Added CHANGELOG.md, CITATION, LICENSE and README.md from physio-public

CHANGELOG.md

+RELEASE INFORMATION
+===============================
+
+Current Release
+---------------
+
+PhysIO_Toolbox_R2017.2
+
+August 03, 2017
+
+Minor Release Notes (R2017.2)
+-----------------------------
+
+- Included Markdown-based documentation via Wiki (also CITATION, LICENSE, CHANGELOG.md)
+- Included FAQ in Wiki
+- Split git repositories into public, dev, examples, and added wiki, to disentangle development from deployed toolbox code and data
+- Bugfix and Typo correction
+- Philips SCANPYHSLOG for their software release 5.1.7.
+
+Minor Release Notes (R2017.1)
+-----------------------------
+
+- Substantially improved Siemens interface, both for VB/VD and 3T/7T releases
+    - several bugfixes
+    - based on extensive user feedback from Berlin and Brisbane
+- New functionality tapas_physio_overlay_contrasts.m to display non-physio 
+  contrasts automatically as well
+
+Major Release Notes (r904 / R2016.1)
+------------------------------------
+
+- Software version for accepted PhysIO Toolbox Paper: doi:10.1016/j.jneumeth.2016.10.019
+- Tested and expanded versions of examples
+- Improved stability by bugfixes and compatibility to Matlab R2016
+- Slice-wise regressor creation
+- Detection of constant physiological time series (detachment, clipping)
+- Refactoring of report_contrasts and compute_tsnr_gains as standalone functionality
+- Improved Read-in capabilities (Siemens respiration data, BioPac .mat)
+- Migration from svn (r904) to git (tnurepository) for version control
+
+Major Release Notes (r835)
+--------------------------
+
+- Software version for Toolbox Paper submission
+- Noise ROIs modeling
+- Extended motion models (24 parameters, Volterra expansion)
+- HRV/RVT models with optional multiple delay regressors
+- Report_contrasts with automatic contrast generation for all regressor groups
+- compute_tsnr_gains for individual physiological regressor groups
+- consistent module naming (scan_timing, preproc)
+- Visualisation improvement (color schemes, legends)
+
+Minor Release Notes (r666)
+--------------------------
+
+- Compatibility tested for SPM12, small bugfixes Batch Dependencies
+- Cleaner Batch Interface with grouped sub-menus (cfg_choice)
+- new model: 'none' to just read out physiological raw data and preprocess,
+  without noise modelling 
+- Philips: Scan-timing via gradient log now automatized (gradient_log_auto)
+- Siemens: Tics-Logfile read-in (proprietary, needs Siemens-agreement)
+- All peak detections (cardiac/respiratory) now via auto_matched algorithm
+- Adapt plots/saving for Matlab R2014b
+
+Major Release Notes (r534)
+--------------------------
+
+- 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???
+- 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)
+--------------------------
+
+- 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)
+- QuickStart-Manual and PhysIO-Background presentation expanded/updated
+- job .m/.mat-files created for all example datasets
+- bugfixes cpulse-initial-select method-handling (auto/manual/load)
+
+Major Release Notes (r429)
+--------------------------
+
+- Cardiac and Respiratory response function regressors integrated in workflow (heart rate and breathing volume computation)
+- Handling of Cardiac and Respiratory Logfiles only
+- expanded documentation (Quickstart.pdf and Handbook.pdf)
+- 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)
+--------------------------
+
+- computation of heart and breathing rate in Philips/PPU/main_PPU.m
+- prefix of functions with tapas_*
+
+Major Release Notes (r241)
+--------------------------
+
+- complete modularization of reading/preprocessing/regressor creation for peripheral physiological data
+- manual selection of missed heartbeats in ECG/pulse oximetry (courtesy of Jakob Heinzle)
+- support for logfiles from GE scanners (courtesy of Steffen Bollmann, KiSpi Zuerich)
+- improved detection of pulse oximetry peaks (courtesy of Steffen Bollmann)
+- improved documentation
+- 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.
+

CITATION

+Please cite this software as follows:
+
+Kasper, L., Bollmann, S., Diaconescu, A.O., Hutton, C., Heinzle, J., 
+Iglesias, S., Hauser, T.U., Sebold, M., Manjaly, Z.-M., Pruessmann, K.P., 
+Stephan, K.E., 2017. The PhysIO Toolbox for Modeling Physiological Noise 
+in fMRI Data. 
+Journal of Neuroscience Methods 276, 56–72. 
+doi:10.1016/j.jneumeth.2016.10.019
+
+For a detailed snippet to be included in the methods section of your manuscript, see the FAQ in the documentation.
\ No newline at end of file

