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TorchIO-project · Jan 30, 2025 · 2f37f69 · 2f37f69
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -61,7 +61,7 @@ body:
         Please run this command in your console and paste the output below
 
         ```shell
-        python <(curl -s https://raw.githubusercontent.com/fepegar/torchio/main/print_system.py)
+        python <(curl -s https://raw.githubusercontent.com/TorchIO-Project/main/print_system.py)
         ```
       placeholder: Your system info
       render: shell
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -1,5 +1,5 @@
 blank_issues_enabled: true
 contact_links:
   - name: ❓ Discussions tab
-    url: https://github.com/fepegar/torchio/discussions/new
+    url: https://github.com/TorchIO-Project/discussions/new
     about: Ask and answer TorchIO-related questions or start a general discussion
diff --git a/.github/ISSUE_TEMPLATE/not_working.yml b/.github/ISSUE_TEMPLATE/not_working.yml
@@ -70,7 +70,7 @@ body:
         Please run this command in your console and paste the output below
 
         ```shell
-        python <(curl -s https://raw.githubusercontent.com/fepegar/torchio/main/print_system.py)
+        python <(curl -s https://raw.githubusercontent.com/TorchIO-Project/main/print_system.py)
         ```
       placeholder: Your system info
       render: shell
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -13,10 +13,10 @@ Fixes #{issue_number}.
 <!-- You do not need to complete all the items by the time you submit the pull
 request, but most likely the changes will only be merged if all the tasks are
 done. See more information about the submission process in the
-CONTRIBUTING (https://github.com/fepegar/torchio/blob/main/CONTRIBUTING.rst) docs. -->
+CONTRIBUTING (https://github.com/TorchIO-Project/blob/main/CONTRIBUTING.rst) docs. -->
 
 <!-- Write an `x` in all the boxes that apply -->
-- [ ] 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`)
+- [ ] I have read the [`CONTRIBUTING`](https://github.com/TorchIO-Project/blob/main/CONTRIBUTING.rst) docs and have a developer setup (especially important are `pre-commit`and `pytest`)
 - [ ] Non-breaking change (would not break existing functionality)
 - [ ] Breaking change (would cause existing functionality to change)
 - [ ] Tests added or modified to cover the changes

diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/CITATION.cff b/CITATION.cff
@@ -5,7 +5,7 @@ authors:
     given-names: Fernando
     orcid: https://orcid.org/0000-0001-9090-3024
 title: "TorchIO"
-repository-code: "https://github.com/fepegar/torchio"
+repository-code: "https://github.com/TorchIO-Project/torchio"
 preferred-citation:
   type: article
   authors:

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -16,7 +16,7 @@ Report bugs
 ~~~~~~~~~~~
 
 Report bugs
-`on GitHub <https://github.com/fepegar/torchio/issues/new?assignees=&labels=bug&template=bug_report.md&title=>`_.
+`on GitHub <https://github.com/TorchIO-Project/issues/new?assignees=&labels=bug&template=bug_report.md&title=>`_.
 
 If you are reporting a bug, please include:
 
@@ -46,7 +46,7 @@ articles, and such.
 Submit feedback
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://github.com/fepegar/torchio/issues.
+The best way to send feedback is to file an issue at https://github.com/TorchIO-Project/issues.
 
 If you are proposing a feature:
 

diff --git a/README.md b/README.md
diff --git a/docs/examples/plot_custom_z_spacing.py b/docs/examples/plot_custom_z_spacing.py
@@ -6,7 +6,7 @@
 image spacing across one axis only.
 
 Inspired by
-`this discussion <https://github.com/fepegar/torchio/discussions/885>`_.
+`this discussion <https://github.com/TorchIO-Project/discussions/885>`_.
 """
 
 import torch

diff --git a/docs/source/README.rst b/docs/source/README.rst
@@ -27,37 +27,37 @@ the `PyTorch Developer Day 2021 <https://pytorch.org/blog/pytorch-developer-day-
 
 Many groups have used TorchIO for their research.
 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
-`dependents list <https://github.com/fepegar/torchio/network/dependents>`_ is
+`dependents list <https://github.com/TorchIO-Project/network/dependents>`_ is
 available on GitHub.
