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Enhanced Spatial Fuzzy C-Means Algorithm for Brain Tissue Segmentation in T1 Images Neuroinformatics (IF 3.0) Pub Date : 2024-04-24 Bahram Jafrasteh, Manuel Lubián-Gutiérrez, Simón Pedro Lubián-López, Isabel Benavente-Fernández
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Growth-Associated Protein 43 and Tensor-Based Morphometry Indices in Mild Cognitive Impairment Neuroinformatics (IF 3.0) Pub Date : 2024-04-17 Homa Seyedmirzaei, Amirhossein Salmannezhad, Hamidreza Ashayeri, Ali Shushtari, Bita Farazinia, Mohammad Mahdi Heidari, Amirali Momayezi, Sara Shaki Baher
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Gradients of Brain Organization: Smooth Sailing from Methods Development to User Community Neuroinformatics (IF 3.0) Pub Date : 2024-04-03
Abstract Multimodal neuroimaging grants a powerful in vivo window into the structure and function of the human brain. Recent methodological and conceptual advances have enabled investigations of the interplay between large-scale spatial trends – or gradients – in brain structure and function, offering a framework to unify principles of brain organization across multiple scales. Strong community enthusiasm
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An Automated Tool to Classify and Transform Unstructured MRI Data into BIDS Datasets Neuroinformatics (IF 3.0) Pub Date : 2024-03-26 Alexander Bartnik, Sujal Singh, Conan Sum, Mackenzie Smith, Niels Bergsland, Robert Zivadinov, Michael G. Dwyer
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DeepN4: Learning N4ITK Bias Field Correction for T1-weighted Images Neuroinformatics (IF 3.0) Pub Date : 2024-03-25
Abstract T1-weighted (T1w) MRI has low frequency intensity artifacts due to magnetic field inhomogeneities. Removal of these biases in T1w MRI images is a critical preprocessing step to ensure spatially consistent image interpretation. N4ITK bias field correction, the current state-of-the-art, is implemented in such a way that makes it difficult to port between different pipelines and workflows, thus
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Updates to the Melbourne Children’s Regional Infant Brain Software Package (M-CRIB-S) Neuroinformatics (IF 3.0) Pub Date : 2024-03-16 Chris L. Adamson, Bonnie Alexander, Claire E. Kelly, Gareth Ball, Richard Beare, Jeanie L. Y. Cheong, Alicia J. Spittle, Lex W. Doyle, Peter J. Anderson, Marc L. Seal, Deanne K. Thompson
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MaPPeRTrac: A Massively Parallel, Portable, and Reproducible Tractography Pipeline Neuroinformatics (IF 3.0) Pub Date : 2024-03-06 Lanya T. Cai, Joseph Moon, Paul B. Camacho, Aaron T. Anderson, Won Jong Chwa, Bradley P. Sutton, Amy J. Markowitz, Eva M. Palacios, Alexis Rodriguez, Geoffrey T. Manley, Shivsundaram Shankar, Peer-Timo Bremer, Pratik Mukherjee, Ravi K. Madduri
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Decentralized Mixed Effects Modeling in COINSTAC Neuroinformatics (IF 3.0) Pub Date : 2024-03-01
Abstract Performing group analysis on magnetic resonance imaging (MRI) data with linear mixed-effects (LME) models is challenging due to its large dimensionality and inherent multi-level covariance structure. In addition, as large-scale collaborative projects become commonplace in neuroimaging, data must increasingly be stored and analyzed from different locations. In such settings, substantial overhead
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Visual Prompting Based Incremental Learning for Semantic Segmentation of Multiplex Immuno-Flourescence Microscopy Imagery Neuroinformatics (IF 3.0) Pub Date : 2024-02-23 Ryan Faulkenberry, Saurabh Prasad, Dragan Maric, Badrinath Roysam
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InSpectro-Gadget: A Tool for Estimating Neurotransmitter and Neuromodulator Receptor Distributions for MRS Voxels Neuroinformatics (IF 3.0) Pub Date : 2024-02-22 Elizabeth McManus, Nils Muhlert, Niall W. Duncan
