Bio


I am a Wu Tsai Interdisciplinary Postdoctoral Scholar, working in collaboration with Dr. Russell Poldrack and Dr. Scott Linderman.
I have a background in cognitive and computational psychology, with a PhD in Neuroscience from McGill University and an MA in Developmental Psychology from Cornell University.

Currently, my research focuses on expanding our statistical toolkit for drawing inferences from high-dimensional, naturalistic datasets measured with modalities such as functional magnetic resonance imaging (fMRI). To do this, I am developing new methods and accompanying open source tools.

Honors & Awards


  • Wu Tsai Interdisciplinary Scholar Award, Wu Tsai Neurosciences Institute (1 June 2022 - 1 June 2024)

Stanford Advisors


Lab Affiliations


All Publications


  • Brain Decoding of the Human Connectome Project Tasks in a Dense Individual fMRI Dataset. NeuroImage Rastegarnia, S., St-Laurent, M., DuPre, E., Pinsard, B., Bellec, P. 2023: 120395

    Abstract

    Brain decoding aims to infer cognitive states from patterns of brain activity. Substantial inter-individual variations in functional brain organization challenge accurate decoding performed at the group level. In this paper, we tested whether accurate brain decoding models can be trained entirely at the individual level. We trained several classifiers on a dense individual functional magnetic resonance imaging (fMRI) dataset for which six participants completed the entire Human Connectome Project (HCP) task battery >13 times over ten separate fMRI sessions. We evaluated nine decoding methods, from Support Vector Machines (SVM) and Multi-Layer Perceptron (MLP) to Graph Convolutional Neural Networks (GCN). All decoders were trained to classify single fMRI volumes into 21 experimental conditions simultaneously, using 7h of fMRI data per participant. The best prediction accuracies were achieved with GCN and MLP models, whose performance (57-67% accuracy) approached state-of-the-art accuracy (76%) with models trained at the group level on >1K hours of data from the original HCP sample. Our SVM model also performed very well (54-62% accuracy). Feature importance maps derived from MLP -our best-performing model- revealed informative features in regions relevant to particular cognitive domains, notably in the motor cortex. We also observed that inter-subject classification achieved substantially lower accuracy than subject-specific models, indicating that our decoders learned individual-specific features. This work demonstrates that densely-sampled neuroimaging datasets can be used to train accurate brain decoding models at the individual level. We expect this work to become a useful benchmark for techniques that improve model generalization across multiple subjects and acquisition conditions.

    View details for DOI 10.1016/j.neuroimage.2023.120395

    View details for PubMedID 37832707

  • The Past, Present, and Future of the Brain Imaging Data Structure (BIDS). ArXiv Poldrack, R. A., Markiewicz, C. J., Appelhoff, S., Ashar, Y. K., Auer, T., Baillet, S., Bansal, S., Beltrachini, L., Bénar, C. G., Bertazzoli, G., Bhogawar, S., Blair, R. W., Bortoletto, M., Boudreau, M., Brooks, T. L., Calhoun, V. D., Castelli, F. M., Clement, P., Cohen, A. L., Cohen-Adad, J., D'Ambrosio, S., de Hollander, G., de la Iglesia-Vayá, M., de la Vega, A., Delorme, A., Devinsky, O., Draschkow, D., Duff, E. P., DuPre, E., Earl, E., Esteban, O., Feingold, F. W., Flandin, G., Galassi, A., Gallitto, G., Ganz, M., Gau, R., Gholam, J., Ghosh, S. S., Giacomel, A., Gillman, A. G., Gleeson, P., Gramfort, A., Guay, S., Guidali, G., Halchenko, Y. O., Handwerker, D. A., Hardcastle, N., Herholz, P., Hermes, D., Honey, C. J., Innis, R. B., Ioanas, H. I., Jahn, A., Karakuzu, A., Keator, D. B., Kiar, G., Kincses, B., Laird, A. R., Lau, J. C., Lazari, A., Legarreta, J. H., Li, A., Li, X., Love, B. C., Lu, H., Maumet, C., Mazzamuto, G., Meisler, S. L., Mikkelsen, M., Mutsaerts, H., Nichols, T. E., Nikolaidis, A., Nilsonne, G., Niso, G., Norgaard, M., Okell, T. W., Oostenveld, R., Ort, E., Park, P. J., Pawlik, M., Pernet, C. R., Pestilli, F., Petr, J., Phillips, C., Poline, J. B., Pollonini, L., Raamana, P. R., Ritter, P., Rizzo, G., Robbins, K. A., Rockhill, A. P., Rogers, C., Rokem, A., Rorden, C., Routier, A., Saborit-Torres, J. M., Salo, T., Schirner, M., Smith, R. E., Spisak, T., Sprenger, J., Swann, N. C., Szinte, M., Takerkart, S., Thirion, B., Thomas, A. G., Torabian, S., Varoquaux, G., Voytek, B., Welzel, J., Wilson, M., Yarkoni, T., Gorgolewski, K. J. 2023

