WheelockLab · AndyEck16 · Jun 3, 2026 · Jun 3, 2026 · Jun 3, 2026 · Jun 3, 2026
diff --git a/+nla/+net/+result/+plot/NetworkTestPlotApp_exported.m b/+nla/+net/+result/+plot/NetworkTestPlotApp_exported.m
@@ -37,6 +37,7 @@
         BrainPlotTypeLabel              matlab.ui.control.Label
         BrainPlotTypeDropDown           matlab.ui.control.DropDown
         Panel_2                         matlab.ui.container.Panel
+        Label                           matlab.ui.control.Label
     end
 
 
@@ -665,7 +666,14 @@ function createComponents(app)
             app.Panel_2 = uipanel(app.UIFigure);
             app.Panel_2.AutoResizeChildren = 'off';
             app.Panel_2.BackgroundColor = [1 1 1];
-            app.Panel_2.Position = [22 298 542 464];
+            app.Panel_2.Position = [22 311 542 451];
+
+            % Create Label
+            app.Label = uilabel(app.UIFigure);
+            app.Label.HorizontalAlignment = 'center';
+            app.Label.FontColor = [0.502 0.502 0.502];
+            app.Label.Position = [28 288 536 22];
+            app.Label.Text = '(Click on significant net -pair blocks above to display brain plots for that net-pair)';
 
             % Show the figure after all components are created
             app.UIFigure.Visible = 'on';

diff --git a/docs/source/_static/design_matrix.png b/docs/source/_static/design_matrix.png
diff --git a/docs/source/_static/fc_average_plot.png b/docs/source/_static/fc_average_plot.png
diff --git a/docs/source/_static/normality_plot.png b/docs/source/_static/normality_plot.png
diff --git a/docs/source/_static/quality_control_gui.png b/docs/source/_static/quality_control_gui.png
diff --git a/docs/source/_static/silhouette_coefficient_plot.png b/docs/source/_static/silhouette_coefficient_plot.png
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -17,6 +17,7 @@ Welcome to documentation for Network Level Analysis
    using_the_gui
    behavior_table
    network_atlases
+   quality_control
    edge_level_tests
    network_level_tests
    network_level_results

diff --git a/docs/source/quality_control.rst b/docs/source/quality_control.rst
@@ -0,0 +1,80 @@
+Quality Control
+==============================
+
+The NLA Toolbox offers various methods to perform quality control on input data before running permutation testing.
+These consist of plots that can be generated in the main ``NLA_GUI`` window, along with a dedicated Quality Control GUI that can be launched from the main window
+
+Quality Plots on Main NLA_GUI
+---------------------------
+
+Network Atlas Plot
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+After selecting a network atlas, the user can visualize the network atlas via the ``View`` button to the right of the ``Network Atlas`` selection button.
+
+The user can select from 3 options for Inflation, which controls how inflated the cortex will be drawn. The options correspond to 'Standard', 'Inflated', and 'Very Inflated'.
+
+If parcel information is available, the user can choose to display (or hide) that information by checking or unchecking the ``Surface parcels`` checkbox.
+
+
+Viewing average Functional Connectivity
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+With both a network atlas and functional connectivity data file loaded, the user can view a lower triangle plot of FC averaged over all current subjects.
+To do this, click the ``View`` button to the right of the button for loading Functional Connectivity.
+
+.. figure:: _static/fc_average_plot.png
+
+    Example plot of average functional connectivity
+
+Design Matrix
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+After loading behavior data and selecting behavior and covariate variables via the behavior table, 
+the user can view the design matrix for the selected variables by clicking the ``View Design Matrix`` button below the behavior table.
+This will also display r-values for colinearity between selected behavior and covariate variables.
+
+.. figure:: _static/design_matrix.png
+
+    Example design matrix
+
+
+Quality Control GUI
+---------------------------
+
+The user can also access a separate dedicated set of quality control tests via the ``Run Quality Control`` button towards the right of the GUI.
+
+This control requires that the user has loaded a Network Atlas, Functional Connectivity, and Behavior data, 
+and has selected a variable for Behavior.
+
+.. figure:: _static/quality_control_gui.png
+
+    Quality Control GUI
+
+
+Check Head Motion
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If your selected behavior data from the main GUI included motion data, select the name of the corresponding variable in the ``Motion Field`` dropdown.
+Then clicking the ``Check Head Motion`` will display quality plots relating to FC-Motion correlation.
+
+View Silhouette Coefficient
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The user can generate a triangle plot for the silhouette coefficent for information on how well the atlas model fits the connectivity data.
+If there is a network the user would like to exclude from the silhouette coefficient calculations (typically a network labeled 'None' or 'Unassigned'), the user can select that network for removal via the ``Unspecified/None "network"`` dropdown.
+To keep all networks provided in the original atlas, the user can set the dropdown to the 'N/A' option.
+
+.. figure:: _static/silhouette_coefficient_plot.png
+
+    Example normality plot
+
+Test Normality
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ``Test Normality`` button runs a Kolmogorov-Smirnov test on the edges within each net-pair block,
+and generates a plot of the p-values for each net-pair.
+
+.. figure:: _static/normality_plot.png
+
+    Example normality plot