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Age Prediction Using Resting-State Functional MRI Neuroinformatics (IF 3.0) Pub Date : 2024-02-11 Jose Ramon Chang, Zai-Fu Yao, Shulan Hsieh, Torbjörn E. M. Nordling
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Network Representation of fMRI Data Using Visibility Graphs: The Impact of Motion and Test-Retest Reliability Neuroinformatics (IF 3.0) Pub Date : 2024-02-09 Govinda R. Poudel, Prabin Sharma, Valentina Lorenzetti, Nicholas Parsons, Ester Cerin
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Preserving Derivative Information while Transforming Neuronal Curves Neuroinformatics (IF 3.0) Pub Date : 2023-11-30 Thomas L. Athey, Daniel J. Tward, Ulrich Mueller, Laurent Younes, Joshua T. Vogelstein, Michael I. Miller
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A Deep Learning-Based Ensemble Method for Early Diagnosis of Alzheimer’s Disease using MRI Images Neuroinformatics (IF 3.0) Pub Date : 2023-12-02 Sina Fathi, Ali Ahmadi, Afsaneh Dehnad, Mostafa Almasi-Dooghaee, Melika Sadegh
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High-Density Exploration of Activity States in a Multi-Area Brain Model Neuroinformatics (IF 3.0) Pub Date : 2023-11-20 David Aquilué-Llorens, Jennifer S. Goldman, Alain Destexhe
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Topological Data Analysis Captures Task-Driven fMRI Profiles in Individual Participants: A Classification Pipeline Based on Persistence Neuroinformatics (IF 3.0) Pub Date : 2023-11-04 Michael J. Catanzaro, Sam Rizzo, John Kopchick, Asadur Chowdury, David R. Rosenberg, Peter Bubenik, Vaibhav A. Diwadkar
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Improving the Eligibility of Task-Based fMRI Studies for Meta-Analysis: A Review and Reporting Recommendations Neuroinformatics (IF 3.0) Pub Date : 2023-11-04 Freya Acar, Camille Maumet, Talia Heuten, Maya Vervoort, Han Bossier, Ruth Seurinck, Beatrijs Moerkerke
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Analyzing Thalamocortical Tract-Tracing Experiments in a Common Reference Space Neuroinformatics (IF 3.0) Pub Date : 2023-10-21 Nestor Timonidis, Mario Rubio-Teves, Carmen Alonso-Martínez, Rembrandt Bakker, María García-Amado, Paul Tiesinga, Francisco Clascá
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Correction to: Geometric Reliability of Super-Resolution Reconstructed Images from Clinical Fetal MRI in the Second Trimester Neuroinformatics (IF 3.0) Pub Date : 2023-09-19 Tommaso Ciceri, Letizia Squarcina, Alessandro Pigoni, Adele Ferro, Florian Montano, Alessandra Bertoldo, Nicola Persico, Simona Boito, Fabio Maria Triulzi, Giorgio Conte, Paolo Brambilla, Denis Peruzzo
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Confounding Effects on the Performance of Machine Learning Analysis of Static Functional Connectivity Computed from rs-fMRI Multi-site Data Neuroinformatics (IF 3.0) Pub Date : 2023-08-15 Oswaldo Artiles, Zeina Al Masry, Fahad Saeed
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Auto-Segmentation and Classification of Glioma Tumors with the Goals of Treatment Response Assessment Using Deep Learning Based on Magnetic Resonance Imaging Neuroinformatics (IF 3.0) Pub Date : 2023-07-17 Zahra Papi, Sina Fathi, Fatemeh Dalvand, Mahsa Vali, Ali Yousefi, Mohammad Hemmatyar Tabatabaei, Alireza Amouheidari, Iraj Abedi
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BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes Neuroinformatics (IF 3.0) Pub Date : 2023-07-03 Thomas L. Athey, Matthew A. Wright, Marija Pavlovic, Vikram Chandrashekhar, Karl Deisseroth, Michael I. Miller, Joshua T. Vogelstein
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Localization and Registration of 2D Histological Mouse Brain Images in 3D Atlas Space Neuroinformatics (IF 3.0) Pub Date : 2023-06-26 Maryam Sadeghi, Arnau Ramos-Prats, Pedro Neto, Federico Castaldi, Devin Crowley, Pawel Matulewicz, Enrica Paradiso, Wolfgang Freysinger, Francesco Ferraguti, Georg Goebel