README.md

+TAPAS PhysIO Toolbox Version 2017
+=================================
+
+> Copyright (C) 2012-2017 Lars Kasper <kasper@biomed.ee.ethz.ch>
+
+> Translational Neuromodeling Unit (TNU)
+
+> Institute for Biomedical Engineering
+
+> University of Zurich and ETH Zurich
+
+Copying
+-------
+
+The PhysIO Toolbox is free software: you can redistribute it and/or
+modify it under the terms of the GNU General Public License as
+published by the Free Software Foundation, either version 3 of the
+License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program (see the file COPYING).  If not, see
+<http://www.gnu.org/licenses/>.
+
+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, 
+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).
+
+Installation
+------------
+
+### Matlab ###
+- Unzip the TAPAS archive
+- Add tapas/physio/code to your matlab path
+
+### SPM ###
+- Certain functionality (Batch Editor GUI, pipeline dependencies, model assessment via F-contrasts) require the installation of SPM
+- Afterwards, the PhysIO Toolbox has to be registered as an SPM toolbox by copying the `physio/code` folder to `spm/toolbox/physio`
+
+
+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.
+
+
+Getting Help/Documentation
+--------------------------
+
+Several documentation files are provided with this toolbox. They have the extension .md (markdown), i.e. are plain text files, but can be conveniently viewed online as the github/gitlab Wiki.
+You can find them in `physio/wikidocs`.
+
+Alternatively, a pdf and html converted version of the following files is found in `physio/docs/documentation.pdf (or .html)`
+
+List of Documentation files:
+- README.md: this file, purpose, installation, getting started, pointer to more help
+- FAQ.md: Frequently asked questions (for users)
+- QUICKSTART.md: Example script and how to use on test data, Intro to Batch Editor GUI
+- 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
+- EXAMPLES.md: List and explanation of all examples
+- CHANGELOG.md: List of all toolbox versions and the respective release notes, i.e. major changes in functionality, bugfixes etc.
+
+
+Background
+----------
+
+The PhysIO Toolbox provides physiological noise correction for fMRI-data 
+from peripheral measures (ECG/pulse oximetry, breathing belt). It is 
+model-based, i.e. creates nuisance regressors from the physiological 
+monitoring that can enter a General Linear Model (GLM) analysis, e.g. 
+SPM8/12. Furthermore, for scanner vendor logfiles (PHILIPS, GE, Siemens), 
+it provides means to statistically assess peripheral data (e.g. heart rate variability) 
+and recover imperfect measures (e.g. distorted R-peaks of the ECG).
+
+Facts about physiological noise in fMRI:
+- Physiological noise can explain 20-60 % of variance in fMRI voxel time 
+  series (Birn2006, Hutton2011, Harvey2008)
+    - Physiological noise affects a lot of brain regions (s. figure, e.g. 
+      brainstem or OFC), especially next to CSF, arteries (Hutton2011). 
+    - If not accounted for, this is a key factor limiting sensitivity for effects of interest.
+- Physiological noise contributions increase with field strength; they 
+  become a particular concern at and above 3 Tesla (Kasper2009, Hutton2011).
+- In resting state fMRI, disregarding physiological noise leads to wrong 
+  connectivity results (Birn2006).
+
+Therefore, some kind of physiological noise correction is highly recommended for every statistical fMRI analysis.
+
+Model-based correction of physiological noise: 
+- Physiological noise can be decomposed into periodic time series following 
+  heart rate and breathing cycle.
+- The Fourier expansion of cardiac and respiratory phases was introduced as 
+  RETROICOR (RETROspective Image CORrection, Glover2000, 
+  see also Josephs1997).
+- These Fourier Terms can enter a General Linear Model (GLM) as nuisance 
+  regressors, analogous to movement parameters.
+- As the physiological noise regressors augment the GLM and explain 
+  variance in the time series, they increase sensitivity in all contrasts 
+  of interest.
+
+		
+Features of this Toolbox
+------------------------
+
+### Physiological Noise Modeling ###
+
+- Modeling physiological noise regressors from peripheral data 
+  (breathing belt, ECG, pulse oximeter) 
