From c9473c26e1913068eb208012314a68fa994c3fad Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
<3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Fri, 13 Oct 2023 23:15:02 +0200
Subject: [PATCH] =?UTF-8?q?DOC:=20http://=20=E2=86=92=20htttps://?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
CONTRIBUTING.md | 2 +-
Dockerfile | 2 +-
docs/links.rst | 6 ++---
docs/usage.rst | 2 +-
smriprep/data/boilerplate.bib | 24 ++++++++++----------
smriprep/data/tests/dataset_description.json | 2 +-
6 files changed, 19 insertions(+), 19 deletions(-)
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 97b5e3d286..c66a89eac8 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -223,7 +223,7 @@ You're awesome. :wave::smiley:
[link_git]: https://git-scm.com/
[link_handbook]: https://guides.github.com/introduction/git-handbook/
-[link_swc_intro]: http://swcarpentry.github.io/git-novice/
+[link_swc_intro]: https://swcarpentry.github.io/git-novice/
[writing_formatting_github]: https://help.github.com/articles/getting-started-with-writing-and-formatting-on-github
[markdown]: https://daringfireball.net/projects/markdown
diff --git a/Dockerfile b/Dockerfile
index 0494a1fd69..a14ec26dfc 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -258,7 +258,7 @@ ARG VERSION
LABEL org.label-schema.build-date=$BUILD_DATE \
org.label-schema.name="sMRIPrep" \
org.label-schema.description="sMRIPrep - robust sMRI preprocessing tool" \
- org.label-schema.url="http://nipreps.org/smriprep" \
+ org.label-schema.url="https://www.nipreps.org/smriprep" \
org.label-schema.vcs-ref=$VCS_REF \
org.label-schema.vcs-url="https://github.com/nipreps/smriprep" \
org.label-schema.version=$VERSION \
diff --git a/docs/links.rst b/docs/links.rst
index 03a607afd1..45827d3e8a 100644
--- a/docs/links.rst
+++ b/docs/links.rst
@@ -1,7 +1,7 @@
.. _fMRIPrep: https://github.com/nipreps/fmriprep
.. _FreeSurfer: https://surfer.nmr.mgh.harvard.edu/
-.. _Nipype: http://nipype.readthedocs.io/en/latest/
-.. _BIDS: http://bids.neuroimaging.io
+.. _Nipype: https://nipype.readthedocs.io/en/latest/
+.. _BIDS: https://bids.neuroimaging.io/
.. _Installation: installation.html
.. _workflows: workflows.html
.. _FSL: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/
@@ -12,4 +12,4 @@
.. _`Docker installation`: https://docs.docker.com/install/
.. _`Docker Hub`: https://hub.docker.com/r/nipreps/smriprep/tags
.. _Singularity: https://github.com/singularityware/singularity
-.. _TACC: https://www.tacc.utexas.edu/
\ No newline at end of file
+.. _TACC: https://www.tacc.utexas.edu/
diff --git a/docs/usage.rst b/docs/usage.rst
index 6887c2e1b6..462502c542 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -14,7 +14,7 @@ The input dataset is required to be in valid :abbr:`BIDS (Brain Imaging Data
Structure)` format, and it must include at least one T1w structural image and
(unless disabled with a flag) a BOLD series.
We highly recommend that you validate your dataset with the free, online
-`BIDS Validator `_.
+`BIDS Validator `_.
The exact command to run *sMRIPrep* depends on the Installation_ method.
The common parts of the command follow the `BIDS-Apps
diff --git a/smriprep/data/boilerplate.bib b/smriprep/data/boilerplate.bib
index 93a5db1b7f..86ace5ba20 100644
--- a/smriprep/data/boilerplate.bib
+++ b/smriprep/data/boilerplate.bib
@@ -69,7 +69,7 @@ @article{fs_reconall
pages = {179-194},
shorttitle = {Cortical Surface-Based Analysis},
title = {Cortical Surface-Based Analysis: I. Segmentation and Surface Reconstruction},
- url = {http://www.sciencedirect.com/science/article/pii/S1053811998903950},
+ url = {https://www.sciencedirect.com/science/article/pii/S1053811998903950},
volume = 9,
year = 1999
}
@@ -82,7 +82,7 @@ @article{mindboggle
number = 2,
pages = {e1005350},
title = {Mindboggling morphometry of human brains},
- url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005350},
+ url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005350},
volume = 13,
year = 2017
}
@@ -130,7 +130,7 @@ @article{ants
pages = {26-41},
shorttitle = {Symmetric diffeomorphic image registration with cross-correlation},
title = {Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain},
- url = {http://www.sciencedirect.com/science/article/pii/S1361841507000606},
+ url = {https://www.sciencedirect.com/science/article/pii/S1361841507000606},
volume = 12,
year = 2008
}
@@ -155,7 +155,7 @@ @article{fieldmapless1
journal = {Frontiers in Neuroinformatics},
language = {English},
title = {Evaluation of Field Map and Nonlinear Registration Methods for Correction of Susceptibility Artifacts in Diffusion {MRI}},
