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‎.github/ISSUE_TEMPLATE/bug_report.yml

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Please run this command in your console and paste the output below
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```shell
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python <(curl -s https://raw.githubusercontent.com/fepegar/torchio/main/print_system.py)
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python <(curl -s https://raw.githubusercontent.com/TorchIO-project/torchio/main/print_system.py)
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```
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placeholder: Your system info
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render: shell

‎.github/ISSUE_TEMPLATE/config.yml

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blank_issues_enabled: true
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contact_links:
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- name: ❓ Discussions tab
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url: https://github.com/fepegar/torchio/discussions/new
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url: https://github.com/TorchIO-project/torchio/discussions/new
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about: Ask and answer TorchIO-related questions or start a general discussion

‎.github/ISSUE_TEMPLATE/not_working.yml

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Please run this command in your console and paste the output below
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```shell
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python <(curl -s https://raw.githubusercontent.com/fepegar/torchio/main/print_system.py)
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python <(curl -s https://raw.githubusercontent.com/TorchIO-project/torchio/main/print_system.py)
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```
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placeholder: Your system info
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render: shell

‎.github/pull_request_template.md

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<!-- You do not need to complete all the items by the time you submit the pull
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request, but most likely the changes will only be merged if all the tasks are
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done. See more information about the submission process in the
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CONTRIBUTING (https://github.com/fepegar/torchio/blob/main/CONTRIBUTING.rst) docs. -->
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CONTRIBUTING (https://github.com/TorchIO-project/torchio/blob/main/CONTRIBUTING.rst) docs. -->
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<!-- Write an `x` in all the boxes that apply -->
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- [ ] I have read the [`CONTRIBUTING`](https://github.com/fepegar/torchio/blob/main/CONTRIBUTING.rst) docs and have a developer setup (especially important are `pre-commit`and `pytest`)
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- [ ] I have read the [`CONTRIBUTING`](https://github.com/TorchIO-project/torchio/blob/main/CONTRIBUTING.rst) docs and have a developer setup (especially important are `pre-commit`and `pytest`)
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- [ ] Non-breaking change (would not break existing functionality)
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- [ ] Breaking change (would cause existing functionality to change)
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- [ ] Tests added or modified to cover the changes

‎CHANGELOG.md

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‎CITATION.cff

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given-names: Fernando
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orcid: https://orcid.org/0000-0001-9090-3024
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title: "TorchIO"
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repository-code: "https://github.com/fepegar/torchio"
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repository-code: "https://github.com/TorchIO-project/torchio"
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preferred-citation:
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type: article
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authors:

‎CONTRIBUTING.rst

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~~~~~~~~~~~
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Report bugs
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`on GitHub <https://github.com/fepegar/torchio/issues/new?assignees=&labels=bug&template=bug_report.md&title=>`_.
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`on GitHub <https://github.com/TorchIO-project/torchio/issues/new?assignees=&labels=bug&template=bug_report.md&title=>`_.
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If you are reporting a bug, please include:
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Submit feedback
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~~~~~~~~~~~~~~~
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The best way to send feedback is to file an issue at https://github.com/fepegar/torchio/issues.
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The best way to send feedback is to file an issue at https://github.com/TorchIO-project/torchio/issues.
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If you are proposing a feature:
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‎README.md

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‎docs/examples/plot_custom_z_spacing.py

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image spacing across one axis only.
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Inspired by
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`this discussion <https://github.com/fepegar/torchio/discussions/885>`_.
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`this discussion <https://github.com/TorchIO-project/torchio/discussions/885>`_.
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"""
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import torch