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Big Brain Data Initiatives in Universiti Sains Malaysia: Data Stewardship to Data Repository and Data Sharing Neuroinformatics (IF 3.0) Pub Date : 2023-06-21 Nurfaten Hamzah, Nurul Hashimah Ahamed Hassain Malim, Jafri Malin Abdullah, Putra Sumari, Ariffin Marzuki Mokhtar, Siti Nur Syamila Rosli, Sharifah Aida Shekh Ibrahim, Zamzuri Idris
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Deep Learning Methods for Identification of White Matter Fiber Tracts: Review of State-of-the-Art and Future Prospective Neuroinformatics (IF 3.0) Pub Date : 2023-06-17 Nayereh Ghazi, Mohammad Hadi Aarabi, Hamid Soltanian-Zadeh
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Applying Joint Graph Embedding to Study Alzheimer’s Neurodegeneration Patterns in Volumetric Data Neuroinformatics (IF 3.0) Pub Date : 2023-06-14 Rosemary He, Daniel Tward
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Single Neuron Modeling Identifies Potassium Channel Modulation as Potential Target for Repetitive Head Impacts Neuroinformatics (IF 3.0) Pub Date : 2023-06-09 Daniel P. Chapman, Stefano Vicini, Mark P. Burns, Rebekah Evans
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Geometric Reliability of Super-Resolution Reconstructed Images from Clinical Fetal MRI in the Second Trimester Neuroinformatics (IF 3.0) Pub Date : 2023-06-07 Tommaso Ciceri, Letizia Squarcina, Alessandro Pigoni, Adele Ferro, Florian Montano, Alessandra Bertoldo, Nicola Persico, Simona Boito, Fabio Maria Triulzi, Giorgio Conte, Paolo Brambilla, Denis Peruzzo
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De-Identification Technique with Facial Deformation in Head CT Images Neuroinformatics (IF 3.0) Pub Date : 2023-05-25 Tatsuya Uchida, Taichi Kin, Toki Saito, Naoyuki Shono, Satoshi Kiyofuji, Tsukasa Koike, Katsuya Sato, Ryoko Niwa, Ikumi Takashima, Hiroshi Oyama, Nobuhito Saito
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CellRemorph: A Toolkit for Transforming, Selecting, and Slicing 3D Cell Structures on the Road to Morphologically Detailed Astrocyte Simulations Neuroinformatics (IF 3.0) Pub Date : 2023-05-03 Laura Keto, Tiina Manninen
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A Method for In-Vivo Mapping of Axonal Diameter Distributions in the Human Brain Using Diffusion-Based Axonal Spectrum Imaging (AxSI) Neuroinformatics (IF 3.0) Pub Date : 2023-04-10 Hila Gast, Assaf Horowitz, Ronnie Krupnik, Daniel Barazany, Shlomi Lifshits, Shani Ben-Amitay, Yaniv Assaf
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Funcmasker-flex: An Automated BIDS-App for Brain Segmentation of Human Fetal Functional MRI data Neuroinformatics (IF 3.0) Pub Date : 2023-03-31 Emily S. Nichols, Susana Correa, Peter Van Dyken, Jason Kai, Tristan Kuehn, Sandrine de Ribaupierre, Emma G. Duerden, Ali R. Khan
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A Minimum Bayes Factor Based Threshold for Activation Likelihood Estimation Neuroinformatics (IF 3.0) Pub Date : 2023-03-28 Tommaso Costa, Donato Liloia, Franco Cauda, Peter T. Fox, Francesca Dalla Mutta, Sergio Duca, Jordi Manuello
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Analysis of Network Models with Neuron-Astrocyte Interactions Neuroinformatics (IF 3.0) Pub Date : 2023-03-23 Tiina Manninen, Jugoslava Aćimović, Marja-Leena Linne
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ABCD_Harmonizer: An Open-source Tool for Mapping and Controlling for Scanner Induced Variance in the Adolescent Brain Cognitive Development Study Neuroinformatics (IF 3.0) Pub Date : 2023-03-20 Jonathan A. Dudley, Thomas C. Maloney, John O. Simon, Gowtham Atluri, Sarah L. Karalunas, Mekibib Altaye, Jeffery N. Epstein, Leanne Tamm
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Automatic Detection of Alzheimer's Disease using Deep Learning Models and Neuro-Imaging: Current Trends and Future Perspectives Neuroinformatics (IF 3.0) Pub Date : 2023-03-08 T. Illakiya, R. Karthik
