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WIP: Example visually showing the stages of tractometry. #1016

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WIP: Example visually showing the stages of tractometry. #1016

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aa8fc54
WIP: Example visually showing the stages of tractometry.
arokem Sep 8, 2023
4ea97d3
Reorganize the bundle order.
arokem Sep 9, 2023
8cbdecb
Reorganize the front page.
arokem Sep 11, 2023
b0e687d
Build tutorials directly into the higher level.
arokem Sep 11, 2023
5b6dfe2
Adding more content to first tutorial.
arokem Sep 11, 2023
fa64cde
Add the custom scalars page back into an index for usage.
arokem Sep 12, 2023
eb64f97
Adds code to make videos.
arokem Sep 15, 2023
93817cf
Increase the number of frames. Save frames to temp location.
arokem Sep 16, 2023
ec8086c
Rewrite to focus on videos.
arokem Sep 16, 2023
ae4f878
Fix this filename.
arokem Sep 16, 2023
10c4a64
Force a space at the bottom of the tract profiles figure.
arokem Sep 17, 2023
b16b787
Include the usage portion of the docs.
arokem Nov 9, 2023
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4 changes: 4 additions & 0 deletions docs/source/conf.py
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Expand Up @@ -221,12 +221,16 @@

from _progressbars import reset_progressbars # noqa

from sphinx_gallery.sorting import ExampleTitleSortKey

sphinx_gallery_conf = {
# path to your examples scripts
'examples_dirs': ['../../examples/howto_examples',
'../../examples/tutorial_examples'],
# path where to save gallery generated examples
'gallery_dirs': ['howto/howto_examples', 'tutorials/tutorial_examples'],
'within_subsection_order': ExampleTitleSortKey,
'ignore_pattern': 'plot_baby_afq.py|cloudknot_hcp_example.py|cloudknot_example.py|add_custom_bundle.py', # noqa
'image_scrapers': image_scrapers,
'reset_modules': (reset_progressbars),
'show_memory': True,
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3 changes: 2 additions & 1 deletion docs/source/howto/index.rst
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Expand Up @@ -8,10 +8,11 @@ software.
:maxdepth: 2

installation_guide
usage
usage/index
contributing
developing/index
getting_help
cite
scalars
howto_examples/index

44 changes: 18 additions & 26 deletions docs/source/index.rst
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Expand Up @@ -7,7 +7,7 @@ Automated Fiber Quantification in Python (pyAFQ)
pyAFQ is an open-source software tool for the analysis of brain white matter in
diffusion MRI measurements. It implements a complete and automated data
processing pipeline for tractometry, from raw DTI data to white matter tract identification
, as well as quantification of tissue properties along the length of the
, as well as quantification of tissue properties along the length of the
major long-range brain white matter connections.


Expand All @@ -22,9 +22,9 @@ major long-range brain white matter connections.
.. note::

Tractography is concerned with the visualization and mapping of white matter
tracts in the brain, while tractometry involves the quantitative analysis of
the structural properties of these tracts. Both techniques are valuable in
understanding the brain's connectivity and can provide insights into various
tracts in the brain, while tractometry involves the quantitative analysis of
the structural properties of these tracts. Both techniques are valuable in
understanding the brain's connectivity and can provide insights into various
neurological conditions and cognitive processes. More information can be found in
the Explanations page.

Expand All @@ -41,29 +41,28 @@ major long-range brain white matter connections.
.. grid:: 2

.. grid-item-card::
:link: howto/index.html
:link: tutorials/index.html

:octicon:`rocket;3em;sd-text-center`
:octicon:`book;3em;sd-text-center`

How To
^^^^^^
Tutorials
^^^^^^^^^

User's guide to pyAFQ. This guide assumes you know
the basics and walks through more commonly used examples.
Beginner's guide to pyAFQ. This guide introduces pyAFQ'S
basic concepts and walks through fundamentals of using the software.

+++


.. grid-item-card::
:link: tutorials/index.html
:link: howto/index.html

:octicon:`book;3em;sd-text-center`
:octicon:`rocket;3em;sd-text-center`

Tutorials
^^^^^^^^^
How To
^^^^^^

Beginner's guide to pyAFQ. This guide introduces pyAFQ'S
basic concepts and walks through fundamentals of using the software.
A set of recipes for specific use-cases. This guide assumes you know
the basics and walks through more commonly used examples.

+++

Expand All @@ -76,10 +75,8 @@ major long-range brain white matter connections.
Explanations
^^^^^^^^^^^^

For more experienced users. This guide contains in depth
explanations on how to use pyAFQ methods. It includes how to
create detailed visualizations and analyses.

More detailed and conceptual, this guide contains in depth
explanations on how to think about the various pyAFQ methods.
+++

.. grid-item-card::
Expand Down Expand Up @@ -116,8 +113,3 @@ R01EB027585) to Eleftherios Garyfallidis and to Ariel Rokem , and by `NSF grant
:align: center
:figclass: align-center
:target: http://brainandeducation.com





7 changes: 0 additions & 7 deletions docs/source/tutorials/index.rst
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