Commit ba7bf037 authored by Lars Kasper's avatar Lars Kasper

updated doc files from public

parent f20b73e6
......@@ -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)
-----------------------------
......
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
......
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