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My current research and engineering work is with the Psychoinformatics Group at the INM-7, Forschungszentrum Jülich, where we develop software and tools for decentralised research data management. This mainly involves DataLad.

I work at the intersection of software engineering, FAIR and decentralized data management, metadata-driven user applications, and open and inclusive research practices, where I focus on building interoperable tools that span all of these domains. In my current work I use version control systems, metadata, web frameworks, and semantic web technologies to build decentralized data catalogs that make datasets discoverable and accessible, even with considerable variation in dataset size, host location, data privacy regulations, level of sensitivity (personal data), storage infrastructure, and data use terms.

Previously, my PhD research focused on two topics within the broad field of functional magnetic resonance imaging (fMRI) analysis:

  1. Developing new signal processing methods the improve the quality of real-time functional MRI signals, for use in clinical applications like neurofeedback
  2. Developing software tools and processes that assist fMRI researchers in implementing best practices for data quality control and methods reporting

My scientific interest stretches beyond these topics and somewhat more broadly into how we can improve transparency and reproducibility in science. I’m particularly interested in developing and sharing tools and methods that make our jobs as researchers easier, while simultaneously improving the scientific record or the way in which it can be queried, summarised and reused. This includes tools and processes for code sharing, data sharing/management, and reproducible analysis environments.

Whenever possible, I try to embed the concepts of collaboration, team science, community-centered project work, and openness into my work.

I have collaborated on and generated some scientific output related to my research interests. Below, I’ll try to list most of the currently relevant ones with links to related content. These outputs often relate to specific software tools.

Articles

Szczepanik, M., Wagner, A.S., Heunis, S. Waite, L.K., Eickhoff, S.B. and Hanke, M. 2024. Teaching Research Data Management with DataLad: A Multi-year, Multi-domain Effort. Neuroinformatics. Links:

Kalantari, A., Szczepanik, M., Heunis, S., Mönch, C., Hanke, M., Wachtler, T. and Aswendt, M. 2023. How to establish and maintain a multimodal animal research dataset using DataLad. Nature Scientific Data 10, 357. Links:

Mara van der Meulen, Simone Dobbelaar, Lina van Drunen, Stephan Heunis, Marinus H. van IJzendoorn, Neeltje E. Blankenstein, and Eveline A. Crone. 2023. Transitioning from childhood into adolescence: A comprehensive longitudinal behavioral and neuroimaging study on prosocial behavior and social inclusion. NeuroImage 284. Links:

Achterberg, M., Mulder, J., Dobbelaar, S., Heunis, S., & Crone, E. 2022. Individual differences in developmental trajectories of social emotion regulation from childhood to emerging adolescence. Links:

DuPre, E., Salo, T., Ahmed, Z., Bandettini, P.A., Bottenhorn, K.L., Caballero-Gaudes, C., Dowdle, L.T., Gonzalez-Castillo, J., Heunis, S., Kundu, P., Laird, A.R., Markello, R., Markiewicz, C.J., Moia, S., Staden, I., Teves, J.B., Uruñuela, E., Vaziri-Pashkam, M., Whitaker, K., Handwerker, D.A., 2021. TE-dependent analysis of multi-echo fMRI with tedana. Journal of Open Source Software 6, 3669. Links:

Gau, R., Noble, S., Heuer, K., Bottenhorn, K.L., Bilgin, I.P., Yang, Y.-F., Huntenburg, J.M., Bayer, J.M.M., Bethlehem, R.A.I., Rhoads, S.A., Vogelbacher, C., Borghesani, V., Levitis, E., Wang, H.-T., Van Den Bossche, S., Kobeleva, X., Legarreta, J.H., Guay, S., Atay, S.M., et. al. 2021. Brainhack: Developing a culture of open, inclusive, community-driven neuroscience. Neuron 109, 1769–1775. Links:

[show all authors] Gau, R., Noble, S., Heuer, K., Bottenhorn, K.L., Bilgin, I.P., Yang, Y.-F., Huntenburg, J.M., Bayer, J.M.M., Bethlehem, R.A.I., Rhoads, S.A., Vogelbacher, C., Borghesani, V., Levitis, E., Wang, H.-T., Van Den Bossche, S., Kobeleva, X., Legarreta, J.H., Guay, S., Atay, S.M., Varoquaux, G.P., Huijser, D.C., Sandström, M.S., Herholz, P., Nastase, S.A., Badhwar, A., Dumas, G., Schwab, S., Moia, S., Dayan, M., Bassil, Y., Brooks, P.P., Mancini, M., Shine, J.M., O’Connor, D., Xie, X., Poggiali, D., Friedrich, P., Heinsfeld, A.S., Riedl, L., Toro, R., Caballero-Gaudes, C., Eklund, A., Garner, K.G., Nolan, C.R., Demeter, D.V., Barrios, F.A., Merchant, J.S., McDevitt, E.A., Oostenveld, R., Craddock, R.C., Rokem, A., Doyle, A., Ghosh, S.S., Nikolaidis, A., Stanley, O.W., Uruñuela, E., Anousheh, N., Arnatkeviciute, A., Auzias, G., Bachar, D., Bannier, E., Basanisi, R., Basavaraj, A., Bedini, M., Bellec, P., Benn, R.A., Berluti, K., Bollmann, Steffen, Bollmann, Saskia, Bradley, C., Brown, J., Buchweitz, A., Callahan, P., Chan, M.Y., Chandio, B.Q., Cheng, T., Chopra, S., Chung, A.W., Close, T.G., Combrisson, E., Cona, G., Constable, R.T., Cury, C., Dadi, K., Damasceno, P.F., Das, S., De Vico Fallani, F., DeStasio, K., Dickie, E.W., Dorfschmidt, L., Duff, E.P., DuPre, E., Dziura, S., Esper, N.B., Esteban, O., Fadnavis, S., Flandin, G., Flannery, J.E., Flournoy, J., Forkel, S.J., Franco, A.R., Ganesan, S., Gao, S., García Alanis, J.C., Garyfallidis, E., Glatard, T., Glerean, E., Gonzalez-Castillo, J., Gould van Praag, C.D., Greene, A.S., Gupta, G., Hahn, C.A., Halchenko, Y.O., Handwerker, D., Hartmann, T.S., Hayot-Sasson, V., Heunis, S., Hoffstaedter, F., Hohmann, D.M., Horien, C., Ioanas, H.-I., Iordan, A., Jiang, C., Joseph, M., Kai, J., Karakuzu, A., Kennedy, D.N., Keshavan, A., Khan, A.R., Kiar, G., Klink, P.C., Koppelmans, V., Koudoro, S., Laird, A.R., Langs, G., Laws, M., Licandro, R., Liew, S.-L., Lipic, T., Litinas, K., Lurie, D.J., Lussier, D., Madan, C.R., Mais, L.-T., Mansour L, S., Manzano-Patron, J.P., Maoutsa, D., Marcon, M., Margulies, D.S., Marinato, G., Marinazzo, D., Markiewicz, C.J., Maumet, C., Meneguzzi, F., Meunier, D., Milham, M.P., Mills, K.L., Momi, D., Moreau, C.A., Motala, A., Moxon-Emre, I., Nichols, T.E., Nielson, D.M., Nilsonne, G., Novello, L., O’Brien, C., Olafson, E., Oliver, L.D., Onofrey, J.A., Orchard, E.R., Oudyk, K., Park, P.J., Parsapoor, M., Pasquini, L., Peltier, S., Pernet, C.R., Pienaar, R., Pinheiro-Chagas, P., Poline, J.-B., Qiu, A., Quendera, T., Rice, L.C., Rocha-Hidalgo, J., Rutherford, S., Scharinger, M., Scheinost, D., Shariq, D., Shaw, T.B., Siless, V., Simmonite, M., Sirmpilatze, N., Spence, H., Sprenger, J., Stajduhar, A., Szinte, M., Takerkart, S., Tam, A., Tejavibulya, L., Thiebaut de Schotten, M., Thome, I., Tomaz da Silva, L., Traut, N., Uddin, L.Q., Vallesi, A., VanMeter, J.W., Vijayakumar, N., di Oleggio Castello, M.V., Vohryzek, J., Vukojević, J., Whitaker, K.J., Whitmore, L., Wideman, S., Witt, S.T., Xie, H., Xu, T., Yan, C.-G., Yeh, F.-C., Yeo, B.T.T., Zuo, X.-N.