    Abstract

    The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS.

    View details for DOI 10.21105/joss.01896

    View details for PubMedID 37744469

    View details for PubMedCentralID PMC10516110

  • Beyond advertising: New infrastructures for publishing integrated research objects PLOS COMPUTATIONAL BIOLOGY DuPre, E., Holdgraf, C., Karakuzu, A., Tetrel, L., Bellec, P., Stikov, N., Poline, J. 2022; 18 (1): e1009651

    View details for DOI 10.1371/journal.pcbi.1009651

    View details for Web of Science ID 001084590400008

    View details for PubMedID 34990466

    View details for PubMedCentralID PMC8735620

  • Centering inclusivity in the design of online conferences-An OHBM-Open Science perspective. GigaScience Levitis, E., van Praag, C. D., Gau, R., Heunis, S., DuPre, E., Kiar, G., Bottenhorn, K. L., Glatard, T., Nikolaidis, A., Whitaker, K. J., Mancini, M., Niso, G., Afyouni, S., Alonso-Ortiz, E., Appelhoff, S., Arnatkeviciute, A., Atay, S. M., Auer, T., Baracchini, G., Bayer, J. M., Beauvais, M. J., Bijsterbosch, J. D., Bilgin, I. P., Bollmann, S., Bollmann, S., Botvinik-Nezer, R., Bright, M. G., Calhoun, V. D., Chen, X., Chopra, S., Chuan-Peng, H., Close, T. G., Cookson, S. L., Craddock, R. C., De La Vega, A., De Leener, B., Demeter, D. V., Di Maio, P., Dickie, E. W., Eickhoff, S. B., Esteban, O., Finc, K., Frigo, M., Ganesan, S., Ganz, M., Garner, K. G., Garza-Villarreal, E. A., Gonzalez-Escamilla, G., Goswami, R., Griffiths, J. D., Grootswagers, T., Guay, S., Guest, O., Handwerker, D. A., Herholz, P., Heuer, K., Huijser, D. C., Iacovella, V., Joseph, M. J., Karakuzu, A., Keator, D. B., Kobeleva, X., Kumar, M., Laird, A. R., Larson-Prior, L. J., Lautarescu, A., Lazari, A., Legarreta, J. H., Li, X. Y., Lv, J., Mansour L, S., 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. A., Qiu, A., Raamana, P. R., Rokem, A., Rutherford, S., Sharan, M., Shaw, T. B., Syeda, W. T., Testerman, M. M., Toro, R., Valk, S. L., Van Den Bossche, S., Varoquaux, G., Váša, F., Veldsman, M., Vohryzek, J., Wagner, A. S., Walsh, R. J., White, T., Wong, F. T., Xie, X., Yan, C. G., Yang, Y. F., Yee, Y., Zanitti, G. E., Van Gulick, A. E., Duff, E., Maumet, C. 2021; 10 (8)

