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‎.github/ISSUE_TEMPLATE/bids_apps_submission.yml‎

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- type: markdown
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attributes:
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value: |
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- Have you checked our [contributing guide](https://github.com/bids-apps/bids-apps.github.io/blob/master/CONTRIBUTING.md)?
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- Have you checked our [contributing guide](https://bids-website.readthedocs.io/en/latest/collaboration/bids_github/CONTRIBUTING.html)?
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It's a helpful resource.
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- Have you checked our [FAQ](https://bids-apps.neuroimaging.io/dev_faq/)?
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- Have you checked our [FAQ](https://bids-website.readthedocs.io/en/latest/faq/bids-apps.html)?
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- type: textarea
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attributes:
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More details here:
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https://github.com/bids-apps/bids-apps.github.io/blob/761bcd927ddce83e80e9f898dce1864d9bcb9b04/_config.yml#L64
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https://github.com/bids-standard/bids-website/blob/81c642691150e00c08ad4450dbdb05eb794f8f9a/data/tools/apps.yml#L3
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For example:
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‎docs/collaboration/governance.md‎

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of the standard, the [PyBIDS](https://github.com/bids-standard/pybids)
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Python and [bids-matlab](https://github.com/bids-standard/bids-matlab)
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libraries allow querying and manipulating BIDS-compliant datasets,
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[BIDS-Apps](https://bids-apps.neuroimaging.io/) for running portable
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[BIDS-Apps](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html) for running portable
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pipelines on validated BIDS datasets, and platforms like
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[OpenNeuro](https://openneuro.org/) store and serve BIDS datasets. Note
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that the associated software does not fall under the same governance

‎docs/collaboration/index.md‎

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There are so many ways to help us build this community.
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- You could help someone else learn the benefits of BIDS by giving a talk in your local organization
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- Or you could work on [building a BIDS App](https://bids-apps.neuroimaging.io/){:target="_blank"}!
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- Or you could work on [building a BIDS App](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html){:target="_blank"}!
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<b>The only requirement is that everyone who contributes adheres to our
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[BIDS Code of Conduct](https://github.com/bids-standard/bids-specification/blob/master/CODE_OF_CONDUCT.md).</b>

