Neurodesk Publications

Scientific publications, technical reports, and research outputs related to Neurodesk’s development and usage.

This page highlights peer-reviewed papers, preprints, and other research outputs that have used or cited Neurodesk in their methods, workflows, or infrastructure.

For instructions on how to cite Neurodesk and specific tools, visit our Citation Guide.

  • Renton, A.I., Dao, T.T., Johnstone, T., Civier, O., Sullivan, R. P., White, D. J., … Narayanan, A. & Bollmann, S. Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging. Nat Methods (2024). https://doi.org/10.1038/s41592-023-02145-x

  • Masson-Trottier, M., Dao, T. T., Narayanan, A., & Bollmann, S. (2025). Toward the Future of Scientific Publishing through Reproducible Research Artefacts Enabled by Neurodesk. Aperture Neuro, 12. https://doi.org/10.52294/001c.143700

  • Dao, T. T., Masson-Trottier, M., Ribeiro, F. L., Scarsbrook, J., Stewart, A., Ye, X., Hamilton, E., Bollmann, S., & Narayanan, A. (2025). Democratizing open neuroimaging: Neurodesk’s approach to open data accessibility and utilization. Aperture Neuro, 5(SI 2). https://doi.org/10.52294/001c.144107

  • Monika Dörig, Michèle Masson-Trottier, Thuy Dao, Kyle Mapue, Andrew Jahn, Fernanda L. Ribeiro, Ashley Stewart, Thomas Shaw, Michal Toth, Marla Pinkert, Paul Taylor, Angela Renton, Daniel A. Handwerker, Giulia Baracchini, Christopher Rorden, Aswin Narayanan, & Bollmann, S. (2026). Developing an Interactive Neuroimaging Education Resource with Neurodesk. EdArXiv. https://doi.org/10.35542/osf.io/7q83c_v1

Neurodesk in action

  • Wright, B. R., Schira, M. M., Paxinos, G., & Kassem, M. S. (2025). Paediatric MRI: High-Resolution in vivo 3T Methods. bioRxiv. https://doi.org/10.1101/2025.10.30.685686

  • Dörig, M., Cole, D. M., Guekos, A., Stämpfli, P., Schuetz, P., Schibli, L., Schweinhardt, P., & Meier, M. L. (2025). Stable Somatotopy in Chronic Low Back Pain: Is Cortical Map Reorganization a Myth? bioRxiv. https://doi.org/10.1101/2025.11.05.686896

  • Arnoldy, L., Gauci, S., Young, L. M., Macpherson, H., Civier, O., Scholey, A., Pipingas, A., & White, D. J. (2025). Assessing the association between the Mediterranean, Dietary Approaches to Stop Hypertension and Mediterranean-DASH Intervention for Neurodegenerative Delay dietary patterns, structural connectivity and cognitive function. Br J Nutr, 133(7), 1-17. https://doi.org/10.1017/S0007114525000406

  • Pruckner, P., Mito, R., Vaughan, D., Jackson, G., Fischmeister, F., Nenning, K. H., Berger, M., Pataraia, E., Baumgartner, C., Dorfer, C., Rossler, K., Czech, T., Kasprian, G., Bonelli, S., & Smith, R. (2025). Surgical white matter disruption leads to downstream atrophy in the non-resected human brain. Brain. https://doi.org/10.1093/brain/awaf344

  • Khalife, S., Bollmann, S., Zalesky, A., & Oestreich, L. K. L. (2025). Magnetic Resonance Imaging-Derived Markers of Acute and Chronic Inflammatory Processes in the Ventral Tegmental Area Associated With Depression. Biol Psychiatry Cogn Neurosci Neuroimaging. https://doi.org/10.1016/j.bpsc.2025.09.003

  • Ribeiro, F. L., Satzger, R., Hoffstaedter, F., Bürger, C., Herholz, P., Linhardt, D., Benson, N. C., Schwarzkopf, D. S., Puckett, A. M., Bollmann, S., & Hebart, M. N. (2025). Predicting functional topography of the human visual cortex from cortical anatomy at scale. bioRxiv. https://doi.org/10.1101/2025.11.27.690210

  • Clements, G. M., Camacho, P., Bowie, D. C., Low, K. A., Sutton, B. P., Gratton, G., & Fabiani, M. (2025). Effects of Aging, Estimated Fitness, and Cerebrovascular Status on White Matter Microstructural Health. Hum Brain Mapp, 46(5), e70168. https://doi.org/10.1002/hbm.70168

  • Essex, C. A., Merenstein, J. L., Overson, D. K., Truong, T. K., Madden, D. J., Bedggood, M. J., Murray, H., Holdsworth, S. J., Stewart, A. W., Morgan, C., Faull, R. L. M., Hume, P., Theadom, A., & Pedersen, M. (2025). Characterizing positive and negative quantitative susceptibility values in the cortex following mild traumatic brain injury: a depth- and curvature-based study. Cereb Cortex, 35(3). https://doi.org/10.1093/cercor/bhaf059

  • Itahashi, T., Tanji, K., Shikauchi, Y., Naoe, T., Okimura, T., Nakamura, M., Ohta, H., & Hashimoto, R. I. (2025). Iron deposition and functional connectivity alterations in the right substantia nigra of adult males with autism. Cereb Cortex, 35(8). https://doi.org/10.1093/cercor/bhaf216

  • Martin, A., Nassif, J., Chaluvadi, L., Schammel, C., Newman-Norlund, R., Bollmann, S., & Absher, J. (2025). Grey matter volume differences across Parkinson’s disease motor subtypes in the supplementary motor cortex. Neuroimage Clin, 45, 103724. https://doi.org/10.1016/j.nicl.2024.103724

  • Monreal-Madrigal, A., Kurban, D., Tse, D. H. Y., Ivanov, D., Boulant, N., & Poser, B. A. (2025). BOLD fMRI at 9.4T with 3D stack-of-spirals readouts. MAGMA. https://doi.org/10.1007/s10334-025-01298-4

  • Shaw, T. B., Ribeiro, F. L., Zhu, X., Aiken, P., Bollmann, S., Bollmann, S., Chang, J., Chidley, K., Dempsey-Jones, H., Eftekhari, Z., Gillespie, J., Henderson, R. D., Kiernan, M. C., Ktena, I., McCombe, P. A., Ngo, S. T., Taubert, S. T., Whelan, B. M., Ye, X.,…Barth, M. (2025). Segmentation of the human tongue musculature using MRI: Field guide and validation in motor neuron disease. Comput Biol Med, 196(Pt B), 110824. https://doi.org/10.1016/j.compbiomed.2025.110824

  • Sokunbi, M. O., Soula, O., Ochieng, B., & Staff, R. T. (2025). Wired Differently? Brain Temporal Complexity and Intelligence in Autism Spectrum Disorder. Brain Sci, 15(8). https://doi.org/10.3390/brainsci15080796

  • Garner, K. G., Leow, L. A., Uchida, A., Nolan, C., Jensen, O., Garrido, M. I., & Dux, P. E. (2024). Assessing the influence of dopamine and mindfulness on the formation of routines in visual search. Psychophysiology, 61(7), e14571. https://doi.org/10.1111/psyp.14571

  • Monreal-Madrigal, A., Kurban, D., Huber, L., Ivanov, D., Boulant, N., & Poser, B. A. (2024). Combining the benefits of 3D acquisitions and spiral readouts for VASO fMRI at UHF. Imaging Neurosci (Camb), 2. https://doi.org/10.1162/imag_a_00308

If you’ve published work using Neurodesk, we’d love to include it here.

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