📝 Document desc-xcp_quality.tsv files (#269)

shnizzedy · web-flow · commit b3ea41519b47 · 2022-01-24T17:03:42.000-05:00
diff --git a/docs/_sources/_static/custom.css b/docs/_sources/_static/custom.css
@@ -1,16 +1,47 @@
+:root {
+  --bg-dark: #11303D;
+  --bg-light: #F0F0F0;
+}
+
+html {
+  background-color: var(--bg-dark, #11303D);
+}
+
+body {
+  background-color: var(--bg-light, #F0F0F0);
+}
+
 div.body {
-    max-width: 100%;
+  max-width: 100%;
+}
+div.bodywrapper p {
+  margin-block: 0;
+}
+div.bodywrapper section {
+  background-color: white;
+  padding: 0 20px 30px 20px;
+}
+div.bodywrapper section h2 {
+  margin-block-start: 0;
+  padding-block-start: 0.83em;
+}
+div.citation p {
+  display: inline;
 }
 div.flowchart-container {
-    max-width: 1200px;
+  max-width: 1200px;
+}
+div.footer {
+  background-color: var(--bg-dark, #11303D);
+}
+div.sphinxsidebar {
+  background-color: var(--bg-light, #F0F0F0);
 }
-
 
 object {
-    max-width: 100%;
+  max-width: 100%;
 }
 
-
 .bibtex .brackets::before {
   content: "[";
 }
diff --git a/docs/_sources/conf.py b/docs/_sources/conf.py
@@ -329,6 +329,8 @@ def _unireplace(release_note, unireplace):
 
 .. toctree::
    :hidden:
+   :titlesonly:
+   :maxdepth: 1
 
    /user/release_notes/{latest}.rst
 """.format(latest=str(t))
@@ -347,6 +349,8 @@ def _unireplace(release_note, unireplace):
 
 .. toctree::
    :hidden:
+   :titlesonly:
+   :maxdepth: 1
 
    {}
 
diff --git a/docs/_sources/developer/index.rst b/docs/_sources/developer/index.rst
@@ -3,26 +3,29 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-.. title:: Developer Documentation
+Developer Documentation
+=======================
 
 Welcome to CPAC's developer documentation!
-==========================================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Contents:
 
 .. toctree::
    :maxdepth: 2
+   :titlesonly:
 
    installation
    pipeline
    nodes
    random_state
    workflow_documentation
    workflows/index
+   xcpqc
    testing
 
 Indices and tables
-==================
+^^^^^^^^^^^^^^^^^^
 
 * :ref:`genindex`
 * :ref:`modindex`
diff --git a/docs/_sources/developer/xcpqc.rst b/docs/_sources/developer/xcpqc.rst
@@ -0,0 +1,12 @@
+eXtensible Connectivity Pipeline-style quality control files
+============================================================
+
+.. automodule:: CPAC.qc.xcp
+    :members:
+
+.. rubric:: References
+
+.. bibliography:: /references/xcpqc_citation.bib
+   :style: cpac_docs_style
+   :cited:
+   :keyprefix: cite-
diff --git a/docs/_sources/index.rst b/docs/_sources/index.rst
@@ -10,6 +10,7 @@ Contents:
 
 .. toctree::
    :maxdepth: 1
+   :titlesonly:
 
    User Guide <user/index>
    Developer Documentation <developer/index>
diff --git a/docs/_sources/references/style.py b/docs/_sources/references/style.py
@@ -75,9 +75,15 @@ def get_book_template(self, entry):
             optional[sentence[date]],
             optional[sentence[href[
                 field('url'),
-                optional[tag('em')[self.format_title(entry, 'title')]]
+                optional[tag('em')[join(sep=', ')[
+                    self.format_title(entry, 'title', as_sentence=False),
+                    optional_field('edition')
+                ]]]
             ]]] if entry.fields.get('url') else optional[sentence[
-                tag('em')[self.format_title(entry, 'title')]
+                tag('em')[join(sep=', ')[
+                    self.format_title(entry, 'title', as_sentence=False),
+                    optional_field('edition')
+                ]]
             ]],
             optional[sentence[
                 join(sep=': ')[
@@ -89,19 +95,20 @@ def get_book_template(self, entry):
         ]
         return template
 
-    def get_incollection_template(self, e):
+    def get_incollection_template(self, entry):
         template = toplevel[optional[
             sentence[self.format_names('author')]],
             optional[sentence[date]],
             optional[sentence[href[
                 field('url'),
-                optional[tag('em')[self.format_title(e, 'title')]]
-            ]] if e.fields.get('url') else optional[sentence[
-                tag('em')[self.format_title(e, 'title')]
-            ]]],
-            optional[sentence[
-                tag('em')[self.format_title(e, 'booktitle')]
+                self.format_title(entry, 'title')
+            ]]] if entry.fields.get('url') else optional[sentence[
+                self.format_title(entry, 'title')
             ]],
+            optional[tag('em')[join(sep=', ')[
+                self.format_title(entry, 'booktitle', as_sentence=False),
+                optional_field('edition')
+            ]]],
             optional[sentence[
                 join(sep=': ')[
                     optional_field('address'),
diff --git a/docs/_sources/references/xcpqc_citation.bib b/docs/_sources/references/xcpqc_citation.bib
@@ -0,0 +1,45 @@
+
+@incollection{BIDS21,
+  title = {Appendix {{IX}}: {{Entities}}},
+  booktitle = {The {{Brain Imaging Data Structure}} ({{BIDS}}) {{Specification}}},
+  author = {{BIDS-contributors}},
+  year = {2021},
+  edition = {1.6.0},
+  url = {https://bids-specification.readthedocs.io/en/v1.6.0/99-appendices/09-entities.html}
+}
+
+@incollection{Ciri19,
+  title = {Quality Control Dictionary},
+  booktitle = {{{xcpEngine}} 1.0 Documentation},
+  author = {Ciric, Rastko and Rosen, Adon F. G. and Erus, Guray and Cieslak, Matthew and Adebimpe, Azeez and Cook, Philip A. and Bassett, Danielle S. and Davatzikos, Christos and Wolf, Daniel H. and Satterthwaite, Theodore D.},
+  year = {2019},
+  edition = {a7254873},
+  url = {https://xcpengine.readthedocs.io/qualitycontrol.html}
+}
+
+@article{Jenk02,
+  title = {Improved Optimization for the Robust and Accurate Linear Registration and Motion Correction of Brain Images},
+  author = {Jenkinson, Mark and Bannister, Peter and Brady, Michael and Smith, Stephen},
+  year = {2002},
+  month = oct,
+  journal = {NeuroImage},
+  volume = {17},
+  number = {2},
+  pages = {825--841},
+  issn = {1053-8119},
+  doi = {10.1006/nimg.2002.1132},
+  abstract = {Linear registration and motion correction are important components of structural and functional brain image analysis. Most modern methods optimize some intensity-based cost function to determine the best registration. To date, little attention has been focused on the optimization method itself, even though the success of most registration methods hinges on the quality of this optimization. This paper examines the optimization process in detail and demonstrates that the commonly used multiresolution local optimization methods can, and do, get trapped in local minima. To address this problem, two approaches are taken: (1) to apodize the cost function and (2) to employ a novel hybrid global\textendash local optimization method. This new optimization method is specifically designed for registering whole brain images. It substantially reduces the likelihood of producing misregistrations due to being trapped by local minima. The increased robustness of the method, compared to other commonly used methods, is demonstrated by a consistency test. In addition, the accuracy of the registration is demonstrated by a series of experiments with motion correction. These motion correction experiments also investigate how the results are affected by different cost functions and interpolation methods.},
+  langid = {english}
+}
+
+@misc{Penn19,
+  title = {{{maskOverlap}}.{{R}}},
+  year = {2019},
+  month = jan,
+  abstract = {Official public repository for the XCP Engine},
+  copyright = {MIT},
+  howpublished = {{The {{Lifespan Informatics and Neuroimaging Center}} at the {{University of Pennylvannia}}}},
+  url = {https://github.com/PennLINC/xcpEngine/blob/640f1c01/utils/maskOverlap.R}
+}
+
+
diff --git a/docs/_sources/user/1.7-1.8-nesting-mappings.rst b/docs/_sources/user/1.7-1.8-nesting-mappings.rst
@@ -2,3 +2,5 @@
    :http-equiv=refresh: 0; url=./pipelines/1.7-1.8-nesting-mappings.rst
 
 .. title:: Filed under 'pipelines'
+
+:orphan:
diff --git a/docs/_sources/user/compute_config.rst b/docs/_sources/user/compute_config.rst
@@ -1,5 +1,3 @@
-:orphan:
-
 Computer Settings
 -----------------
 .. figure:: /_images/compute_gui.png
diff --git a/docs/_sources/user/default.rst b/docs/_sources/user/default.rst
@@ -2,3 +2,5 @@
    :http-equiv=refresh: 0; url=./pipelines/default
 
 .. title:: Filed under 'pipelines'
+
+:orphan:
diff --git a/docs/_sources/user/design_a_pipeline.rst b/docs/_sources/user/design_a_pipeline.rst
@@ -2,3 +2,5 @@
    :http-equiv=refresh: 0; url=./pipelines/design_a_pipeline
 
 .. title:: Filed under 'pipelines'
+
+:orphan:
diff --git a/docs/_sources/user/index.rst b/docs/_sources/user/index.rst
@@ -3,8 +3,11 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
+User Documentation
+==================
+
 Welcome to C-PAC's user guide!
-==============================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The C-PAC Mission
 ^^^^^^^^^^^^^^^^^
@@ -98,6 +101,7 @@ User Guide Index
 .. toctree::
    :maxdepth: 2
    :includehidden:
+   :titlesonly:
 
    1. C-PAC Quickstart <quick>
    2. Specify Your Data <subject_list_config>
diff --git a/docs/_sources/user/output_config.rst b/docs/_sources/user/output_config.rst
@@ -1,5 +1,3 @@
-:orphan:
-
 Output Settings
 ----------------
 
diff --git a/docs/_sources/user/pipeline_config.rst b/docs/_sources/user/pipeline_config.rst
@@ -2,3 +2,5 @@
    :http-equiv=refresh:  0; url=./pipelines/pipeline_config
 
 .. title:: Filed under 'pipelines'
+
+:orphan:
diff --git a/docs/_sources/user/pipelines/configurable-settings.rst b/docs/_sources/user/pipelines/configurable-settings.rst
@@ -0,0 +1,16 @@
+Configurable Settings
+---------------------
+
+.. raw:: html
+
+    <div class="flowchart-container"><object data="../_static/flowcharts/pipeline-individual.svg" type="image/svg+xml"></object></div>
+
+.. toctree::
+   :maxdepth: 1
+
+   ALFF and f/ALFF </user/alff>
+   ReHo </user/reho>
+   Network Centrality </user/centrality>
+   SCA/Dual Regression </user/sca>
+   VMHC </user/vmhc>
+   PyPEER Integration </user/pypeer>
diff --git a/docs/_sources/user/pipelines/data-environment.rst b/docs/_sources/user/pipelines/data-environment.rst
@@ -0,0 +1,7 @@
+Data Management and Environment Settings
+'''''''''''''''''''''''''''''''''''''''''
+.. toctree::
+   :maxdepth: 1
+
+   /user/compute_config
+   /user/output_config
diff --git a/docs/_sources/user/pipelines/derivatives.rst b/docs/_sources/user/pipelines/derivatives.rst
@@ -0,0 +1,11 @@
+Derivatives
+'''''''''''
+
+.. toctree::
+   :maxdepth: 1
+
+   Seed-based Correlation Analysis (SCA) and Dual Regression - Analyze the connectivity between brain regions. </user/sca>
+   Voxel-mirrored Homotopic Connectivity (VMHC) - Investigate connectivity between hemispheres. </user/vmhc>
+   Amplitude of Low Frequency Fluctuations (ALFF) and fractional ALFF (fALFF) - Measure the power of slow fluctuations in brain activity. </user/alff>
+   Regional Homogeneity (ReHo) - Measure the similarity of activity patterns across neighboring voxels. </user/reho>
+   Network Centrality - Analyze the structure of functional networks. </user/centrality>
diff --git a/docs/_sources/user/pipelines/design_a_pipeline.rst b/docs/_sources/user/pipelines/design_a_pipeline.rst
@@ -25,9 +25,9 @@ C-PAC offers a graphical interface you can use to quickly and easily modify the
 
     See :ref:`using_a_text_editor` for configuring a custom pipeline without the GUI.
     
