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"] }