updates R2020a-v7.3.0

CHANGELOG.md

 RELEASE INFORMATION
-===============================
+===================
 
 Current Release
 ---------------
 
-*Current version: PhysIO Toolbox Release R2019b, v7.2.0*
+*Current version: PhysIO Toolbox Release R2020a, v7.3.0*
 
-August 20, 2019
+July 10th, 2020
+
+
+SCHEDULED Minor Release Notes (v7.4.0)
+----------------------------------------------
+
+### Added
+- Brain Imaging Data Structure (BIDS) export format (`.tsv.gz`, `.json`) to save raw physiological recordings after synchronization with scanner timing (internal gitlab issue #91)
+    - following current BIDS specification on [continuous physiological recordings](https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/06-physiological-and-other-continuous-recordings.html) and its [metadata]( https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#tabular-files)
+    - single tab-separated values file with columns for cardiac and respiratory recordings
+        - if sampling frequencies of the two differ, upsampling to higher frequency is performed
+
+### Changed
+
+### Fixed
+
+
+Minor Release Notes (R2020a, v7.3.0)
+------------------------------------
+
+### Added
+
+- Added descriptive names for the multiple regressors matrix.
+    - Closes GitLab issue #82.
+    - Now possible to straightforwardly inspect `physio.model.R` and the
+      contents of `physio.model.output_multiple_regressors` using
+      `physio.model.R_column_names`.
+    - Added `tapas_physio_guess_regressor_names()` to maintain backwards
+      compatibility.
+- New example datasets Siemens VB PPU3T with DICOM Sync (courtesy of Alexander Ritter, Jena, Germany)
+- More versatile control on figure visibility, saving and closing during `main` and `review` runs of PhysIO
+    - feature provided by Stephan Heunis, TU Eindhoven, The Netherlands (github issue #89)
+    - figures can now be plotted in the background without disturbing interactive Matlab sessions, and can be (more) selectively saved and closed during execution of `tapas_physio_review`
+    - more comprehensive support within `tapas_physio_main_create_regressors` to follow
+
+
+Bugfix Release Notes (v7.2.8)
+-----------------------------
+
+### Fixed
+- Bug(s) when checking SPM and PhysIO paths in `tapas_physio_init` under
+  certain particular Matlab path environment settings (Gitlab merge request !37)
+    - e.g., when add `physio-public/code` manually without subfolder
+    - or if spm existed as a folder name without being added to path
+
+
+Bugfix Release Notes (v7.2.7)
+-----------------------------
+
+### Changed
+- Reimplemented `tapas_physio_filter_respiratory.m`.
+    - Closes GitLab issue #98.
+    - Reduces the cut-off frequency of the high-pass filter, so as to behave
+      more like a detrending step. Previous value of 0.1 Hz could distort e.g.
+      sigh breaths, which can easily last upwards of 10 s.
+    - Reimplements the filters themselves, with a higher filter order, extra
+      padding, and a two step high-pass and low-pass procedure (i.e. rather
+      than band pass) to improve the overall stability.
+
+
+Bugfix Release Notes (v7.2.6)
+-----------------------------
+
+### Fixed
+- Meaningful error message for `auto_matched` peak detection, if time series is too short
+    - at least 20 peaks (and pulse templates) are required to create a pulse template
+    - this is now stated explicitly, if time series is too short
+    - reported by Joy Schuurmans Stekhoven, TNU, as gitlab issue #92
+
+
+Bugfix Release Notes (v7.2.5)
+-----------------------------
+
+### Fixed
+- Corrected documentation for ` preproc.cardiac.initial_cpulse_select.min` parameter
+    - threshold for peak relative to z-scored time series, *not* correlation
+    - reported by Sam Harrison, TNU, as gitlab issue #95
+
+
+Bugfix Release Notes (v7.2.4)
+-----------------------------
+
+### Fixed
+- Stop docked figure default throwing error with `-nodisplay`
+    - allows generating saved figure without a display, e.g., on remote server
+    - bugfix provided by Sam Harrison, TNU
+
+
+Bugfix Release Notes (v7.2.3)
+-----------------------------
+
+### Fixed
+- Bugfix manual peak selection (Github issue #85, Gitlab #90)
+    - did not work because of figure handling
+
+
+Bugfix Release Notes (v7.2.2)
+-----------------------------
+
+### Fixed
+- Bugfix Siemens VB (`*.resp, *.puls, *.ecg`)
+    - Synchronization to DICOM time stamp did not work for extended physiological recordings (not starting/ending with functional run) due to ignored absolute start time stamp
+    - reported by Alexander Ritter, Jena, Germany (Github issue #55, Gitlab #87)
+    - probably fixes Github issue #63 (Gitlab #86) as well
+
+
+Bugfix Release Notes (v7.2.1)
+-----------------------------
+
+### Changed
+- PhysIO: removed Matlab statistics toolbox dependency for PCA by SVD implementation (thanks to Benoît Beranger, [pull request 64](https://github.com/translationalneuromodeling/tapas/pull/64))
+    - new function `tapas_physio_pca` allows for switch between stats and native SVD implementation of PCA
+    - comes with unit tests checking equivalency
 
 
 Minor Release Notes (R2019b, v7.2.0)
@@ -44,6 +156,7 @@ Batch Editor and Matlab-only configuration scripts. Reference data provided in
 - visualization error for regressor orthogonalization (github issue #57), 
   when only `'RETROICOR'` set was chosen
 