Levitis, E., Praag, C.G. van, Gau, R., Heunis, S., …, Maumet, C., 2021. Centering inclusivity in the design of online conferences—An OHBM–Open Science perspective. GigaScience 10, giab051. Links:

[show all authors] Levitis, E., Praag, C.G. van, Gau, R., Heunis, S., DuPre, E., Kiar, G., Bottenhorn, K., Glatard, T., Nikolaidis, A., Whitaker, K., Mancini, M., Niso, G., Afyouni, S., Ortiz, E.A., Appelhoff, S., Arnatkeviciute, A., Atay, M.S., Auer, T., Baracchini, G., Bayer, J.M.M., Beauvais, M.J.S., Bijsterbosch, J., Bilgin, I.P., Bollmann, Saskia, Bollmann, Steffen, Botvinik-Nezer, R., Bright, M.G., Calhoun, V.D., Chen, X., Chopra, S., Chuan-Peng, H., Close, T., Cookson, S., Craddock, C., Vega, A.D.L., Leener, B.D., Demeter, D., Maio, P.D., Dickie, E.W., Eickhoff, S.B., Esteban, O., Finc, K., Frigo, M., Ganesan, S., Ganz, M., Garner, K., Garza-Villarreal, E.A., Gonzalez-Escamilla, G., Goswami, R., Griffiths, J., Grootswagers, T., Guay, S., Guest, O., Handwerker, D.A., Herholz, P., Heuer, K., Huijser, D., Iacovella, V., Joseph, M., Karakuzu, A., Keator, D., Kobeleva, X., Kumar, M., Laird, A., Larson-Prior, L.J., Lautarescu, A., Lazari, A., Gorroño, J.H.L., Li, X.-Y., Lv, J., Mansour, S.L., Meunier, D., Moraczewski, D., Nandi, T., Nastase, S.A., Nau, M., Noble, S., Norgaard, M., Obungoloch, J., Oostenveld, R., Orchard, E.R., Pinho, A.L., Poldrack, R., Qiu, A., Raamana, P.R., Rokem, A., Rutherford, S., Sharan, M., Shaw, T., Syeda, W.T., Testerman, M., Toro, R., Valk, S.L., Bossche, S.V.D., Varoquaux, G., Vasa, F., Veldsman, M., Vohryzek, J., Wagner, A.S., Walsh, R., White, T., zuxfoucault, Xie, X., Yan, C.-G., Yang, Y.-F., Yee, Y., Zanitti, G.E., Gulick, A.V., Duff, E., Maumet, C.

Heunis, S., Breeuwer, M., Caballero-Gaudes, C., Hellrung, L., Huijbers, W., Jansen, J.F., Lamerichs, R., Zinger, S., and Aldenkamp, A.P. 2021. The effects of multi-echo fMRI combination and rapid T2*-mapping on offline and real-time BOLD sensitivity. NeuroImage 238, 118244. Links:

Heunis, S., Breeuwer, M., Caballero-Gaudes, C., Hellrung, L., Huijbers, W., Jansen, J.F., Lamerichs, R., Zinger, S., and Aldenkamp, A.P. 2020. rt-me-fMRI: A task and resting state dataset for real-time, multi-echo fMRI methods development and validation. F1000Research. Links:

Bannier, E., Barker, G., Borghesani, V., … , Wang, F., Wang, C., Zhu, H. 2021. The Open Brain Consent: Informing Research Participants and Obtaining Consent to Share Brain Imaging Data. Human Brain Mapping. Links:

[show all authors] Bannier, E., Barker, G., Borghesani, V., Broeckx, N., Clement, P., Emblem, K.E., Ghosh, S., Glerean, E., Gorgolewski, K.J., Havu, M., Halchenko, Y.O., Herholz, P., Hespel, A., Heunis, S., Hu, Y., Hu, C.-P., Huijser, D., Vayá, M. de la I., Jancalek, R., Katsaros, V.K., Kieseler, M.-L., Maumet, C., Moreau, C.A., Mutsaerts, H.-J., Oostenveld, R., Ozturk‐Isik, E., Espinosa, N.P.L., Pellman, J., Pernet, C.R., Pizzini, F.B., Trbalić, A.Š., Toussaint, P.-J., Castello, M.V. di O., Wang, F., Wang, C., Zhu, H.