 
-The code is available on `GitHub <https://github.com/fepegar/torchio>`_.
+The code is available on `GitHub <https://github.com/TorchIO-Project>`_.
 If you like TorchIO, please go to the repository and star it!
 
 .. raw:: html
 
-   <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>
+   <a class="github-button" href="https://github.com/TorchIO-Project" data-icon="octicon-star" data-show-count="true" aria-label="Star TorchIO-Project on GitHub">Star</a>
    <script async defer src="https://buttons.github.io/buttons.js"></script>
 
 See :doc:`Getting started <quickstart>` for installation instructions and a
 usage overview.
 
 Contributions are more than welcome.
-Please check our `contributing guide <https://github.com/fepegar/torchio/blob/main/CONTRIBUTING.rst>`_
+Please check our `contributing guide <https://github.com/TorchIO-Project/blob/main/CONTRIBUTING.rst>`_
 if you would like to contribute.
 
 If you have questions, feel free to ask in the discussions tab:
 
 .. raw:: html
 
-   <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>
+   <a class="github-button" href="https://github.com/TorchIO-Project/discussions" data-icon="octicon-comment-discussion" aria-label="Discuss TorchIO-Project on GitHub">Discuss</a>
    <script async defer src="https://buttons.github.io/buttons.js"></script>
 
 If you found a bug or have a feature request, please open an issue:
 
 .. raw:: html
 
    <!-- Place this tag where you want the button to render. -->
-   <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>
+   <a class="github-button" href="https://github.com/TorchIO-Project/issues" data-icon="octicon-issue-opened" data-show-count="true" aria-label="Issue TorchIO-Project on GitHub">Issue</a>
    <!-- Place this tag in your head or just before your close body tag. -->
    <script async defer src="https://buttons.github.io/buttons.js"></script>
 
@@ -78,35 +78,35 @@ If you found a bug or have a feature request, please open an issue:
    :alt: Conda version
 
 .. |Google-Colab-notebook| image:: https://colab.research.google.com/assets/colab-badge.svg
-   :target: https://github.com/fepegar/torchio/blob/main/tutorials/README.md
+   :target: https://github.com/TorchIO-Project/blob/main/tutorials/README.md
    :alt: Google Colab notebooks
 
 .. |Docs-status| image:: https://img.shields.io/readthedocs/torchio?label=Docs&logo=Read%20the%20Docs
    :target: https://torchio.rtfd.io/?badge=latest
    :alt: Documentation status
 
-.. |Tests-status| image:: https://github.com/fepegar/torchio/actions/workflows/tests.yml/badge.svg
-   :target: https://github.com/fepegar/torchio/actions/workflows/tests.yml
+.. |Tests-status| image:: https://github.com/TorchIO-Project/actions/workflows/tests.yml/badge.svg
+   :target: https://github.com/TorchIO-Project/actions/workflows/tests.yml
    :alt: Tests status
 
 .. |Ruff| image:: https://camo.githubusercontent.com/bb88127790fb054cba2caf3f3be2569c1b97bb45a44b47b52d738f8781a8ede4/68747470733a2f2f696d672e736869656c64732e696f2f656e64706f696e743f75726c3d68747470733a2f2f7261772e67697468756275736572636f6e74656e742e636f6d2f636861726c6965726d617273682f727566662f6d61696e2f6173736574732f62616467652f76312e6a736f6e
    :target: https://docs.astral.sh/ruff/
    :alt: Code style: Ruff
 
-.. |Coverage-codecov| image:: https://codecov.io/gh/fepegar/torchio/branch/main/graphs/badge.svg