+
 Minor Release Notes (R2019a, v7.1.0)
 ------------------------------------
 

README.md

 TAPAS PhysIO Toolbox 
 ====================
 
-*Current version: Release 2019b, v7.2.0*
+*Current version: Release 2020a, v7.3.0*
 
-> Copyright (C) 2012-2019  
+> Copyright (C) 2012-2020  
 > Lars Kasper  
 > <kasper@biomed.ee.ethz.ch>  
 >  
@@ -18,7 +18,9 @@ Download
 - Please download the latest stable versions of the PhysIO Toolbox on GitHub as part of the 
   [TAPAS software releases of the TNU](https://github.com/translationalneuromodeling/tapas/releases).
 - Older versions are available on the [TNU website](http://www.translationalneuromodeling.org/tapas).
-- The latest bugfixes can be found in the [GitHub Issue Forum](https://github.com/translationalneuromodeling/tapas/issues) or by request to the authors. 
+- The latest bugfixes can be found in the 
+  [development branch of TAPAS](https://github.com/translationalneuromodeling/tapas/tree/development) 
+  and are announced in the [GitHub Issue Forum](https://github.com/translationalneuromodeling/tapas/issues). 
 - Changes between all versions are documented in the 
   [CHANGELOG](https://gitlab.ethz.ch/physio/physio-doc/blob/master/CHANGELOG.md).
 
@@ -204,7 +206,7 @@ data from imperfect peripheral measures. Read-in of the following formats is
 currently supported (alphabetic order):
 
 - Biopac `.mat` and `.txt` -export
-- Brain Imaging Data Structure (BIDS)
+- Brain Imaging Data Structure ([BIDS](http://bids.neuroimaging.io/bids_spec.pdf) for `*_physio.tsv[.gz]/.json` files)
 - Custom logfiles: should contain one amplitude value per line, one logfile per 
   device. Sampling interval(s) are provided as a separate parameter to the toolbox.
 - General Electric
@@ -249,15 +251,14 @@ Contributors
 - Project Team: 
     - Steffen Bollmann, Centre for Advanced Imaging, University of Queensland, Australia
     - Saskia Bollmann, Centre for Advanced Imaging, University of Queensland, Australia
+    - Sam Harrison, TNU Zurich
 - Contributors (Code):
     - Eduardo Aponte, TNU Zurich
     - Tobias U. Hauser, FIL London, UK
-    - Sam Harrison, TNU Zurich
     - Jakob Heinzle, TNU Zurich
     - Chloe Hutton, FIL London, UK (previously)
     - Miriam Sebold, Charite Berlin, Germany
-    - External TAPAS contributors listed in its [Contributor License Agreement]
-    (https://github.com/translationalneuromodeling/tapas/blob/master/Contributor-License-Agreement.md)
+    - External TAPAS contributors are listed in the [Contributor License Agreement](https://github.com/translationalneuromodeling/tapas/blob/master/Contributor-License-Agreement.md)
 - Contributors (Examples):
     - listed in [EXAMPLES.md](https://gitlab.ethz.ch/physio/physio-doc/wikis/EXAMPLES)
 
@@ -268,7 +269,7 @@ Requirements
 - All specific software requirements and their versions are in a separate file
   in this folder, `requirements.txt`.
 - In brief:
-    - PhysIO needs Matlab to run, and some of its toolboxes.
+    - PhysIO needs Matlab to run, and a few of its toolboxes.
     - Some functionality requires SPM (GUI, nuisance regression, contrast reporting, 
       writing residual and SNR images).
 
@@ -304,6 +305,7 @@ Journal of Neuroscience Methods 276, 56–72. https://doi.org/10.1016/j.jneumeth
 The [FAQ](https://gitlab.ethz.ch/physio/physio-doc/wikis/FAQ#3-how-do-i-cite-physio) 
 contains a complete suggestion for a snippet in your methods section.
 
+
 ### Related Papers (Implemented noise correction algorithms and optimal parameter choices)
 
 The following sections list papers that 
@@ -317,21 +319,20 @@ paper. The list is by no means complete, and we are happy to add any relevant pa
 suggested to us. 
 
 #### RETROICOR 
-2. Glover, G.H., Li, T.Q. & Ress, D. Image‐based method for retrospective correction
+2. Glover, G.H., Li, T.Q. & Ress, D. Image�based method for retrospective correction
 of PhysIOlogical motion effects in fMRI: RETROICOR. Magn Reson Med 44, 162-7 (2000).
 
 3. Hutton, C. et al. The impact of Physiological noise correction on fMRI at 7 T.
-NeuroImage 57, 101‐112 (2011).
+NeuroImage 57, 101�112 (2011).
 
 4. Harvey, A.K. et al. Brainstem functional magnetic resonance imaging:
 Disentangling signal from PhysIOlogical noise. Journal of Magnetic Resonance
-Imaging 28, 1337‐1344 (2008).
+Imaging 28, 1337�1344 (2008).
 
 5. Bollmann, S., Puckett, A.M., Cunnington, R., Barth, M., 2018. 
 Serial correlations in single-subject fMRI with sub-second TR. 
 NeuroImage 166, 152–166. https://doi.org/10.1016/j.neuroimage.2017.10.043
 
-
 #### aCompCor / Noise ROIs 
 6. Behzadi, Y., Restom, K., Liau, J., Liu, T.T., 2007. A component based noise
 correction method (CompCor) for BOLD and perfusion based fMRI. NeuroImage 37,