This page lists research that used Neurodesk in its methods, workflows, or infrastructure, along with the Neurodesk team’s papers describing the platform.
For instructions on how to cite Neurodesk and specific tools, visit our Citation Guide.
Papers describing the platform, written by the Neurodesk team.
Main Neurodesk paper · please cite this when you use Neurodesk
Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging
Renton, A. I., Dao, T. T., Johnstone, T., Civier, O., Sullivan, R. P., White, D. J., … Narayanan, A., & Bollmann, S. Nature Methods, 21(5), 804–808, 2024.Developing an Interactive Neuroimaging Education Resource with Neurodesk
Dörig, M., Masson-Trottier, M., Dao, T. T., Mapue, K., Jahn, A., Ribeiro, F. L., Stewart, A., Shaw, T., Toth, M., Pinkert, M., Taylor, P., Renton, A., Handwerker, D. A., Baracchini, G., Rorden, C., Narayanan, A., & Bollmann, S. Aperture Neuro, 2026.Democratizing open neuroimaging: Neurodesk’s approach to open data accessibility and utilization
Dao, T. T., Masson-Trottier, M., Ribeiro, F. L., Scarsbrook, J., Stewart, A., Ye, X., Hamilton, E., Bollmann, S., & Narayanan, A. Aperture Neuro, 5(SI 2), 2025.Studies, tools and protocols by researchers who used Neurodesk in their methods or infrastructure. Click a bar, a year or a topic tag to filter the list.
A geometry aware framework enhances noninvasive mapping of whole human brain dynamics
Wang, S., Lou, K., Wei, C., Sheng, Z., Tang, J., Peng, K., Shen, X., Mei, S., Chen, L., Gu, D., & Liu, Q. Nature Biomedical Engineering, 2026.Effects of a 24-week resistance exercise program on Alzheimer’s disease brain signatures in cognitively unimpaired older adults: a secondary analysis of the AGUEDA randomized controlled trial
Sanchez-Martinez, J., Solis-Urra, P., Fernandez-Gamez, B., Fernandez-Ortega, J., Sanchez-Aranda, L., Erickson, K. I., Ortega, F. B., & Esteban-Cornejo, I. Age and Ageing, 55(4), 2026.White matter changes in reward circuits of amyotrophic lateral sclerosis: a fixel-based study of appetite loss
Chang, J., Lipscombe, H., Lv, J., McCombe, P. A., Henderson, R. D., Ngo, S. T., Steyn, F. J., & Shaw, T. B. BMC Medicine, 24(1), 2026.Surgical white matter disruption leads to downstream atrophy in the non-resected human brain
Pruckner, P., Mito, R., Vaughan, D. N., Jackson, G. D., Fischmeister, F., Nenning, K.-H., Berger, M., Pataraia, E., Baumgartner, C., Dorfer, C., Rössler, K., Czech, T., Kasprian, G., Bonelli, S., & Smith, R. E. Brain, 149(2), 548–562, 2026.Divergent recovery trajectories after mild traumatic brain injury are characterized by distinct acute profiles of neurofilament light, 4R-tau, and white matter diffusivity
Papini, M. G., Thorne, J., Gozt, A. K., Avila, A. N. C., Ellery, C. S., Gilroy, R., Gill, G., Buhagiar, F., Thomas, E., Armstrong, A., Pedrini, S., Taddei, K., Martins, R. N., Ring, A., Arendts, G., Celenza, A., Iliff, J. C., Xu, D., Honeybul, S., Cowen, G., Smedley, B., Fatovich, D., Bynevelt, M., Pestell, C., Fitzgerald, M., & Hellewell, S. C. Journal of Neurology, 273(9), 548, 2026.Stable Mechanoreceptive Somatotopy in Chronic Low Back Pain: Is Cortical Map Reorganization a Myth?
