Reducing the efforts to create reproducible analysis code with FieldTrip

Reducing the efforts to create reproducible analysis code with FieldTrip - Published in JOSS (2024)

https://github.com/fieldtrip/fieldtrip

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • CITATION.cff file
  • codemeta.json file
    Found codemeta.json file
  • .zenodo.json file
    Found .zenodo.json file
  • DOI references
    Found 4 DOI reference(s) in README and JOSS metadata
  • Academic publication links
    Links to: scholar.google, zenodo.org
  • Committers with academic emails
    27 of 226 committers (11.9%) from academic institutions
  • Institutional organization owner
  • JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

analysis beamformer bids brain connectivity dipole donders ecog eeg fieldtrip ieeg matlab meg neuroimaging neuroscience seeg statistics time-frequency

Keywords from Contributors

electroencephalography magnetoencephalography electrocorticography mne mesh parallel cryptocurrencies dicom fem finite-elements

Scientific Fields

Engineering Computer Science - 40% confidence
Last synced: 6 months ago · JSON representation

Repository

The MATLAB toolbox for MEG, EEG and iEEG analysis

Basic Info
Statistics
  • Stars: 914
  • Watchers: 48
  • Forks: 746
  • Open Issues: 103
  • Releases: 16
Topics
analysis beamformer bids brain connectivity dipole donders ecog eeg fieldtrip ieeg matlab meg neuroimaging neuroscience seeg statistics time-frequency
Created about 13 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Code of conduct Citation Codeowners

README.md

Open in MATLAB Online GitHub contributors Last commit GitHub commit activity (branch) GitHub Repo stars License: GPL-3.0 DOI

FieldTrip

FieldTrip is the MATLAB software toolbox for MEG, EEG and iEEG analysis that is being developed at the Donders Institute for Brain, Cognition and Behaviour in Nijmegen, the Netherlands together with collaborating institutes.

The toolbox offers advanced analysis methods of MEG, EEG, and invasive electrophysiological data, such as time-frequency analysis, source reconstruction using dipoles, distributed sources and beamformers and non-parametric statistical testing. It supports the data formats of all major MEG systems (CTF, Neuromag/Elekta/Megin, BTi/4D, Yokogawa/Ricoh, FieldLine) and of most popular EEG systems, and new formats can be added easily. FieldTrip contains high-level functions that you can use to construct your own analysis protocols in MATLAB. Furthermore, it easily allows methods researchers to incorporate new methods for EEG/MEG analysis.

For more information, documentation, and tutorials, please visit https://www.fieldtriptoolbox.org

Installation

To install the FieldTrip toolbox on your computer, you can clone this repository or download the zip file, unzip it, and add it to your MATLAB path. Subsequently you call the ft_defaults function, which will add the required subdirectories to the path.

We recommend that you add the addpath(...) and the ft_defaults command to your startup.m file. See also https://www.fieldtriptoolbox.org/faq/installation/

Note that you should not use addpath(genpath(...)) and we recommend not to use the "add with subdirectories" button in the graphical path setup tool, as there are a number of external toolboxes and backward compatibility directories that you should not add to your path. If those directories are needed, then ft_defaults and ft_hastoolbox will take care of them.

Copyright

The FieldTrip software is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. See the file COPYING for more details.

The functions in the FieldTrip toolbox are copyrighted by their respective authors:

  • Robert Oostenveld, DCCN, FCDC, SMI, MBFYS
  • Jan-Mathijs Schoffelen, DCCN, MPI, CCNi, FCDC
  • Pascal Fries, FCDC
  • Eric Maris, DCC, FCDC
  • Arjen Stolk, DCCN
  • Eelke Spaak, DCCN
  • Ingrid Nieuwenhuis, DCCN, FCDC
  • Jens Schwarzbach, FCDC
  • Jorn Horschig, DCCN
  • Lilla Magyari, MPI, DCCN
  • Markus Siegel, FCDC, UKE
  • Martin Vinck, DCCN, SILS
  • Ole Jensen, FCDC
  • Roemer van der Meij, DCC
  • Saskia Haegens, DCCN, FCDC
  • Vladimir Litvak, UCL
  • and many other contributors

The authors are or were working at a range of academic institutions:

  • Copyright (C) 2008-2025, Donders Institute for Brain, Cognition and Behaviour, Radboud University, The Netherlands (DCCN, DCC, DCN)
  • Copyright (C) 2014-2025, Karolinska Institute, Stockholm, Sweden (NatMEG)
  • Copyright (C) 2012-2018, Max Planck Institute for Psycholinguistics, The Netherlands (MPI)
  • Copyright (C) 2008-2017, The Wellcome Trust Centre for Neuroimaging, University College London, UK (UCL)
  • Copyright (C) 2010-2013, Swammerdam Institute for Life Sciences, University of Amsterdam (SILS)
  • Copyright (C) 2008-2009, Centre for Cognitive Neuroimaging in Glasgow, United Kingdom (CCNi)
  • Copyright (C) 2009-2009, Netherlands Institute for Neuroscience (NIN)
  • Copyright (C) 2003-2008, F.C. Donders Centre, Radboud University Nijmegen, The Netherlands (FCDC)
  • Copyright (C) 2004-2007, Nijmegen Institute for Cognition and Information, The Netherlands (NICI)
  • Copyright (C) 2004-2005, Universitatsklinikum Hamburg-Eppendorf, Germany (UKE)
  • Copyright (C) 2003-2004, Center for Sensory Motor Interaction, University Aalborg, Denmark (SMI)
  • Copyright (C) 1999-2003, Department of Medical Physics, Radboud University Nijmegen, The Netherlands (MBFYS)

The FieldTrip software is a toolbox, i.e. a library with functions, which in turn an depend on other functions. The release of this toolbox includes functions from other toolboxes that are covered under their respective licenses. See fieldtrip/external for details. Unauthorised copying and distribution of functions that are not explicitly covered by the GPL is not allowed.