‎docs/source/README.rst

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Many groups have used TorchIO for their research.
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The complete list of citations is available on `Google Scholar <https://scholar.google.co.uk/scholar?cites=8711392719159421861&sciodt=0,5&hl=en>`_, and the
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`dependents list <https://github.com/fepegar/torchio/network/dependents>`_ is
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`dependents list <https://github.com/TorchIO-project/torchio/network/dependents>`_ is
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available on GitHub.
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The code is available on `GitHub <https://github.com/fepegar/torchio>`_.
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The code is available on `GitHub <https://github.com/TorchIO-project/torchio>`_.
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If you like TorchIO, please go to the repository and star it!
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.. raw:: html
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<a class="github-button" href="https://github.com/fepegar/torchio" data-icon="octicon-star" data-show-count="true" aria-label="Star fepegar/torchio on GitHub">Star</a>
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<a class="github-button" href="https://github.com/TorchIO-project/torchio" data-icon="octicon-star" data-show-count="true" aria-label="Star TorchIO-project/torchio on GitHub">Star</a>
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<script async defer src="https://buttons.github.io/buttons.js"></script>
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See :doc:`Getting started <quickstart>` for installation instructions and a
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usage overview.
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Contributions are more than welcome.
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Please check our `contributing guide <https://github.com/fepegar/torchio/blob/main/CONTRIBUTING.rst>`_
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Please check our `contributing guide <https://github.com/TorchIO-project/torchio/blob/main/CONTRIBUTING.rst>`_
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if you would like to contribute.
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If you have questions, feel free to ask in the discussions tab:
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.. raw:: html
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<a class="github-button" href="https://github.com/fepegar/torchio/discussions" data-icon="octicon-comment-discussion" aria-label="Discuss fepegar/torchio on GitHub">Discuss</a>
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<a class="github-button" href="https://github.com/TorchIO-project/torchio/discussions" data-icon="octicon-comment-discussion" aria-label="Discuss TorchIO-project/torchio on GitHub">Discuss</a>
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<script async defer src="https://buttons.github.io/buttons.js"></script>
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If you found a bug or have a feature request, please open an issue:
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.. raw:: html
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<!-- Place this tag where you want the button to render. -->
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<a class="github-button" href="https://github.com/fepegar/torchio/issues" data-icon="octicon-issue-opened" data-show-count="true" aria-label="Issue fepegar/torchio on GitHub">Issue</a>
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<a class="github-button" href="https://github.com/TorchIO-project/torchio/issues" data-icon="octicon-issue-opened" data-show-count="true" aria-label="Issue TorchIO-project/torchio on GitHub">Issue</a>
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<!-- Place this tag in your head or just before your close body tag. -->
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<script async defer src="https://buttons.github.io/buttons.js"></script>
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:alt: Conda version
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.. |Google-Colab-notebook| image:: https://colab.research.google.com/assets/colab-badge.svg
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:target: https://github.com/fepegar/torchio/blob/main/tutorials/README.md
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:target: https://github.com/TorchIO-project/torchio/blob/main/tutorials/README.md
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:alt: Google Colab notebooks
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.. |Docs-status| image:: https://img.shields.io/readthedocs/torchio?label=Docs&logo=Read%20the%20Docs
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:target: https://torchio.rtfd.io/?badge=latest
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:alt: Documentation status
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.. |Tests-status| image:: https://github.com/fepegar/torchio/actions/workflows/tests.yml/badge.svg
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:target: https://github.com/fepegar/torchio/actions/workflows/tests.yml
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.. |Tests-status| image:: https://github.com/TorchIO-project/torchio/actions/workflows/tests.yml/badge.svg
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:target: https://github.com/TorchIO-project/torchio/actions/workflows/tests.yml
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:alt: Tests status
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.. |Ruff| image:: https://camo.githubusercontent.com/bb88127790fb054cba2caf3f3be2569c1b97bb45a44b47b52d738f8781a8ede4/68747470733a2f2f696d672e736869656c64732e696f2f656e64706f696e743f75726c3d68747470733a2f2f7261772e67697468756275736572636f6e74656e742e636f6d2f636861726c6965726d617273682f727566662f6d61696e2f6173736574732f62616467652f76312e6a736f6e
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:target: https://docs.astral.sh/ruff/
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:alt: Code style: Ruff
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.. |Coverage-codecov| image:: https://codecov.io/gh/fepegar/torchio/branch/main/graphs/badge.svg
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:target: https://app.codecov.io/github/fepegar/torchio
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.. |Coverage-codecov| image:: https://codecov.io/gh/TorchIO-project/torchio/branch/main/graphs/badge.svg
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:target: https://app.codecov.io/github/TorchIO-project/torchio
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:alt: Coverage status
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.. |Code-Quality| image:: https://img.shields.io/scrutinizer/g/fepegar/torchio.svg?label=Code%20quality&logo=scrutinizer
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:target: https://scrutinizer-ci.com/g/fepegar/torchio/?branch=main
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.. |Code-Quality| image:: https://img.shields.io/scrutinizer/g/TorchIO-project/torchio.svg?label=Code%20quality&logo=scrutinizer
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:target: https://scrutinizer-ci.com/g/TorchIO-project/torchio/?branch=main
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:alt: Code quality
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.. |YouTube| image:: https://img.shields.io/youtube/views/UEUVSw5-M9M?label=watch&style=social
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:target: https://www.youtube.com/watch?v=UEUVSw5-M9M
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:alt: YouTube
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.. |Code-Maintainability| image:: https://api.codeclimate.com/v1/badges/518673e49a472dd5714d/maintainability
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:target: https://codeclimate.com/github/fepegar/torchio
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:target: https://codeclimate.com/github/TorchIO-project/torchio
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:alt: Maintainability
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.. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white