-   :target: https://app.codecov.io/github/fepegar/torchio
+.. |Coverage-codecov| image:: https://codecov.io/gh/TorchIO-Project/branch/main/graphs/badge.svg
+   :target: https://app.codecov.io/github/TorchIO-Project
    :alt: Coverage status
 
-.. |Code-Quality| image:: https://img.shields.io/scrutinizer/g/fepegar/torchio.svg?label=Code%20quality&logo=scrutinizer
-   :target: https://scrutinizer-ci.com/g/fepegar/torchio/?branch=main
+.. |Code-Quality| image:: https://img.shields.io/scrutinizer/g/TorchIO-Project.svg?label=Code%20quality&logo=scrutinizer
+   :target: https://scrutinizer-ci.com/g/TorchIO-Project/?branch=main
    :alt: Code quality
 
 .. |YouTube| image:: https://img.shields.io/youtube/views/UEUVSw5-M9M?label=watch&style=social
    :target: https://www.youtube.com/watch?v=UEUVSw5-M9M
    :alt: YouTube
 
 .. |Code-Maintainability| image:: https://api.codeclimate.com/v1/badges/518673e49a472dd5714d/maintainability
-   :target: https://codeclimate.com/github/fepegar/torchio
+   :target: https://codeclimate.com/github/TorchIO-Project
    :alt: Maintainability
 
 .. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white

diff --git a/docs/source/_templates/layout.html b/docs/source/_templates/layout.html
@@ -20,7 +20,7 @@
 
 {% block document %}
 {{super()}}
-    <a href="https://github.com/fepegar/torchio">
+    <a href="https://github.com/TorchIO-Project">
         <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">
     </a>
 {% endblock %}
diff --git a/docs/source/datasets.rst b/docs/source/datasets.rst
@@ -15,7 +15,7 @@ GitHub repository:
 
 .. raw:: html
 
-   <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>
+   <a class="github-button" href="https://github.com/TorchIO-Project/discussions" data-icon="octicon-comment-discussion" aria-label="Discuss TorchIO-Project on GitHub">Discuss</a>
    <script async defer src="https://buttons.github.io/buttons.js"></script>
 
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -12,5 +12,5 @@
     datasets
     interfaces/index
     auto_examples/index
-    GitHub repository <https://github.com/fepegar/torchio>
+    GitHub repository <https://github.com/TorchIO-Project>
     Paper <https://www.sciencedirect.com/science/article/pii/S0169260721003102>
diff --git a/docs/source/quickstart.rst b/docs/source/quickstart.rst
@@ -27,7 +27,7 @@ If you would like to install Matplotlib to use the plotting features, use::
 
 
 If you are on Windows and have
-`trouble installing TorchIO <https://github.com/fepegar/torchio/issues/343>`_,
+`trouble installing TorchIO <https://github.com/TorchIO-Project/issues/343>`_,
 try `installing PyTorch <https://pytorch.org/get-started/locally/>`_ with
 `conda <https://docs.conda.io/en/latest/miniconda.html>`_ before pip-installing
 TorchIO.
@@ -113,7 +113,7 @@ Tutorials
 |Google-Colab-notebook|
 
 The best way to quickly understand and try the library is the
-`Jupyter Notebooks <https://github.com/fepegar/torchio/blob/main/tutorials/README.md>`_
+`Jupyter Notebooks <https://github.com/TorchIO-Project/blob/main/tutorials/README.md>`_
 hosted on Google Colab.
 
 They include multiple examples and visualization of most of the classes,
@@ -122,5 +122,5 @@ brain segmentation on :math:`T_1`-weighted MRI with full volumes and
 with subvolumes (aka patches or windows).
