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Changelog

TAPAS toolbox

[4.0.0] 2020-09-09

Added

  • ceode: Toolbox to integrate delay differential equations (DDEs) underlying convolution based Dynamic Causal Models for ERPs.
  • task/FDT: Filter Detection Task version 0.2.2
  • citation information

Changed

  • rDCM: version v1.2
  • HUGE: removed deprecated functions
  • external toolboxes are now managed as matlab packages

Fixed

  • Fixed name collision issue due to mcmcdiag toolbox (see issue 106)

Known issues

  • h2gf (beta): demo script currently does not work

[3.3.0] 2020-07-17

Added

  • h2gf: Hierarchical inference for the HGF, beta version released
  • SERIA: Added the Watanabe Akaike information criterion (WAIC) as output.
  • SERIA: Added computation of early and late response likelihood.
  • SERIA: Added delta plots to output summary.

Changed

  • HGF: v6.0 released
  • SERIA: The constraints matrix is now automatically plot by tapas_sem_display_posterior.m
  • SERIA: Python code is now updated to python 3.7 and the requirement file now uses the latest libraries (numpy, scipy, cython).
  • SERIA: Posterior plots includes fits of the complete group.
  • SERIA: Summaries are automatically generated when preparing the posterior.
  • PhysIO: PhysIO Toolbox Release R2020a, v7.3.0
  • PhysIO: removed Matlab statistics toolbox dependency for PCA by SVD implementation (thanks to Benoît Beranger, pull request 64)

Fixed

  • HUGE: fixed tick labels

Known issues

  • TAPAS uses the mcmcdiag toolbox for Monte Carlo convergence diagnostics, which shadows a number of matlab built-in functions. Affected functions include: Contents.m, cusum.m, join.m and score.m. Workaround: If you use one of these functions in your own code, remove the tapas folder from your matlab path when you are not using the TAPAS toolbox.

[3.2.0] 2019-09-29

Added

  • HUGE: introduced object-oriented interface in addition to old interface
  • HUGE: build-in unit tests
  • HUGE: user manual
  • PhysIO (details in tapas/PhysIO/CHANGELOG.md)
    • more unit testing and integration testing for examples
    • bandpass-filtering for cardiac data in preprocessing, user-defined max heart rate for peak detection

Fixed

  • PhysIO: Bugfix RVT/HRV convolution had erroneous half-width shift

Changed

  • HUGE: demo script reflect interface changes

[3.1.0] 2019-03-26

Added

  • Get revision info from Matlab.
  • PhysIO R2018.1.2: BioPac txt-file reader (for single file, resp/cardiac/trigger data in different columns)
  • SERIA: Automatic plotting of the seria model.
  • SERIA: Example for single subject.

Fixed

  • Huge: minor bugs.

Changed

  • Huge: Improved documentation.
  • New version of the HGF toolbox (v5.3). Details in tapas/HGF/README.md
  • New version of the rDCM toolbox (v1.1). Details in tapas/rDCM/CHANGELOG.md.
  • New version of the PhysIO Toolbox (R2019a-v7.1.0)
    • BIDS and BioPac readers; code sorted in modules (readin, preproc etc.), also reflected in figure names
    • Updated and extended all examples, and introduced unit testing
    • Full details in tapas/PhysIO/CHANGELOG.md
  • Improved the documentation of SERIA.

[3.0.1] 2018-10-17

Fixed

  • PhysIO R2018.1.2: fixed bug for 3D nifti array read-in in tapas_physio_create_noise_rois_regressors (github issue #24, gitlab #52)

Added

[3.0.0] 2018-09-09

Added

  • tapas_get_tapas_revision.m outputs the branch and hash of the repository.
  • Revision is printed when initiliazing tapas.
  • Contributor License Agreement (CLA) file
  • CONTRIBUTING.md explaining coding and style guidelines, signing procedure for CLA file
  • Include the function tapas_get_current_version.m.
  • Implements download of example data from the server using tapas_download_example_data.
  • Now there is log file that list the versions of tapas, the download link and the hash of the file that is downloaded.
  • Use the an external file to do the md5 check sum. See external javamd5.
  • HUGE toolbox: hierarchical unsupervised generative embedding
    https://doi.org/10.1016/j.neuroimage.2018.06.073
  • rDCM toolbox: Regression dynamic causal modeling
    https://doi.org/10.1016/j.neuroimage.2017.02.090
    https://doi.org/10.1016/j.neuroimage.2018.05.058

Changed

  • README.md to include reference to CONTRIBUTING.md and explanation of CLA
  • Dropped 4 digits versioning for 3.
  • The version of tapas is now read from misc/log_tapas.txt. It is the first line of this file.
  • Updated the documentation of SEM.
  • Updated SEM to include hierarchical models for inference.
  • New version of the HGF toolbox (5.2.0). Details in tapas/HGF/README.md.
  • New version of the PhysIO toolbox (R2018.1). Details in tapas/PhysIO/CHANGELOG.md.
  • tapas_init.m displays a message to download the data in case the examples directory is not present.
  • Update MPDCM for supporting up to cuda 9.0 and openmp.

Removed

  • Deleted the gpo folder.

[2.7.4.1] 2018-01-24

Added

  • includes PhysIO R2017.3
    • new Readers: Human Connectome Project (HCP) and Siemens multiband (CMRR) WIP Physlog files
    • extended documentation and FAQ via Wiki

[2.7.3.2] 2018-01-19

Changed

  • README.md includes references to github, new support policy, links to toolbox documentation

Fixed

  • tapas_version typo
  • tapas_print_logo with T=Translational instead of TNU

[2.7.3.1] 2017-08-18

Changed

  • CHANGELOG.md includes value for hot fixes.

Fixed

  • Repair links to the wiki in the readme file.
  • Typos in SEM documentation.

[2.7.3.0] 2017-08-17

Added

  • Added condhalluc_obs and condhalluc_obs2 models.

Changed

  • Introduced kappa1 in all binary HGF models.

[2.7.2.0] 2017-08-17

Added

  • New PhysIO CHANGELOG.md specific file.

Changed

  • Specified in PhysIO/CHANGELOG.md.

[2.7.1.0] 2017-08-17

Added

  • Added a CHANGELOG.md file

Changed

  • Now the README.txt file is in markdown format.
  • The documentation is integrated with the wiki in github.