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phys2bids

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phys2bids is a python3 library meant to format physiological files in BIDS. At the moment, it supports:

• .acq, .txt, and .mat AcqKnowledge format (BIOPAC)
• .txt and .mat LabChart format (ADInstruments)
• .smr Spike2 format (CED)
• GE MRI file format (GE)

We want to offer as much support as possible! If you have a file format that you want to see added, open an issue about it!

If you use phys2bids in your work, please support it by citing the zenodo DOI of the version you used. You can find the latest version here

We also support gathering all relevant citations via DueCredit.

Read the latest documentation for more information on phys2bids!

Shortcuts:

• Requirements
• Installation
• Usage
• How to use phys2bids
• Contributing to phys2bids
• Developer installation
• Contributor guide
• Code of Conduct
• Developer calls calendar

Tested OSs

All versions until 2.6.2 were tested on Linux and Windows. However, starting from version 2.7 onwards we had to drop Windows testing. The reason for this is related to the cost of running such tests: for each Windows test, we can run up to 8 tests on Linux instead. Partial Windows testing might be reintroduced in future releases.

Hence, while we cannot ensure that phys2bids will run on Windows or MacOS/iOS, we don't see any reason it shouldn't. Besides, it will run on Linux Subsystems.

We apologise for any discomfort.

<!-- ## Hacktoberfest Hacktoberfest participants, welcome! We have some issues for you [here](https://github.com/physiopy/phys2bids/issues?q=is%3Aissue+is%3Aopen+label%3Ahacktoberfest)! However, feel free to tackle any issue you'd like. Depending on the issue and extent of contribution, Hacktoberfest related PRs might not count toward being listed as contributors and authors (unless there is the specific interest). You can ask about it in the issue itself! Feel free to ask help to the contributors through issues or contactign directly Stefano, happy coding and (hopefully) enjoy your tee (or tree)!-->

Contributors ✨

We're always looking for code contributors, but any suggestion/bug report is welcome! Feel free to open issues!

This project follows the all-contributors specification. Contributions of any kind welcome!

Thanks goes to these wonderful people (emoji key):

<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section --> <!-- prettier-ignore-start --> <!-- markdownlint-disable --> <table> <tbody> <tr> <td align="center" valign="top" width="25%"><a href="https://github.com/danalclop"><img src="https://avatars0.githubusercontent.com/u/38854309?v=4?s=100" width="100px;" alt="Daniel Alcalá"/><br />_{<b>Daniel Alcalá</b>}</a><br /><a href="#design-danalclop" title="Design">🎨</a></td> <td align="center" valign="top" width="25%"><a href="https://github.com/AyyagariA"><img src="https://avatars1.githubusercontent.com/u/50453337?v=4?s=100" width="100px;" alt="Apoorva Ayyagari"/><br />_{<b>Apoorva Ayyagari</b>}</a><br /><a href="#content-AyyagariA" title="Content">🖋</a> <a href="#data-AyyagariA" title="Data">🔣</a> <a href="https://github.com/physiopy/phys2bids/commits?author=AyyagariA" title="Documentation">📖</a></td> <td align="center" valign="top" width="25%"><a href="https://github.com/62442katieb"><img src="https://avatars1.githubusercontent.com/u/14095475?v=4?s=100" width="100px;" alt="Katie Bottenhorn"/><br />_{<b>Katie Bottenhorn</b>}</a><br /><a href="https://github.com/physiopy/phys2bids/commits?author=62442katieb" title="Code">💻</a> <a href="#mentoring-62442katieb" title="Mentoring">🧑‍🏫</a> <a href="https://github.com/physiopy/phys2bids/pulls?q=is%3Apr+reviewed-by%3A62442katieb" title="Reviewed Pull Requests">👀</a> <a href="#content-62442katieb" title="Content">🖋</a></td> <td align="center" valign="top" width="25%"><a href="http://brightlab.northwestern.edu"><img src="https://avatars2.githubusercontent.com/u/32640425?v=4?s=100" width="100px;" alt="Molly Bright"/><br />_{<b>Molly Bright</b>}</a><br /><a href="#content-BrightMG" title="Content">🖋</a> <a href="#data-BrightMG" title="Data">🔣</a> <a href="#ideas-BrightMG" title="Ideas, Planning, & Feedback">🤔</a></td> </tr> <tr> <td align="center" valign="top" width="25%"><a href="https://github.com/CesarCaballeroGaudes"><img src="https://avatars1.githubusercontent.com/u/7611340?v=4?s=100" width="100px;" alt="Cesar Caballero Gaudes"/><br />_{<b>Cesar Caballero Gaudes</b>}</a><br /><a href="#content-CesarCaballeroGaudes" title="Content">🖋</a> <a href="#data-CesarCaballeroGaudes" title="Data">🔣</a> <a href="#ideas-CesarCaballeroGaudes" title="Ideas, Planning, & Feedback">🤔</a></td> <td align="center" valign="top" width="25%"><a href="https://github.com/ineschh"><img src="https://avatars0.githubusercontent.com/u/72545702?v=4?s=100" width="100px;" alt="Inés Chavarría"/><br />_{<b>Inés Chavarría</b>}</a><br /><a href="https://github.com/physiopy/phys2bids/commits?author=ineschh" title="Code">💻</a></td> <td align="center" valign="top" width="25%"><a href="https://github.com/nw-duncan"><img src="https://avatars.githubusercontent.com/u/23524584?v=4?s=100" width="100px;" alt="Niall Duncan"/><br />_{<b>Niall Duncan</b>}</a><br /><a href="https://github.com/physiopy/phys2bids/commits?author=nw-duncan" title="Code">💻</a> <a href="https://github.com/physiopy/phys2bids/commits?author=nw-duncan" title="Documentation">📖</a> <a href="#data-nw-dunca