‎docs/faq/bids-apps.md‎

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## Can I add more arguments to the API of my App?
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# BIDS apps
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Every BIDS App must use the mandatory arguments mentioned above, but you are
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free to add more that are specific to the task your App will perform.
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!!! note
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We recommend you follow the guidelines mentioned in the
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[BIDS extension proposal 027](https://bids.neuroimaging.io/bep027)
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for more information on specifying the API of your App.
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Make sure to check out the [nipreps wesbite](https://www.nipreps.org/)
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for more information on using and creating BIDS apps.
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## For users
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### How can I check a version of a container I have available locally?
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## How can I check a version of a container I have available locally?
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For many bids-app you should be able to run something like:
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```bash
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docker run bids/example --version
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```
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Inside each BIDS App there is a /version file with the version number.
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Inside each BIDS App there is a `/version` file with the version number.
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This file is automatically populated with tag used to trigger the build on the CI server.
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docker pull bids/example:v0.0.5
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```
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## How do I upload my BIDS App to the BIDS App Github org?
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You can release BIDS Apps using your own or your lab's account.
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However, if you want to be added to the BIDS docker hub,
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please message the [BIDS maintainers](mailto:[email protected])
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to have a repo created for you.
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If you base your code on <https://github.com/bids-apps/example> deployment on
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docker hub will happen automatically via Circle-ci.
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If you want your App to show on the BIDS App website
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[here](https://bids-apps.neuroimaging.io/apps/), you will in any case have to
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update the `_config.yml` in the
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[BIDS App website repository](https://github.com/bids-apps/bids-apps.github.io.git).
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## How should I version my BIDS App?
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Since most BIDS Apps are just thin wrappers around existing pipelines it would
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be most sensible to use the same version as the software they are wrapping.
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For example in case of HCP Pipelines this would be `v3.17.0`.
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## How to tag a new release?
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```bash
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git tag v0.0.1
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git push
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```
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## What do the analysis levels (`participant` and `group`) mean?
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## I want to release a new version of a BIDS App, but the pipeline version is the same?
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Generally, `participant` means individual level analysis (for instance: single subject).
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The `group` level analysis can be thought of as the second step,
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where the input becomes the output of the `participant` level analysis.
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This can happen when only the runscript or the Dockerfile changed?
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According to semantic versioning we should use the `+` signed followed by the build number.
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Unfortunately Docker Hub does not support semantic versioning.
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The best option is to use the `-` sign followed by the build number.
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For example `v3.17.0-3`.
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For example, generating statistic maps of each subject's brain could be considered `participant`,
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while generating the average of these maps across the dataset could be considered `group`.
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## Is it mandatory to first check the dataset validity using the BIDS-validator?
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## For developers
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It is an extremely helpful feature to have validation of the dataset as part of your tool.
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However, it's not considered mandatory.
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For instance: many Apps will
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simply fail with an error message if the dataset is not BIDS compliant.
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### Getting started
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## Is there a BIDS App template?
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#### Is there a BIDS App template?
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Have a look at the
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[example BIDS App repository](https://github.com/bids-apps/example). A
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minimalist example of a BIDS App consisting of a Dockerfile and a simple entry
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point script (written in this case in Python) accepting the standard BIDS Apps
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command line arguments.
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## What do the analysis levels (`participant` and `group`) mean?
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[example BIDS App repository](https://github.com/bids-apps/example).
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A minimalist example of a BIDS App consisting of a Dockerfile
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and a simple entry point script (written in this case in Python)
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accepting the standard BIDS Apps command line arguments.
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Generally, `participant` means individual level analysis (for instance: single
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subject) The group level analysis can be thought of as the second step, where
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the input becomes the output of the `participant` level analysis.
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#### Which container should I use to start building my app?
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For example, generating statistic maps of each subject's brain could be
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considered `participant`, while generating the average of these maps across the
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dataset could be considered `group`.
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The only minimum requirements of a BIDS App's container is its ability to run your pipeline.
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So for example, if your App is mostly Python based it should be sufficient
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to start with any image that has Python and include your environment dependencies.
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## What do we do if our application does not have any use for the group level analysis?
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### API
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If your pipeline has no need for group level analysis, it is fine if it is only
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valid for the analysis_level argument (see
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[fmriprep](https://fmriprep.readthedocs.io/en/latest/usage.html))
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## What should the API of my BIDS App look like?
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#### What should the API of my BIDS App look like?
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The obligatory arguments of the API of any BIDS App are:
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app_name bids_dir output_dir analysis_level
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```
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## When is a new image deposited to Docker Hub?
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#### What do we do if my application does not have any use for the group level analysis?
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Even though Docker image is being build on the CI server each time
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you push a commit to the repository it is not automatically being pushed to Docker Hub.
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Only if you tag a commit, push the tag to GitHub,
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and the tests you configured pass a new image will be deposited in Docker Hub.
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If your pipeline has no need for group level analysis,
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it is fine if it is only valid for the analysis_level argument
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(see [fmriprep](https://fmriprep.readthedocs.io/en/latest/usage.html)).
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## Where can I can data to test my app
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#### Can I add more arguments to the API of my App?
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Every BIDS App must use the mandatory arguments mentioned above,
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but you are free to add more that are specific to the task your App will perform.
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We recommend you follow the guidelines mentioned in the [BIDS apps specification](https://bids-standard.github.io/execution-spec/)
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for more information on specifying the API of your App.
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### Testing
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#### Where can I can get data to test my app?
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For both lightweight and full datasets to test your BIDS App, you can choose
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from one of these
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[example datasets](https://bids-standard.github.io/bids-starter-kit/dataset_examples.html)
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## Where should I describe changes between versions?
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#### Is it mandatory to first check the dataset validity using the BIDS-validator?
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It is an extremely helpful feature to have validation of the dataset as part of your tool.
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However, it's not considered mandatory.
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For instance: many Apps will simply fail with an error message if the dataset is not BIDS compliant.
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### Version
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#### How should I version my BIDS App?
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Since most BIDS Apps are just thin wrappers around existing pipelines it would
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be most sensible to use the same version as the software they are wrapping.
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For example in case of HCP Pipelines this would be `v3.17.0`.
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#### How to tag a new release?
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```bash
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git tag v0.0.1
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git push
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```
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#### I want to release a new version of a BIDS App, but the pipeline version is the same?
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This can happen when only the runscript or the Dockerfile changed?
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According to semantic versioning we should use the `+` signed followed by the build number.
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Unfortunately Docker Hub does not support semantic versioning.
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The best option is to use the `-` sign followed by the build number.
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For example `v3.17.0-3`.
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#### Where should I describe changes between versions?
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After tagging a new release it is important to provide a list of changes
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on the GitHub Releases page.
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Here's an [example](https://github.com/bids-apps/example/releases).
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## Which container should I use to start building my app?
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### Deplopying
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#### How do I upload my BIDS App to the BIDS App Github org?
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The only minimum requirements of a BIDS App's container is its ability to run
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your pipeline. So for example, if your App is mostly Python based it should be
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sufficient to start with any image that has Python and include your environment
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dependencies.
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You can release BIDS Apps using your own or your lab's account.
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However, if you want to be added to the BIDS docker hub,
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please message the [BIDS maintainers](mailto:[email protected])
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to have a repo created for you.
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If you base your code on <https://github.com/bids-apps/example> deployment
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on docker hub will happen automatically via Circle-ci.
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<hr>
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If you want your App to show on the [BIDS website](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html),
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you will have to update the `data/tools/apps.yml` in the
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[BIDS website repository](https://github.com/bids-standard/bids-website/tree/main).
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Generated by [FAQtory](https://github.com/willmcgugan/faqtory)
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#### When is a new image deposited to Docker Hub?
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Even though Docker image is being build on the CI server each time
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you push a commit to the repository it is not automatically being pushed to Docker Hub.
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Only if you tag a commit, push the tag to GitHub,
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and the tests you configured pass a new image will be deposited in Docker Hub.

