Removed CWAS and BASC from documentation.

Author: jpellman

docs/user/_sources/data_config.txt

@@ -4,7 +4,7 @@ In order to run CPAC, you must specify a list of subjects and data files to proc
 
 .. figure:: /_images/subject_list_gui.png
 
-**Note: If you are loading a previously created subject list, make sure that you click the 'Load' button on the main CPAC screen (left of the 'Subject Lists' box) instead of 'Load Settings' on this screen.  'Load Settings' is intended for data configuration files generated by the subject list setup interface and other YAML files will not work.**
+**Note: If you are loading a previously created subject list, make sure that you click the 'Load' button on the main CPAC screen (right of the 'Subject Lists' box) instead of 'Load Settings' on this screen.  'Load Settings' is intended for data configuration files generated by the subject list setup interface and other YAML files will not work.**
 
 Defining File Path Templates
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

docs/user/_sources/outputs.txt

@@ -29,10 +29,8 @@ Derivatives are the processed individual-level outputs of C-PAC.  These include
 * :doc:`Dual Regression </dual_reg>` - Compare large-scale networks.
 * :doc:`Amplitude of Low Frequency Fluctuations (ALFF) and fractional ALFF (fALFF) </alff>` - Measure the power of slow fluctuations in brain activity.
 * :doc:`Voxel-mirrored Homotopic Connectivity (VMHC) </vmhc>` - Investigate connectivity between hemispheres.
-* :doc:`Bootstrap Analysis of Stable Clusters (BASC) </basc>` - Quantify the stable characteristics of networks.
 * :doc:`Regional Homogeneity (ReHo) </reho>` - Measure the similarity of activity patterns across neighboring voxels.
 * :doc:`Network Centrality </centrality>` - Analyze the structure of functional networks.
-* :doc:`Connectome-wide Association Studies (CWAS) </cwas>` - Explore the relationship between patterns of functional connectivity and phenotypes.
 
 C-PAC also makes it easy to :doc:`export timeseries information </tse>` from your data. You can choose to extract timeseries from regions of interest, and individual voxels.  
 

docs/user/_sources/use.txt

@@ -80,10 +80,8 @@ Alternately, it is of course possible to simply view CPAC outputs using the appl
 
 Running Group-Level Analysis
 ----------------------------
-To run BASC, CWAS, or FSL Group Analysis you must have already run preprocessing and individual-level analysis. To configure group-level analysis, select a pipeline for which you have run preprocessing and individual-level anlaysis, then click Edit. See the following pages for information on configuring group-level analysis functions:
+To run FSL Group Analysis you must have already run preprocessing and individual-level analysis. To configure group-level analysis, select a pipeline for which you have run preprocessing and individual-level anlaysis, then click Edit. See the following page for information on configuring group-level analysis functions:
 
-* :doc:`Bootstrap Analysis of Stable Clusters </basc>`
-* :doc:`Connectome-wide Association Studies </cwas>`
 * :doc:`FSL Group Analysis </fsl_ga>`
 
 When you are finished configuring the pipeline for group-level analysis, click save.