The DataLad Handbook

Wagner, Adina; Waite, Laura K.; Meyer, Kyle; K., Heckner, Marisa; Kadelka, Tobias; Reuter, Niels; Waite, Alexander Q.; Poldrack, Benjamin; Markiewicz, Christopher J.; Halchenko, Yaroslav; Vavra, Peter; Chormai, Pattarawat; Poline, Jean‐Baptiste; Paas, Lya K.; Herholz, Peer; Mochalski, Lisa N.; Kraljevic, Nevena; Lisa, Wiersch,; Hutton, Alexandre; Pustina, Dorian; Baagil, Hamzah Hamid; Glatard, Tristan; Oliveira, Sarah Christina Caldas; Ippoliti, Giulia; Mönch, Christian; Huijser, Dorien; Hanke, Michael

doi:10.5281/zenodo.3905791

Cited by 5 publications

(3 citation statements)

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“…The majority of the steps involved in preparing and preprocessing the MRI data employed recently developed tools and workflows aimed at enhancing standardization and reproducibility of task-based fMRI studies (for a similar data processing pipeline, see e.g., Esteban et al, 2019a; Wittkuhn and Schuck, 2021). Version-controlled data and code management was performed using DataLad (version 0.13.0; Halchenko et al, 2019, 2021), supported by the DataLad handbook (Wagner et al, 2020). Following successful acquisition, all study data were arranged according to the brain imaging data structure (BIDS) specification (Gorgolewski et al, 2016) using the HeuDiConv tool (version 0.8.0.2; freely available from https://github.com/ReproNim/reproin or https://hub.docker.com/r/repronim/reproin) in combination with the ReproIn heuristic (Visconti di Oleggio Castello et al, 2020) (version 0.6.0) that allows automated creation of BIDS data sets from the acquired Digital Imaging and Communications in Medicine (DICOM) images.…”

Section: Methodsmentioning

confidence: 99%

Statistical learning of successor representations is related to on-task replay

Wittkuhn

Krippner

2022

Preprint

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Humans automatically infer higher-order relationships between events in the environment from their statistical co-occurrence, often without conscious awareness. Neural replay of task representations, which has been described as sampling from a learned transition structure of the environment, is a candidate mechanism by which the brain could use or even learn such relational information in the service of adaptive behavior. Human participants viewed sequences of images that followed probabilistic transitions determined by ring-like graph structures. Behavioral modeling revealed that participants acquired multi-step transition knowledge through gradual updating of an internal successor representation (SR) model, although half of participants did not indicate any knowledge about the sequential task structure. To investigate neural replay, we analyzed dynamics of multivariate functional magnetic resonance imaging (fMRI) patterns during short pauses from the ongoing statistical learning task. Evidence for sequential replay consistent with the probabilistic task structure was found in occipito-temporal and sensorimotor cortices during short on-task intervals. These findings indicate that implicit learning of higher-order relationships establishes an internal SR-based map of the task, and is accompanied by cortical on-task replay.

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Section: Methodsmentioning

confidence: 99%

Statistical learning of successor representations is related to on-task replay

Wittkuhn

Krippner

2022

Preprint

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“…These subdatasets can be independently manipulated and have their own standalone version history. For a primer on using DataLad, we recommend the DataLad Handbook 221 (http://handbook.datalad.org/).…”

Section: "It's Not the Fall That Gets You"mentioning

confidence: 99%

The “Narratives” fMRI dataset for evaluating models of naturalistic language comprehension

et al. 2021

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The “Narratives” collection aggregates a variety of functional MRI datasets collected while human subjects listened to naturalistic spoken stories. The current release includes 345 subjects, 891 functional scans, and 27 diverse stories of varying duration totaling ~4.6 hours of unique stimuli (~43,000 words). This data collection is well-suited for naturalistic neuroimaging analysis, and is intended to serve as a benchmark for models of language and narrative comprehension. We provide standardized MRI data accompanied by rich metadata, preprocessed versions of the data ready for immediate use, and the spoken story stimuli with time-stamped phoneme- and word-level transcripts. All code and data are publicly available with full provenance in keeping with current best practices in transparent and reproducible neuroimaging.

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“…from documentation, user training, or tutorials, and also an individual’s interest in doing so. Efforts such as Repro-Nim’s ( repronim.org ) webinars, teaching resource collections, and teaching fellowships, or in-depth, user-focused documentation formats such as the DataLad Handbook ( Wagner et al, 2020 ) facilitate this.…”

Section: Drdm Perspective: One Laboratory or Researchermentioning

confidence: 99%

In defense of decentralized research data management

et al. 2021

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Decentralized research data management (dRDM) systems handle digital research objects across participating nodes without critically relying on central services. We present four perspectives in defense of dRDM, illustrating that, in contrast to centralized or federated research data management solutions, a dRDM system based on heterogeneous but interoperable components can offer a sustainable, resilient, inclusive, and adaptive infrastructure for scientific stakeholders: An individual scientist or laboratory, a research institute, a domain data archive or cloud computing platform, and a collaborative multisite consortium. All perspectives share the use of a common, self-contained, portable data structure as an abstraction from current technology and service choices. In conjunction, the four perspectives review how varying requirements of independent scientific stakeholders can be addressed by a scalable, uniform dRDM solution and present a working system as an exemplary implementation.

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The DataLad Handbook

Cited by 5 publications

References 0 publications

Statistical learning of successor representations is related to on-task replay

Statistical learning of successor representations is related to on-task replay

The “Narratives” fMRI dataset for evaluating models of naturalistic language comprehension

In defense of decentralized research data management

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