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PhysIO Wiki Main Page
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=====================
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Several documentation files are provided with this toolbox, and are linked in this wiki. They have the extension .md (markdown), i.e. are plain text files, but can be conveniently viewed online as the github/gitlab Wiki.
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You can find them in `physio/docs`.
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List of Documentation files:
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* [x] [HOME](HOME): This page. Landing Page of Wiki. Navigation to all other files and this explanation
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* [x] [FAQ](FAQ): Frequently asked questions (for users)
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* [x] [QUICKSTART](QUICKSTART): Example script and how to use on test data, Intro to Batch Editor GUI
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* [x] [EXAMPLES](EXAMPLES): List and explanation of all examples
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* [ ] [MANUAL](MANUAL): Reference Manual (mostly for developers) listing all functions, and rationales of the toolbox, disecting its modular structure
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- [READIN](MANUAL_PART_READIN)
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* [x] [README](https://tnurepository.ethz.ch/physio/physio-public/blob/master/README.md): from main physio-public repository, similar info to this page
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* [x] [CHANGELOG](https://tnurepository.ethz.ch/physio/physio-public/blob/master/CHANGELOG.md): List of all toolbox versions and the respective release notes, i.e. major changes in functionality, bugfixes etc. |
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This Wiki contains the most up-to date User Guide to the PhysIO Toolbox. It is most conveniently viewed online with gitlab-formatting. Its content can also be retrieved offline after downloading the toolbox, in folder `physio/wikidocs` as
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- plain text `.md` markdown files
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- as single HTML and PDF file: `documentation.{html,pdf}`
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List of current Wiki files
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--------------------------
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- [HOME](HOME): This page. Landing Page of PhysIO Wiki. Navigation to all other files and this explanation.
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- [FAQ](FAQ): Frequently asked questions (for users) (also frequently updated!)
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- [QUICKSTART](QUICKSTART): Example script and how to use it on test data, Intro to Batch Editor GUI
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- [EXAMPLES](EXAMPLES): List and explanation of all examples available for download
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- [MANUAL](MANUAL): Detailed overview of the toolbox functionality, following its modular structure
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- *These pages are under construction, therefore also check the `physio/docs/QuickStart_PhysIO_Toolbox.pdf` for now, which contains a slightly out-dated, but in principle valid documentation of the toolbox structure*
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- [Read-In of Logfiles](MANUAL_PART_READIN)
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- **TODO** [Preprocessing Physiological Data](MANUAL_PART_PREPROC)
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- **TODO** [Physiological Noise Modeling](MANUAL_PART_MODEL)
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- **TODO** [Performance Assessment](MANUAL_PART_ASSESS)
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- **TODO** [Technical Documentation](MANUAL_PART_DEVELOPERS) For developers, list of all functions, see header of `.m` files for now
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Other sources of Documentation
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------------------------------
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Documentation for this toolbox is also provided in the following forms:
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1. Overview and guide to further documentation: README.md and CHANGELOG.md
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- [README.md](https://gitlab.ethz.ch/physio/physio-doc/blob/master/README.md): purpose, installation, getting started, pointer to more help
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- [CHANGELOG.md](https://gitlab.ethz.ch/physio/physio-doc/blob/master/CHANGELOG.md): List of all toolbox versions and the respective release notes,
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i.e. major changes in functionality, bugfixes etc.
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2. Within SPM: All toolbox parameters and their settings are explained in the
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Help Window of the SPM Batch Editor
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3. Within Matlab: Extensive header at the start of each `tapas_physio_*` function and commenting
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- accessible via `help` and `doc` commands from Matlab command line
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- starting point for all parameters (comments within file): `edit tapas_physio_new`
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- also useful for developers (technical documentation)
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4. Scientific Documentation: Our [paper](https://doi.org/10.1016/j.jneumeth.2016.10.019) on the PhysIO Toolbox explains both the scientific background on physiological noise modeling, as well as the modular structure of the toolbox as comprehensivce yet succinct as we (and the reviewers) could. |
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