From 2ead358072d41ca3419e1ce8e082c3f792fdd068 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Thu, 28 Sep 2023 17:33:53 +0200 Subject: [PATCH 1/2] =?UTF-8?q?MNT:=20http://=20=E2=86=92=20https://?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- Dockerfile | 2 +- docs/Makefile | 2 +- docs/installation.rst | 2 +- docs/links.rst | 4 ++-- docs/outputs.rst | 8 ++++---- docs/sphinxext/github_link.py | 4 ++-- docs/usage.rst | 15 ++++++--------- 7 files changed, 17 insertions(+), 20 deletions(-) diff --git a/Dockerfile b/Dockerfile index 8c8498884..cc389d914 100644 --- a/Dockerfile +++ b/Dockerfile @@ -267,7 +267,7 @@ ARG VERSION LABEL org.label-schema.build-date=$BUILD_DATE \ org.label-schema.name="fMRIPrep" \ org.label-schema.description="fMRIPrep - robust fMRI preprocessing tool" \ - org.label-schema.url="http://fmriprep.org" \ + org.label-schema.url="https://fmriprep.org" \ org.label-schema.vcs-ref=$VCS_REF \ org.label-schema.vcs-url="https://github.com/nipreps/fmriprep" \ org.label-schema.version=$VERSION \ diff --git a/docs/Makefile b/docs/Makefile index adb9cd853..6a720dff2 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -9,7 +9,7 @@ BUILDDIR = _build # User-friendly check for sphinx-build ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) - $(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don\'t have Sphinx installed, grab it from http://sphinx-doc.org/) + $(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don\'t have Sphinx installed, grab it from https://www.sphinx-doc.org/) endif # Internal variables. diff --git a/docs/installation.rst b/docs/installation.rst index 0d729d6b3..631bb056a 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -94,6 +94,6 @@ Sherlock enables `the following data transfer options `_. Alternatively, more comprehensive solutions such as `Datalad -`_ will handle data transfers with the appropriate +`_ will handle data transfers with the appropriate settings and commands. Datalad also performs version control over your data. diff --git a/docs/links.rst b/docs/links.rst index f8c5defab..67d6a480d 100644 --- a/docs/links.rst +++ b/docs/links.rst @@ -1,5 +1,5 @@ -.. _Nipype: http://nipype.readthedocs.io/en/latest/ -.. _BIDS: http://bids.neuroimaging.io +.. _Nipype: https://nipype.readthedocs.io/en/latest/ +.. _BIDS: https://bids.neuroimaging.io/ .. _`BIDS Derivatives`: https://bids-specification.readthedocs.io/en/stable/05-derivatives/01-introduction.html .. _`BEP 011`: https://bids-specification.readthedocs.io/en/bep011/05-derivatives/04-structural-derivatives.html .. _`BEP 012`: https://bids-specification.readthedocs.io/en/bep012/05-derivatives/05-functional-derivatives.html diff --git a/docs/outputs.rst b/docs/outputs.rst index cdd1c6e26..c7b63ef3c 100644 --- a/docs/outputs.rst +++ b/docs/outputs.rst @@ -607,7 +607,7 @@ the following invocation:: .. [Behzadi2007] Behzadi Y, Restom K, Liau J, Liu TT, A component-based noise correction method (CompCor) for BOLD and perfusion-based fMRI. NeuroImage. 2007. - doi:`10.1016/j.neuroimage.2007.04.042 `_ + doi:`10.1016/j.neuroimage.2007.04.042 `_ .. [Ciric2017] Ciric R, Wolf DH, Power JD, Roalf DR, Baum GL, Ruparel K, Shinohara RT, Elliott MA, Eickhoff SB, Davatzikos C., Gur RC, Gur RE, Bassett DS, Satterthwaite TD. @@ -617,7 +617,7 @@ the following invocation:: .. [Greve2013] Greve DN, Brown GG, Mueller BA, Glover G, Liu TT, A Survey of the Sources of Noise in fMRI. Psychometrika. 2013. - doi:`10.1007/s11336-013-9344-2 `_ + doi:`10.1007/s11336-013-9344-2 `_ .. [Friston1996] Friston KJ1, Williams S, Howard R, Frackowiak RS, Turner R, Movement‐Related effects in fMRI time‐series. Magnetic Resonance in Medicine. 1996. @@ -634,7 +634,7 @@ the following invocation:: .. [Muschelli2014] Muschelli J, Nebel MB, Caffo BS, Barber AD, Pekar JJ, Mostofsky SH, Reduction of motion-related artifacts in resting state fMRI using aCompCor. NeuroImage. 