Subject-centered multi-view feature fusion for neuroimaging retrieval and classification

Multi-View neuroimaging retrieval and classification play an important role in computer-aided-diagnosis of brain disorders, as multi-view features could provide more insights of the disease pathology and potentially lead to more accurate diagnosis than single-view features. The large inter-feature and inter-subject variations make the multi-view neuroimaging analysis a challenging task. Many multi-view or multi-modal feature fusion methods have been proposed to reduce the impact of inter-feature variations in neuroimaging data. However, there is not much in-depth work focusing on the inter-subject variations. In this study, we propose a subject-centered multi-view feature fusion method for neuroimaging retrieval and classification based on the propagation graph fusion (PGF) algorithm. Two main advantages of the proposed method are: 1) it evaluates the query online and adaptively reshapes the connections between subjects according to the query; 2) it measures the affinity of the query to the subjects using the subject-centered affinity matrices, which can be easily combined and efficiently solved. Evaluated using a public accessible neuroimaging database, our algorithm outperforms the state-of-the-art methods in retrieval and achieves comparable performance in classification

Content-Based Retrieval of Brain Diffusion Magnetic Resonance Image

The content-based retrieval of diffusion magnetic resonance (dMR) imaging data would enable a wide range of analyses on large databases with dMR images.This paper proposes a content-based retrieval framework for dMR images to explore the use of Diffusion Tensor Imaging (DTI) - derived parameters. The propagation graph algorithm is proposed for the query-centric retrieval of dMR subjects and the fusion of different features. The proposed framework was evaluated with ADNI database with 233 baseline dMR images. The preliminary results show that the proposed retrieval framework is able to retrieve subjects with similar neurodegenerative patterns

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

MVPAlab: A machine learning decoding toolbox for multidimensional electroencephalography data

This research was supported by the Spanish Ministry of Sci- ence and Innovation under the PID2019–111187GB-I00 grant, by the MCIN/AEI/10.13039/50110 0 011033/ and FEDER “Una manera de hacer Europa’’ under the RTI2018-098913-B100 project, by the Consejería de Economía, Innovación, Ciencia y Empleo (Junta de Andalucía) and FEDER under CV20-45250, A-TIC-080-UGR18, B- TIC-586-UGR20 and P20-00525 projects. The first author of this work is supported by a scholarship from the Spanish Ministry of Science and Innovation (BES-2017–079769). Funding for open ac- cess charge: Universidad de Granada / CBUA. The sample EEG dataset was extracted from an original experiment previously ap- proved by the Ethics Committee of the University of Granada.Background and Objective: The study of brain function has recently expanded from classical univariate to multivariate analyses. These multivariate, machine learning-based algorithms afford neuroscientists extracting more detailed and richer information from the data. However, the implementation of these procedures is usually challenging, especially for researchers with no coding experience. To address this problem, we have developed MVPAlab, a MATLAB-based, flexible decoding toolbox for multidimensional electroencephalography and magnetoencephalography data. Methods: The MVPAlab Toolbox implements several machine learning algorithms to compute multivariate pattern analyses, cross-classification, temporal generalization matrices and feature and frequency contri- bution analyses. It also provides access to an extensive set of preprocessing routines for, among others, data normalization, data smoothing, dimensionality reduction and supertrial generation. To draw statisti- cal inferences at the group level, MVPAlab includes a non-parametric cluster-based permutation approach. Results: A sample electroencephalography dataset was compiled to test all the MVPAlab main function- alities. Significant clusters (p < 0.01) were found for the proposed decoding analyses and different config- urations, proving the software capability for discriminating between different experimental conditions. Conclusions: This toolbox has been designed to include an easy-to-use and intuitive graphic user interface and data representation software, which makes MVPAlab a very convenient tool for users with few or no previous coding experience. In addition, MVPAlab is not for beginners only, as it implements several high and low-level routines allowing more experienced users to design their own projects in a highly flexible manner.Spanish Government PID2019-111187GB-I00 BES-2017-079769MCIN/AEIFEDER "Una manera de hacer Europa'' RTI2018-098913-B100Junta de AndalucíaEuropean Commission CV20-45250 A-TIC-080-UGR18 BTIC-586-UGR20 P20-00525Universidad de Granada/CBU

Multimodal neuroimaging computing: a review of the applications in neuropsychiatric disorders

Multimodal neuroimaging is increasingly used in neuroscience research, as it overcomes the limitations of individual modalities. One of the most important applications of multimodal neuroimaging is the provision of vital diagnostic data for neuropsychiatric disorders. Multimodal neuroimaging computing enables the visualization and quantitative analysis of the alterations in brain structure and function, and has reshaped how neuroscience research is carried out. Research in this area is growing exponentially, and so it is an appropriate time to review the current and future development of this emerging area. Hence, in this paper, we review the recent advances in multimodal neuroimaging (MRI, PET) and electrophysiological (EEG, MEG) technologies, and their applications to the neuropsychiatric disorders. We also outline some future directions for multimodal neuroimaging where researchers will design more advanced methods and models for neuropsychiatric research

Interactive Visualization of Multimodal Brain Connectivity: Applications in Clinical and Cognitive Neuroscience

Magnetic resonance imaging (MRI) has become a readily available prognostic and diagnostic method, providing invaluable information for the clinical treatment of neurological diseases. Multimodal neuroimaging allows integration of complementary data from various aspects such as functional and anatomical properties; thus, it has the potential to overcome the limitations of each individual modality. Specifically, functional and diffusion MRI are two non-invasive neuroimaging techniques customized to capture brain activity and microstructural properties, respectively. Data from these two modalities is inherently complex, and interactive visualization can assist with data comprehension. The current thesis presents the design, development, and validation of visualization and computation approaches that address the need for integration of brain connectivity from functional and structural domains. Two contexts were considered to develop these approaches: neuroscience exploration and minimally invasive neurosurgical planning. The goal was to provide novel visualization algorithms and gain new insights into big and complex data (e.g., brain networks) by visual analytics. This goal was achieved through three steps: 3D Graphical Collision Detection: One of the primary challenges was the timely rendering of grey matter (GM) regions and white matter (WM) fibers based on their 3D spatial maps. This challenge necessitated pre-scanning those objects to generate a memory array containing their intersections with memory units. This process helped faster retrieval of GM and WM virtual models during the user interactions. Neuroscience Enquiry (MultiXplore): A software interface was developed to display and react to user inputs by means of a connectivity matrix. This matrix displays connectivity information and is capable to accept selections from users and display the relevant ones in 3D anatomical view (with associated anatomical elements). In addition, this package can load multiple matrices from dynamic connectivity methods and annotate brain fibers. Neurosurgical Planning (NeuroPathPlan): A computational method was provided to map the network measures to GM and WM; thus, subject-specific eloquence metric can be derived from related resting state networks and used in objective assessment of cortical and subcortical tissue. This metric was later compared to apriori knowledge based decisions from neurosurgeons. Preliminary results show that eloquence metric has significant similarities with expert decisions