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Neuroinformatics, Volume 22

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Volume 22, Number 1, January 2024

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John Darrell Van Horn:
Editorial: On the Economics of Neuroscientific Data Sharing. 1-4
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Freya Acar, Camille Maumet, Talia Heuten, Maya Vervoort, Han Bossier, Ruth Seurinck, Beatrijs Moerkerke:
Improving the Eligibility of Task-Based fMRI Studies for Meta-Analysis: A Review and Reporting Recommendations. 5-22
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Nestor Timonidis, Mario Rubio-Teves, Carmen Alonso-Martínez, Rembrandt Bakker, María García-Amado, Paul H. E. Tiesinga, Francisco Clascá:
Analyzing Thalamocortical Tract-Tracing Experiments in a Common Reference Space. 23-43
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Michael J. Catanzaro, Sam Rizzo, John J. Kopchick, Asadur Chowdury, David R. Rosenberg, Peter Bubenik, Vaibhav A. Diwadkar:
Topological Data Analysis Captures Task-Driven fMRI Profiles in Individual Participants: A Classification Pipeline Based on Persistence. 45-62
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Thomas L. Athey, Daniel Jacob Tward, Ulrich Mueller, Laurent Younes, Joshua T. Vogelstein, Michael I. Miller:
Preserving Derivative Information while Transforming Neuronal Curves. 63-74
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David Aquilué-Llorens, Jennifer S. Goldman, Alain Destexhe:
High-Density Exploration of Activity States in a Multi-Area Brain Model. 75-87
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Sina Fathi, Ali Ahmadi, Afsaneh Dehnad, Mostafa Almasi-Dooghaee, Melika Sadegh:
A Deep Learning-Based Ensemble Method for Early Diagnosis of Alzheimer's Disease using MRI Images. 89-105

Volume 22, Number 2, April 2024

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Govinda R. Poudel, Prabin Sharma, Valentina Lorenzetti, Nicholas Parsons, Ester Cerin:
Network Representation of fMRI Data Using Visibility Graphs: The Impact of Motion and Test-Retest Reliability. 107-118
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Jose Ramon Chang, Zai-Fu Yao, Shulan Hsieh, Torbjörn E. M. Nordling:
Age Prediction Using Resting-State Functional MRI. 119-134
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Elizabeth McManus, Nils Muhlert, Niall W. Duncan:
InSpectro-Gadget: A Tool for Estimating Neurotransmitter and Neuromodulator Receptor Distributions for MRS Voxels. 135-145
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Ryan Faulkenberry, Saurabh Prasad, Dragan Maric, Badrinath Roysam:
Visual Prompting Based Incremental Learning for Semantic Segmentation of Multiplex Immuno-Flourescence Microscopy Imagery. 147-162
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Sunitha Basodi, Rajikha Raja, Harshvardhan Gazula, Javier Tomas Romero, Sandeep R. Panta, Thomas Maullin-Sapey, Thomas E. Nichols, Vince D. Calhoun:
Decentralized Mixed Effects Modeling in COINSTAC. 163-175
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Lanya T. Cai, Joseph Y. Moon, Paul B. Camacho, Aaron T. Anderson, Won Jong Chwa, Bradley P. Sutton, Amy J. Markowitz, Eva M. Palacios, Alexis A. Rodriguez, Geoffrey T. Manley, Shivsundaram Shankar, Peer-Timo Bremer, Pratik Mukherjee, Ravi K. Madduri, Shankar Gopinath, Ramesh Grandhi, C. Dirk Keene, Michael A. McCrea, Randall Merchant, Laura B. Ngwenya, Ava M. Puccio, David Schnyer, Sabrina R. Taylor, John K. Yue, Esther L. Yuh, Ross Zafonte:
MaPPeRTrac: A Massively Parallel, Portable, and Reproducible Tractography Pipeline. 177-191
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Praitayini Kanakaraj, Tianyuan Yao, Leon Y. Cai, Ho Hin Lee, Nancy R. Newlin, Michael E. Kim, Chenyu Gao, Kimberly R. Pechman, Derek B. Archer, Timothy J. Hohman, Angela L. Jefferson, Lori L. Beason-Held, Susan M. Resnick, Eleftherios Garyfallidis, Adam W. Anderson, Kurt G. Schilling, Bennett A. Landman, Daniel Moyer:
DeepN4: Learning N4ITK Bias Field Correction for T1-weighted Images. 193-205
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Christopher 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:
Updates to the Melbourne Children's Regional Infant Brain Software Package (M-CRIB-S). 207-223