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Multimodal 3D Mouse Brain Atlas Framework with the Skull-Derived Coordinate System Neuroinformatics (IF 3.0) Pub Date : 2023-02-21 Johanna Perens, Casper Gravesen Salinas, Urmas Roostalu, Jacob Lercke Skytte, Carsten Gundlach, Jacob Hecksher-Sørensen, Anders Bjorholm Dahl, Tim B. Dyrby
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On the Long-term Archiving of Research Data Neuroinformatics (IF 3.0) Pub Date : 2023-02-01 Cyril Pernet, Claus Svarer, Ross Blair, John D. Van Horn, Russell A. Poldrack
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NiftyPAD - Novel Python Package for Quantitative Analysis of Dynamic PET Data Neuroinformatics (IF 3.0) Pub Date : 2023-01-09 Jieqing Jiao, Fiona Heeman, Rachael Dixon, Catriona Wimberley, Isadora Lopes Alves, Juan Domingo Gispert, Adriaan A. Lammertsma, Bart N. M. van Berckel, Casper da Costa-Luis, Pawel Markiewicz, David M. Cash, M Jorge Cardoso, Sebastién Ourselin, Maqsood Yaqub, Frederik Barkhof
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IABC: A Toolbox for Intelligent Analysis of Brain Connectivity Neuroinformatics (IF 3.0) Pub Date : 2023-01-07 Yuhui Du, Yanshu Kong, Xingyu He
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Correction to: Deconvolution of the Functional Ultrasound Response in the Mouse Visual Pathway Using Block-Term Decomposition Neuroinformatics (IF 3.0) Pub Date : 2022-12-26 Aybüke Erol, Chagajeg Soloukey, Bastian Generowicz, Nikki van Dorp, Sebastiaan Koekkoek, Pieter Kruizinga, Borbála Hunyadi
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Consent Codes: Maintaining Consent in an Ever-expanding Open Science Ecosystem Neuroinformatics (IF 3.0) Pub Date : 2022-12-15 Stephanie O. M. Dyke, Kathleen Connor, Victoria Nembaware, Nchangwi S. Munung, Kathy Reinold, Giselle Kerry, Mamana Mbiyavanga, Lyndon Zass, Mauricio Moldes, Samir Das, John M. Davis, Jordi Rambla De Argila, J. Dylan Spalding, Alan C. Evans, Nicola Mulder, Jason Karamchandani
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Co-alteration Network Architecture of Major Depressive Disorder: A Multi-modal Neuroimaging Assessment of Large-scale Disease Effects Neuroinformatics (IF 3.0) Pub Date : 2022-12-05 Jodie P. Gray, Jordi Manuello, Aaron F. Alexander-Bloch, Cassandra Leonardo, Crystal Franklin, Ki Sueng Choi, Franco Cauda, Tommaso Costa, John Blangero, David C. Glahn, Helen S. Mayberg, Peter T. Fox
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Chronic Mild Traumatic Brain Injury: Aberrant Static and Dynamic Connectomic Features Identified Through Machine Learning Model Fusion Neuroinformatics (IF 3.0) Pub Date : 2022-12-02 Nicholas J. Simos, Katina Manolitsi, Andrea I. Luppi, Antonios Kagialis, Marios Antonakakis, Michalis Zervakis, Despina Antypa, Eleftherios Kavroulakis, Thomas G. Maris, Antonios Vakis, Emmanuel A. Stamatakis, Efrosini Papadaki
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Scalable Query Answering Under Uncertainty to Neuroscientific Ontological Knowledge: The NeuroLang Approach Neuroinformatics (IF 3.0) Pub Date : 2022-11-29 Gaston E. Zanitti, Yamil Soto, Valentin Iovene, Maria Vanina Martinez, Ricardo O. Rodriguez, Gerardo I. Simari, Demian Wassermann
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Federated Analysis in COINSTAC Reveals Functional Network Connectivity and Spectral Links to Smoking and Alcohol Consumption in Nearly 2,000 Adolescent Brains Neuroinformatics (IF 3.0) Pub Date : 2022-11-25 Harshvardhan Gazula, Kelly Rootes-Murdy, Bharath Holla, Sunitha Basodi, Zuo Zhang, Eric Verner, Ross Kelly, Pratima Murthy, Amit Chakrabarti, Debasish Basu, Subodh Bhagyalakshmi Nanjayya, Rajkumar Lenin Singh, Roshan Lourembam Singh, Kartik Kalyanram, Kamakshi Kartik, Kumaran Kalyanaraman, Krishnaveni Ghattu, Rebecca Kuriyan, Sunita Simon Kurpad, Gareth J Barker, Rose Dawn Bharath, Sylvane Desrivieres