Owner

  • Name: FieldTrip toolbox
  • Login: fieldtrip
  • Kind: organization
  • Location: Nijmegen, The Netherlands

JOSS Publication

Reducing the efforts to create reproducible analysis code with FieldTrip
Published
February 21, 2024
Volume 9, Issue 94, Page 5566
Authors
Mats W.j. van Es ORCID
Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands, Oxford Centre for Human Brain Activity, Department of Psychiatry, University of Oxford, United Kingdom, Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, United Kingdom
Eelke Spaak ORCID
Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands
Jan-Mathijs Schoffelen ORCID
Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands
Robert Oostenveld ORCID
Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands, NatMEG, Karolinska Institutet, Stockholm, Sweden
Editor
Claudia Solis-Lemus ORCID
Tags
FieldTrip Toolbox reproducibility analysis pipeline open science MEG EEG

GitHub Events

Total
  • Issues event: 64
  • Watch event: 73
  • Delete event: 5
  • Issue comment event: 189
  • Push event: 135
  • Pull request review comment event: 5
  • Pull request review event: 5
  • Pull request event: 71
  • Fork event: 24
  • Create event: 34
Last Year
  • Issues event: 64
  • Watch event: 73
  • Delete event: 5
  • Issue comment event: 189
  • Push event: 137
  • Pull request review comment event: 5
  • Pull request review event: 5
  • Pull request event: 71
  • Fork event: 24
  • Create event: 34

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 18,061
  • Total Committers: 226
  • Avg Commits per committer: 79.916
  • Development Distribution Score (DDS): 0.533
Past Year
  • Commits: 190
  • Committers: 14
  • Avg Commits per committer: 13.571
  • Development Distribution Score (DDS): 0.474
Top Committers
Name Email Commits
Robert Oostenveld r****d@g****m 8,427
Jan Mathijs Schoffelen j****n@d****l 1,485
Jan-Mathijs Schoffelen j****n@d****l 1,403
Jorn Horschig j****g@d****l 569
Cristiano Micheli m****2@g****m 562
Roemer van der Meij r****j@d****l 536
Martin Vinck m****k@g****m 496
Eelke Spaak e****k@d****l 478
Stefan Klanke s****e@d****l 411
Marcel van Gerven m****n@g****m 285
Arjen Stolk a****k@d****l 281
StolkArjen a****8@g****m 210
Johanna Zumer j****r@d****l 184
Nikolaas N. Oosterhof n****f@u****t 179
Boris Reuderink b****k@g****m 154
Vladimir Litvak v****k@u****k 151
Roemer van der Meij r****j@g****m 111
Jim Herring j****g@d****l 98
Diego Lozano Soldevilla d****a@d****l 95
Lilla Magyari l****i@d****l 87
Ingrid Nieuwenhuis i****s@g****m 80
Sarang Dalal s****g@c****k 78
Joseph Dien j****7@m****m 71
helenacockx h****x@d****l 63
Tim Engelkes t****s@d****l 62
Mats m****s@d****l 59
Saskia Haegens s****s@g****m 56
Jörn M. Horschig j****n@a****m 53
Craig Richter c****r@g****m 52
Tilmann Sander-Thoemmes T****s@p****e 50
and 196 more...

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 86
  • Total pull requests: 234
  • Average time to close issues: 9 months
  • Average time to close pull requests: 2 months
  • Total issue authors: 45
  • Total pull request authors: 54
  • Average comments per issue: 2.77
  • Average comments per pull request: 2.26
  • Merged pull requests: 147
  • Bot issues: 0
  • Bot pull requests: 3
Past Year
  • Issues: 35
  • Pull requests: 76
  • Average time to close issues: 12 days
  • Average time to close pull requests: 8 days
  • Issue authors: 22
  • Pull request authors: 17
  • Average comments per issue: 1.31
  • Average comments per pull request: 2.54
  • Merged pull requests: 56
  • Bot issues: 0
  • Bot pull requests: 2
Top Authors
Issue Authors
  • schoffelen (14)
  • robertoostenveld (13)
  • arnodelorme (6)
  • vlitvak (3)
  • NirOfir (3)
  • GuilleSGCUPO (2)
  • mcpiastra (2)
  • asalazar4 (2)
  • contsili (2)
  • sinamakhdoomi (2)
  • tchaase (2)
  • chrisNatMEG (2)
  • JoaoAmaro2001 (1)
  • CDog1994 (1)
  • VlastaKoudelka (1)
Pull Request Authors
  • schoffelen (69)
  • robertoostenveld (31)
  • thht (9)
  • nno (9)
  • contsili (8)
  • gpiantoni (7)
  • mrkdsmith (6)
  • matsvanes (6)
  • mcpiastra (5)
  • dnacombo (4)
  • chrisNatMEG (4)
  • StolkArjen (4)
  • marcelzwiers (4)
  • roemervandermeij (4)
  • yarikoptic (3)
Top Labels
Issue Labels
bug (42) unconfirmed (42) question (17) enhancement (16) inactive (1) summer project (1) work in progress (1) dependencies (1) help wanted (1) documentation (1)
Pull Request Labels
dependencies (3) github_actions (2) codex (2) work in progress (1) bug (1) unconfirmed (1) summer project (1)