diff --git a/docs/conf.py b/docs/conf.py index 9ce87527a..ebcc656b3 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -47,6 +47,7 @@ # Add any Sphinx extension module names here, as strings. # They can be extensions coming with Sphinx (named "sphinx.ext.*") or your custom ones. extensions = [ + "hoverxref.extension", "nbsphinx", "nipype.sphinxext.apidoc", "nipype.sphinxext.plot_workflow", @@ -330,6 +331,19 @@ bibtex_reference_style = "author_year" bibtex_footbibliography_header = "" +# -- +# hoverxref +# -- +hoverxref_auto_ref = True +hoverxref_mathjax = True +hoverxref_roles = [ + "numref", + "confval", + "setting", + "term", + "footcite", +] + def setup(app): """Add extra formatting files.""" diff --git a/docs/glossary.rst b/docs/glossary.rst new file mode 100644 index 000000000..5d7c722d2 --- /dev/null +++ b/docs/glossary.rst @@ -0,0 +1,26 @@ +.. include:: links.rst + +.. glossary:: + + ASL + Arterial spin labeling. + + CBF + Cerebral blood flow. ASLPrep provides CBF results in mL/100 g/min. + + |Delta-M| + :math:`\Delta{M}` is a time series produced by subtracting labelled volumes in the ASL time + series from the associated control volumes. + + .. math:: + \Delta{M} = M_{C} - M_{L} + + |lambda| + Brain-blood partition coefficient. + Set to 0.9 g/mL :footcite:p:`alsop_recommended_2015`. + + +References +========== + +.. footbibliography:: \ No newline at end of file diff --git a/docs/links.rst b/docs/links.rst index c85764037..1e8878862 100644 --- a/docs/links.rst +++ b/docs/links.rst @@ -12,3 +12,6 @@ .. _Nipype: http://nipype.readthedocs.io/en/latest/ .. _Singularity: https://github.com/singularityware/singularity .. _SPM: https://www.fil.ion.ucl.ac.uk/spm/software/spm12/ + +.. |Delta-M| replace:: :math:`\Delta{M}` +.. |lambda| replace:: :math:`\lambda` diff --git a/docs/workflows.rst b/docs/workflows.rst index aab72b1d8..06b86e67b 100644 --- a/docs/workflows.rst +++ b/docs/workflows.rst @@ -288,7 +288,8 @@ ASL data consist of multiple pairs of labeled and control images. In the absence of M0 images or an M0 estimate provided in the metadata, the average of control images is used as the reference image. -After :ref:`preprocessing `, the pairs of labeled and control images are subtracted: +After :ref:`preprocessing `, the pairs of labeled and control images are subtracted +to produce a :term:`|Delta-M|` time series: .. math:: \Delta{M} = M_{C} - M_{L} @@ -313,8 +314,9 @@ model :footcite:p:`alsop_recommended_2015`. :math:`\tau` : Labeling duration, in seconds. - :math:`\lambda` : Brain-blood partition coefficient. - Set to 0.9 g/mL :footcite:p:`alsop_recommended_2015`. + :term:`lambda <|lambda|>` + + :term:`|lambda| ` :math:`\alpha` : Labeling efficiency. This may be directly encoded in the ASL file's sidecar file with the ``LabelingEfficiency`` field. diff --git a/pyproject.toml b/pyproject.toml index 62f0f26f8..30aae8f18 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -60,6 +60,7 @@ doc = [ "recommonmark", "sphinx >= 6.2.1", "sphinx-argparse", + "sphinx-hoverxref", "sphinx-markdown-tables", "sphinx_rtd_theme >= 1.2.2", "sphinxcontrib-apidoc",