Dörig, M., Cole, D. M., Guekos, A., Stämpfli, P., Schütz, P., Schibli, L., Schweinhardt, P., & Meier, M. L. The Journal of Neuroscience, 46(19), e2069252026, 2026.The Austrian MS database and the Austrian MS cohort: a national effort towards data harmonization and prospective data collection
Bsteh, G., Föttinger, F., Ponleitner, M., Berek, K., Di Pauli, F., Heschl, B., Wurth, S., Deisenhammer, F., Enzinger, C., Berger, T., Khalil, M., Hegen, H., Austrian Multiple Sclerosis Database, & Austrian MS cohort study group. Wiener Klinische Wochenschrift, 138(13–14), 394–402, 2026.Orchestrating neuroimaging data processing using the ‘Snakemake’ workflow manager
Mannion, D. J., Quiroga, M. del M., Paul, J. M., & Garrido, M. I. Brain Structure and Function, 231(8), 131, 2026.Seamless neuroimaging visualization: The NiiVue wrapper ecosystem
Eckstein, K., Androulakis, A., Dao, T. T., Drake, C., Hanayik, T., O’Reilly, C., Prahm, C., Wang, Z., Wighton, P., Dalca, A., Bollmann, S., & Rorden, C. Aperture Neuro, 6, 2026.Effects of high-intensity interval training with or without resistance training on Alzheimer’s disease brain signatures in individuals with coronary artery disease: The Heart-Brain randomized controlled trial
Sanchez-Martinez, J., Solis-Urra, P., Toval, A., Coca-Pulido, A., Rodriguez Palacios, M. T., Sanchez-Aranda, L., Bakker, E. A., Martin Fuentes, I., Fernandez-Ortega, J., Alonso-Cuenca, R. M., Olvera-Rojas, M., Fernandez Gamez, B., Erickson, K. I., Moreno Escobar, E., Garcia-Orta, R., Esteban-Cornejo, I., & Ortega, F. B. medRxiv, 2026.Automated Segmentation of Prostatic Gold Fiducial Markers for MR-Only Radiotherapy Planning Using Multi-Model Consensus Deep Learning
Stewart, A. W., Goodwin, J., Richardson, M., Robinson, S. D., O’Brien, K., Jin, J., Barth, M., & Bollmann, S. bioRxiv, 2026.Quantifying Amyloid Burden Across the Alzheimer’s Continuum: A Reproducible Centiloid Pipeline For Analysis in Resource-Constrained Settings
Adeniyi, A., Oladeji, D., Anene-Ogbe, C. M., Babari, B., Freddia, M., Ibe, C. K., Nwasike, N. C. C., Elvira, N. A., Fajardo, A., Nkwam, P., Akinmuleya, O. I., Anazodo, U., Mohamed, A. Z., Draper, E., & Anene-Ogbe, M. protocols.io, 2026.Predicting functional topography of the human visual cortex from cortical anatomy at scale
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. eLife (Reviewed Preprint), 15, 2026.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
Arnoldy, L., Gauci, S., Young, L. M., Macpherson, H., Civier, O., Scholey, A., Pipingas, A., & White, D. J. British Journal of Nutrition, 133(7), 1–17, 2025.Effects of Aging, Estimated Fitness, and Cerebrovascular Status on White Matter Microstructural Health
Clements, G. M., Camacho, P., Bowie, D. C., Low, K. A., Sutton, B. P., Gratton, G., & Fabiani, M. Human Brain Mapping, 46(5), e70168, 2025.Characterizing positive and negative quantitative susceptibility values in the cortex following mild traumatic brain injury: a depth- and curvature-based study
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. Cerebral Cortex, 35(3), 2025.Iron deposition and functional connectivity alterations in the right substantia nigra of adult males with autism
Itahashi, T., Tanji, K., Shikauchi, Y., Naoe, T., Okimura, T., Nakamura, M., Ohta, H., & Hashimoto, R. I. Cerebral Cortex, 35(8), 2025.Grey matter volume differences across Parkinson’s disease motor subtypes in the supplementary motor cortex
Martin, A., Nassif, J., Chaluvadi, L., Schammel, C., Newman-Norlund, R., Bollmann, S., & Absher, J. NeuroImage: Clinical, 45, 103724, 2025.BOLD fMRI at 9.4T with 3D stack-of-spirals readouts
Monreal-Madrigal, A., Kurban, D., Tse, D. H. Y., Ivanov, D., Boulant, N., & Poser, B. A. MAGMA, 2025.Segmentation of the human tongue musculature using MRI: Field guide and validation in motor neuron disease
Shaw, T. B., Ribeiro, F. L., Zhu, X., Aiken, P., 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. Computers in Biology and Medicine, 196(Pt B), 110824, 2025.Assessing the influence of dopamine and mindfulness on the formation of routines in visual search
Garner, K. G., Leow, L. A., Uchida, A., Nolan, C., Jensen, O., Garrido, M. I., & Dux, P. E. Psychophysiology, 61(7), e14571, 2024.Combining the benefits of 3D acquisitions and spiral readouts for VASO fMRI at UHF
Monreal-Madrigal, A., Kurban, D., Huber, L., Ivanov, D., Boulant, N., & Poser, B. A. Imaging Neuroscience, 2, 2024.
Have you used Neurodesk in your research or teaching? We welcome community contributions to this list.
Alternatively, email the core team or tag us on social media.