‎docs/source/_templates/layout.html

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{% extends "!layout.html" %}
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{% block footer %} {{ super() }}
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{% extends "!layout.html" %} {% block footer %} {{ super() }}
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<style>
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/* Sidebar header (and topbar for mobile) */
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.wy-side-nav-search, .wy-nav-top {
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background: #d45848;
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}
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/* Make full screen */
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/* .wy-nav-content { max-width: none; } */
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.wy-menu > .caption > span.caption-text {
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color: #d45848;
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}
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/* .property {
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<style>
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/* Sidebar header (and topbar for mobile) */
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.wy-side-nav-search,
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.wy-nav-top {
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background: #d45848;
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}
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/* Make full screen */
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/* .wy-nav-content { max-width: none; } */
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.wy-menu > .caption > span.caption-text {
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color: #d45848;
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}
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/* .property {
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} */
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</style>
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{% endblock %}
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{% block document %}
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{{super()}}
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<a href="https://github.com/fepegar/torchio">
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<img style="position: absolute; top: 0; right: 0; border: 0;" src="https://s3.amazonaws.com/github/ribbons/forkme_right_darkblue_121621.png" alt="Fork me on GitHub">
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</a>
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</style>
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{% endblock %} {% block document %} {{super()}}
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<a href="https://github.com/TorchIO-project/torchio">
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<img
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style="position: absolute; top: 0; right: 0; border: 0"
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src="https://s3.amazonaws.com/github/ribbons/forkme_right_darkblue_121621.png"
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alt="Fork me on GitHub"
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/>
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</a>
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{% endblock %}

‎docs/source/datasets.rst

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.. raw:: html
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<a class="github-button" href="https://github.com/fepegar/torchio/discussions" data-icon="octicon-comment-discussion" aria-label="Discuss fepegar/torchio on GitHub">Discuss</a>
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<a class="github-button" href="https://github.com/TorchIO-project/torchio/discussions" data-icon="octicon-comment-discussion" aria-label="Discuss TorchIO-project/torchio on GitHub">Discuss</a>
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<script async defer src="https://buttons.github.io/buttons.js"></script>
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‎docs/source/index.rst

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datasets
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interfaces/index
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auto_examples/index
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GitHub repository <https://github.com/fepegar/torchio>
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GitHub repository <https://github.com/TorchIO-project/torchio>
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Paper <https://www.sciencedirect.com/science/article/pii/S0169260721003102>

‎docs/source/quickstart.rst

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If you are on Windows and have
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`trouble installing TorchIO <https://github.com/fepegar/torchio/issues/343>`_,
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`trouble installing TorchIO <https://github.com/TorchIO-project/torchio/issues/343>`_,
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try `installing PyTorch <https://pytorch.org/get-started/locally/>`_ with
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`conda <https://docs.conda.io/en/latest/miniconda.html>`_ before pip-installing
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TorchIO.
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|Google-Colab-notebook|
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The best way to quickly understand and try the library is the
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`Jupyter Notebooks <https://github.com/TorchIO-project/torchio/blob/main/tutorials/README.md>`_
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hosted on Google Colab.
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They include multiple examples and visualization of most of the classes,
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with subvolumes (aka patches or windows).
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.. |Google-Colab-notebook| image:: https://colab.research.google.com/assets/colab-badge.svg
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:target: https://github.com/fepegar/torchio/blob/main/tutorials/README.md
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:target: https://github.com/TorchIO-project/torchio/blob/main/tutorials/README.md
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:alt: Google Colab notebook

‎pyproject.toml

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[project.urls]
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Homepage = "http://torchio.rtfd.io"
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Source = "https://github.com/fepegar/torchio"
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"Issue tracker" = "https://github.com/fepegar/torchio/issues"
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Source = "https://github.com/TorchIO-project/torchio"
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"Issue tracker" = "https://github.com/TorchIO-project/torchio/issues"
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"Release notes" = "https://github.com/fepegar/torchio/releases"
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"Release notes" = "https://github.com/TorchIO-project/torchio/releases"
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[dependency-groups]
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dev = [

‎src/torchio/constants.py

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REPO_URL = 'https://github.com/TorchIO-project/torchio/'
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# Data repository
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DATA_REPO = 'https://github.com/fepegar/torchio-data/raw/main/data/'
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DATA_REPO = 'https://github.com/TorchIO-project/torchio-data/raw/main/data/'
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MIN_FLOAT_32 = torch.finfo(torch.float32).eps

‎src/torchio/data/image.py

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if 'channels_last' in kwargs:
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message = (
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'The "channels_last" keyword argument is deprecated after'
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' https://github.com/fepegar/torchio/pull/685 and will be'
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' https://github.com/TorchIO-project/torchio/pull/685 and will be'
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' removed in the future'
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)
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warnings.warn(message, DeprecationWarning, stacklevel=2)
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' will be instances of torchio.Subject with 5D images. Replace'
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' your PyTorch DataLoader with a torchio.SubjectsLoader so that'
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' the collated batch becomes a dictionary, as expected. See'
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' https://github.com/fepegar/torchio/issues/1179 for more'
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' https://github.com/TorchIO-project/torchio/issues/1179 for more'
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' context about this issue.'
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)
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warnings.warn(message, stacklevel=1)
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if path is None:
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# https://github.com/TorchIO-project/torchio/pull/838
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raise TypeError('The path argument cannot be a dictionary')
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‎src/torchio/data/inference/aggregator.py

