https://github.com/carpentries-incubator/sdc-bids-intromri
Introduction to MRI and BIDS
https://github.com/carpentries-incubator/sdc-bids-intromri
alpha bids binder carpentries-incubator english helpwanted-list lesson mri neuroimaging python
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Introduction to MRI and BIDS
- Host: GitHub
- URL: https://github.com/carpentries-incubator/sdc-bids-intromri
- Owner: carpentries-incubator
- License: other
- Created: 2019-11-07T17:52:56.000Z (almost 6 years ago)
- Default Branch: main
- Last Pushed: 2025-06-17T00:46:42.000Z (4 months ago)
- Last Synced: 2025-06-17T01:37:43.743Z (4 months ago)
- Topics: alpha, bids, binder, carpentries-incubator, english, helpwanted-list, lesson, mri, neuroimaging, python
- Language: Jupyter Notebook
- Homepage: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI
- Size: 29.6 MB
- Stars: 26
- Watchers: 8
- Forks: 20
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION
- Authors: AUTHORS
Awesome Lists containing this project
README
# Introduction to Working with MRI Data in Python
[![Create a Slack Account with us][create_slack_svg]][slack_heroku_invite]
[![Slack Status][slack_channel_status]][slack_channel_url]
[![Binder][binder_svg]][binder_url]
An introduction to working with magnetic resonance imaging (MRI) data in Python.
## About the Lesson
This lesson teaches:
- a (re?) introduction to MR nomenclature - with BIDS
- how neuroimaging data is stored
- "converting" your data to BIDS
- BIDS apps
- queueing up neuroimaging pipelines
## Episodes
| \# | Episode | Time | Question(s) |
| --: | :------ | :--: | :------------------------------------------------------------------------- |
| 1 | [Before we start][episode01] | 30 | What is Python and why should I learn it? |
| 2 | [From the scanner to our computer][episode02] | 30 | What are the main MRI modalities?
What's the first step necessary to start working with MRI data? |
| 3 | [Anatomy of a NIfTI][episode03] | 25 | How are MRI data represented digitally? |
| 4 | [Data organization with BIDS][episode04] | 45 | |
| 5 | [Exploring open MRI datasets][episode05] | 45 | How does standardizing neuroimaging data ease the data exploration process |
| 6 | [BIDS derivatives][episode06] | 45 | |
## Contributing
We welcome all contributions to improve the lesson! Maintainers will do their best to help you if you have any
questions, concerns, or experience any difficulties along the way.
We'd like to ask you to familiarize yourself with our [Contribution Guide](CONTRIBUTING.md) and have a look at
the [more detailed guidelines][lesson-example] on proper formatting, ways to render the lesson locally, and even
how to write new episodes.
Please see the current list of [issues][link_issues] for ideas for contributing to this
repository. For making your contribution, we use the GitHub flow, which is
nicely explained in the chapter [Contributing to a Project](https://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project) in Pro Git
by Scott Chacon.
Look for the tag . This indicates that the maintainers will welcome a pull request fixing this issue.
## Maintainer(s)
Current maintainers of this lesson are
- [Michael Joseph][michael_joseph]
- [Jerrold Jeyachandra][jerrold_jeyachandra]
## Authors
A list of contributors to the lesson can be found in [AUTHORS](AUTHORS)
## License
Instructional material from this lesson is made available under the Creative
Commons Attribution (CC BY 4.0) license. Except where otherwise noted, example
programs and software included as part of this lesson are made available under
the MIT license. For more information, see [LICENSE](LICENSE.md).
## Citation
To cite this lesson, please consult with [CITATION](CITATION)
[slack_heroku_invite]: https://swc-slack-invite.herokuapp.com
[create_slack_svg]: https://img.shields.io/badge/Create_Slack_Account-The_Carpentries-071159.svg
[slack_channel_url]: https://swcarpentry.slack.com/messages/CCJBHKCHZ
[slack_channel_status]: https://img.shields.io/badge/Slack_Channel-neuroimaging-E01563.svg
[binder_url]: https://mybinder.org/v2/gh/carpentries-incubator/SDC-BIDS-IntroMRI/gh-pages?filepath=code%2F
[binder_svg]: https://mybinder.org/badge_logo.svg
[episode01]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/before-we-start.html
[episode02]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/scanner-to-computer.html
[episode03]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/anatomy-of-nifti.html
[episode04]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/data-organization-bids.html
[episode05]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/open-mri-datasets.html
[episode06]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/bids-derivatives.html
[lesson-example]: https://carpentries.github.io/lesson-example
[link_issues]: https://github.com/conp-pcno-training/SDC-BIDS-IntroMRI/issues
[michael_joseph]: https://github.com/josephmje
[jerrold_jeyachandra]: https://github.com/jerdra