-.. seealso::
-
-    :doc:`Details about mapping the older syntax to the new. </user/pipelines/1.7-1.8-nesting-mappings>`
+   .. seealso::
+   
+       :doc:`Details about mapping the older syntax to the new. </user/pipelines/1.7-1.8-nesting-mappings>`
 
 .. figure:: /_images/gui_home1.png
 
@@ -52,6 +52,7 @@ Or you can provide it to the C-PAC Singularity container like so:
             -B /tmp:/tmp \
             -B /Users/You/Documents:/configs \
             fcpindi_c-pac_latest-{date}-{hash value}.img s3://fcp-indi/data/Projects/ADHD200/RawDataBIDS /outputs participant --pipeline_file /configs/pipeline_config.yml
+
 **Reporting errors and getting help**
 
-Please report errors on the `C-PAC github page issue tracker <https://github.com/FCP-INDI/C-PAC/issues>`_. Please use the `C-PAC google group <https://groups.google.com/forum/#!forum/cpax_forum>`_ for help using C-PAC and this application.
+Please report errors on the `C-PAC github page issue tracker <https://github.com/FCP-INDI/C-PAC/issues>`_. Please use the `C-PAC google group <https://groups.google.com/forum/#!forum/cpax_forum>`_ for help using C-PAC and this application.
diff --git a/docs/_sources/user/pipelines/pipeline_config.rst b/docs/_sources/user/pipelines/pipeline_config.rst
@@ -69,7 +69,7 @@ Pipeline configuration files, like the data settings and data configuration file
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :start_at: pipeline_setup:
+   :start-at: pipeline_setup:
    :end-before: working_directory:
 
 An example of a pipeline configuration YAML file can be found :doc:`here </user/pipelines/default>`.  Tables explaining the keys and their potential values can be found on the individual pages for each of the outputs C-PAC is capable of producing. All pipeline setup configuration files should have the keys in the :doc:`Output Settings </user/output_config>` table defined.
@@ -125,10 +125,23 @@ Derivatives
 * :doc:`Network Centrality </user/centrality>` - Analyze the structure of functional networks.
 
 
-.. rubric:: Reference
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+
+   preconfig
+   configurable-settings
+   data-environment
+   pre-and-post
+   derivatives
+   quality
+
+
+Reference
+---------
 
 
 .. bibliography:: /references/glossary.bib
     :style: cpac_docs_style
     :cited:
-    :keyprefix: glossary-
+    :keyprefix: glossary-
diff --git a/docs/_sources/user/pipelines/pre-and-post.rst b/docs/_sources/user/pipelines/pre-and-post.rst
@@ -0,0 +1,10 @@
+Pre- and post-processing
+'''''''''''''''''''''''''
+.. toctree::
+   :maxdepth: 1
+
+   Anatomical Preprocessing </user/anat>
+   Functional Preprocessing </user/func>
+   Nuisance Corrections </user/nuisance>
+   Time Series Extraction </user/tse>
+   After Warp Settings </user/after_warp>
diff --git a/docs/_sources/user/pipelines/quality.rst b/docs/_sources/user/pipelines/quality.rst
@@ -0,0 +1,8 @@
+Quality Control
+'''''''''''''''
+
+.. toctree::
+   :maxdepth: 1
+
+   QC Pages - Visual Data Quality Control </user/qc_interface>
+   XCP QC files - eXtensible Connectivity Pipeline-style quality control files </user/xcpqc>
diff --git a/docs/_sources/user/preconfig.rst b/docs/_sources/user/preconfig.rst
@@ -2,3 +2,5 @@
    :http-equiv=refresh:  0; url=./pipelines/preconfig
 
 .. title:: Filed under 'pipelines'
+
+:orphan:
diff --git a/docs/_sources/user/xcpqc.rst b/docs/_sources/user/xcpqc.rst

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,3 @@`
`1`		`-:orphan:`
`2`		`-`
`3`	`1`	`Computer Settings`
`4`	`2`	`-----------------`
`5`	`3`	`.. figure:: /_images/compute_gui.png`