updated doc files from public

CHANGELOG.md

@@ -4,9 +4,23 @@ RELEASE INFORMATION
 Current Release
 ---------------
 
-PhysIO_Toolbox_R2017.2
+PhysIO_Toolbox_R2017.3
 
-August 03, 2017
+January 24, 2018
+
+Minor Release Notes (R2017.3)
+-----------------------------
+
+- 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`)
+- Updated Siemens Reader for Multiband patches(CMRR), versions EJA_1
+    - including multi-echo data (4,5 columns)
+    - multi-channel ECG data
+    - significant speed up of read-in
+    - generalized framework for later changes to format
+    - interpolation of different sampling rates RESP/CARDIAC
+- updated README about documentation, new support policy and [TAPAS on GitHub](https://translationalneuromodeling.github.io/tapas)
+- extended FAQ
 
 Minor Release Notes (R2017.2)
 -----------------------------

README.md

-TAPAS PhysIO Toolbox Version 2017
-=================================
+TAPAS PhysIO Toolbox 
+====================
 
-> Copyright (C) 2012-2017 Lars Kasper <kasper@biomed.ee.ethz.ch>
+*Current version: 2017.3*
+
+> Copyright (C) 2012-2018 Lars Kasper <kasper@biomed.ee.ethz.ch>
 
 > Translational Neuromodeling Unit (TNU)
 
@@ -13,26 +15,41 @@ TAPAS PhysIO Toolbox Version 2017
 Download
 --------
 
-Please download the latest stable version of the PhysIO Toolbox with the 
-[TAPAS software collection of the TNU](www.translationalneuromodeling.org/tapas). 
-Older or newer, bug-fixed versions are available on request to the authors. 
-
-Changes between all versions are documented in the 
-[CHANGELOG](https://gitlab.ethz.ch/physio/physio-doc/blob/master/CHANGELOG.md)
+- 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. 
+- Changes between all versions are documented in the 
+  [CHANGELOG](https://gitlab.ethz.ch/physio/physio-doc/blob/master/CHANGELOG.md).
 
 
 Purpose
 -------
 
-The PhysIO Toolbox provides model-based physiological noise correction of 
-fMRI data using peripheral measures of respiration and cardiac pulsation. 
-It incorporates noise models of cardiac/respiratory phase (RETROICOR, 
+The general purpose of this Matlab toolbox is the model-based physiological noise 
+correction of fMRI data using peripheral measures of respiration and cardiac 
+pulsation. It incorporates noise models of cardiac/respiratory phase (RETROICOR, 
 Glover et al. 2000), as well as heart rate variability and respiratory 
 volume per time (cardiac response function, Chang et. al, 2009, respiratory 
-response function, Birn et al. 2006). The toolbox is usable via the SPM 
-batch editor, performs automatic pre-processing of noisy peripheral data 
-and outputs nuisance regressor files directly suitable for SPM 
-(multiple_regressors.txt).
+response function, Birn et al. 2006), and extended motion models. 
+While the toolbox is particularly well integrated with SPM via the Batch Editor GUI, its 
+simple output nuisance regressor text files can be incorporated into any major 
+neuroimaging analysis package.
+
+Core design goals for the toolbox were: *flexibility*, *robustness*, and *quality assurance* 
+to enable physiological noise correction for large-scale and multi-center studies. 
+
+Some highlights:
+1. Robust automatic preprocessing of peripheral recordings via iterative peak 
+   detection, validated in noisy data and patients.
+2. Flexible support of peripheral data formats (Siemens, Philips, HCP, GE, Biopac, ...) 
+   and noise models (RETROICOR, RVHRCOR).
+3. Fully automated noise correction and performance assessment for group studies.
+4. Integration in fMRI pre-processing pipelines as SPM Toolbox (Batch Editor GUI).
+
+The accompanying technical paper about the toolbox concept and methodology 
+can be found at: https://doi.org/10.1016/j.jneumeth.2016.10.019
+
 