    Abstract

    As the global health crisis unfolded, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical, and legal barriers and effectively enabled many individuals from groups that have traditionally been underrepresented to join and participate. A number of studies have outlined how moving online made it possible to gather a more global community and has increased opportunities for individuals with various constraints, e.g., caregiving responsibilities. Yet, the mere existence of online conferences is no guarantee that everyone can attend and participate meaningfully. In fact, many elements of an online conference are still significant barriers to truly diverse participation: the tools used can be inaccessible for some individuals; the scheduling choices can favour some geographical locations; the set-up of the conference can provide more visibility to well-established researchers and reduce opportunities for early-career researchers. While acknowledging the benefits of an online setting, especially for individuals who have traditionally been underrepresented or excluded, we recognize that fostering social justice requires inclusivity to actively be centered in every aspect of online conference design. Here, we draw from the literature and from our own experiences to identify practices that purposefully encourage a diverse community to attend, participate in, and lead online conferences. Reflecting on how to design more inclusive online events is especially important as multiple scientific organizations have announced that they will continue offering an online version of their event when in-person conferences can resume.

    View details for DOI 10.1093/gigascience/giab051

    View details for PubMedID 34414422

  • Analysis of task-based functional MRI data preprocessed with fMRIPrep. Nature protocols Esteban, O., Ciric, R., Finc, K., Blair, R. W., Markiewicz, C. J., Moodie, C. A., Kent, J. D., Goncalves, M., DuPre, E., Gomez, D. E., Ye, Z., Salo, T., Valabregue, R., Amlien, I. K., Liem, F., Jacoby, N., Stojic, H., Cieslak, M., Urchs, S., Halchenko, Y. O., Ghosh, S. S., De La Vega, A., Yarkoni, T., Wright, J., Thompson, W. H., Poldrack, R. A., Gorgolewski, K. J. 2020

    Abstract

    Functional magnetic resonance imaging (fMRI) is a standard tool to investigate the neural correlates of cognition. fMRI noninvasively measures brain activity, allowing identification of patterns evoked by tasks performed during scanning. Despite the long history of this technique, the idiosyncrasies of each dataset have led to the use of ad-hoc preprocessing protocols customized for nearly every different study. This approach is time consuming, error prone and unsuitable for combining datasets from many sources. Here we showcase fMRIPrep (http://fmriprep.org), a robust tool to prepare human fMRI data for statistical analysis. This software instrument addresses the reproducibility concerns of the established protocols for fMRI preprocessing. By leveraging the Brain Imaging Data Structure to standardize both the input datasets (MRI data as stored by the scanner) and the outputs (data ready for modeling and analysis), fMRIPrep is capable of preprocessing a diversity of datasets without manual intervention. In support of the growing popularity of fMRIPrep, this protocol describes how to integrate the tool in a task-based fMRI investigation workflow.

    View details for DOI 10.1038/s41596-020-0327-3

    View details for PubMedID 32514178

  • fMRIPrep: a robust preprocessing pipeline for functional MRI NATURE METHODS Esteban, O., Markiewicz, C. J., Blair, R. W., Moodie, C. A., Isik, A., Erramuzpe, A., Kent, J. D., Goncalves, M., DuPre, E., Snyder, M., Oya, H., Ghosh, S. S., Wright, J., Durnez, J., Poldrack, R. A., Gorgolewski, K. J. 2019; 16 (1): 111-+
  • PyBIDS: Python tools for BIDS datasets. Journal of open source software Yarkoni, T., Markiewicz, C. J., de la Vega, A., Gorgolewski, K. J., Salo, T., Halchenko, Y. O., McNamara, Q., DeStasio, K., Poline, J., Petrov, D., Hayot-Sasson, V., Nielson, D. M., Carlin, J., Kiar, G., Whitaker, K., DuPre, E., Wagner, A., Tirrell, L. S., Jas, M., Hanke, M., Poldrack, R. A., Esteban, O., Appelhoff, S., Holdgraf, C., Staden, I., Thirion, B., Kleinschmidt, D. F., Lee, J. A., Visconti di Oleggio Castello, M., Notter, M. P., Blair, R. 2019; 4 (40)

    View details for DOI 10.21105/joss.01294

    View details for PubMedID 32775955