2014. - doi:`10.1016/j.neuroimage.2014.03.028 `_ + doi:`10.1016/j.neuroimage.2014.03.028 `_ .. [Parkes2018] Parkes L, Fulcher B, Yücel M, Fornito A, An evaluation of the efficacy, reliability, and sensitivity of motion correction strategies for resting-state functional MRI. NeuroImage. 2018. @@ -653,7 +653,7 @@ the following invocation:: doi:`10.1016/j.neuroimage.2011.10.018 `_ .. [Power2016] Power JD, A simple but useful way to assess fMRI scan qualities. NeuroImage. 2016. - doi:`10.1016/j.neuroimage.2016.08.009 `_ + doi:`10.1016/j.neuroimage.2016.08.009 `_ .. [Provins2022] Provins C et al., Quality control and nuisance regression of fMRI, looking out where signal should not be found. Proc. Intl. Soc. Mag. Reson. Med. 31, London (UK). 2022 diff --git a/docs/sphinxext/github_link.py b/docs/sphinxext/github_link.py index 47ff2a76f..f15ff9138 100644 --- a/docs/sphinxext/github_link.py +++ b/docs/sphinxext/github_link.py @@ -30,10 +30,10 @@ def _linkcode_resolve(domain, info, package, url_fmt, revision): >>> _linkcode_resolve('py', {'module': 'tty', ... 'fullname': 'setraw'}, ... package='tty', - ... url_fmt='http://hg.python.org/cpython/file/' + ... url_fmt='https://hg.python.org/cpython/file/' ... '{revision}/Lib/{package}/{path}#L{lineno}', ... revision='xxxx') - 'http://hg.python.org/cpython/file/xxxx/Lib/tty/tty.py#L18' + 'https://hg.python.org/cpython/file/xxxx/Lib/tty/tty.py#L18' """ if revision is None: diff --git a/docs/usage.rst b/docs/usage.rst index bc72f2668..503753811 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -18,7 +18,7 @@ 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 *fMRIPRep* depends on the Installation_ method. The common parts of the command follow the `BIDS-Apps @@ -188,27 +188,24 @@ Because processing this emerging type of datasets (*densely sampled neuroimaging Troubleshooting --------------- -Logs and crashfiles are outputted into the +Logs and crashfiles are output into the ``/fmriprep/sub-/log`` directory. -Information on how to customize and understand these files can be found on the -`nipype debugging `_ -page. **Support and communication**. -The documentation of this project is found here: http://fmriprep.readthedocs.org/en/latest/. +The documentation of this project is found here: https://fmriprep.readthedocs.org/en/latest/. All bugs, concerns and enhancement requests for this software can be submitted here: https://github.com/nipreps/fmriprep/issues. If you have a problem or would like to ask a question about how to use *fMRIPRep*, -please submit a question to `NeuroStars.org `_ with an ``fmriprep`` tag. +please submit a question to `NeuroStars.org `_ with an ``fmriprep`` tag. NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics. Previous questions about *fMRIPRep* are available here: -http://neurostars.org/tags/fmriprep/ +https://neurostars.org/tag/fmriprep/ To participate in the *fMRIPRep* development-related discussions please use the -following mailing list: http://mail.python.org/mailman/listinfo/neuroimaging +following mailing list: https://mail.python.org/mailman/listinfo/neuroimaging Please add *[fmriprep]* to the subject line when posting on the mailing list. From 96700bea7cdd887e070cc200f730e616134c355d Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Mon, 2 Oct 2023 22:22:33 +0200 Subject: [PATCH 2/2] Put back a (current) link to Debugging Nipype --- docs/usage.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/usage.rst b/docs/usage.rst index 503753811..438defbb2 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -190,6 +190,9 @@ Troubleshooting --------------- Logs and crashfiles are output into the ``/fmriprep/sub-/log`` directory. +Information on how to customize and understand these files can be found on the +`Debugging Nipype Workflows `_ +page. **Support and communication**. The documentation of this project is found here: https://fmriprep.readthedocs.org/en/latest/.