 Installation
 ------------
@@ -49,8 +66,9 @@ Installation
 Getting Started
 ---------------
 
-Run `example_main_ECG3T.m` in subdirectory `Philips/ECG3T` of the toolbox example repository `physio-examples`.
-See subdirectory `physio/docs` and next section of this document.
+1. Download the toolbox example repository `physio-examples` from our [website](https://www.tnu.ethz.ch/en/software/tapas/data.html)
+2. Run `example_main_ECG3T.m` in subdirectory `Philips/ECG3T`
+3. See subdirectory `physio/docs` and the next two section of this document for help.
 
 
 Contact/Support
@@ -73,22 +91,24 @@ pointers and templates. Before you contact us, please try the following:
 Documentation
 -------------
 
-Several documentation files are provided with this toolbox. You can find them 
-- in `physio/wikidocs` (plain text .md markdown files) or 
-- as a pdf and html converted version in `physio/docs/documentation.pdf (or .html)`
-- online at http://gitlab.ethz.ch/physio/physio-doc.
-
-List of included Documentation files:
-- README.md: this file, purpose, installation, getting started, pointer to more help
-- Wiki
-    - FAQ.md: Frequently asked questions (for users)
-    - QUICKSTART.md: Example script and how to use on test data, Intro to Batch Editor GUI
-    - EXAMPLES.md: List and explanation of all examples
-    - MANUAL.md: Reference Manual (mostly for developers) listing all functions, and rationales of the toolbox, disecting its modular structure
-        - not provided yet; see the old version in `physio/docs/QuickStart_PhysIO_Toolbox.pdf` for source code documentation
-    - HOME.md: Landing Page of Wiki. Navigation to all other files and this explanation
-- CHANGELOG.md: List of all toolbox versions and the respective release notes, i.e. major changes in functionality, bugfixes etc.
-
+Documentation for this toolbox is provided in the following forms
+
+1. Overview and guide to further documentation: README.md and CHANGELOG.md
+    - [README.md](README.md): this file, purpose, installation, getting started, pointer to more help
+    - [CHANGELOG.md](CHANGELOG.md): List of all toolbox versions and the respective release notes, 
+      i.e. major changes in functionality, bugfixes etc.
+2. User Guide: The markdown-based [GitLab Wiki](https://gitlab.ethz.ch/physio/physio-doc/wikis/home), including an FAQ
+    - online (and frequently updated) at http://gitlab.ethz.ch/physio/physio-doc/wikis/home.
+    - offline (with stables releases) as part of the toolbox in folder `physio/wikidocs`: 
+        - plain text `.md` markdown files
+        - as single HTML and PDF  file: `documentation.{html,pdf}`
+3. Within SPM: All toolbox parameters and their settings are explained in the 
+   Help Window of the SPM Batch Editor
+4. Within Matlab: Extensive header at the start of each `tapas_physio_*` function and commenting
+    - accessible via `help` and `doc` commands from Matlab command line
+    - starting point for all parameters (comments within file): `edit tapas_physio_new` 
+    - also useful for developers (technical documentation)
+    
 
 Background
 ----------
@@ -157,8 +177,9 @@ data from imperfect peripheral measures.
 
 - General Electric
 - Philips SCANPHYSLOG files (all versions from release 2.6 to 5.3)
-- Siemens VB (files `.ecg`, `.resp`, `.puls`
-- Siemens VD (files (`*_ECG.log`, `*_RESP.log`, `*_PULS.log`)
+- Siemens VB (files `.ecg`, `.resp`, `.puls`)
+- Siemens VD (files `*_ECG.log`, `*_RESP.log`, `*_PULS.log`)
+- Siemens Human Connectome Project (preprocessed files `*Physio_log.txt`)
 - Biopac .mat-export
     - assuming the following variables (as columns): `data`, `isi`, `isi_units`, `labels`, `start_sample`, `units`
     - See `tapas_physio_read_physlogfiles_biopac_mat.m` for details