 
 .. |Google-Colab-notebook| image:: https://colab.research.google.com/assets/colab-badge.svg
-   :target: https://github.com/fepegar/torchio/blob/main/tutorials/README.md
+   :target: https://github.com/TorchIO-Project/blob/main/tutorials/README.md
    :alt: Google Colab notebook
diff --git a/pyproject.toml b/pyproject.toml
@@ -65,10 +65,10 @@ torchio-transform = "torchio.cli.apply_transform:app"
 
 [project.urls]
 Homepage = "http://torchio.rtfd.io"
-Source = "https://github.com/fepegar/torchio"
-"Issue tracker" = "https://github.com/fepegar/torchio/issues"
+Source = "https://github.com/TorchIO-Project"
+"Issue tracker" = "https://github.com/TorchIO-Project/issues"
 Documentation = "http://torchio.rtfd.io"
-"Release notes" = "https://github.com/fepegar/torchio/releases"
+"Release notes" = "https://github.com/TorchIO-Project/releases"
 
 [dependency-groups]
 dev = [

diff --git a/src/torchio/constants.py b/src/torchio/constants.py
@@ -24,10 +24,10 @@
 CHANNELS_DIMENSION = 1
 
 # Code repository
-REPO_URL = 'https://github.com/fepegar/torchio/'
+REPO_URL = 'https://github.com/TorchIO-Project/'
 
 # Data repository
-DATA_REPO = 'https://github.com/fepegar/torchio-data/raw/main/data/'
+DATA_REPO = 'https://github.com/TorchIO-Project-data/raw/main/data/'
 
 # Floating point error
 MIN_FLOAT_32 = torch.finfo(torch.float32).eps

diff --git a/src/torchio/data/image.py b/src/torchio/data/image.py
@@ -168,7 +168,7 @@ def __init__(
         if 'channels_last' in kwargs:
             message = (
                 'The "channels_last" keyword argument is deprecated after'
-                ' https://github.com/fepegar/torchio/pull/685 and will be'
+                ' https://github.com/TorchIO-Project/pull/685 and will be'
                 ' removed in the future'
             )
             warnings.warn(message, DeprecationWarning, stacklevel=2)
@@ -242,7 +242,7 @@ def _check_data_loader() -> None:
                 ' will be instances of torchio.Subject with 5D images. Replace'
                 ' your PyTorch DataLoader with a torchio.SubjectsLoader so that'
                 ' the collated batch becomes a dictionary, as expected. See'
-                ' https://github.com/fepegar/torchio/issues/1179 for more'
+                ' https://github.com/TorchIO-Project/issues/1179 for more'
                 ' context about this issue.'
             )
             warnings.warn(message, stacklevel=1)
@@ -480,7 +480,7 @@ def _parse_path(
         if path is None:
             return None
         elif isinstance(path, dict):
-            # https://github.com/fepegar/torchio/pull/838
+            # https://github.com/TorchIO-Project/pull/838
             raise TypeError('The path argument cannot be a dictionary')
         elif self._is_paths_sequence(path):
             return [self._parse_single_path(p) for p in path]  # type: ignore[union-attr]

diff --git a/src/torchio/data/inference/aggregator.py b/src/torchio/data/inference/aggregator.py
@@ -24,7 +24,7 @@ class GridAggregator:
             function. See the `grid aggregator tests`_ for a raw visualization
             of the three modes.
 
-    .. _grid aggregator tests: https://github.com/fepegar/torchio/blob/main/tests/data/inference/test_aggregator.py
+    .. _grid aggregator tests: https://github.com/TorchIO-Project/blob/main/tests/data/inference/test_aggregator.py
 
     .. note:: Adapted from NiftyNet. See `this NiftyNet tutorial
         <https://niftynet.readthedocs.io/en/dev/window_sizes.html>`_ for more
@@ -232,7 +232,7 @@ def get_output_tensor(self) -> torch.Tensor:
             assert isinstance(self._avgmask_tensor, torch.Tensor)  # for mypy
             # true_divide is used instead of / in case the PyTorch version is
             # old and one the operands is int:
-            # https://github.com/fepegar/torchio/issues/526
+            # https://github.com/TorchIO-Project/issues/526
             output = torch.true_divide(
                 self._output_tensor,
                 self._avgmask_tensor,

diff --git a/src/torchio/data/queue.py b/src/torchio/data/queue.py
@@ -91,7 +91,7 @@ class Queue(Dataset):
     and the :class:`~torch.utils.data.DataLoader` used to pop batches from the
     queue.
 
-    .. image:: https://raw.githubusercontent.com/fepegar/torchio/main/docs/images/diagram_patches.svg
+    .. image:: https://raw.githubusercontent.com/TorchIO-Project/main/docs/images/diagram_patches.svg
         :alt: Training with patches
 
     This sketch can be used to experiment and understand how the queue works.

