How to cite us

How should you cite Neurodesk and the tools you use through the platform?

Citing Neurodesk

Please cite the Neurodesk paper and if you used Neurodesktop, add the version that was used (e.g. v2024-12-06).

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

 @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}
        }

Check our preprint here Neurodesk Preprint

Citing specific tools

To guarantee reproducibility, we recommend specifying the name, version number and builddate for any containerised applications used through Neurodesk. You can find this information here.

In addition to citing Neurodesk, please remember to cite any papers associated with the tools you use. You find this information in the README.m for each tool, or when opening the application through the menu in Neurodesktop.

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 (v2024-12-06, Renton et al, 2022)”

“EEGlab (2020.0_20211026, Delorme & Makeig, 2004) was run in Neurodesk (v2024-12-06, Renton et al, 2022) part of the AEDAPT project.”

References

  1. 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
  2. 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
  3. 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
Last modified January 23, 2025: extend sshfs example (5869a61)