Changelog

TAPAS toolbox

[6.0.1] 2022-05-17

Fixed

HGF: Version 7.1: Fixed bug in tapas_simModel.

[6.0.0] 2022-04-08

For this major release of TAPAS, we have decided to move currently unmaintained toolboxes to a dedicated TAPAS Legacy repository.

Added

PhysIO Version 8.1.0: BIDS Read-in for separate cardiac/respiratory trace files (e.g., due to different sampling frequencies)
- Compatibility of whole code base with Matlab compiler in order to run spm_make_standalone.

Changed

Moved MICP,VBLM,h2gf and mpdcm toolboxes to TAPAS Legacy repository.
HGF Version 7.0: Numerical stability improvements, various enhancements
rDCM Version 1.4: The update includes a new function that can convert the rDCM output to the SPM format. Additionally, some small bug fixes and changes have been made. No changes to the main functionality of rDCM have been made.

Fixed

[5.1.2] 2021-09-06

Fixed

TOOLS: Fixed a bug in the computation of WAIC (function tapas_waic.m). Added new function to compute log-exp_sum (function tapas_logsumexp.m).

[5.1.1] 2021-06-22

Fixed

Added references to TAPAS paper (in collection and toolboxes)
HGF: Version 6.3: Minor improvements
rDCM: Version v1.3: Corrected bug in construction of the full posterior covariance matrix (from the region-wise posterior covariance matrices)

[5.1.0] 2021-04-23

Added

HUGE: Added Monte Carlo based inference (https://doi.org/10.1002/hbm.25431)

Fixed

Fixed typos

[5.0.0] 2021-03-15

Added

genbed: Python package for Generative Embedding
UniQC: unified neuroimaging quality control (beta release)
task/BLT: breathing learning task
PhysIO: Release 2021a-v8.0; new method for estimating respiratory volume per unit time (RVT) via the Hilbert transform (Harrison et al., NeuroImage 230 (2021))
- also: robust respiratory preprocessing: optional de-spiking (median filter) and window-padded detrending

[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
- For details on the bug, its impact and fix, see our specific Release Info on RVT/HRV Bugfix

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.