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function. See the `grid aggregator tests`_ for a raw visualization
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of the three modes.
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.. _grid aggregator tests: https://github.com/fepegar/torchio/blob/main/tests/data/inference/test_aggregator.py
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.. _grid aggregator tests: https://github.com/TorchIO-project/torchio/blob/main/tests/data/inference/test_aggregator.py
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.. note:: Adapted from NiftyNet. See `this NiftyNet tutorial
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<https://niftynet.readthedocs.io/en/dev/window_sizes.html>`_ for more
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# old and one the operands is int:
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# https://github.com/fepegar/torchio/issues/526
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# https://github.com/TorchIO-project/torchio/issues/526
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‎src/torchio/data/queue.py

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and the :class:`~torch.utils.data.DataLoader` used to pop batches from the
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queue.
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.. image:: https://raw.githubusercontent.com/fepegar/torchio/main/docs/images/diagram_patches.svg
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.. image:: https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/diagram_patches.svg
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:alt: Training with patches
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‎src/torchio/data/sampler/label.py

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raise RuntimeError(message)
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crop_fin_i, crop_fin_j, crop_fin_k = crop_fin = (patch_size - 1) // 2
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fin_i, fin_j, fin_k = spatial_shape - crop_fin
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# See https://github.com/fepegar/torchio/issues/458
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# See https://github.com/TorchIO-project/torchio/issues/458
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label_map = label_map[:, ini_i:fin_i, ini_j:fin_j, ini_k:fin_k]
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multichannel = label_map.shape[0] > 1
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# See https://github.com/fepegar/torchio/issues/458
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# See https://github.com/TorchIO-project/torchio/issues/458
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padding = ini_k, crop_fin_k, ini_j, crop_fin_j, ini_i, crop_fin_i
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‎src/torchio/data/sampler/weighted.py

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[ 6808, 6804, 6942, 6809, 6946, 6988, 7002, 6826, 7041]])
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"""
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# Get first value larger than random number ensuring the random number
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# is not exactly 0 (see https://github.com/fepegar/torchio/issues/510)
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# is not exactly 0 (see https://github.com/TorchIO-project/torchio/issues/510)
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random_number = max(MIN_FLOAT_32, torch.rand(1).item()) * cdf[-1]
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random_location_index = np.searchsorted(cdf, random_number)
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message = (
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'Error retrieving probability in weighted sampler.'
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' Please report this issue at'
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' https://github.com/fepegar/torchio/issues/new?labels=bug&template=bug_report.md'
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' https://github.com/TorchIO-project/torchio/issues/new?labels=bug&template=bug_report.md'
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)
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raise RuntimeError(message)
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‎src/torchio/data/subject.py

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Original file line numberDiff line numberDiff line change
@@ -322,7 +322,7 @@ def check_consistent_space(self) -> None:
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'As described above, some images in the subject are not in the'
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' same space. You probably can use the transforms ToCanonical'
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' and Resample to fix this, as explained at'
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' https://github.com/fepegar/torchio/issues/647#issuecomment-913025695'
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' https://github.com/TorchIO-project/torchio/issues/647#issuecomment-913025695'
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)
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raise RuntimeError(message) from e
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‎src/torchio/datasets/ixi.py

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Original file line numberDiff line numberDiff line change
@@ -172,7 +172,7 @@ class IXITiny(SubjectsDataset):
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:class:`~torchio.transforms.transform.Transform`.
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download: If set to ``True``, will download the data into :attr:`root`.
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.. _notebook: https://github.com/fepegar/torchio/blob/main/tutorials/README.md
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.. _notebook: https://github.com/TorchIO-project/torchio/blob/main/tutorials/README.md
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"""
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url = 'https://www.dropbox.com/s/ogxjwjxdv5mieah/ixi_tiny.zip?dl=1'

‎src/torchio/datasets/mni/colin.py

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Original file line numberDiff line numberDiff line change
@@ -73,7 +73,7 @@ def __init__(self, version=1998):
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filename=self.filename,
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)
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# Fix label map (https://github.com/fepegar/torchio/issues/220)
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# Fix label map (https://github.com/TorchIO-project/torchio/issues/220)
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if version == 2008:
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path = self.download_root / 'colin27_cls_tal_hires.nii'
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cls_image = LabelMap(path)

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