Volume 22, Number 3, July 2024

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Campbell Coleman, John Darrell Van Horn:
Towards Comprehensive Connectivity Modeling. 225-227
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Alexander Bartnik, Sujal Singh, Conan Sum, Mackenzie T. Smith, Niels Bergsland, Robert Zivadinov, Michael G. Dwyer:
An Automated Tool to Classify and Transform Unstructured MRI Data into BIDS Datasets. 229-238
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Homa Seyedmirzaei, Amirhossein Salmannezhad, Hamidreza Ashayeri, Ali Shushtari, Bita Farazinia, Mohammad Mahdi Heidari, Amirali Momayezi, Sara Shaki Baher:
Growth-Associated Protein 43 and Tensor-Based Morphometry Indices in Mild Cognitive Impairment. 239-250
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Nicolas Rault, Tido Bergmans, Natasja Delfstra, Bisley J. Kleijnen, Fleur Zeldenrust, Tansu Celikel:
Where Top-Down Meets Bottom-Up: Cell-Type Specific Connectivity Map of the Whisker System. 251-268
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Alexander Bartnik, Lucas M. Serra, Mackenzie T. Smith, William D. Duncan, Lauren Wishnie, Alan Ruttenberg, Michael G. Dwyer, Alexander D. Diehl:
MRIO: the Magnetic Resonance Imaging Acquisition and Analysis Ontology. 269-283
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Hao Wang, Yanting Liu, Yanrui Ding:
Identifying Diagnostic Biomarkers for Autism Spectrum Disorder From Higher-order Interactions Using the PED Algorithm. 285-296
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Harsh Sinha, Pradeep Reddy Raamana:
Solving the Pervasive Problem of Protocol Non-Compliance in MRI using an Open-Source tool mrQA. 297-315
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André S. B. Oliveira, Luciano C. P. C. Leonel, Megan M. J. Bauman, Alessandro De Bonis, Edward R. LaHood, Stephen Graepel, Michael J. Link, Carlos D. Pinheiro-Neto, Nirusha Lachman, Jonathan M. Morris, Maria Peris-Celda:
Photogrammetry scans for neuroanatomy education - a new multi-camera system: technical note. 317-327
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Sander M. Boelders, Wouter De Baene, Eric O. Postma, Karin Gehring, Lee-Ling Sharon Ong:
Predicting Cognitive Functioning for Patients with a High-Grade Glioma: Evaluating Different Representations of Tumor Location in a Common Space. 329-352
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Jéssica Leite, Fabiano Nhoatto, Antonio Jacob Jr., Roberto Santana, Fábio Manoel França Lobato:
Computational Tools for Neuronal Morphometric Analysis: A Systematic Search and Review. 353-377
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Nikolay Aseyev, Anastasia Borodinova, Svetlana Pavlova, Marina Roshchina, Matvey Roshchin, Evgeny S. Nikitin, Pavel M. Balaban:
CADENCE - Neuroinformatics Tool for Supervised Calcium Events Detection. 379-387
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Ahmed Nebli, Christian Schiffer, Meiqi Niu, Nicola Palomero-Gallagher, Katrin Amunts, Timo Dickscheid:
Generative Modelling of Cortical Receptor Distributions from Cytoarchitectonic Images in the Macaque Brain. 389-402