Tomas Ros, Stefanie Enriquez-Geppert, Vadim Zotev, Kymberly Young, … , Robert T. Thibault. 2020. Consensus on the reporting and experimental design of clinical and cognitive-behavioural neurofeedback studies (CRED-nf checklist). Brain. 2020; 143, 1674–1685, Links:

[show all authors] Tomas Ros, Stefanie Enriquez-Geppert, Vadim Zotev, Kymberly Young, Guilherme Wood, Susan Whitfield-Gabrieli, Patrik Vuilleumier,Feng Wan, François Vialatte, Dimitri Van De Ville, Doron Todder, Tanju Surmeli, James Sulzer, Ute Strehl, Barry Sterman, Naomi Steiner, Bettina Sorger, Surjo Soekadar, Ranganatha Sitaram, Leslie Sherlin, Michael Schönenberg, Frank Scharnowski, Manuel Schabus, Katya Rubia, Agostinho Rosa, Miriam Reiners, Jaime Pineda, Christian Paret, Alexei Ossadtchi,Andrew Nicholson, Wenya Nan, Javier Minguez, Jean-Arthur Micoulaud-Franchi, David M. A. Mehler, Michael Lührs, Joel Lubar, Fabien Lotte, David E. J. Linden, Jarrod Lewis-Peacock, Mikhail Lebedev, Ruth Lanius, Andrea Kübler,Cornelia Kranczioch, Yury Koush, Lilian Konicar, Simon H. Kohl, Silivia E. Kober, Manousos Klados, Camille Jeunet, Tieme Janssen, Rene J. Huster, Kerstin Hoedlmoser, Laurence Hirshberg, Stephan Heunis, Talma Hendler, Michelle Hampson, Adrian Guggisberg, John Gruzelier,Rainer Göbel, Nicolas Gninenko, Alireza Gharabaghi, Paul Frewen, Thomas Fovet, Thalia Fernandez, Carlos Escolano, Ann-Christine Ehlis, Renate Drechsler, R Christopher deCharms, Stefan Debener, Dirk De Ridder, Eddy Davelaar, Marco Congedo, Marc Cavazza, Rien M. H. M. Breteler, Daniel Brandeis, Jerzy Bodurka, Niels Birbaumer, Olga Bazanova, Robert Bauer, Beatrix Barth, Panagiotis Bamidis, Tibor Auer, Martijn Arns, Robert T. Thibault.

Botvinik-Nezer, R., Holzmeister, F., Camerer, C.F., Dreber, A., … , Nichols, T.E., Poldrack, R.A., Schonberg, T., 2019. Variability in the analysis of a single neuroimaging dataset by many teams. Nature 582, 84–88 (2020). Links:

[show all authors] Botvinik-Nezer, R., Holzmeister, F., Camerer, C.F., Dreber, A., Huber, J., Johannesson, M., Kirchler, M., Iwanir, R., Mumford, J.A., Adcock, A., Avesani, P., Baczkowski, B., Bajracharya, A., Bakst, L., Ball, S., Barilari, M., Bault, N., Beaton, D., Beitner, J., Benoit, R., Berkers, R., Bhanji, J., Biswal, B., Bobadilla-Suarez, S., Bortolini, T., Bottenhorn, K., Bowring, A., Braem, S., Brooks, H., Brudner, E., Calderon, C., Camilleri, J., Castrellon, J., Cecchetti, L., Cieslik, E., Cole, Z., Collignon, O., Cox, R., Cunningham, W., Czoschke, S., Dadi, K., Davis, C., Luca, A.D., Delgado, M., Demetriou, L., Dennison, J., Di, X., Dickie, E., Dobryakova, E., Donnat, C., Dukart, J., Duncan, N.W., Durnez, J., Eed, A., Eickhoff, S., Erhart, A., Fontanesi, L., Fricke, G.M., Galvan, A., Gau, R., Genon, S., Glatard, T., Glerean, E., Goeman, J., Golowin, S., González-García, C., Gorgolewski, K., Grady, C., Green, M., Moreira, J.G., Guest, O., Hakimi, S., Hamilton, J.P., Hancock, R., Handjaras, G., Harry, B., Hawco, C., Herholz, P., Herman, G., Heunis, S., Hoffstaedter, F., Hogeveen, J., Holmes, S., Hu, C.-P., Huettel, S., Hughes, M., Iacovella, V., Iordan, A., Isager, P., Isik, A.I., Jahn, A., Johnson, M., Johnstone, T., Joseph, M., Juliano, A., Kable, J., Kassinopoulos, M., Koba, C., Kong, X.-Z., Koscik, T., Kucukboyaci, N.E., Kuhl, B., Kupek, S., Laird, A., Lamm, C., Langner, R., Lauharatanahirun, N., Lee, H., Lee, S., Leemans, A., Leo, A., Lesage, E., Li, F., Li, M., Lim, P.C., Lintz, E., Liphardt, S., Vermeer, A.L., Love, B., Mack, M., Malpica, N., Marins, T., Maumet, C., McDonald, K., McGuire, J., Melero, H., Leal, A.M., Meyer, B., Meyer, K., Mihai, P., Mitsis, G., Moll, J., Nielson, D., Nilsonne, G., Notter, M., Olivetti, E., Onicas, A., Papale, P., Patil, K., Peelle, J.E., Pérez, A., Pischedda, D., Poline, J.-B., Prystauka, Y., Ray, S., Reuter-Lorenz, P., Reynolds, R., Ricciardi, E., Rieck, J., Rodriguez-Thompson, A., Romyn, A., Salo, T., Samanez-Larkin, G., Sanz-Morales, E., Schlichting, M., Schultz, D., Shen, Q., Sheridan, M., Shiguang, F., Silvers, J., Skagerlund, K., Smith, A., Smith, D., Sokol-Hessner, P., Steinkamp, S., Tashjian, S., Thirion, B., Thorp, J., Tinghög, G., Tisdall, L., Tompson, S., Toro-Serey, C., Torre, J., Tozzi, L., Truong, V., Turella, L., Veer, A.E. van’t, Verguts, T., Vettel, J., Vijayarajah, S., Vo, K., Wall, M., Weeda, W.D., Weis, S., White, D., Wisniewski, D., Xifra-Porxas, A., Yearling, E., Yoon, S., Yuan, R., Yuen, K., Zhang, L., Zhang, X., Zosky, J., Nichols, T.E., Poldrack, R.A., Schonberg, T.