‎docs/faq/bids-extensions.md‎

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[bids-specification issue #1177](https://github.com/bids-standard/bids-specification/issues/1177)
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for an example of the reasoning that led to the application of an entity
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previously used for functional data to anatomical MRI.
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<hr>
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Generated by [FAQtory](https://github.com/willmcgugan/faqtory)

‎docs/faq/eeg.md‎

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For a formatted example on how to deal with this in the BIDS context,
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please see this
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[template](https://github.com/bids-standard/bids-starter-kit/blob/main/templates/sub-01/ses-01/eeg/sub-01_ses-01_task-ReferenceExample_eeg.json).
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<hr>
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Generated by [FAQtory](https://github.com/willmcgugan/faqtory)

‎docs/faq/general.md‎

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If you plan to put your dataset on [openneuro](https://openneuro.org/),
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you should use a CC0 or a PDDL license as explained in their [FAQ](https://openneuro.org/faq).
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<hr>
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Generated by [FAQtory](https://github.com/willmcgugan/faqtory)

‎docs/faq/mri.md‎

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- [Fieldtrip](http://www.fieldtriptoolbox.org/faq/how_can_i_anonymize_an_anatomical_mri/) under matlab can do it.
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- SPM8 and SPM12: when in the batch editor go to: `SPM menu --> Util --> Deface`
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<hr>
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Generated by [FAQtory](https://github.com/willmcgugan/faqtory)

‎docs/faq/phenotype.md‎

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[epilepsyClassification2017](https://github.com/bids-standard/bids-starter-kit/blob/main/interactiveTreeVisualization/epilepsyClassification2017/tree.html)
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and follow the examples in the
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[phenotype templates](https://github.com/bids-standard/bids-starter-kit/tree/main/templates/phenotype).
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<hr>
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Generated by [FAQtory](https://github.com/willmcgugan/faqtory)

‎docs/impact/index.md‎

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| statistical model | ![PyPI - Downloads](https://img.shields.io/pypi/dm/bsmschema) |
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For the number of docker pulls of the BIDS apps, please check the
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[BIDS app dashboard](https://bids-apps.neuroimaging.io/apps/).
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[BIDS app dashboard](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html).
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### Contributors
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