Merge remote-tracking branch 'upstream/master' into next

nipreps · Nov 10, 2023 · 619b157 · 619b157
2 parents c238409 + 1b3da52
commit 619b157
Show file tree

Hide file tree

Showing 9 changed files with 24 additions and 25 deletions.
diff --git 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
@@ -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
@@ -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/
+.. _TACC: https://www.tacc.utexas.edu/
diff --git 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 <http://bids-standard.github.io/bids-validator/>`_.
+`BIDS Validator <https://bids-standard.github.io/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
@@ -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/io_spec.json b/smriprep/data/io_spec.json
@@ -155,13 +155,12 @@
           ".nii.gz",
           ".nii"
         ]
-      }
     }
   },
   "patterns": [
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio>}.{extension<nii|nii.gz|json>|nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}.{extension<txt|h5>}",
-    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}]_hemi-{hemi<L|R>}_{suffix<white|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|thickness|sulc|curv>}.{extension<surf.gii|shape.gii>}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}]_hemi-{hemi<L|R>}[_space-{space}][_desc-{desc}]_{suffix<white|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|thickness|sulc|curv>}.{extension<surf.gii|shape.gii>}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}]_desc-{desc}_{suffix<mask>|mask}.{extension<nii|nii.gz|json>|nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}.{extension<nii|nii.gz|json>|nii.gz}"
   ]

diff --git 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"]
 }
diff --git a/smriprep/interfaces/workbench.py b/smriprep/interfaces/workbench.py
@@ -399,7 +399,7 @@ class SurfaceModifySphere(WBCommand):
     a sphere, which can suffer from problems generally not present in
     -surface-sphere-project-unproject.  If the sphere should already be
     centered around the origin, using -recenter may still shift it slightly
-    before changing the radius, which is likely to be undesireable.
+    before changing the radius, which is likely to be undesirable.
 
     If <sphere-in> is not close to spherical, or not centered around the
     origin and -recenter is not used, a warning is printed.

diff --git a/wrapper/smriprep_docker.py b/wrapper/smriprep_docker.py
@@ -164,9 +164,9 @@ def _get_posargs(usage):
 
     # Make sure we're not clobbering options we don't mean to
     overlap = set(w_flags).intersection(t_flags)
-    expected_overlap = set(
-        ["h", "version", "w", "d", "fs-license-file", "use-plugin", "fs-subjects-dir"]
-    )
+    expected_overlap = {
+        "h", "version", "w", "d", "fs-license-file", "use-plugin", "fs-subjects-dir"
+    }
 
     assert overlap == expected_overlap, "Clobbering options: {}".format(
         ", ".join(overlap - expected_overlap)