Abstract
Multicentre studies are of utmost importance to confirm hypotheses. The lack of established standards and the ensuing complexity of their data management often hamper their implementation. The Brain Imaging Data Structure (BIDS) is an initiative for organizing and describing neuroimaging and electrophysiological data. Building on BIDS, we have developed two software programs: BIDS Manager and BIDS Uploader. The former has been designed to collect, organise and manage the data and the latter has been conceived to handle their transfer and anonymisation from the partner centres. These two programs aim at facilitating the implementation of multicentre study by providing a standardised framework.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Notes
available here: http://meg.univ-amu.fr/wiki/AnyWave
GDPR defines in Article 3 pseudo-anonymisation as “the processing of personal data in such a way that the data can no longer be attributed to a specific data subject without the use of additional information.” Such “additional information” must be “kept separately and subject to technical and organisational measures to ensure non-attribution to an identified or identifiable person.”
available at: http://meg.univ-amu.fr/wiki/GARDEL:presentation
References
Atkinson, I. (2012). Accuracy of data transfer: Double data entry and estimating levels of error. Journal of Clinical Nursing, 21(19-20), 2730–2735. https://doi.org/10.1111/j.1365-2702.2012.04353.x.
Cheng, A., Kessler, D., Mackinnon, R., Chang, T.P., Nadkarni, V.M., Hunt, E.A., Duval-Arnould, J., Lin, Y., Pusic, M., & Auerbach, M. (2017). Conducting multicenter research in healthcare simulation: Lessons learned from the INSPIRE network. Advances in Simulation, 2(1), 1–14. https://doi.org/10.1186/s41077-017-0039-0.
Colombet, B., Woodman, M., Badier, J., & Bénar, C.G. (2015). AnyWave: A cross-platform and modular software for visualizing and processing electrophysiological signals. Journal of Neuroscience Methods, 242, 118–126. https://doi.org/10.1016/j.jneumeth.2015.01.017.
Cox, R.W., Ashburner, J., Breman, H., Fissell, K., Haselgrove, C., Holmes, C.J., Lancaster, J.L., Rex, D.E., Smith, S.M., Woodward, J.B., & Strother, S.C. (2004). A (sort of) new image data format standard: {NIfTI-1}. NeuroImage 22(May 2014):1. http://nifti.nimh.nih.gov/dfwg/NIFTI-1-Abstract.html.
Dashevsky, B.Z., Bercu, Z.L., Bhosale, P.R., Burton, K.R., Chatterjee, A.R., Frigini, L.A.R., Heacock, L., Herskovits, E.H., Lee, J.T., Subhas, N., Wasnik, A.P., & Gyftopoulos, S. (2018). Multicenter research studies in radiology. Academic Radiology, 25(1), 18–25. https://doi.org/10.1016/j.acra.2017.05.019.
Delorme, A., & Makeig, S. (2004). EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics. Journal of Neuroscience Methods, 13, 9–21. https://doi.org/10.1016/j.jneumeth.2003.10.009.
Feistel, H. (1973). Cryptography and computer privacy. Scientific American, 228(5), 15–23. https://doi.org/10.1038/scientificamerican0573-15.
Gorgolewski, K.J., Auer, T., Calhoun, V.D., Craddock, R.C., Das, S., Duff, E.P., Flandin, G., Ghosh, S.S., Glatard, T., Halchenko, Y.O., Handwerker, D.A., Hanke, M., Keator, D., Li, X., Michael, Z., Maumet, C., Nichols, B.N., Nichols, T.E., Pellman, J., Poline, J.B., Rokem, A., Schaefer, G., Sochat, V., Triplett, W., Turner, J.A., Varoquaux, G., & Poldrack, R.A. (2016). The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Scientific Data, 3, 1–9. https://doi.org/10.1038/sdata.2016.44.
Gorgolewski, K.J., Alfaro-Almagro, F., Auer, T., Bellec, P., Capotă, M., Chakravarty, M.M., Churchill, N.W., Cohen, A.L., Craddock, R.C., Devenyi, G.A., Eklund, A., Esteban, O., Flandin, G., Ghosh, S.S., Guntupalli, J.S., Jenkinson, M., Keshavan, A., Kiar, G., Liem, F., Raamana, P.R., Raffelt, D., Steele, C.J., Quirion, P.O., Smith, R.E., Strother, S.C., Varoquaux, G., Wang, Y., Yarkoni, T., & Poldrack, R.A. (2017). BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. PLoS Computational Biology, 13(3), 1–16. https://doi.org/10.1371/journal.pcbi.1005209.
Gramfort, A., Luessi, M., Larson, E., Engemann, D.A., Strohmeier, D., Brodbeck, C., Goj, R., Jas, M., Brooks, T., Parkkonen, L., & Hämäläinen, M. (2013). MEG and EEG data analysis with MNE-Python. Frontiers in Neuroscience, 7(7 DEC), 1–13. https://doi.org/10.3389/fnins.2013.00267.
Holdgraf, C., Appelhoff, S., Bickel, S., Bouchard, K., D’Ambrosio, S., David, O., Devinsky, O., Dichter, B., Flinker, A., Foster, B.L., Gorgolewski, K.J., Groen, I., Groppe, D., Gunduz, A., Hamilton, L., Honey, C.J., Jas, M., Knight, R., Lachaux, J.P., Lau, J.C., Lee-Messer, C., Lundstrom, B.N., Miller, K.J., Ojemann, J.G., Oostenveld, R., Petridou, N., Piantoni, G., Pigorini, A., Pouratian, N., Ramsey, N.F., Stolk, A., Swann, N.C., Tadel, F., Voytek, B., Wandell, B.A., Winawer, J., Whitaker, K., Zehl, L., & Hermes, D. (2019). iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology. Scientific Data, 6(1), 102. https://doi.org/10.1038/s41597-019-0105-7. http://www.nature.com/articles/s41597-019-0105-7.