Volume 22, Number 4, October 2024

Special Issue on Data Science Methods and Neuroinformatics Applications / Special Issue on Neuroinformatics and Analysis of Traumatic Brain Injury and Related Conditions / Special Issue on Bridging the Gap: How Neuroinformatics is Preparing the Next Generation of Neuroscience Researchers

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Ivo D. Dinov:
Neuroinformatics Applications of Data Science and Artificial Intelligence. 403-405
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Bahram Jafrasteh, Manuel Lubián-Gutiérrez, Simón Pedro Lubián-López, Isabel Benavente-Fernández:
Enhanced Spatial Fuzzy C-Means Algorithm for Brain Tissue Segmentation in T1 Images. 407-420
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Qiu Ge, Matthew Lock, Xue Yang, Yuejiao Ding, Juan Yue, Na Zhao, Yun-Song Hu, Yong Zhang, Minliang Yao, Yufeng Zang:
Utilizing fMRI to Guide TMS Targets: the Reliability and Sensitivity of fMRI Metrics at 3 T and 1.5 T. 421-435
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Rongke Lyu, Marina Vannucci, Suprateek Kundu:
Bayesian Tensor Modeling for Image-based Classification of Alzheimer's Disease. 437-455
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Sharmistha Guha, Jose Rodriguez-Acosta, Ivo D. Dinov:
A Bayesian Multiplex Graph Classifier of Functional Brain Connectivity Across Diverse Tasks of Cognitive Control. 457-472
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Ofek Ophir, Orit Shefi, Ofir Lindenbaum:
Classifying Neuronal Cell Types Based on Shared Electrophysiological Information from Humans and Mice. 473-486
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Gabriel R. Palma, Conor Thornberry, Sean Commins, Rafael A. Moral:
Understanding Learning from EEG Data: Combining Machine Learning and Feature Engineering Based on Hidden Markov Models and Mixed Models. 487-497
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Ashima Tyagi, Vibhav Prakash Singh, Manoj Madhava Gore:
Detection of Schizophrenia from EEG Signals using Selected Statistical Moments of MFC Coefficients and Ensemble Learning. 499-520
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Elham Ahmadi Moghadam, Farhad Abedinzadeh Torghabeh, Seyyed Abed Hosseini, Mohammad Hossein Moattar:
Improved ADHD Diagnosis Using EEG Connectivity and Deep Learning through Combining Pearson Correlation Coefficient and Phase-Locking Value. 521-537
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Heitor Mynssen, Kamilla Avelino-de-Souza, Khallil Taverna Chaim, Vanessa Lanes Ribeiro, Nina Patzke, Bruno Mota:
Stitcher: A Surface Reconstruction Tool for Highly Gyrified Brains. 539-554
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Wentao Jiang, Xinyi Liu, Ming Song, Zhengyi Yang, Lan Sun, Tianzi Jiang:
MBV-Pipe: A One-Stop Toolbox for Assessing Mouse Brain Morphological Changes for Cross-Scale Studies. 555-568
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Andrei Irimia:
Neuroinformatics and Analysis of Traumatic Brain Injury and Related Conditions. 569-572
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Xiaojian Kang, Byung C. Yoon, Emily Grossner, Maheen M. Adamson:
Characteristics of the Structural Connectivity in Patients with Brain Injury and Chronic Health Symptoms: A Pilot Study. 573-589
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Kevin H. Guo, Nikhil N. Chaudhari, Tamara Jafar, Nahian F. Chowdhury, Paul Bogdan, Andrei Irimia:
Anatomic Interpretability in Neuroimage Deep Learning: Saliency Approaches for Typical Aging and Traumatic Brain Injury. 591-606
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Rachel M. Edelstein, Sterling Gutterman, Benjamin Newman, John Darrell Van Horn:
Assessment of Sports Concussion in Female Athletes: A Role for Neuroinformatics? 607-618
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Mathew Birdsall Abrams, John Darrell Van Horn:
Bridging the Gap: How Neuroinformatics is Preparing the Next Generation of Neuroscience Researchers. 619-622
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  - journals/ni/RoyerPVKHPBLYJSMB24
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Jessica Royer, Casey Paquola, Sofie L. Valk, Matthias Kirschner, Seok-Jun Hong, Bo-yong Park, Richard A. I. Bethlehem, Robert Leech, B. T. Thomas Yeo, Elizabeth Jefferies, Jonathan Smallwood, Daniel S. Margulies, Boris C. Bernhardt:
Gradients of Brain Organization: Smooth Sailing from Methods Development to User Community. 623-634
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Michal Szczepanik, Adina S. Wagner, Stephan Heunis, Laura K. Waite, Simon B. Eickhoff, Michael Hanke:
Teaching Research Data Management with DataLad: A Multi-year, Multi-domain Effort. 635-645
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Ariel Rokem, Noah C. Benson:
Hands-On Neuroinformatics Education at the Crossroads of Online and In-Person: Lessons Learned from NeuroHackademy. 647-655
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Alice Geminiani, Judith Kathrein, Alper Yegenoglu, Franziska Vogel, Marcelo Armendáriz, Ziv Ben-Zion, Petrut Antoniu Bogdan, Joana Covelo, Marissa Díaz Pier, Karin Grasenick, Vitali Karasenko, Wouter Klijn, Tina Kokan, Carmen Alina Lupascu, Anna Lührs, Tara Mahfoud, Taylan Özden, Jens Egholm Pedersen, Luca Peres, Ingrid Reiten, Nikola Simidjievski, Inga Ulnicane, Michiel van der Vlag, Lyuba Zehl, Alois Saria, Sandra Diaz-Pier, Johannes Passecker:
Interdisciplinary and Collaborative Training in Neuroscience: Insights from the Human Brain Project Education Programme. 657-678
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Joshua K. Marchant, Natalie G. Ferris, Diana Grass, Magdelena S. Allen, Vivek Gopalakrishnan, Mark D. Olchanyi, Devang Sehgal, Maxina Sheft, Amelia Strom, Berkin Bilgic, Brian L. Edlow, Elizabeth M. C. Hillman, Meher R. Juttukonda, Laura Lewis, Shahin Nasr, Aapo Nummenmaa, Jonathan R. Polimeni, Roger B. H. Tootell, Lawrence L. Wald, Hui Wang, Anastasia Yendiki, Susie Y. Huang, Bruce R. Rosen, Randy L. Gollub:
Mesoscale Brain Mapping: Bridging Scales and Modalities in Neuroimaging - A Symposium Review. 679-706
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Simon H. Geukes, Mariana P. Branco, Erik J. Aarnoutse, Annike Bekius, Julia Berezutskaya, Nick F. Ramsey:
Effect of Electrode Distance and Size on Electrocorticographic Recordings in Human Sensorimotor Cortex. 707-717
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Roman Peter, Petr Hrobar, Josef Navratil, Martin Vagenknecht, Jindrich Soukup, Keiko Tsuji, Nestor X. Barrezueta, Anna C. Stoll, Renee C. Gentzel, Jonathan A. Sugam, Jacob Marcus, Danny A. Bitton:
AnNoBrainer, An Automated Annotation of Mouse Brain Images using Deep Learning. 719-730
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Maysam Orouskhani, Negar Firoozeh, Huayu Wang, Yan Wang, Hanrui Shi, Weijing Li, Beibei Sun, Jianjian Zhang, Xiao Li, Huilin Zhao, Mahmud Mossa-Basha, Jenq-Neng Hwang, Chengcheng Zhu:
Morphology and Texture-Guided Deep Neural Network for Intracranial Aneurysm Segmentation in 3D TOF-MRA. 731-744
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Jiaxuan Wang, Rui Gong, Shahrokh Heidari, Mitchell Rogers, Toshiki Tani, Hiroshi Abe, Noritaka Ichinohe, Alexander Woodward, Patrice J. Delmas:
A Deep Learning-based Pipeline for Segmenting the Cerebral Cortex Laminar Structure in Histology Images. 745-761

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