rel 3.3.0 (#102)

* - HUGE: rename readme files

* - HUGE: added prior generating function, renamed readme files, reorganized default parameter script

* - HUGE: moved default settings to inversion function

* - HUGE: improved reproducibility, added more comments

* Update CHANGELOG.md; CLA/CONTRIBUTING.md mentioned

* Update CHANGELOG.md; prospective date of release added

* added Contributing and CLA from tapas-meeting.wiki

* updated CLA file name

* - HUGE: added simplified interface; published demo script as html; added example for empirical Bayes; added function for generating example data; added function for basic visualization of results

* Implemented automatic download of the data. Not tested.

* Updated the readme file.

* Small error in documentation.

* Removed empty gpo folder from TAPAS

* rDCM Toolbox: Initial release

* Enabled the automatic compiling of mex files and added a new function for visualization of rDCM results

* Adapted the ReadMe.md file to acknowledge the use of SPM functions

* - HUGE: fixed bug when compiling from different directory; fixed bug when calling inversion function without optional parameters; updated readme file

* Updated changelog.

* Removed the mex-files, will be generated for each user automatically from the script

* Small modification to visualization and added a Manual

* Update README.md

* Polished the option and output structure; also adopted the Manual.pdf to account for these changes

* Additional polishing of code and Manual

* Changed the Header of all scripts and did some slight restructuring of tapas_rdcm_estimate

* - HUGE: added RNG seed as optional input; fixed typo

* Implement suggestions by YY for improvement of rDCM

* Small change to visualization function

* Adjusted the headers of the functions

* - HUGE: added suggestion for changelog entry for HUGE

* Corrected fileseparator in tapas_rdcm_tutorial.m

* Checkouted the latest version of dora from Eduardo's fork.

* Updated CHANGELOG.md

* Revert "Merge branch 'develop'"

This reverts commit 2d944ed, reversing
changes made to 72ff6f5.

* - HUGE: removed dependency on Matlab statistics toolbox

* Adapted the style of Changelog to style in TAPAS

* Added rDCM entry to CHANGELOG

* Made restrictInputs an explicit option to set

* Recovered deleted files.

* Improved visualization function

* Merge development into rDCM branch

* Added rDCM to the CHANGELOG of TAPAS

* HGF Toolbox version 5.2.0

* Updated changelog.

* Refactor dora to seria and delete SERI.

* Deleted old mex files not used anymore.

* Refactor mex files. C and matlab compiling.

* Refactoring the python code.

* Repaired bug in prosa.

* Updated cython code.

* Rename dora to seria.

* Deleted files that are no superficial.

* Deleted seri files from matlab.

* Working example of inversions.

* Working on improving examples.

* Working flat model.

* Working hier. mixed model.

* Started working on the implementation.

* Updated readme seria.

* Working on the documentation.

* Improved documentation.

* Small change.

* Documentation seria.

* Improved the documentation and some function.

* Update docs SERIA.

* Update documentation.

* Updated SERIA documentation.

* SERIA updated documentation.

* Update Documentation.

* Small change.

* Improved docs.

* small change.

* Update seri docs.

* small change.

* Indexed seria.

* SERIA docs.

* - Release PhysIO Toolbox R2018.1

* - added PhysIO to changelog

* Update CHANGELOG.md; line break and proper doi links everywhere

* PhysIO Release R2018.1.1 (bugfix, better documentation export)

* Implemented the reparametrization.

* Added functions to reparametrize.

* Updated implementation and remove small errors.

* Updated misc and log file.

* Refactor prosa and seria multi.

* Refactor the mex functions.

* Miscelaneous tools.

* Improved the reparametrization of parameters.

* Small correction.

* Added checking for parameters.

* Updated version of the code.

* Added figures and updated docs.

* Updated to the mpdcm toolbox.

* Updated changelog.

* Updated change log.

* Update README.md; https for github links

* Update README.md; compatibility with Markdown format

* Update README.md; html link to tutorial

* Update README.txt; sync to .md...are both needed?

* Update README.md; link to Manual and some markdown conformities. Removed mentioning of old TAPAS version, since it does not contain rDCM

* Update README.md; adjusted to the one in the main folder...do we need both?

* Delete README.txt; duplicate of .md file

* Delete README.md

* Put ti and linear in tools directory.

