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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!

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physiopy/phys2bids

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Phys2BIDS

phys2bids

DOI Join the chat at https://gitter.im/phys2bids/community

All Contributors

Phys2bids is a python3 library meant to format physiological files in BIDS. It was born for AcqKnowledge files (BIOPAC), and at the moment it supports .acq files as well as .txt files obtained by labchart (ADInstruments). It doesn't support physiological files recorded with the MRI, as you can find a software for it here.

It requires python 3.6 or above, as well as the modules:

  • numpy >= 1.9.3
  • matplotlib >= 3.1.1

In order to process .acq files, it needs bioread, an excellent module that can be found at this link.

Linux and mac installation

Donwload the package as zip from github and uncompress or if you have git use the command:

git clone https://github.com/smoia/phys2bids.git

open a terminal in the phy2bids folder and execute the command:

pip3 install .

type the command:

phys2bids -v

if your output is: phys2bids 1.2.0-beta or similar, phys2bids is ready to be used.

The project is currently under development. Any suggestion/bug report is welcome! Feel free to open an issue.

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

Contributors ✨

Thanks goes to these wonderful people (emoji key):


Daniel Alcalá

🎨

Apoorva Ayyagari

🔣 📖 🖋

Molly Bright

🔣 🤔 🖋

Vicente Ferrer

🐛 💻 📖 👀

Cesar Caballero Gaudes

🔣 🤔 🖋

Soichi Hayashi

🐛

Ross Markello

🐛 💻 🤔 🚇 👀 ⚠️

Stefano Moia

💻 🔣 🤔 🚇 📆 👀 📖 🖋

Rachael Stickland

🐛 🔣 📖 📓

Eneko Uruñuela

🐛 🚇 👀 ⚠️

Kristina Zvolanek

🔣 📖 🖋

License

Copyright 2019, 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.