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Inline flowchart SVGs
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‎docs/_sources/_static/custom.css‎

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:root {
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--bg-dark: #11303D;
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--bg-light: #F0F0F0;
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}
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html {
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background-color: var(--bg-dark, #11303D);
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}
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body {
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background-color: var(--bg-light, #F0F0F0);
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}
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div.body {
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max-width: 100%;
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}
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div.bodywrapper p {
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margin-block: 0;
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}
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div.bodywrapper section {
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background-color: white;
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padding: 0 20px 30px 20px;
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}
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div.bodywrapper section > p {
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padding-bottom: 1ex;
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}
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div.bodywrapper section h2 {
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margin-block-start: 0;
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padding-block-start: 0.83em;
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}
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div.citation p {
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display: inline;
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}
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div.flowchart-container {
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max-width: 1200px;
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}
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div.footer {
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background-color: var(--bg-dark, #11303D);
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}
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div.sphinxsidebar {
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background-color: var(--bg-light, #F0F0F0);
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}
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object {
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max-width: 100%;
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}
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.bibtex .brackets::before {
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content: "[";
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}
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.bibtex .brackets::after {
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content: "]"
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}
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.bibtex.label {
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display: grid;
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}
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section[id^="Tutorial:"] p img {
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max-width: 80%;
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.svg-flowchart > svg {
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width: 100%;
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height: auto;
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}

‎docs/_sources/conf.py‎

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# so a file named 'default.css' will overwrite the builtin 'default.css'.
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html_static_path = ['_static']
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# These paths are either relative to html_static_path
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# or fully qualified paths (eg. https://...)
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html_css_files = [
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'custom.css',
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]
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# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
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# using the given strftime format.
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# html_last_updated_fmt = '%b %d, %Y'

‎docs/_sources/developer/continuous_integration.rst‎

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Our continous integration flow relies on GitHub Actions, GitHub Container Registry, CircleCI and Docker Hub. GitHub Actions builds staging images based on changes to Dockerfiles and pushes those images to GitHub Container Registry. On each push, once staging images are built or determined to be up to date, GitHub Actions installs C-PAC into a development image for each variant (standard, lite, fMRIPrep-LTS, and ABCD-HCP). CircleCI runs tests in both Docker and Singularity for each of these images and generates a coverage report if all tests pass. On release, CircleCI also pushes production images to Docker Hub.
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.. raw:: html
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.. container:: svg-flowchart
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<a href="../_static/flowcharts/CI-flow.svg"><img src="../_static/flowcharts/CI-flow.svg" /></a>
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.. raw:: html
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:file: ../_static/flowcharts/CI-flow.svg
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`Open image <../_static/flowcharts/CI-flow.svg>`_

‎docs/_sources/developer/logging.rst‎

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Most C-PAC logging is handled by the built-in Python ``logging`` library. When logging, take care to choose an appropriate ``getLogger`` function or method. While :py:func:`CPAC.utils.monitoring.custom_logging.getLogger` and ``nipype.utils.logger.Logging.getLogger`` each fall back on ``logging.getLogger``,
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.. raw:: html
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.. container:: svg-flowchart
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<a href="../_static/flowcharts/getLogger.svg"><img src="../_static/flowcharts/getLogger.svg" /></a>
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.. raw:: html
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:file: ../_static/flowcharts/getLogger.svg
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`Open image <../_static/flowcharts/getLogger.svg>`_
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each have their own intended use cases.

‎docs/_sources/user/anat.rst‎

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Anatomical Preprocessing
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------------------------
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.. raw:: html
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.. container:: svg-flowchart
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<a href="../_static/flowcharts/anatomical.svg"><img src="../_static/flowcharts/anatomical.svg" /></a>
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.. raw:: html
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:file: ../_static/flowcharts/anatomical.svg
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`Open image <../_static/flowcharts/anatomical.svg>`_
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Surface Analysis
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Anatomical Tissue Segmentation
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. raw:: html
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.. container:: svg-flowchart
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.. raw:: html
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:file: ../_static/flowcharts/segmentation.svg
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<a href="../_static/flowcharts/segmentation.svg"><img src="../_static/flowcharts/segmentation.svg" /></a>
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`Open image <../_static/flowcharts/segmentation.svg>`_
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C-PAC uses `FSL/FAST <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST>`_ to automatically segment brain images into white matter, gray matter, and CSF. This is done using probability maps that contain information about the likelihood that a given voxel will be of a particular tissue type. Users specify a probability threshold such that voxels meeting a minimum probability of being a particular tissue will be classified as such. This results in masks containing voxels of only a single tissue type.
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‎docs/_sources/user/func.rst‎

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Functional Preprocessing
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-------------------------
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.. raw:: html
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.. container:: svg-flowchart
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<a href="../_static/flowcharts/functional.svg"><img src="../_static/flowcharts/functional.svg" /></a>
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.. raw:: html
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:file: ../_static/flowcharts/functional.svg
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`Open image <../_static/flowcharts/functional.svg>`_
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Initial Preprocessing
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^^^^^^^^^^^^^^^^^^^^^

‎docs/_sources/user/longitudinal.rst‎

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Longitudinal Preprocessing
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--------------------------
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.. container:: svg-flowchart
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<a href="../_static/flowcharts/longitudinal.svg"><img src="../_static/flowcharts/longitudinal.svg" /></a>
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.. raw:: html
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:file: ../_static/flowcharts/longitudinal.svg
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`Open image <../_static/flowcharts/longitudinal.svg>`_
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Background
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^^^^^^^^^^

‎docs/_sources/user/pipelines/configurable-settings.rst‎

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Configurable Settings
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---------------------
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.. container:: svg-flowchart
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<a href="../../_static/flowcharts/pipeline-individual.svg"><img src="../../_static/flowcharts/pipeline-individual.svg" /></a>
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.. raw:: html
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:file: ../../_static/flowcharts/pipeline-individual.svg
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`Open image <../../_static/flowcharts/pipeline-individual.svg>`_
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.. toctree::
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:maxdepth: 1

‎docs/_sources/user/pipelines/pipeline_config.rst‎

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Configurable Settings
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------------------------------
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.. container:: svg-flowchart
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<a href="../../_static/flowcharts/pipeline-individual.svg"><img src="../../_static/flowcharts/pipeline-individual.svg" /></a>
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.. raw:: html
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:file: ../../_static/flowcharts/pipeline-individual.svg
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`Open image <../../_static/flowcharts/pipeline-individual.svg>`_
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Data Management and Environment Settings
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'''''''''''''''''''''''''''''''''''''''''

‎docs/_sources/user/preprocessing.rst‎

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====================
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.. container:: svg-flowchart
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<a href="../_static/flowcharts/pipeline-individual.svg"><img src="../_static/flowcharts/pipeline-individual.svg" /></a>
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.. raw:: html
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:file: ../_static/flowcharts/pipeline-individual.svg
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`Open image <../_static/flowcharts/pipeline-individual.svg>`_
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The following index provides links to pages containing overviews and configuration instructions for the various pre-processing steps that C-PAC performs. For more information about how to set up a pipeline configuration, see the :doc:`pipeline configuration page </user/pipelines/pipeline_config>`.
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