https://github.com/physiopy/phys2bids
Python3 library to format physiological files in BIDS. At the moment, it supports Acqknowledge and Labchart. BrainHack participants, check the issues with the BrainHack labels!
https://github.com/physiopy/phys2bids
acqknowledge bids brainweb closember ge hacktoberfest labchart physiological-recordings physiological-signals physiology python3-library spike2
Last synced: 5 days ago
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Python3 library to format physiological files in BIDS. At the moment, it supports Acqknowledge and Labchart. BrainHack participants, check the issues with the BrainHack labels!
- Host: GitHub
- URL: https://github.com/physiopy/phys2bids
- Owner: physiopy
- License: apache-2.0
- Created: 2019-09-16T17:49:07.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2025-11-10T19:54:23.000Z (2 months ago)
- Last Synced: 2025-11-10T21:22:29.541Z (2 months ago)
- Topics: acqknowledge, bids, brainweb, closember, ge, hacktoberfest, labchart, physiological-recordings, physiological-signals, physiology, python3-library, spike2
- Language: Python
- Homepage: https://phys2bids.readthedocs.io
- Size: 57.6 MB
- Stars: 66
- Watchers: 5
- Forks: 48
- Open Issues: 59
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: docs/contributing.rst
- License: LICENSE
- Zenodo: .zenodo.json
Awesome Lists containing this project
README
phys2bids
=========
[](https://github.com/physiopy/phys2bids/releases)
[](https://github.com/physiopy/phys2bids/releases)
[](https://github.com/intuit/auto)
[](https://phys2bids.readthedocs.io/en/latest/?badge=latest)
[](https://zenodo.org/badge/latestdoi/208861898)
[](https://github.com/physiopy/phys2bids/blob/master/LICENSE)
[](https://codecov.io/gh/physiopy/phys2bids)
[](https://circleci.com/gh/physiopy/phys2bids)
[](https://phys2bids.readthedocs.io/en/latest/?badge=latest)
[](https://pypi.org/project/phys2bids/)
[](https://pypi.org/project/phys2bids/)
[](https://github.com/intuit/auto)
[](https://pypi.org/project/phys2bids/)
[](#contributors)
``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](https://doi.org/10.5281/zenodo.3470091)
> We also support gathering all relevant citations via [DueCredit](http://duecredit.org).
[Read the latest documentation](https://phys2bids.readthedocs.io/en/latest/) for more information on phys2bids!
Shortcuts:
- [Requirements](https://phys2bids.readthedocs.io/en/latest/installation.html#requirements)
- [Installation](https://phys2bids.readthedocs.io/en/latest/installation.html#linux-and-mac-installation)
- [Usage](https://phys2bids.readthedocs.io/en/latest/cli.html)
- [How to use phys2bids](https://phys2bids.readthedocs.io/en/latest/howto.html)
- [Contributing to phys2bids](https://phys2bids.readthedocs.io/en/latest/contributing.html)
- [Developer installation](https://phys2bids.readthedocs.io/en/latest/contributing.html#linux-and-mac-developer-installation)
- [**Contributor guide**](https://phys2bids.readthedocs.io/en/latest/contributorfile.html)
- [**Code of Conduct**](https://phys2bids.readthedocs.io/en/latest/conduct.html)
- [Developer calls calendar](https://calendar.google.com/calendar/u/0?cid=amoycDQ1MTdhMWdpaHNuNzlnOW1ucHJkMjRAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ)
## 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.
## 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](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
Daniel Alcalá
🎨
Apoorva Ayyagari
🖋 🔣 📖
Katie Bottenhorn
💻 🧑🏫 👀 🖋
Molly Bright
🖋 🔣 🤔
Cesar Caballero Gaudes
🖋 🔣 🤔
Inés Chavarría
💻
Niall Duncan
💻 📖 🔣 ⚠️ 🤔
Vicente Ferrer
🐛 💻 📖 👀 ⚠️
Yaroslav Halchenko
🚇
Soichi Hayashi
🐛
Vittorio Iacovella
💻
François Lespinasse
🐛 💻 🖋 ⚠️
Ross Markello
🐛 💻 🖋 🤔 🚇 👀 ⚠️ 🧑🏫
m-miedema
✅ 📋
Stefano Moia
💻 🖋 🔣 🤔 🚇 📆 👀 📖 🧑🏫 📢 📣 🚧 ✅
Robert Oostenveld
🤔 👀
Basile
💻 ⚠️
David Romero-Bascones
🐛 💻 📖 🖋
Taylor Salo
🤔 💻 👀 🚇
Rachael Stickland
🐛 💻 🔣 📖 📓 👀 🚇
Eneko Uruñuela
🐛 💻 🚇 👀 ⚠️ 🧑🏫
Merel van der Thiel
💻
Hao-Ting Wang
💻 📖 🔣 ⚠️ 🤔
Kristina Zvolanek
🔣 🖋 📖
Marcel Zwiers
🔌
victox5
📖
Marie-Eve Picard
👀
License
-------
Copyright 2019-2020, The Phys2BIDS community.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
