Toward a woven literature: Open-source infrastructure for reproducible publishing
Agah Karakuzu
Parkinson’s disease in the spinal cord: an exploratory study to establish T2*w, MTR and diffusion-weighted imaging metric values
Jupyter Notebook PythonSamuelle St-Onge, Camille Coustaury, Caroline Landelle, Linda Solstrand Dahlberg, Ovidiu Lungu, Julien Doyon, Benjamin De Leener
Computational examples of software for white matter tractometry
Jupyter Notebook PythonJohn Kruper, Ariel Rokem
Representation in Brain Imaging Research: A Quebec demographic overview
Jupyter NotebookTudor Sintu, Olujide Oyeniran, Udunna Anazodo, Benjamin De Leener, Eva Alonso-Ortiz
NeuroMOSAICS: A collection of neurostimulation datasets - Multi-scale Open-Source Across Interfaces Conditions & Species
Jupyter Notebook PythonLison Kardassevitch, Davide Burchielli, Numa Dancause, Marco Bonizzato
Little Science, Big Science, and Beyond: How Amateurs Shape the Scientific Landscape
Jupyter NotebookEvelyn McLean, Jane Abdo, Nadia Blostein, Nikola Stikov
Integrating Structural, Functional, and Biochemical Brain Imaging Data with MRShiny Brain - An Interactive Web Application
RJessica Archibald, Alexander Mark Weber, Paulina S. Scheuren, Oscar Ortiz, Cassandra Choles, Jaimie J. Lee, Niklaus Zölch, Erin L. MacMillan, John L.k Kramer
Vendor-neutral sequences and their implications for the reproducibility of quantitative MRI
R Nextflow Jupyter NotebookAgah Karakuzu, Labonny Biswas, Julien Cohen-Adad, Nikola Stikov
Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"
Jupyter NotebookDaniel Papp, Kyle M. Gilbert, Gaspard Cereza, Alexandre D’Astous, Nibardo Lopez-Rios, Mathieu Boudreau, Marcus Couch, Pedram Yazdanbakhsh, Robert L. Barry, Eva Alonso Ortiz, Julien Cohen-Adad
Paper is not enough: Crowdsourcing the T1 mapping common ground via the ISMRM reproducibility challenge
Jupyter NotebookMathieu Boudreau, Agah Karakuzu, Julien Cohen-Adad, Ecem Bozkurt, Madeline Carr, Marco Castellaro, Luis Concha, Mariya Doneva, Seraina A. Dual, Alex Ensworth, Alexandru Foias, Véronique Fortier, Refaat E. Gabr, Guillaume Gilbert, Carri K. Glide-Hurst, Matthew Grech-Sollars, Siyuan Hu, Oscar Jalnefjord, Jorge Jovicich, Kübra Keskin, Peter Koken, Anastasia Kolokotronis, Simran Kukran, Nam. G. Lee, Ives R. Levesque, Bochao Li, Dan Ma, Burkhard Mädler, Nyasha Maforo, Jamie Near, Erick Pasaye, Alonso Ramirez-Manzanares, Ben Statton, Christian Stehning, Stefano Tambalo, Ye Tian, Chenyang Wang, Kilian Weis, Niloufar Zakariaei, Shuo Zhang, Ziwei Zhao, Nikola Stikov
Leveraging Large Language Models for Interactive Exploration of MRI Research Reproducibility: A Self-Evolving Review
Jupyter Notebook PythonAgah Karakuzu, Mathieu Boudreau, Nikola Stikov
A database of the healthy human spinal cord morphometry in the PAM50 template space
Jupyter NotebookJan Valošek, Sandrine Bédard, Miloš Keřkovský, Tomáš Rohan, Julien Cohen-Adad
Longitudinal stability of brain and spinal cord quantitative MRI measures
Jupyter NotebookMathieu Boudreau, Agah Karakuzu, Arnaud Boré, Basile Pinsard, Kiril Zelenkovski, Eva Alonso-Ortiz, Julie Boyle, Pierre Bellec, Julien Cohen-Adad
Results of the ISMRM 2020 joint Reproducible Research & Quantitative MR study groups reproducibility challenge on phantom and human brain T1 mapping
Jupyter NotebookMathieu Boudreau, Agah Karakuzu, Julien Cohen-Adad, Ecem Bozkurt, Madeline Carr, Marco Castellaro, Luis Concha, Mariya Doneva, Seraina Dual, Alex Ensworth, Alexandru Foias, Véronique Fortier, Refaat E. Gabr, Guillaume Gilbert, Carri K. Glide-Hurst, Matthew Grech-Sollars, Siyuan Hu, Oscar Jalnefjord, Jorge Jovicich, Kübra Keskin, Peter Koken, Anastasia Kolokotronis, Simran Kukran, Nam. G. Lee, Ives R. Levesque, Bochao Li, Dan Ma, Burkhard Mädler, Nyasha Maforo, Jamie Near, Erick Pasaye, Alonso Ramirez-Manzanares, Ben Statton, Christian Stehning, Stefano Tambalo, Ye Tian, Chenyang Wang, Kilian Weis, Niloufar Zakariaei, Shuo Zhang, Ziwei Zhao, Nikola Stikov
A reproducible benchmark of resting-state fMRI denoising strategies using fMRIPrep and Nilearn
Jupyter Notebook PythonHao-Ting Wang, Steven L. Meisler, Hanad Sharmarke, Natasha Clarke, François Paugam, Nicolas Gensollen, Christopher J. Markiewicz, Bertrand Thirion, Pierre Bellec
Parcellating the parcellation issue - a proof of concept for reproducible analyses using Neurolibre
Jupyter NotebookPierre Bellec, Saâd Jbabdi, R. Cameron Craddock
NiMARE: Neuroimaging Meta-Analysis Research Environment
Jupyter Notebook JavaScript PythonTaylor Salo, Tal Yarkoni, Thomas E. Nichols, Jean-Baptiste Poline, Murat Bilgel, Katherine L. Bottenhorn, Dorota Jarecka, James D. Kent, Adam Kimbler, Dylan M. Nielson, Kendra M. Oudyk, Julio A. Peraza, Alexandre Pérez, Puck C. Reeders, Julio A. Yanes, Angela R. Laird
An interactive meta-analysis of MRI biomarkers of myelin
R Jupyter NotebookMatteo Mancini, Agah Karakuzu, Julien Cohen-Adad, Mara Cercignani, Thomas E. Nichols, Nikola Stikov
Quantitative T1 MRI
Jupyter NotebookMathieu Boudreau, Kathryn E. Keenan, Nikola Stikov
