Commit 705944de authored by Lars Kasper's avatar Lars Kasper

updated doc files from public

parent c94a17f4
......@@ -4,42 +4,80 @@ RELEASE INFORMATION
Current Release
---------------
PhysIO_Toolbox_R2018.1.3
*Current version: PhysIO Toolbox Release R2019a, v7.1.0*
October 30, 2018
March 19, 2019
WIP Release Notes (R2018.2.0)
-----------------------------
*not released yet*
Unreleased
----------
### CHANGED
- put all functions in `code` into subfolders relating to different modules: `readin`, `sync`, `preproc`, `model`, `assess`, `utils` (gitlab-issue #58)
- updated deployment `tapas_physio_init` because of that
### Changed
- Toned down and replaced irrelevant peak height and missing cardiac pulse warnings (github issue #51)
Minor Release Notes (R2019a, v7.1.0)
------------------------------------
Bugfix Release Notes (R2018.1.3)
--------------------------------
### Added
- BIDS reader and example (Brain Imaging Data Structure,
http://bids.neuroimaging.io/bids_spec.pdf) for `*_physio.tsv[.gz]/.json` files
- Added BioPac txt-File read-in and example
- Template example with all physio-fields for matlab script and settings as in default SPM batch
- Started unit testing framework in folder `tests`
- example functions for findpeaks and BIDS readin
- reference data saved with example data in subfolder `TestReferenceResults`
- reference data reflects physio structure after running example scripts
with PhysIO R2019a
### Changed
- put all functions in `code` into subfolders relating to different modules:
`readin`, `sync`, `preproc`, `model`, `assess`, `utils` (gitlab-issue #58)
- updated deployment `tapas_physio_init` because of that
- updated figure names to reflect respective code module
- matlab-script examples now contain more comments
- fixed internal bug that prepended absolute paths to input logfiles in automatic example generation
- `tapas_physio_create_noise_rois_regressors` with more flexible ROI reslicing
options (speed-up) and uses `spm_erode` (no Matlab image processing toolbox needed),
thanks to a [contribution by Benoît Béranger](https://github.com/translationalneuromodeling/tapas/pull/34)
- introduced semantic version numbers for all previous releases, and changed
Release numbering to R<YEAR><LETTER> style
- extended documentation (FAQ, new read-in BIDS)
- several bugfixes (Sep 18 - Mar 19), see
[GitHub Issues](https://github.com/translationalneuromodeling/tapas/issues?q=label:physio)
### Removed
- `tapas_physio_findpeaks` now refers to current Matlab signal processing
toolbox implementation, instead of copy of older version
- some Matlab toolbox dependencies by custom simplified functions (e.g.,
`suptitle`)
Bugfix Release Notes (R2018.1.3, v7.0.3)
----------------------------------------
### Changed
- fixed bug for matching of Philips SCANPHYSLOG-files (Gitlab #62), if
physlogs were acquired on different days, but similar times
Bugfix Release Notes (R2018.1.2)
--------------------------------
### Changed
- fixed bug for 3D nifti array read-in in tapas_physio_create_noise_rois_regressors (github issue #24, gitlab #52)
Bugfix Release Notes (R2018.1.2, v7.0.2)
----------------------------------------
### Added
- BioPac txt-file reader (for single file, resp/cardiac/trigger data in different columns)
Bugfix Release Notes (R2018.1.1)
-------------------------------
### Changed
- fixed bug for 3D nifti array read-in in tapas_physio_create_noise_rois_regressors (github issue #24, gitlab #52)
Bugfix Release Notes (R2018.1.1, v7.0.1)
----------------------------------------
### Changed
- documentation.{html,pdf} export nicer with different FAQ numbering
Major Release Notes (R2018.1)
-----------------------------
Major Release Notes (R2018.1, v7.0.0)
-------------------------------------
### Added
- initialization function `tapas_physio_init()` to check Matlab paths, including SPM for batch processing
......@@ -53,8 +91,9 @@ Major Release Notes (R2018.1)
- Updated `README.md` to reflect changes to example download, new references
- Extended Wiki documentation, in particular examples and read-in formats
Minor Release Notes (R2017.3)
-----------------------------
Minor Release Notes (R2017.3, v6.3.0)
-------------------------------------
- Included references to external [ETH gitlab physio-doc repo and wiki](https://gitlab.ethz.ch/physio/physio-doc)
- New Human Connectome Project reader for preprocessed Siemens 3-column logfiles (`*Physio_log.txt`)
......@@ -67,8 +106,9 @@ Minor Release Notes (R2017.3)
- updated README about documentation, new support policy and [TAPAS on GitHub](https://translationalneuromodeling.github.io/tapas)
- extended FAQ
Minor Release Notes (R2017.2)
-----------------------------
Minor Release Notes (R2017.2, v6.2.0)
-------------------------------------
- Included Markdown-based documentation via Wiki (also CITATION, LICENSE, CHANGELOG.md)
- Included FAQ in Wiki
......@@ -76,8 +116,9 @@ Minor Release Notes (R2017.2)
- Bugfix and Typo correction
- Philips SCANPYHSLOG for their software release 5.1.7.
