diff --git a/+nla/+net/+result/+plot/NetworkTestPlotApp_exported.m b/+nla/+net/+result/+plot/NetworkTestPlotApp_exported.m index 62cf3e19..084b0398 100644 --- 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 new file mode 100644 index 00000000..b36ba328 Binary files /dev/null and b/docs/source/_static/design_matrix.png differ diff --git a/docs/source/_static/fc_average_plot.png b/docs/source/_static/fc_average_plot.png new file mode 100644 index 00000000..39c251d9 Binary files /dev/null and b/docs/source/_static/fc_average_plot.png differ diff --git a/docs/source/_static/normality_plot.png b/docs/source/_static/normality_plot.png new file mode 100644 index 00000000..dc4ce3be Binary files /dev/null and b/docs/source/_static/normality_plot.png differ diff --git a/docs/source/_static/quality_control_gui.png b/docs/source/_static/quality_control_gui.png new file mode 100644 index 00000000..46839457 Binary files /dev/null and b/docs/source/_static/quality_control_gui.png differ diff --git a/docs/source/_static/silhouette_coefficient_plot.png b/docs/source/_static/silhouette_coefficient_plot.png new file mode 100644 index 00000000..6cfbc801 Binary files /dev/null and b/docs/source/_static/silhouette_coefficient_plot.png differ diff --git a/docs/source/index.rst b/docs/source/index.rst index 1ce0658a..1105eb93 100644 --- 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 index e69de29b..63e82d44 100644 --- 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 \ No newline at end of file