How to cite us

How to cite Neurodesk and the tools used through the platform.

If you used Neurodesk in your research or teaching, please cite our main paper and the relevant containerized tools to ensure reproducibility and proper attribution.

Citing Neurodesk

Please cite the Neurodesk paper. You can also access it via the open access link or refer to the preprint version.

If you used Neurodesktop, please include the version used (e.g., v2025-06-10). See examples below.

Full citation: 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

BibTeX:

 @article{Renton2024,
            author = {Renton, Angela I and Dao, Thuy T and Johnstone, Tom and Civier, Oren and Sullivan, Ryan P and White, David J and Lyons, Paris and Slade, Benjamin M and Abbott, David F and Amos, Toluwani J and Bollmann, Saskia and Botting, Andy and Campbell, Megan E J and Chang, Jeryn and Close, Thomas G and D{\"{o}}rig, Monika and Eckstein, Korbinian and Egan, Gary F and Evas, Stefanie and Flandin, Guillaume and Garner, Kelly G and Garrido, Marta I and Ghosh, Satrajit S and Grignard, Martin and Halchenko, Yaroslav O and Hannan, Anthony J and Heinsfeld, Anibal S and Huber, Laurentius and Hughes, Matthew E and Kaczmarzyk, Jakub R and Kasper, Lars and Kuhlmann, Levin and Lou, Kexin and Mantilla-Ramos, Yorguin-Jose and Mattingley, Jason B and Meier, Michael L and Morris, Jo and Narayanan, Akshaiy and Pestilli, Franco and Puce, Aina and Ribeiro, Fernanda L and Rogasch, Nigel C and Rorden, Chris and Schira, Mark M and Shaw, Thomas B and Sowman, Paul F and Spitz, Gershon and Stewart, Ashley W and Ye, Xincheng and Zhu, Judy D and Narayanan, Aswin and Bollmann, Steffen},
            doi = {10.1038/s41592-023-02145-x},
            issn = {1548-7105},
            journal = {Nature Methods},
            number = {5},
            pages = {804--808},
            title = {{Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging}},
            url = {https://doi.org/10.1038/s41592-023-02145-x},
            volume = {21},
            year = {2024}
        }

Citing specific tools

For reproducibility, please include the tool name, version number, and build date for any containerized application used in Neurodesk. This information is available in our application list.

In addition to citing Neurodesk, please remember to cite any original publication associated with each tool you use. Citation details can be found:

in the tool’s README.md under neurocontainers/recipes
Or in the tool’s interface within Neurodesktop

Citing EEG/MEG related tools

If you used any EEG/MEG/electrophysiology tools, please also cite the AEDAPT project.

Examples

Here are some example excerts of how to cite Neurodesk:

“TGV QSM (v1.0.0_20210629, Langkammer et al, 2015) was run in Neurodesk (v2025-06-10, Renton et al, 2022)”

EEG example: “EEGlab (2020.0_20211026, Delorme & Makeig, 2004) was run in Neurodesk (v2025-06-10, Renton et al, 2022) part of the AEDAPT project.”

References

Langkammer, C; Bredies, K; Poser, BA; Barth, M; Reishofer, G; Fan, AP; Bilgic, B; Fazekas, F; Mainero; C; Ropele, S. Fast Quantitative Susceptibility Mapping using 3D EPI and Total Generalized Variation. Neuroimage. 2015 May 1;111:622-30. doi: 10.1016/j.neuroimage.2015.02.041
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). 10.1038/s41592-023-02145-x
Delorme A & Makeig S (2004) EEGLAB: an open-source toolbox for analysis of single-trial EEG dynamics, Journal of Neuroscience Methods 134:9-21. doi: 10.1016/j.jneumeth.2003.10.009