- url = {http://journal.frontiersin.org/article/10.3389/fninf.2017.00017/full},
+ url = {https://www.frontiersin.org/articles/10.3389/fninf.2017.00017/full},
volume = 11,
year = 2017
}
@@ -179,7 +179,7 @@ @article{fieldmapless3
number = 3,
pages = {e0152472},
title = {Characterization and Correction of Geometric Distortions in 814 Diffusion Weighted Images},
- url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152472},
+ url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152472},
volume = 11,
year = 2016
}
@@ -188,7 +188,7 @@ @article{flirt
title = {A global optimisation method for robust affine registration of brain images},
volume = {5},
issn = {1361-8415},
- url = {http://www.sciencedirect.com/science/article/pii/S1361841501000366},
+ url = {https://www.sciencedirect.com/science/article/pii/S1361841501000366},
doi = {10.1016/S1361-8415(01)00036-6},
number = {2},
urldate = {2018-07-27},
@@ -207,7 +207,7 @@ @article{mcflirt
number = 2,
pages = {825-841},
title = {Improved Optimization for the Robust and Accurate Linear Registration and Motion Correction of Brain Images},
- url = {http://www.sciencedirect.com/science/article/pii/S1053811902911328},
+ url = {https://www.sciencedirect.com/science/article/pii/S1053811902911328},
volume = 17,
year = 2002
}
@@ -233,7 +233,7 @@ @article{aroma
pages = {267-277},
shorttitle = {ICA-AROMA},
title = {ICA-{AROMA}: A robust {ICA}-based strategy for removing motion artifacts from fMRI data},
- url = {http://www.sciencedirect.com/science/article/pii/S1053811915001822},
+ url = {https://www.sciencedirect.com/science/article/pii/S1053811915001822},
volume = 112,
year = 2015
}
@@ -246,7 +246,7 @@ @article{power_fd_dvars
number = {Supplement C},
pages = {320-341},
title = {Methods to detect, characterize, and remove motion artifact in resting state fMRI},
- url = {http://www.sciencedirect.com/science/article/pii/S1053811913009117},
+ url = {https://www.sciencedirect.com/science/article/pii/S1053811913009117},
volume = 84,
year = 2014
}
@@ -259,7 +259,7 @@ @article{lanczos
number = 1,
pages = {76-85},
title = {Evaluation of Noisy Data},
- url = {http://epubs.siam.org/doi/10.1137/0701007},
+ url = {https://epubs.siam.org/doi/10.1137/0701007},
volume = 1,
year = 1964
}
@@ -272,7 +272,7 @@ @article{compcor
number = 1,
pages = {90-101},
title = {A component based noise correction method ({CompCor}) for {BOLD} and perfusion based fMRI},
- url = {http://www.sciencedirect.com/science/article/pii/S1053811907003837},
+ url = {https://www.sciencedirect.com/science/article/pii/S1053811907003837},
volume = 37,
year = 2007
}
@@ -285,7 +285,7 @@ @article{hcppipelines
pages = {105-124},
series = {Mapping the Connectome},
title = {The minimal preprocessing pipelines for the Human Connectome Project},
- url = {http://www.sciencedirect.com/science/article/pii/S1053811913005053},
+ url = {https://www.sciencedirect.com/science/article/pii/S1053811913005053},
volume = 80,
year = 2013
}
diff --git a/smriprep/data/tests/dataset_description.json b/smriprep/data/tests/dataset_description.json
index fed83d6935..4081f38b3a 100644
--- a/smriprep/data/tests/dataset_description.json
+++ b/smriprep/data/tests/dataset_description.json
@@ -1,6 +1,6 @@
{
"BIDSVersion": "1.0.0",
- "License": "This dataset is made available under the Public Domain Dedication and License \nv1.0, whose full text can be found at \nhttp://www.opendatacommons.org/licenses/pddl/1.0/. \nWe hope that all users will follow the ODC Attribution/Share-Alike \nCommunity Norms (http://www.opendatacommons.org/norms/odc-by-sa/); \nin particular, while not legally required, we hope that all users \nof the data will acknowledge the OpenfMRI project and NSF Grant \nOCI-1131441 (R. Poldrack, PI) in any publications.",
+ "License": "This dataset is made available under the Public Domain Dedication and License \nv1.0, whose full text can be found at \nhttps://opendatacommons.org/licenses/pddl/1-0/. \nWe hope that all users will follow the ODC Attribution/Share-Alike \nCommunity Norms (https://opendatacommons.org/norms/odc-by-sa/); \nin particular, while not legally required, we hope that all users \nof the data will acknowledge the OpenfMRI project and NSF Grant \nOCI-1131441 (R. Poldrack, PI) in any publications.",
"Name": "Balloon Analog Risk Task",
"ReferencesAndLinks": ["Schonberg TS, Fox CR, Mumford JA, Congdon E, Trepel C, Poldrack RA (2012). Decreasing ventromedial prefrontal cortex activity during sequential risk-taking: An fMRI investigation of the Balloon Analogue Risk Task. Frontiers in Decision Neuroscience, 6:80 doi: 10.3389/fnins.2012.00080"]
}