Fix some links in docs (#1213)

fepegar · Sep 24, 2024 · 0314926 · 0314926
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diff --git a/README.md b/README.md
@@ -42,7 +42,7 @@ at [OpenAI](https://openai.com/) ([link](https://jack-clark.net/2020/03/17/)).
             <a href="https://torchio.rtfd.io/?badge=latest">
                 <img src="https://img.shields.io/readthedocs/torchio?label=Docs&logo=Read%20the%20Docs" alt="Documentation status">
             </a>
-            <a href="https://codecov.io/github/fepegar/torchio">
+            <a href="https://app.codecov.io/github/fepegar/torchio">
                 <img src="https://codecov.io/gh/fepegar/torchio/branch/main/graphs/badge.svg" alt="Coverage status">
             </a>
         </td>
@@ -58,7 +58,7 @@ at [OpenAI](https://openai.com/) ([link](https://jack-clark.net/2020/03/17/)).
             <a href="https://scrutinizer-ci.com/g/fepegar/torchio/?branch=main">
                 <img src="https://img.shields.io/scrutinizer/g/fepegar/torchio.svg?label=Code%20quality&logo=scrutinizer" alt="Code quality">
             </a>
-            <a href="https://codeclimate.com/github/fepegar/torchio/maintainability">
+            <a href="https://codeclimate.com/github/fepegar/torchio">
                 <img src="https://api.codeclimate.com/v1/badges/518673e49a472dd5714d/maintainability" alt="Code maintainability">
             </a>
             <a href="https://github.com/pre-commit/pre-commit">

diff --git a/docs/source/README.rst b/docs/source/README.rst
@@ -94,7 +94,7 @@ If you found a bug or have a feature request, please open an issue:
    :alt: Code style: Ruff
 
 .. |Coverage-codecov| image:: https://codecov.io/gh/fepegar/torchio/branch/main/graphs/badge.svg
-   :target: https://codecov.io/github/fepegar/torchio
+   :target: https://app.codecov.io/github/fepegar/torchio
    :alt: Coverage status
 
 .. |Code-Quality| image:: https://img.shields.io/scrutinizer/g/fepegar/torchio.svg?label=Code%20quality&logo=scrutinizer
@@ -118,7 +118,7 @@ If you found a bug or have a feature request, please open an issue:
    :alt: Twitter commits
 
 .. |Code-Maintainability| image:: https://api.codeclimate.com/v1/badges/518673e49a472dd5714d/maintainability
-   :target: https://codeclimate.com/github/fepegar/torchio/maintainability
+   :target: https://codeclimate.com/github/fepegar/torchio
    :alt: Maintainability
 
 .. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white

diff --git a/src/torchio/datasets/bite.py b/src/torchio/datasets/bite.py
@@ -49,7 +49,7 @@ class BITE3(BITE):
     Please check the `BITE website`_ for more information and
     acknowledgments instructions.
 
-    .. _BITE website: http://nist.mni.mcgill.ca/bite-brain-images-of-tumors-for-evaluation-database/
+    .. _BITE website: https://nist.mni.mcgill.ca/bite-brain-images-of-tumors-for-evaluation-database/
 
     Args:
         root: Root directory to which the dataset will be downloaded.

diff --git a/src/torchio/datasets/mni/colin.py b/src/torchio/datasets/mni/colin.py
@@ -26,7 +26,7 @@ class Colin27(SubjectMNI):
     r"""Colin27 MNI template.
 
     More information can be found in the website of the
-    `1998 <http://nist.mni.mcgill.ca/colin-27-average-brain/>`_ and
+    `1998 <https://nist.mni.mcgill.ca/colin-27-average-brain/>`_ and
     `2008 <http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres>`_
     versions.
 

diff --git a/src/torchio/datasets/mni/mni.py b/src/torchio/datasets/mni/mni.py
@@ -5,7 +5,7 @@
 class SubjectMNI(_RawSubjectCopySubject):
     """Atlases from the Montreal Neurological Institute (MNI).
 
-    See `the website <http://nist.mni.mcgill.ca/?page_id=714>`_ for more
+    See `the website <https://nist.mni.mcgill.ca/?page_id=714>`_ for more
     information.
     """
 

diff --git a/src/torchio/datasets/mni/pediatric.py b/src/torchio/datasets/mni/pediatric.py
@@ -25,10 +25,10 @@ def format_age(n):
 class Pediatric(SubjectMNI):
     """MNI pediatric atlases.
 
-    See `the MNI website <http://nist.mni.mcgill.ca/pediatric-atlases-4-5-18-5y/>`_
+    See `the MNI website <https://nist.mni.mcgill.ca/pediatric-atlases-4-5-18-5y/>`_
     for more information.
 
-    .. image:: http://nist.mni.mcgill.ca/wp-content/uploads/2016/04/nihpd_asym_all_sm.jpg
+    .. image:: https://nist.mni.mcgill.ca/wp-content/uploads/2016/04/nihpd_asym_all_sm.jpg
         :alt: Pediatric MNI template
 
     Arguments:

diff --git a/src/torchio/transforms/preprocessing/intensity/histogram_standardization.py b/src/torchio/transforms/preprocessing/intensity/histogram_standardization.py
@@ -118,7 +118,7 @@ def train(
             cutoff: Optional minimum and maximum quantile values,
                 respectively, that are used to select a range of intensity of
                 interest. Equivalent to :math:`pc_1` and :math:`pc_2` in
-                `Nyúl and Udupa's paper <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.204.102&rep=rep1&type=pdf>`_.
+                `Nyúl and Udupa's paper <https://pubmed.ncbi.nlm.nih.gov/10571928/>`_.
             mask_path: Path (or list of paths) to a binary image that will be
                 used to select the voxels use to compute the stats during
                 histogram training. If ``None``, all voxels in the image will