diff --git a/Dockerfile b/Dockerfile index 79d93da07..5a19036ea 100644 --- a/Dockerfile +++ b/Dockerfile @@ -138,7 +138,7 @@ ARG VCS_REF LABEL org.label-schema.build-date=$BUILD_DATE \ org.label-schema.name="MRIQC" \ org.label-schema.description="MRIQC - Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain" \ - org.label-schema.url="http://mriqc.readthedocs.io" \ + org.label-schema.url="https://mriqc.readthedocs.io" \ org.label-schema.vcs-ref=$VCS_REF \ org.label-schema.vcs-url="https://github.com/nipreps/mriqc" \ org.label-schema.version=$VERSION \ diff --git a/NOTICE b/NOTICE index 07d35eae9..a7e7c982c 100644 --- a/NOTICE +++ b/NOTICE @@ -9,7 +9,7 @@ Psychology at Stanford University, Stanford, CA, US. This software contains code ultimately derived from the PCP Quality Assessment Protocol (QAP; -http://preprocessed-connectomes-project.github.io/quality-assessment-protocol) +http://preprocessed-connectomes-project.org/quality-assessment-protocol) by C. Craddock, S. Giavasis, D. Clark, Z. Shezhad, and J. Pellman. This software is also distributed as a Docker container image. diff --git a/README.rst b/README.rst index 8850ef08e..d4ae03314 100644 --- a/README.rst +++ b/README.rst @@ -11,7 +11,7 @@ MRIQC is an open-source project, developed under the following software engineering principles: #. **Modularity and integrability**: MRIQC implements a - `nipype `_ workflow to integrate modular + `nipype `_ workflow to integrate modular sub-workflows that rely upon third party software toolboxes such as ANTs and AFNI. @@ -20,8 +20,8 @@ software engineering principles: processed derivatives. #. **Interoperability and standards**: MRIQC follows the the `brain imaging data structure - (BIDS) `_, and it adopts the `BIDS-App - `_ standard. + (BIDS) `_, and it adopts the `BIDS-App + `_ standard. #. **Reliability and robustness**: the software undergoes frequent vetting sprints by testing its robustness against data variability (acquisition parameters, @@ -39,7 +39,7 @@ Citation Support and communication ------------------------- -The documentation of this project is found here: http://mriqc.readthedocs.io/. +The documentation of this project is found here: https://mriqc.readthedocs.io/. Users can get help using the `mriqc-users google group `_. @@ -54,7 +54,7 @@ of the *NiPreps framework*. *MRIQC* originally derives from, and hence is heavily influenced by, the `PCP Quality Assessment Protocol -`__. +`__. Please check the ``NOTICE`` file for further information. License diff --git a/docs/source/conf.py b/docs/source/conf.py index cf6d112db..946a89ae7 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -322,7 +322,7 @@ "nibabel": ("https://nipy.org/nibabel/", None), "nipype": ("https://nipype.readthedocs.io/en/latest/", None), "numpy": ("https://numpy.org/doc/stable/", None), - "pandas": ("http://pandas.pydata.org/pandas-docs/dev", None), + "pandas": ("https://pandas.pydata.org/pandas-docs/dev/", None), "python": ("https://docs.python.org/3/", None), "scipy": ("https://docs.scipy.org/doc/scipy/reference", None), } diff --git a/docs/source/docker.rst b/docs/source/docker.rst index c120beed7..9b5374cb3 100644 --- a/docs/source/docker.rst +++ b/docs/source/docker.rst @@ -7,11 +7,11 @@ Preliminaries ------------- #. Get the Docker Engine (https://docs.docker.com/engine/installation/) #. Have your data organized in BIDS - (`get BIDS specification `_, - `see BIDS paper `_). -#. Validate your data (http://incf.github.io/bids-validator/). You can - safely use the BIDS-validator since no data is uploaded to the server, - works locally in your browser. + (`get BIDS specification `_, + `see BIDS paper `_). +#. Validate your data (https://bids-standard.github.io/bids-validator/). + You can safely use the BIDS-validator since no data is uploaded to the + server, it works locally in your browser. .. warning :: diff --git a/mriqc/data/tests/ds000005/README b/mriqc/data/tests/ds000005/README index fc6b833bd..d9684e73b 100644 --- a/mriqc/data/tests/ds000005/README +++ b/mriqc/data/tests/ds000005/README @@ -14,9 +14,9 @@ Release history: This dataset is made available under the Public Domain Dedication and License v1.0, whose full text can be found at -http://www.opendatacommons.org/licenses/pddl/1.0/. +https://opendatacommons.org/licenses/pddl/1-0/. We hope that all users will follow the ODC Attribution/Share-Alike -Community Norms (http://www.opendatacommons.org/norms/odc-by-sa/); +Community Norms (https://opendatacommons.org/norms/odc-by-sa/); in particular, while not legally required, we hope that all users of the data will acknowledge the OpenfMRI project and NSF Grant OCI-1131441 (R. Poldrack, PI) in any publications. diff --git a/mriqc/interfaces/diffusion.py b/mriqc/interfaces/diffusion.py index 0ee98a074..c694e70ba 100644 --- a/mriqc/interfaces/diffusion.py +++ b/mriqc/interfaces/diffusion.py @@ -514,7 +514,7 @@ def _rms(estimator, X): Callable to pass to GridSearchCV that will calculate a distance score. To consider: using `MDL - `__ + `__ """ if len(np.unique(estimator.cluster_centers_)) < estimator.n_clusters: diff --git a/mriqc/qc/__init__.py b/mriqc/qc/__init__.py index afd30cf8f..e103e0888 100644 --- a/mriqc/qc/__init__.py +++ b/mriqc/qc/__init__.py @@ -45,7 +45,7 @@ Most of the :abbr:`IQMs (image quality metrics)` in this module are adapted, derived or reproduced from the :abbr:`QAP (quality assessment protocols)` project [QAP]_. - We particularly thank Steve Giavasis (`@sgiavasis `_) and + We particularly thank Steve Giavasis (`@sgiavasis `_) and Krishna Somandepali for their original implementations of the code in this module that we took from the [QAP]_. The [QAP]_ has a very good description of the :abbr:`IQMs (image quality metrics)` @@ -66,7 +66,7 @@ `_. .. [QAP-measures] `The Quality Assessment Protocols website: Taxonomy of QA Measures - `_. + `_. """ diff --git a/mriqc/qc/anatomical.py b/mriqc/qc/anatomical.py index e6479af0b..6f9a4a3ae 100644 --- a/mriqc/qc/anatomical.py +++ b/mriqc/qc/anatomical.py @@ -171,7 +171,7 @@ .. [Dietrich2007] Dietrich et al., *Measurement of SNRs in MR images: influence of multichannel coils, parallel imaging and reconstruction filters*, JMRI 26(2):375--385. - 2007. doi:`10.1002/jmri.20969 `_. + 2007. doi:`10.1002/jmri.20969 `_. .. [Ganzetti2016] Ganzetti et al., *Intensity inhomogeneity correction of structural MR images: a data-driven approach to define input algorithm parameters*. Front Neuroinform 10:10. 2016. @@ -180,15 +180,15 @@ .. [Magnota2006] Magnotta, VA., & Friedman, L., *Measurement of signal-to-noise and contrast-to-noise in the fBIRN multicenter imaging study*. J Dig Imag 19(2):140-147, 2006. doi:`10.1007/s10278-006-0264-x - `_. + `_. .. [Mortamet2009] Mortamet B et al., *Automatic quality assessment in structural brain magnetic resonance imaging*, Mag Res Med 62(2):365-372, - 2009. doi:`10.1002/mrm.21992 `_. + 2009. doi:`10.1002/mrm.21992 `_. .. [Tustison2010] Tustison NJ et al., *N4ITK: improved N3 bias correction*, IEEE Trans Med Imag, 29(6):1310-20, - 2010. doi:`10.1109/TMI.2010.2046908 `_. + 2010. doi:`10.1109/TMI.2010.2046908 `_. .. [Shehzad2015] Shehzad Z et al., *The Preprocessed Connectomes Project Quality Assessment Protocol - a resource for measuring the quality of MRI data*, diff --git a/mriqc/qc/functional.py b/mriqc/qc/functional.py index 4c86a0bee..593153703 100644 --- a/mriqc/qc/functional.py +++ b/mriqc/qc/functional.py @@ -170,41 +170,41 @@ .. [Atkinson1997] Atkinson et al., *Automatic correction of motion artifacts in magnetic resonance images using an entropy focus criterion*, IEEE Trans Med Imag 16(6):903-910, 1997. - doi:`10.1109/42.650886 `_. + doi:`10.1109/42.650886 `_. .. [Friedman2008] Friedman, L et al., *Test--retest and between‐site reliability in a multicenter fMRI study*. Hum Brain Mapp, 29(8):958--972, 2008. doi:`10.1002/hbm.20440 - `_. + `_. .. [Giannelli2010] Giannelli et al., *Characterization of Nyquist ghost in EPI-fMRI acquisition sequences implemented on two clinical 1.5 T MR scanner systems: effect of readout bandwidth and echo spacing*. J App Clin Med Phy, 11(4). 2010. - doi:`10.1120/jacmp.v11i4.3237 `_. + doi:`10.1120/jacmp.v11i4.3237 `_. .. [Jenkinson2002] Jenkinson et al., *Improved Optimisation for the Robust and Accurate Linear Registration and Motion Correction of Brain Images*. NeuroImage, 17(2), 825-841, 2002. - doi:`10.1006/nimg.2002.1132 `_. + doi:`10.1006/nimg.2002.1132 `_. .. [Kruger2001] Krüger et al., *Physiological noise in oxygenation-sensitive magnetic resonance imaging*, Magn. Reson. Med. 46(4):631-637, 2001. - doi:`10.1002/mrm.1240 `_. + doi:`10.1002/mrm.1240 `_. .. [Nichols2013] Nichols, `Notes on Creating a Standardized Version of DVARS - `_, + `_, 2013. .. [Power2012] Power et al., *Spurious but systematic correlations in functional connectivity MRI networks arise from subject motion*, NeuroImage 59(3):2142-2154, 2012, doi:`10.1016/j.neuroimage.2011.10.018 - `_. + `_. .. [Saad2013] Saad et al. *Correcting Brain-Wide Correlation Differences in Resting-State FMRI*, Brain Conn 3(4):339-352, 2013, doi:`10.1089/brain.2013.0156 - `_. + `_. """ import os.path as op diff --git a/mriqc/reports/__init__.py b/mriqc/reports/__init__.py index 3e2216950..60f9d4c61 100644 --- a/mriqc/reports/__init__.py +++ b/mriqc/reports/__init__.py @@ -33,7 +33,7 @@ :abbr:`IQMs (image quality metrics)`, so it is particularly easy to identify the cases that are outliers for each metric. The plots are interactive, such that clicking on any particular sample opens the corresponding individual report of that case. Examples of group and individual -reports for the ABIDE dataset are available online at `mriqc.org `_. +reports for the ABIDE dataset are available online at `mriqc.org `_. .. toctree:: :maxdepth: 3