Heunis, S., Lamerichs, R., Zinger, S., Caballero‐Gaudes, C., Jansen, J.F.A., Aldenkamp, B., Breeuwer, M., 2020. Quality and denoising in real‐time functional magnetic resonance imaging neurofeedback: A methods review. Human Brain Mapping. 2020; 41: 3439–3467. Links:

Heunis, S., Besseling, R., Lamerichs, R., de Louw, A., Breeuwer, M., Aldenkamp, B., Bergmans, J., 2018. Neu3CA-RT: A framework for real-time fMRI analysis. Psychiatry Research: Neuroimaging 282, 90–102. Links:

Besseling, R., Lamerichs, R., Michels, B., Heunis, S., de Louw, A., Tijhuis, A., Bergmans, J., Aldenkamp, B., 2018. Functional network abnormalities consistent with behavioral profile in Autism Spectrum Disorder. Psychiatry Research: Neuroimaging 275, 43–48. Links:

Conference Posters

Szczepanik, M., Heunis, S., Mönch, C., Wagner, A., Waite, A. Q., Waite, L., & Hanke, M. 2023. Distributed data management for large collaborative projects: DataLad ecosystem in Collaborative Research Center 1451. INCF Neuroinformatics Assembly 2023. Links:

Stefano Moia, Hao-Ting Wang, Anibal S. Heinsfeld, Dorota Jarecka, Yu Fang Yang, Stephan Heunis, et al. 2024. Proceedings of the OHBM Brainhack 2022. Aperture Neuro. Links:

Stephan Heunis, Christian Mönch, Benjamin Poldraxk, and Michael Hanke. 2022. DataCat: generate a user-friendly data browser from structured metadata. Poster and software demonstration at the 2022 annual meeting of the Organization of Human Brain Mapping. Glasgow, Scotland. Links:

Heunis, S., Hellrung, L., Meer, V.D., Bergert, S., Sladky, R., Pamplona, G.S.P., Scharnowski, F., Koush, Y., Mehler, D., Falcon, C., Gispert, J.D., Molinuevo, J.L., Skouras, S., 2019. rtQC: an open-source toolbox for real-time fMRI quality control. Poster and software demonstration at the 2019 annual meeting of the Organization of Human Brain Mapping. Rome, Italy. Links:

Heunis, J.S., Lamerichs, R., Song, G., Zinger, S., Aldenkamp, B., 2019. Improving BOLD sensitivity with real-time multi-echo echo-planar imaging - Towards a cleaner neurofeedback signal. Poster at the 1th annual meeting of the Benelux Chapter of the International Society for Magnetic Resonance in Medicine. Leiden, The Netherlands. Links:

Heunis, J.S., Besseling, R., Lamerichs, R., De Louw, A., Aldenkamp, B., Bergmans, J., 2018. Dynamic T2star and S0 mapping towards real-time multi-echo fMRI denoising. Poster at the 10th annual meeting of the Benelux Chapter of the International Society for Magnetic Resonance in Medicine. Antwerpen, Belgium.