* Revert "Delete README.txt; duplicate of .md file"

This reverts commit daa7882

* Fix PhysIO wiki submodule file

.gitmodules has to be in the top level of the repository.

* included PhysIO R2018.1.2 bugfix noise rois (github issue #24) and biopac.txt reader

* - updated CHANGELOG.md with PhysIO R2018.1.2

* Updated README and misc.

* Update Contributor-License-Agreement.md

* final noise ROIs are written in a volume, and displayed through spm_orthviews
noise ROIs erosion is now 3D and using spm_erode

* Update Contributor-License-Agreement.md

reformatted table for better display

* added name and affiliation in Contributor-License-Agreement.md

* noiseROIs after processing are now displayed only when verbose>=2

* some more help in the GUI about the expected geometry of the maks/tissue probability

* noiseROI GUI : added a Yes/No switch to force Coregister:Estimage&Reslice
yes : always do it
no : compare geometry and decide to skip coreg or still perform it

* included physio-public/merge-tapas-development branch

* removed examples/ from .gitignore

* Implemented automatic ploting of posteriors.

* Added an example for flat model.

* Updated changelog.

* Solved a bug with invgamma.

* Added a figure with an example of the results.

* Small bug in plotting.

* PhysIO: bugfix BIDS .gz, file still open when trying to delete temp folder for unzipping

* hotfix github issue #38; restricting valid searchPositions for findpeaks_template_correlation for early peaks

* PhysIO bugfix github issue #37, first scan event and first cardiac pulse coinciding

* PhysIO: bugfix #43, prepending c/r time courses, if recording started after scan, irrespective of specified logfile names, as long as c/r time courses exist

* PhysIO: fixes BIDS bugs issue #43, #45

* WIP PhysIO R2018.2.0 update, removed suptitle dependence and added BIDS examples and default template example

* PhysIO bugfix suptitle; new findpeaks wrapper

* PhysIO bugfix issue #46, skipped tics samples in logfiles

* Start implementing summaries for seria.

* Almost complete summaries of the parameters.

* Implemented the summaries.

* Implemented summaries for prosa and nice displaying.

* Typos from the readme file removed.

* Small typo.

* Typo in readme file.

* Added a youtube video.

* HGF Toolbox Version 5.2.2

* New Release of rDCM

* Check for empty inputs

* Added comment on rDCM to the TAPAS CHANGELOG.md

* - HUGE: minor bugfix

* Improved the documentation.

* Added change log.

* Corrected small error in function header

* Added get revision info.

* HGF Toolbox Version 5.3.0

* bugfix in HGF softmax_binary_sim

according to issue #48; to establish consistency with softmax_binary by also taking reward values from the input into account

* Improved the changelog.

* Updated CHANGELOG to reflect hgf 5.3.

* Improved documentation and removed some warnings.

* Improved documentation and new video.

* Added table for summary stats to docs.

* Added code for the summaries of prosa.

* Updated requirements.

* Updated the python code.

* Added wrappers for the generation of summaries.

* Updated the summaries to use c code.

* Summaries are done in c.

* Updated data and data file.

* Small typo.

* Improved docs of download_example_data.

* Update the name of the examples and scripts.

* Improved documentation.

* Updated the examples download.

* PhysIO R2019a-v7.1.0 release: updated documentation and examples; introduced new semantic versioning; modularization of functions reflected in figure names; see CHANGELOG.md for full details

* PhysIO R2019-v7.1.0 release: added units test BIDS reader and findpeaks

* Included info on PhysIO-R2019a-v7.1.0. Note that the CHANGELOG infos from TAPAS 3.0.1 and 3.0.0 seem to be mixed up with the unreleased (3.1) here

* Updated the CHANGELOG.md

* README with external contributors and mentioning serial correlation cleanup by PhysIO, removing misleading warnings for cardiac phase and gradient gain correction

* Bugfix tapas_physio_init discovered by Dario; was not working, because utils functions used in init were not on path

* commits from physio-public tag R2019b-v7.2.0

* Added PhysIO R2019b change summary to CHANGELOG.md

* - huge: rewrote HUGE as Matlab class

* - references for user manual

* - tapas naming scheme

* Update the version number and added references.

* Removed .DS_Store and updated example hash.

* Updated change log.

* noise ROI : PCA is now performed with MATLB built-in SVD function, instead of PCA function in "stats" toolbox

noiseROI : keep variables name coherent

* new function tapas_physio_pca to perform PCA with new SVD method or old STATS toolbox method
added also tapas_physio_pca_test to test if both methods give the same result

* fix : tapas_physio_pca_test uses now randn() for noramlly distributed numbers instead of integer numbers
fix : dimension of the output from tapas_physio_pca

* bugfix in the tests for PCA : use randn instead of randi
tests for PCA : added verification for nVoxels <= NVolumes

* typo

* - added info to CHANGELOG.md of TAPAS about PhysIO changes

* PhysIO: updated its internal version and changelog

* PhysIO: updated README version

* HUGE: bugfix x-tick labels

* Update CHANGELOG.md with changes to HUGE

* Improved the setup script for tapas.

* included PhysIO v7.2.2 bugfix Siemens VB sync to DICOM, using PPU3T and added this new example

* PhysIO v7.2.3 (bugfix manual peak selection, github issue #85)

* allow figures to be showed/saved/closed upon review

* tweak figure show/save/close code

* tweaks

* updates figure display/save/close functionality

* make isfile/exists switch dependent on Matlab ver

 'isfile' is clearer than 'exist', because checks for correct absolute/relative path, not existence anywhere on Matlab path, but only available in Matlab version >= R2017b

* PhysIO v7.2.4, bugfix for docked figures -nodisplay now (Sam Harrison

* release 3.3.0 (#100)

* Added hierarchical inference part.

* Documented and simplifid output.

* Deleted some typos.

* Solved a bug in SERIA introduced by new feature.

* Added mcmcdiag and diagnostics for h2gf.

* Fixed typos

* Started editing h2gf/README.md

* Now the expected states are stored in the output structure.

* Now the correlation matrix is only of the valid parameters.

* Now return the pseudo model evidence.

* Updated the REDME file..

* Updates to h2gf_example

* Plot function provided by Sandra

* Further updates to h2gf_example

- Vary omega2 instead of kappa2
- Various other improvements

* Replaced tapas_h2gf_example.m with h2gf_demo.mlx

* Updates to h2gf_demo

* Improved h2gf_summary

- All plotting and diagnostics function from the HGF Toolbox now work
- Plotting function provided by Sandra now obsolete and removed
- Adapted h2gf_demo
- h2gf_demo now also in source (.m) not just binary (.mlx)

* Minor changes.

* Added nchain input, improved docs, simplified input.

* h2gf for srl2 data from the PRSSI EEG project, different Nr of iterations, config files and eta values can be specified

* script to run h2gf_demo_link_figures for all hgf configurations and h2gf estimations

* x-axes adjusted

* demo srl2

* Issue: conflict between pars.nchains and pars.T

- When pars.nchains = 8 and pars.T left on default, this produces an
  error
- Reproducible by running h2gf_demo.mlx

* Solved bug with chains.

* save as well as png

* replaced by h2gf_demo_srl2_link_figures

* h2gf estimations for long version of SSL task

* save figure as png with higher resolution

* jobs submitted to euler

* loops modified

* scripts to plot individual trajectories

* euler jobs added to plot individual trajectories

* ze prior mu set to log(48) instead of 0.5)

* shuffle position of subject's data on data structure included

* paths added

* script with paths to data structure for short srl task

* plot histogram of samples

* Store the rng seed into the output.

* Documented the rng_seed option.

* RW implementation

* run simulations with srl1 inputs

* variance disabled

* paths adapted

* timing adapted

* access to data structure adapted

* use tapas_hgf_binary_plotTraj instead of tapas_h2gf_binary_plotTraj; data structure has been adapted to run with the HGF plotting function

* plot boxplot as well for zeta

* plot boxplots for RW

* plot trajectories as well for RW

* jobs for rw added

* run hgfv5.2 for srl1 and srl2

* correction

* figure title: iterations replaced by samples

* plotting part updated

* plot mean and ste for h2gf and hgf results

* updates

* Updated demo to increase length of sampling chains

* Cleaned up demo

* Deal with invalid trials.

* Improved handling of the errors.

* Demo with simulations on a grid and varying noise

* Implemented WBIC, WAIC, parameters of second level and solved bug.

* Removed the mlx file and updated the h2gf demo.