Minor Release Notes (R2017.1)
-----------------------------
Minor Release Notes (R2017.1, v6.1.0)
-------------------------------------
- Substantially improved Siemens interface, both for VB/VD and 3T/7T releases
- several bugfixes
......@@ -85,8 +126,9 @@ Minor Release Notes (R2017.1)
- New functionality tapas_physio_overlay_contrasts.m to display non-physio
contrasts automatically as well
Major Release Notes (r904 / R2016.1)
------------------------------------
Major Release Notes (r904 / R2016.1, v6.0.0)
--------------------------------------------
- Software version for accepted PhysIO Toolbox Paper: doi:10.1016/j.jneumeth.2016.10.019
- Tested and expanded versions of examples
......@@ -97,8 +139,9 @@ Major Release Notes (r904 / R2016.1)
- Improved Read-in capabilities (Siemens respiration data, BioPac .mat)
- Migration from svn (r904) to git (tnurepository) for version control
Major Release Notes (r835)
--------------------------
Major Release Notes (r835, v5.0.0)
----------------------------------
- Software version for Toolbox Paper submission
- Noise ROIs modeling
......@@ -109,8 +152,9 @@ Major Release Notes (r835)
- consistent module naming (scan_timing, preproc)
- Visualisation improvement (color schemes, legends)
Minor Release Notes (r666)
--------------------------
Minor Release Notes (r666, v4.1.0)
----------------------------------
- Compatibility tested for SPM12, small bugfixes Batch Dependencies
- Cleaner Batch Interface with grouped sub-menus (cfg_choice)
......@@ -121,16 +165,19 @@ Minor Release Notes (r666)
- All peak detections (cardiac/respiratory) now via auto_matched algorithm
- Adapt plots/saving for Matlab R2014b
Major Release Notes (r534)
--------------------------
Major Release Notes (r534, v4.0.0)
----------------------------------
- Read-in of Siemens plain text log files; new example dataset for Siemens
- Speed up and debugging of auto-detection method for noisy cardiac data => new method thresh.cardiac.initial_cpulse_select.method = ???auto_matched???
- Speed up and debugging of auto-detection method for noisy cardiac data => new
method thresh.cardiac.initial_cpulse_select.method = 'auto_matched'
- Error handling for temporary breathing belt failures (Eduardo Aponte, TNU Zurich)
- slice-wise regressors can be created by setting sqpar.onset_slice to a index vector of slices
Major Release Notes (r497)
--------------------------
Major Release Notes (r497, v3.0.0)
----------------------------------
- SPM matlabbatch GUI implemented (Call via Batch -> SPM -> Tools -> TAPAS PhysIO Toolbox)
- improved, automatic heartbeat detection for noisy ECG now standard for ECG and Pulse oximetry (courtesy of Steffen Bollmann)
......@@ -138,8 +185,9 @@ Major Release Notes (r497)
- job .m/.mat-files created for all example datasets
- bugfixes cpulse-initial-select method-handling (auto/manual/load)
Major Release Notes (r429)
--------------------------
Major Release Notes (r429, v2.0.0)
----------------------------------
- Cardiac and Respiratory response function regressors integrated in workflow (heart rate and breathing volume computation)
- Handling of Cardiac and Respiratory Logfiles only
......@@ -147,14 +195,16 @@ Major Release Notes (r429)
- read-in of custom log files, e.g. for BrainVoyager peripheral data
- more informative plots and commenting (especially in tapas_physio_new).
Minor Release Notes (r354)
--------------------------
Minor Release Notes (r354, v1.1.0)
----------------------------------
- computation of heart and breathing rate in Philips/PPU/main_PPU.m
- prefix of functions with tapas_*
Major Release Notes (r241)
--------------------------
Major Release Notes (r241, v1.0.0)
----------------------------------
- complete modularization of reading/preprocessing/regressor creation for peripheral physiological data
- manual selection of missed heartbeats in ECG/pulse oximetry (courtesy of Jakob Heinzle)
......@@ -164,4 +214,3 @@ Major Release Notes (r241)
- consistent function names (prefixed by "physio_")
NOTE: Your main_ECG/PPU.m etc. scripts from previous versions (<=r159) will not work with this one any more. Please adapt one of the example scripts for your needs (~5 min of work). The main benefit of this version is a complete new variable structure that is more sustainable and makes the code more readable.
TAPAS PhysIO Toolbox
====================
*Current version: 2018.1.3*
*Current version: Release 2019a, v7.1.0*
> Copyright (C) 2012-2018
> Copyright (C) 2012-2019
> Lars Kasper
> <kasper@biomed.ee.ethz.ch>
>
......
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