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https://unfmontreal.github.io/Dcm2Bids/
Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
https://unfmontreal.github.io/Dcm2Bids/
bids neuroimaging neuroscience
Last synced: about 2 months ago
JSON representation
Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
- Host: GitHub
- URL: https://unfmontreal.github.io/Dcm2Bids/
- Owner: UNFmontreal
- License: gpl-3.0
- Created: 2016-05-24T14:40:03.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2024-04-15T13:03:13.000Z (5 months ago)
- Last Synced: 2024-04-16T02:02:43.605Z (5 months ago)
- Topics: bids, neuroimaging, neuroscience
- Language: Python
- Homepage: https://UNFmontreal.github.io/Dcm2Bids/
- Size: 11.6 MB
- Stars: 147
- Watchers: 7
- Forks: 79
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.txt
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION.cff
Awesome Lists containing this project
- awesome-bids - Dcm2Bids
README
# dcm2bids
Your friendly DICOM converter.
[](https://unfmontreal.github.io/Dcm2Bids)
[](https://zenodo.org/badge/latestdoi/59581295)
[](https://anaconda.org/conda-forge/dcm2bids)
[](https://github.com/unfmontreal/Dcm2Bids/actionsk)
[](https://codecov.io/gh/unfmontreal/Dcm2Bids)
[](https://github.com/psf/black)
[](https://pypi.org/project/dcm2bids)
[](https://pypi.org/project/dcm2bids)
[](https://anaconda.org/conda-forge/dcm2bids)
[](https://hub.docker.com/r/unfmontreal/dcm2bids)
[](/docs/LICENSE.txt)
---
`dcm2bids` reorganises NIfTI files using [dcm2niix][dcm2niix-github] into the [Brain Imaging Data Structure][bids] (BIDS).
## Major upgrade with dcm2bids >=3.0.0
⚠️ Breaking changes alert ⚠️
**dcm2bids>=3.0.0 is not compatible with config files made for v2.1.9 and below**.
In order to develop dcm2bids new features we had to rewrite some of its code.
Since v3.0.0, dcm2bids has become **more powerful** and **more flexible** while reducing the burden of creating config files. Porting your config file should be relatively easy by following the [How-to upgrade][dcm2bids-upgrade] page.
If you have any issues with it don't hesitate to report it on [Neurostars][neurostars-dcm2bids].
## Scope
`dcm2bids` is a community-centered project. It aims to be a friendly,
easy-to-use tool to convert your dicoms. Our main goal is to make the dicom
to BIDS conversion as effortless as possible. Even if in the near future
more advanced features will be added, we'll keep the focus on your day
to day use case without complicating anything. That's the promise of the `dcm2bids` project.
## Documentation
Please take a look at the [documentation][dcm2bids-doc] to:
* [Learn about bids][bids-spec] with some dataset [examples][bids-examples]
* [Install dcm2bids][dcm2bids-install]
* [Use docker and Apptainer/Singularity][dcm2bids-container]
* [Follow the tutorials][dcm2bids-tutorial]
* [Seek for more advanced usage][dcm2bids-advanced]
## Issues and Questions
We work hard to make sure `dcm2bids` is robust and we welcome comments and questions to make sure it meets your use case! Here's our preferred workflow:
- If you have a usage question :raising_hand:, we encourage you to post your question on [Neurostars][neurostars] with [dcm2bids][neurostars-dcm2bids] as an optional tag. The tag is really important because [Neurostars][neurostars-dcm2bids] will notify the `dcm2bids` team only if the tag is present. [Neurostars][neurostars-dcm2bids] is a question and answer forum for neuroscience researchers, infrastructure providers and software developers, and free to access.
Before posting your question, you may want to first browse through questions that were tagged with the [dcm2bids tag][neurostars-dcm2bids]. If your question persists, feel free to comment on previous questions or ask your own question.
- If you think you've found a bug :bug:, please open an issue on [our repository][dcm2bids-issues]. To do this, you'll need a GitHub account. See our [contributing guide](CONTRIBUTING/#open-an-issue-or-choose-one-to-fix) for more details.
[bids]: http://bids.neuroimaging.io/
[bids-examples]: https://github.com/bids-standard/bids-examples
[bids-spec]: https://bids-specification.readthedocs.io/en/stable/
[dcm2bids-doc]: https://unfmontreal.github.io/Dcm2Bids
[dcm2bids-install]: https://unfmontreal.github.io/Dcm2Bids/latest/get-started/install/
[dcm2bids-tutorial]: https://unfmontreal.github.io/Dcm2Bids/latest/tutorial/first-steps/#tutorial-first-steps
[dcm2bids-advanced]: https://unfmontreal.github.io/Dcm2Bids/latest/advanced/
[dcm2bids-container]: https://unfmontreal.github.io/Dcm2Bids/latest/how-to/container/
[dcm2bids-upgrade]: https://unfmontreal.github.io/Dcm2Bids/dev/upgrade/
[dcm2bids-issues]: https://github.com/UNFmontreal/Dcm2Bids/issues
[dcm2niix-install]: https://github.com/rordenlab/dcm2niix#install
[dcm2niix-github]: https://github.com/rordenlab/dcm2niix
[neurostars]: https://neurostars.org/
[neurostars-dcm2bids]: https://neurostars.org/tag/dcm2bids
[dcm2bids-contributing]: https://unfmontreal.github.io/Dcm2Bids/latest/how-to/contributing/
## Please cite dcm2bids
If you use dcm2bids in your research or as part of your developments, please always cite the reference below.
### APA
> Boré, A., Guay, S., Bedetti, C., Meisler, S., & GuenTher, N. (2023). Dcm2Bids (Version 3.1.1) [Computer software]. https://doi.org/10.5281/zenodo.8436509
### BibTeX
```
@software{Bore_Dcm2Bids_2023,
author = {Boré, Arnaud and Guay, Samuel and Bedetti, Christophe and Meisler, Steven and GuenTher, Nick},
doi = {10.5281/zenodo.8436509},
month = aug,
title = {{Dcm2Bids}},
url = {https://github.com/UNFmontreal/Dcm2Bids},
version = {3.1.1},
year = {2023}
```