+    - State of the art RETROICOR cardiac and respiratory phase expansion
+    - Cardiac response function (Chang et al, 2009) and respiratory response 
+      function (Birn et al. 2006) modelling of heart-rate variability and 
+      respiratory volume  per time influence on physiological noise
+    - Flexible expansion orders to model different contributions of cardiac, 
+      respiratory and interaction terms (see Harvey2008, Hutton2011)
+- Data-driven noise regressors
+    - PCA extraction from nuisance ROIs (CSF, white matter), similar to aCompCor (Behzadi2007)
+
+### Automatization and Performance Assessment ###
+- Automatic creation of nuisance regressors, full integration into standard 
+  GLMs, tested for SPM8/12 ("multiple_regressors.mat")
+- Integration in SPM Batch Editor: GUI for parameter input, dependencies to integrate physiological noise correction in preprocessing pipeline
+- Performance Assessment: Automatic F-contrast and tSNR Map creation and display for groups of physiological noise regressors, using SPM GLM tools
+
+### Flexible Read-in ###
+
+The toolbox is dedicated to seamless integration into a clinical research s
+etting and therefore offers correction methods to recover physiological 
+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`)
+- 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
+- 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.
+
+
+
+Compatibility and Support
+-------------------------
+
+- Matlab Toolbox
+- Input: 
+    - Fully integrated to work with physiological logfiles for Philips MR systems (SCANPHYSLOG)
+    - tested for General Electric (GE) log-files
+    - implementation for Siemens log-files
+    - also: interface for 'Custom', i.e. general heart-beat time stamps 
+      & breathing volume time courses from other log formats
+- Output: 
+    - Nuisance regressors for mass-univariate statistical analysis with SPM5,8,12
+      or as text file for export to any other package
+    - raw and processed physiological logfile data
+- Part of the TAPAS Software Collection of the Translational Neuromodeling Unit (TNU) Zurich:long term support and ongoing development
+
+
+Contributors
+------------
+
+- Lead Programmer: 
+    - Lars Kasper, TNU & MR-Technology Group, IBT, University of Zurich & ETH Zurich
+- Project Team: 
+    - Steffen Bollmann, Centre for Advanced Imaging, University of Queensland, Australia
+    - Saskia Bollmann, Centre for Advanced Imaging, University of Queensland, Australia
+- Contributors:
+    - Eduardo Aponte, TNU Zurich
+    - Tobias U. Hauser, FIL London, UK
+    - Jakob Heinzle, TNU Zurich
+    - Chloe Hutton, FIL London, UK (previously)
+    - Miriam Sebold, Charite Berlin, Germany
+
+
+Contact
+-------
+Send bug reports and suggestions either to 
+1) our mailing list: tapas@sympa.ethz.ch, or
+2) as an issue on our TAPAS github account : https://github.com/translationalneuromodeling/tapas/issues
+
+
+References
+----------
+
+### Main Toolbox Reference ###
+1. Kasper, L., Bollmann, S., Diaconescu, A.O., Hutton, C., Heinzle, J., Iglesias, S., Hauser, T.U., Sebold, M., Manjaly, Z.-M., Pruessmann, K.P., Stephan, K.E., 2017. The PhysIO Toolbox for Modeling Physiological Noise in fMRI Data. Journal of Neuroscience Methods 276, 56–72. doi:10.1016/j.jneumeth.2016.10.019
+
+### Related Papers (Implemented noise correction algorithms) ###
+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).
+
+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).
+
+5. 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,
+90–101. doi:10.1016/j.neuroimage.2007.04.042
+    
+6. Birn, R.M., Smith, M.A., Jones, T.B., Bandettini, P.A., 2008. The respiration response
+function: The temporal dynamics of fMRI s ignal fluctuations related to changes in
+respiration. NeuroImage 40, 644–654. doi:10.1016/j.neuroimage.2007.11.059
+    
+7. Chang, C., Cunningham, J.P., Glover, G.H., 2009. Influence of heart rate on the
+BOLD signal: The cardiac response function. NeuroImage 44, 857–869.
+doi:10.1016/j.neuroimage.2008.09.029
+    
+8. Siegel, J.S., Power, J.D., Dubis, J.W., Vogel, A.C., Church, J.A., Schlaggar, B.L.,
+Petersen, S.E., 2014. Statistical improvements in functional magnetic resonance
+imaging analyses produced by censoring high-motion data points. Hum. Brain Mapp.
+35, 1981–1996. doi:10.1002/hbm.22307