Irving, S.Y., & Curley, M.A. (2008). Challenges to conducting multicenter clinical research. AACN Advanced Critical Care, 19(2), 164–169. https://doi.org/10.1097/01.aacn.0000318119.67061.0f.
Keerie, C., Tuck, C., Milne, G., Eldridge, S., Wright, N., & Lewis, S.C. (2018). Data sharing in clinical trials - practical guidance on anonymising trial datasets. Trials, 19(1), 1–8. https://doi.org/10.1186/s13063-017-2382-9.
Kupzyk, K.A., & Cohen, M.Z. (2015). Data validation and other strategies for data entry. Western Journal of Nursing Research, 37(4), 546–556. https://doi.org/10.1177/0193945914532550.
Latha, M., Bellary, S., & Krishnankutty, B. (2014). Basics of case report form designing in clinical research. Perspectives in Clinical Research, 5(4), 159. https://doi.org/10.4103/2229-3485.140555.
Litvak, V., Mattout, J., Kiebel, S., Phillips, C., Henson, R., Kilner, J., Barnes, G., Oostenveld, R., Daunizeau, J., Flandin, G., Penny, W., & Friston, K. (2011). EEG And MEG data analysis in SPM8. Computational Intelligence and Neuroscience 2011, https://doi.org/10.1155/2011/852961 .
Marcus, D.S., Olsen, T.R., Ramaratnam, M., & Buckner, R.L. (2007). The extensible neuroimaging archive toolkit an informatics platform for managing, exploring, and sharing neuroimaging data. Neuroinformatics, 5(4), 11–33. https://doi.org/10.1385/NI:5:1:11. http://www.springerlink.com/index/X74873723718574K.pdf.
Medina Villalon, S., Paz, R., Roehri, N., Lagarde, S., Pizzo, F., Colombet, B., Bartolomei, F., Carron, R., & Bénar, C.G. (2018). EpiTools, A software suite for presurgical brain mapping in epilepsy: Intracerebral EEG. Journal of Neuroscience Methods, 303, 7–15. https://doi.org/10.1016/j.jneumeth.2018.03.018.
Niso, G., Gorgolewski, K.J., Bock, E., Brooks, T.L., Flandin, G., Gramfort, A., Henson, R.N., Jas, M., Litvak, V.T., Moreau, J., Oostenveld, R., Schoffelen, J.M., Tadel, F., Wexler, J., & Baillet, S. (2018). MEG-BIDS, the brain imaging data structure extended to magnetoencephalography. Scientific Data, 5, 180,110. https://doi.org/10.1038/sdata.2018.110. http://www.nature.com/articles/sdata2018110.
Oostenveld, R., Fries, P., Maris, E., & Schoffelen, J.M. (2011). Fieldtrip: Open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data. Computational Intelligence and Neuroscience 2011. https://doi.org/10.1155/2011/156869.
Paulsen, A., Overgaard, S., & Lauritsen, J.M. (2012). Quality of data entry using single entry, double entry and automated forms processing-an example based on a study of patient-reported outcomes. PLoS ONE, 7(4), 1–6. https://doi.org/10.1371/journal.pone.0035087.
Pernet, C.R., Appelhoff, S., Gorgolewski, K.J., Flandin, G., Phillips, C., Delorme, A., & Oostenveld, R. (2019). EEG-BIDS, an extension to the brain imaging data structure for electroencephalography. Scientific Data, 6(1), 103. https://doi.org/10.1038/s41597-019-0104-8.
Schmitt, C.P., & Burchinal, M. (2011). Data management practices for collaborative research. Frontiers in Psychiatry, 2(JUL), 1–8. https://doi.org/10.3389/fpsyt.2011.00047.
Scott, A., Courtney, W., Wood, D., de la Garza, R., Lane, S., King, M., Wang, R., Roberts, J., Turner, J.A., & Calhoun, V.D. (2011). Coins: An innovative informatics and neuroimaging tool suite built for large heterogeneous datasets. Frontiers in Neuroinformatics, 5(December), 1–15. https://doi.org/10.3389/fninf.2011.00033.
Tadel, F., Baillet, S., Mosher, J.C., Pantazis, D., & Leahy, R.M. (2011). Brainstorm: a user-friendly application for MEG/EEG analysis. Computational Intelligence and Neuroscience 2011. https://doi.org/10.1155/2011/879716.
Acknowledgments
NR was supported by the French national clinical project SPREAD [PHRCN-16-0685 sponsored by University Hospitals of Strasbourg, IDRCB No. 2017-A00497-46]. This work was partially supported by the RHU EPINOV [A*MIDEX project (ANR-17-RHUS-0004) funded by the ‘Investissements d‘Avenir’ French Government]. AJ has received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreement No. 785907 (Human Brain Project SGA2). We would like to thank Dr Olivier David who shared the code of the uploader used in the F-TRACT project (f-tract.eu) which served as the starting point of BIDS Uploader described above.
Author information
Authors and Affiliations
Contributions
NR drafted the manuscript. NR, SMV, BC, BG, AP, FB and CGB designed the framework. NR developed BIDS Manager and SMV developed BIDS Uploader. AJ contributed in programming BIDS Manager. All the authors contributed to reviewing and editing the manuscript.
Corresponding author
Ethics declarations
Conflict of interests
The authors declare no competing interests.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Roehri, N., Medina Villalon, S., Jegou, A. et al. Transfer, Collection and Organisation of Electrophysiological and Imaging Data for Multicentre Studies. Neuroinform 19, 639–647 (2021). https://doi.org/10.1007/s12021-020-09503-6
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12021-020-09503-6