diff --git a/src/torchio/data/sampler/label.py b/src/torchio/data/sampler/label.py
@@ -117,7 +117,7 @@ def get_probabilities_from_label_map(
             raise RuntimeError(message)
         crop_fin_i, crop_fin_j, crop_fin_k = crop_fin = (patch_size - 1) // 2
         fin_i, fin_j, fin_k = spatial_shape - crop_fin
-        # See https://github.com/fepegar/torchio/issues/458
+        # See https://github.com/TorchIO-Project/issues/458
         label_map = label_map[:, ini_i:fin_i, ini_j:fin_j, ini_k:fin_k]
 
         multichannel = label_map.shape[0] > 1
@@ -141,7 +141,7 @@ def get_probabilities_from_label_map(
         if multichannel:
             probability_map = probability_map.sum(dim=0, keepdim=True)
 
-        # See https://github.com/fepegar/torchio/issues/458
+        # See https://github.com/TorchIO-Project/issues/458
         padding = ini_k, crop_fin_k, ini_j, crop_fin_j, ini_i, crop_fin_i
         probability_map = torch.nn.functional.pad(
             probability_map,

diff --git a/src/torchio/data/sampler/weighted.py b/src/torchio/data/sampler/weighted.py
@@ -227,7 +227,7 @@ def sample_probability_map(
                    [ 6808,  6804,  6942,  6809,  6946,  6988,  7002,  6826,  7041]])
         """
         # Get first value larger than random number ensuring the random number
-        # is not exactly 0 (see https://github.com/fepegar/torchio/issues/510)
+        # is not exactly 0 (see https://github.com/TorchIO-Project/issues/510)
         random_number = max(MIN_FLOAT_32, torch.rand(1).item()) * cdf[-1]
 
         random_location_index = np.searchsorted(cdf, random_number)
@@ -242,7 +242,7 @@ def sample_probability_map(
             message = (
                 'Error retrieving probability in weighted sampler.'
                 ' Please report this issue at'
-                ' https://github.com/fepegar/torchio/issues/new?labels=bug&template=bug_report.md'
+                ' https://github.com/TorchIO-Project/issues/new?labels=bug&template=bug_report.md'
             )
             raise RuntimeError(message)
 

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

diff --git a/src/torchio/datasets/ixi.py b/src/torchio/datasets/ixi.py
@@ -172,7 +172,7 @@ class IXITiny(SubjectsDataset):
             :class:`~torchio.transforms.transform.Transform`.
         download: If set to ``True``, will download the data into :attr:`root`.
 
-    .. _notebook: https://github.com/fepegar/torchio/blob/main/tutorials/README.md
+    .. _notebook: https://github.com/TorchIO-Project/blob/main/tutorials/README.md
     """
 
     url = 'https://www.dropbox.com/s/ogxjwjxdv5mieah/ixi_tiny.zip?dl=1'

diff --git a/src/torchio/datasets/mni/colin.py b/src/torchio/datasets/mni/colin.py
@@ -73,7 +73,7 @@ def __init__(self, version=1998):
                 filename=self.filename,
             )
 
-            # Fix label map (https://github.com/fepegar/torchio/issues/220)
+            # Fix label map (https://github.com/TorchIO-Project/issues/220)
             if version == 2008:
                 path = self.download_root / 'colin27_cls_tal_hires.nii'
                 cls_image = LabelMap(path)

diff --git a/src/torchio/transforms/augmentation/spatial/random_affine.py b/src/torchio/transforms/augmentation/spatial/random_affine.py
@@ -348,7 +348,7 @@ def get_affine_transform(self, image):
         # the input space. Intuitively, the passed arguments should take us
         # from the input space to the output space, so we need to invert the
         # transform.
-        # More info at https://github.com/fepegar/torchio/discussions/693
+        # More info at https://github.com/TorchIO-Project/discussions/693
         transform = transform.GetInverse()
 
         if self.invert_transform:

diff --git a/src/torchio/transforms/preprocessing/label/keep_largest_component.py b/src/torchio/transforms/preprocessing/label/keep_largest_component.py
@@ -15,7 +15,7 @@ class KeepLargestComponent(LabelTransform):
         maps with a background and a foreground class. If you are interested in
         extending this transform, please `open a new issue`_.
 
-    .. _open a new issue: https://github.com/fepegar/torchio/issues/new?assignees=&labels=enhancement&template=feature_request.md&title=Improve%20KeepLargestComponent%20transform
+    .. _open a new issue: https://github.com/TorchIO-Project/issues/new?assignees=&labels=enhancement&template=feature_request.md&title=Improve%20KeepLargestComponent%20transform
     """
 
     def apply_transform(self, subject: Subject) -> Subject: