Updates to subject list text body

Author: jpellman

docs/user/_sources/pipeline_config.txt

@@ -23,11 +23,11 @@ For instance, :file:`_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM
 
 Using a Text Editor
 -------------------
-Pipeline configuration files, like the data configuration file discussed in the `subject list builder section <subject_list_config>`_, are also stored as YAML files.  Similarly, each of the parameters used by C-PAC to assemble your pipeline can be specified as key-value pairs, so a pipeline configuration YAML would have multiple lines of the form::
+Pipeline configuration files, like the data configuration and subject list files discussed in the `subject list builder section <subject_list_config>`_, are stored as YAML files.  Similarly, each of the parameters used by C-PAC to assemble your pipeline can be specified as key-value pairs, so a pipeline configuration YAML would have multiple lines of the form::
 
     key : value
 
-An example of a pipeline configuration YAML file can be found `here <https://raw.githubusercontent.com/FCP-INDI/C-PAC/master/configs/pipeline_config.yml>`_.  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 configuration files should have the keys in the Output Settings,Preprocessing Workflow options, and derivatives settings tables defined (see below for links to the documents where these tables are contained).
+An example of a pipeline configuration YAML file can be found `here <https://raw.githubusercontent.com/FCP-INDI/C-PAC/master/configs/pipeline_config.yml>`_.  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 configuration files should have the keys in the :doc:`Output Settings </output_config>`,`Preprocessing Workflow Options </preprocwf_config>`, and `Derivatives Settings </deriv_config>` tables defined (see below for links to the documents where these tables are contained).
 
 Why a list?
 '''''''''''
@@ -37,12 +37,13 @@ Using the GUI
 -------------
 Opening the GUI 
 ''''''''''''''''
-To open the CPAC GUI, simply enter the command ``cpac_gui`` in a terminal window.  Then, on the main screen click on *New* next to *Pipelines*.  For each of the settings in the lefthand pane, refer to the pages linked to below in the *Configurable Settings* section.
-**Note: You may receive an error about a 'known incorrect sRGB profile' if you are running the GUI within Anaconda/Miniconda on some machines.  This will not affect C-PAC performance and can be ignored.**
+If the C-PAC GUI is not open already, type the command ``cpac_gui`` in a terminal window as you would with the subject list builder.  Then, on the main screen click on *New* next to *Pipelines*.  For each of the settings in the lefthand pane, refer to the pages linked to below in the *Configurable Settings* section.
+
+**Note: As mentioned in the previous section you may receive an error about a 'known incorrect sRGB profile' if you are running the GUI on some machines.  This will not affect C-PAC performance and can be ignored.**
 
 When you have finished configuring your pipeline, click *Save*. You will be asked to specify a location to save a configuration file containing information about the pipeline, and to specify a name for the pipeline.
 
-To modify an existing pipeline, select it and click *Edit*. To use a previously configured pipeline, click *Load* and select the appropriate ``.yml`` configuration file. If you have loaded multiple pipelines, use the checkboxes to select which pipelines you would like to run. 
+To modify an existing pipeline, select it and click *Edit*. To use a previously configured pipeline, click *Load* and select the appropriate pipeline configuration file. If you have loaded multiple pipelines, use the checkboxes to select which pipelines you would like to run. 
 
 Configurable Settings
 ---------------------