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Deconvolution of the Functional Ultrasound Response in the Mouse Visual Pathway Using Block-Term Decomposition Neuroinformatics (IF 3.0) Pub Date : 2022-11-15 Aybüke Erol, Chagajeg Soloukey, Bastian Generowicz, Nikki van Dorp, Sebastiaan Koekkoek, Pieter Kruizinga, Borbála Hunyadi
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Assessing the Repeatability of Multi-Frequency Multi-Layer Brain Network Topologies Across Alternative Researcher’s Choice Paths Neuroinformatics (IF 3.0) Pub Date : 2022-11-14 Stavros I. Dimitriadis
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An Algorithm Based on a Cable-Nernst Planck Model Predicting Synaptic Activity throughout the Dendritic Arbor with Micron Specificity Neuroinformatics (IF 3.0) Pub Date : 2022-11-08 Claire Guerrier, Tristan Dellazizzo Toth, Nicolas Galtier, Kurt Haas
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Correction to: Bayesian Coherence Analysis for Microcircuit Structure Learning Neuroinformatics (IF 3.0) Pub Date : 2022-10-13 Rong Chen
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Review Paper: Reporting Practices for Task fMRI Studies Neuroinformatics (IF 3.0) Pub Date : 2022-10-06 Freya Acar, Camille Maumet, Talia Heuten, Maya Vervoort, Han Bossier, Ruth Seurinck, Beatrijs Moerkerke
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Bayesian Coherence Analysis for Microcircuit Structure Learning Neuroinformatics (IF 3.0) Pub Date : 2022-10-05 Rong Chen
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Polymer Physics-Based Classification of Neurons Neuroinformatics (IF 3.0) Pub Date : 2022-10-03 Kiri Choi, Won Kyu Kim, Changbong Hyeon
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Automatic Cerebral Hemisphere Segmentation in Rat MRI with Ischemic Lesions via Attention-based Convolutional Neural Networks Neuroinformatics (IF 3.0) Pub Date : 2022-09-30 Juan Miguel Valverde, Artem Shatillo, Riccardo De Feo, Jussi Tohka
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Dementia in Convolutional Neural Networks: Using Deep Learning Models to Simulate Neurodegeneration of the Visual System Neuroinformatics (IF 3.0) Pub Date : 2022-09-09 Jasmine A. Moore, Anup Tuladhar, Zahinoor Ismail, Pauline Mouches, Matthias Wilms, Nils D. Forkert
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Semi-Automated Quantitative Evaluation of Neuron Developmental Morphology In Vitro Using the Change-Point Test Neuroinformatics (IF 3.0) Pub Date : 2022-09-07 Ashlee S. Liao, Wenxin Cui, Yongjie Jessica Zhang, Victoria A. Webster-Wood
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Deep Learning Classification of Treatment Response in Diabetic Painful Neuropathy: A Combined Machine Learning and Magnetic Resonance Neuroimaging Methodological Study Neuroinformatics (IF 3.0) Pub Date : 2022-08-26 Kevin Teh, Paul Armitage, Solomon Tesfaye, Dinesh Selvarajah
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ABLE: Automated Brain Lines Extraction Based on Laplacian Surface Collapse Neuroinformatics (IF 3.0) Pub Date : 2022-08-26 Alberto Fernández-Pena, Daniel Martín de Blas, Francisco J. Navas-Sánchez, Luis Marcos-Vidal, Pedro M. Gordaliza, Javier Santonja, Joost Janssen, Susanna Carmona, Manuel Desco, Yasser Alemán-Gómez
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Multi-Subject Analysis for Brain Developmental Patterns Discovery via Tensor Decomposition of MEG Data Neuroinformatics (IF 3.0) Pub Date : 2022-08-24 Irina Belyaeva, Ben Gabrielson, Yu-Ping Wang, Tony W. Wilson, Vince D. Calhoun, Julia M. Stephen, Tülay Adali
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EBRAINS Live Papers - Interactive Resource Sheets for Computational Studies in Neuroscience Neuroinformatics (IF 3.0) Pub Date : 2022-08-20 Shailesh Appukuttan, Luca L. Bologna, Felix Schürmann, Michele Migliore, Andrew P. Davison