Feature/surface v1.8 (#251)

Author: shnizzedy

docs/_sources/_images/anat_surface.png

@@ -5,6 +5,27 @@
 
     <div class="flowchart-container"><object data="../_static/flowcharts/anatomical.svg" type="image/svg+xml"></object></div>
 
+Surface Analysis
+^^^^^^^^^^^^^^^^
+
+Surface analysis runs FreeSurfer recon-all and generates CSF, WM, GM masks, pial surface mesh, smoothed surface mesh, spherical surface mesh, white matter surface mesh, sulcal depth surface maps, cortical thickness surface maps and cortical volume surface maps.
+
+Configuring CPAC to run surface analysis:
+"""""""""""""""""""""""""""""""""""""""""
+
+.. figure:: /_images/anat_surface.png
+
+#. **FreeSurfer - [On,Off]:** FreeSurfer recon-all. Default is Off.
+
+Configuration Without the GUI
+""""""""""""""""""""""""""""""
+
+The following nested key/value pairs that will be set to these defaults if not defined in your :doc:`pipeline configuration YAML </user/pipelines/pipeline_config>`:
+
+.. literalinclude:: /references/default_pipeline.yml
+   :language: YAML
+   :lines: 152-159
+
 Initial Preprocessing
 ^^^^^^^^^^^^^^^^^^^^^
 

docs/_sources/user/anat.rst

@@ -73,7 +73,7 @@ Pipeline configuration files, like the data settings and data configuration file
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 10-53
+   :lines: 10-51
 
 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.