their application to fMRI activation mapping
- 2014
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Ingår i: [Host publication title missing]. - 1557-170X. ; , s. 1039-1042
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Konferensbidrag (refereegranskat)abstract
- Wavelet-based statistical parametric mapping (WSPM) is an extension of the classical approach in fMRI activation mapping that combines wavelet processing with voxel-wise statistical testing. We recently showed how WSPM, using graph wavelets tailored to the full gray-matter (GM) structure of each individual’s brain, can improve brain activity detection compared to using the classical wavelets that are only suited for the Euclidian grid. However, in order to perform analysis on a subject-invariant graph, canonical graph wavelets should be designed in normalized brain space. We here introduce an approach to define a fixed template graph of the cerebellum, an essential component of the brain, using the SUIT cerebellar template. We construct a corresponding set of canonical cerebellar graph wavelets, and adopt them in the analysis of both synthetic and real data. Compared to classical SPM, WSPM using cerebellar graph wavelets shows superior type-I error control, an empirical higher sensitivity on real data, as well as the potential to capture subtle patterns of cerebellar activity.
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| 8. |
- Behjat, Hamid, et al.
(författare)
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Characterization of Spatial Dynamics of Fmri Data in White Matter Using Diffusion-Informed White Matter Harmonics
- 2021
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Ingår i: 2021 IEEE 18th International Symposium On Biomedical Imaging (ISBI). - : Institute of Electrical and Electronics Engineers (IEEE). - 1945-7928 .- 1945-8452. - 9781665412469 - 9781665429474
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Konferensbidrag (refereegranskat)abstract
- In this work, we leverage the Laplacian eigenbasis of voxelwise white matter (WM) graphs derived from diffusionweighted MRI data, dubbed WM harmonics, to characterize the spatial structure of WM fMRI data. Our motivation for such a characterization is based on studies that show WM fMRI data exhibit a spatial correlational anisotropy that coincides with underlying fiber patterns. By quantifying the energy content of WM fMRI data associated with subsets of WM harmonics across multiple spectral bands, we show that the data exhibits notable subtle spatial modulations under functional load that are not manifested during rest. WM harmonics provide a novel means to study the spatial dynamics of WM fMRI data, in such way that the analysis is informed by the underlying anatomical structure.
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| 9. |
- Behjat, Hamid
(författare)
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Domain-Informed Signal Processing with Application to Analysis of Human Brain Functional MRI Data
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Standard signal processing techniques are implicitly based on the assumption that the signal lies on a regular, homogeneous domain. In practice, however, many signals lie on an irregular or inhomogeneous domain. An application area where data are naturally defined on an irregular or inhomogeneous domain is human brain neuroimaging. The goal in neuroimaging is to map the structure and function of the brain using imaging techniques. In particular, functional magnetic resonance imaging (fMRI) is a technique that is conventionally used in non-invasive probing of human brain function. This doctoral dissertation deals with the development of signal processing schemes that adapt to the domain of the signal. It consists of four papers that in different ways deal with exploiting knowledge of the signal domain to enhance the processing of signals. In each paper, special focus is given to the analysis of brain fMRI data, either as the main theme (Paper I) or as proof of practical significance of the proposed schemes (Papers II, III and IV). Paper I presents a framework for enhanced fMRI activation mapping through exploiting filters that adapt to the brain anatomy. A novel procedure for constructing brain graphs, with subgraphs that separately encode the topology of the cerebral and cerebellar gray matter, is presented. Graph wavelets tailored to the convoluted boundaries of brain gray matter are designed and exploited to implement an anatomically-informed spatial transformation on fMRI data. Compared to conventional brain activation mapping schemes, the proposed approach shows superior type-I error control. Results on real data suggest a higher detection sensitivity as well as capability to capture subtle, connected patterns of brain activity. Paper II presents a graph-based signal decomposition scheme that adapts to the domain of the data as well as to the spectral content of a given signal set. The construction starts from the design of a prototype Meyer-type system of kernels with uniform subbands. The adaptivity of the approach is introduced by exploiting the ensemble energy spectral density. Using the ensemble energy spectral density, the prototype design is warped such that the resulting subbands each capture an equal amount of energy for the given signal class. Results on fMRI data and Monte Carlo simulations illustrate the superiority of signal-adapted frames over frames blind to signal characteristics in representing data and in denoising. Paper III presents a generic interpolation scheme for reconstructing signal samples from an inhomogeneous domain. The interpolation adapts to the inhomogeneity of the domain. The adaptation is incorporated by introducing a domain-similarity metric that characterises the domain in the adjacency of each sample point. The interpolation is shown to satisfy the domain-informed consistency principle, a principle that we define as an extension of the classical consistency principle. As proof of concept, domain-informed linear interpolation is presented as an extension of standard linear interpolation. Results from applying the proposed approach on fMRI data demonstrated its potential to reveal subtle details. Paper IV extends the theory in Paper III to enable reconstruction of signals with varying degrees of spatial smoothness. In particular, conventional shift-invariant B-spline interpolation is extended to a shift-variant, domain-informed interpolation. This is done by constructing a domain-informed generating basis that satisfies stability properties. The benefit of domain-informed interpolation over standard B-spline interpolation is demonstrated through Monte Carlo simulations across a range of B-spline orders. The practical significance of domain-informed spline interpolation is demonstrated on fMRI data. The results show the benefit of incorporating domain knowledge so that an interpolant consistent to the anatomy of the brain can be recovered by the proposed interpolation.
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| 10. |
- Behjat, Hamid, et al.
(författare)
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Domain-Informed Spline Interpolation
- 2019
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Ingår i: IEEE Transactions on Signal Processing. - 1053-587X. ; 67:15, s. 3909-3921
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Tidskriftsartikel (refereegranskat)abstract
- Standard interpolation techniques are implicitly based on the assumption that the signal lies on a single homogeneous domain. In contrast, many naturally occurring signals lie on an inhomogeneous domain, such as brain activity associated to different brain tissue. We propose an interpolation method that instead exploits prior information about domain inhomogeneity, characterized by different, potentially overlapping, subdomains. As proof of concept, the focus is put on extending conventional shift-invariant B-spline interpolation. Given a known inhomogeneous domain, B-spline interpolation of a given order is extended to a domain-informed, shift-variant interpolation. This is done by constructing a domain-informed generating basis that satisfies stability properties. We illustrate example constructions of domain-informed generating basis and show their property in increasing the coherence between the generating basis and the given inhomogeneous domain. By advantageously exploiting domain knowledge, we demonstrate the benefit of domain-informed interpolation over standard B-spline interpolation through Monte Carlo simulations across a range of B-spline orders. We also demonstrate the feasibility of domain-informed interpolation in a neuroimaging application where the domain information is available by a complementary image contrast. The results show the benefit of incorporating domain knowledge so that an interpolant consistent to the anatomy of the brain is obtained.
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