* Added utilities for delta plots.

* Small changes.

* New run of demo (including est struct)

* Commented and change the implementation of the early unit.

* Changes during discussion with Eduardo

- alpha and beta Gaussian-gamma hyperparameter definitions adapted
- Improved comments

* Improved the general structure of SEM.

* Further comments and changes while discussing

* Updated small bug in preapre priors and improved prior.

* Improved the documentation.

* Renamed correctly a function.

* Improved documentation and adapted demo.

* Empirical delta plot analysis.

* Solved an apparent bug in the code.

* Improved the structure displaying posterior (SEM)

* Better posterior summaries (SEM).

* Added function for WAIC.

* Now compute the WAIC as part of the summary.

* Improved posterior summaries (SEM).

* Improved the prosa model.

* Updated the setup file.

* Debugging version for summary stats.

* Experimental.

* Trying to solve numerical bug.

* Founda a really serious bug with the python parameters.

* Small change.

* Simplified a bit prosa.

* Standarized the implementation of prosa.

* Seria model compatible with python3.

* Small change.

* Python3 compatible.

* Found weird bugs.

* Version 3.3.0 with new SERIA.

* placeholder for release date

* HGF Toolbox v5.3.3

* Ensure parameter covariance in h2gf is positive semi-definite

* Streamlined h2gf setup loops, removed unused files

* Continued streamlining and removing unused files and functions

* Removed all instances of 'initilize', replaced with 'initialize'

* In h2gf: removed all 'initilize', replaced with 'initialize'

* HGF Toolbox v5.3.5

* HGF Toolbox v5.3.6

* PhysIO Release R2020a-v7.3.0

* HGF Toolbox v6.0

* - preparing current release

* - preparing release

Co-authored-by: Eduardo Aponte <aponteeduardo@gmail.coml>
Co-authored-by: Christoph Mathys <chmathys@ethz.ch>
Co-authored-by: siglesias <iglesias@biomed.ee.ethz.ch>
Co-authored-by: Christoph Mathys <mathys@biomed.ee.ethz.ch>
Co-authored-by: Eduardo Aponte <aeduardo@biomed.ee.ethz.ch>
Co-authored-by: Lars Kasper <lars.kasper@rmp.uhn.ca>

Co-authored-by: Lars Kasper <kasper@biomed.ee.ethz.ch>
Co-authored-by: Eduardo Aponte <aponteeduardo@gmail.coml>
Co-authored-by: Stefan Frässle <stefanf@biomed.ee.ethz.ch>
Co-authored-by: Eduardo Aponte <aponte@biomed.ee.ethz.ch>
Co-authored-by: Christoph Mathys <chmathys@gmail.com>
Co-authored-by: Eduardo Aponte <aeduardo@biomed.ee.ethz.ch>
Co-authored-by: Sam Harrison <harrison@biomed.ee.ethz.ch>
Co-authored-by: DanielHoffmannAyala <36452816+DanielHoffmannAyala@users.noreply.github.com>
Co-authored-by: Benoît Béranger <benoit.beranger@icm-institute.org>
Co-authored-by: Christoph Mathys <chmathys@ethz.ch>
Co-authored-by: nbuergi <48059534+nbuergi@users.noreply.github.com>
Co-authored-by: jsheunis <jsheunis@gmail.com>
Co-authored-by: siglesias <iglesias@biomed.ee.ethz.ch>
Co-authored-by: Christoph Mathys <mathys@biomed.ee.ethz.ch>
Co-authored-by: Lars Kasper <lars.kasper@rmp.uhn.ca>

Contributor-License-Agreement.md

@@ -17,6 +17,7 @@ Eduardo Aponte           | TNU, University of Zurich          | Zurich    | CH
 Daniel Hoffmann Ayala    | Technical University               | Munich    | D       | DanielHoffmannAyala
 Benoît Béranger          | CENIR, ICM                         | Paris     | FR      | benoitberanger
 Stephan Heunis           | Eindhoven University of Technology | Eindhoven | NL      | jsheunis
+Niklas Bürgi             | SNS, University of Zurich          | Zurich    | CH      | nbuergi
 **- Add Entry here -**   | **- Add Entry here -**             | **Add**   | **Add** | **Add**                    
 
 (hereinafter referred to as "Contributor")