Merge pull request #1532 from softmatterlab/ac-ConnectivityOrderedMultiplexPipeline

Ac connectivity ordered multiplex pipeline

Author: giovannivolpe

braph2genesis/measures/_MultilayerCommunityStructure.gen.m

@@ -161,10 +161,10 @@
         it(:,i)=M(ii(i));
     end
     it = it(ii,:);
-    if norm(full(it-it')) > 2*eps
-        error([BRAPH2.STR ':MultilayerCommunityStructure:' BRAPH2.WRONG_INPUT], ...
-            'Function handle does not correspond to a symmetric matrix. Deviation: %i', norm(full(it-it')))
-    end
+%     if norm(full(it-it')) > 2*eps
+%         error([BRAPH2.STR ':MultilayerCommunityStructure:' BRAPH2.WRONG_INPUT], ...
+%             'Function handle does not correspond to a symmetric matrix. Deviation: %i', norm(full(it-it')))
+%     end
 else
     n = length(OM);
     S = (1:n)';

braph2genesis/neuralnetworks/_NNClassifierCrossValidation.gen.m

@@ -266,6 +266,8 @@
     else
         pr = PanelPropCell('EL', nncv, 'PROP', NNClassifierCrossValidation.FEATURE_IMPORTANCE, varargin{:});
     end
+else
+    pr = PanelPropCell('EL', nncv, 'PROP', NNClassifierCrossValidation.FEATURE_IMPORTANCE, varargin{:});
 end
 
 %% ¡props_update!

braph2genesis/neuralnetworks/_NNClassifierEvaluator.gen.m

@@ -46,6 +46,8 @@ under the ROC curve (AUC), and the confusion matrix.
     else
         pr = PanelPropCell('EL', nne, 'PROP', NNClassifierEvaluator.FEATURE_MASK, varargin{:});
     end
+else
+    pr = PanelPropCell('EL', nne, 'PROP', NNClassifierEvaluator.FEATURE_MASK, varargin{:});
 end
 
 %%% ¡prop!
@@ -130,6 +132,8 @@ under the ROC curve (AUC), and the confusion matrix.
     else
         pr = PanelPropCell('EL', nne, 'PROP', NNClassifierEvaluator.FEATURE_PERMUTATION_IMPORTANCE, varargin{:});
     end
+else
+    pr = PanelPropCell('EL', nne, 'PROP', NNClassifierEvaluator.FEATURE_PERMUTATION_IMPORTANCE, varargin{:});
 end
 
 %%% ¡prop!

braph2genesis/pipelines/connectivity multiplex group_average/example_CON_MP_GA_WU.m

@@ -28,7 +28,7 @@
 
 gr2 = im_gr2.get('GR');
 
-%% Analysis Group CON_MP WU
+%% Analysis Group CON_MP GA WU
 a_WU1 = AnalyzeGroup_CON_MP_GA_WU( ...
     'GR', gr1 ...
     );

braph2genesis/pipelines/connectivity multiplex group_average/pipeline_connectivity_multiplex_group_analysis_wu.braph2

@@ -2,8 +2,7 @@
 
 % This is the pipeline script to analyze a group of subjects using connectivity multiplex data averaged by group and a weighted undirected graph.
 % 1. It loads a brain atlas from an XLS file (e.g., desikan_atlas.xlsx).
-% 2.1 It loads the connectivity data of one group of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
-% 2.2 It loads the connectivity data of one group of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
+% 2. It loads the connectivity data of one group of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
 % 3. It analyzes the data using connectivity multiplex analysis (CON_MP) based on weighted undirected graphs (WU) averaged by group (GA).
 
 %% Brain Atlas

braph2genesis/pipelines/connectivity multiplex/pipeline_connectivity_multiplex_analysis_bud.braph2

@@ -2,8 +2,7 @@
 
 % This is the pipeline script to analyze a group of subjects using connectivity multiplex data and a binary undirected graph at fixed densities.
 % 1. It loads a brain atlas from an XLS file (e.g., aal90_atlas.xlsx).
-% 2.1 It loads the connectivity data of one group of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
-% 2.2 It loads the connectivity data of one group of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
+% 2. It loads the connectivity data of one group of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
 % 3. It analyzes the data using connectivity multiplex analysis (CON_MP) based on a binary undirected graph at fixed densities (BUD).
 
 %% Brain Atlas

braph2genesis/pipelines/connectivity multiplex/pipeline_connectivity_multiplex_analysis_but.braph2

@@ -2,8 +2,7 @@
 
 % This is the pipeline script to analyze a group of subjects using connectivity multiplex data and a binary undirected graph at fixed thresholds.
 % 1. It loads a brain atlas from an XLS file (e.g., aal90_atlas.xlsx).
-% 2.1 It loads the connectivity data of one group of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
-% 2.2 It loads the connectivity data of one group of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
+% 2. It loads the connectivity data of one group of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
 % 3. It analyzes the data using connectivity multiplex analysis (CON_MP) based on a binary undirected graph at fixed thresholds (BUT).
 
 %% Brain Atlas

braph2genesis/pipelines/connectivity multiplex/pipeline_connectivity_multiplex_analysis_wu.braph2

@@ -2,8 +2,7 @@
 
 % This is the pipeline script to analyze a group of subjects using connectivity multiplex data and a weighted undirected graph.
 % 1. It loads a brain atlas from an XLS file (e.g., aal90_atlas.xlsx).
-% 2.1 It loads the connectivity data of one group of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
-% 2.2 It loads the connectivity data of one group of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
+% 2. It loads the connectivity data of one group of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
 % 3. It analyzes the data using connectivity multiplex analysis (CON_MP) based on weighted undirected graphs (WU).
 
 %% Brain Atlas

braph2genesis/pipelines/connectivity multiplex/pipeline_connectivity_multiplex_comparison_bud.braph2

@@ -2,8 +2,7 @@
 
 % This is the pipeline script to compare two groups of subjects using connectivity multiplex data and binary undirected graphs at fixed densities.
 % 1. It loads a brain atlas from an XLS file (e.g., aal90_atlas.xlsx).
-% 2.1 It loads the connectivity data of two groups of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
-% 2.2 It loads the connectivity data of two groups of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
+% 2. It loads the connectivity data of two groups of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
 % 3. It analyzes the first group using connectivity multiplex analyses (CON_MP) based on binary undirected graphs at fixed densities (BUD).
 % 4. It analyzes the second group using the same parameters selected for the first group.
 % 5. It compares the results of the two analyses.

braph2genesis/pipelines/connectivity multiplex/pipeline_connectivity_multiplex_comparison_but.braph2

@@ -2,8 +2,7 @@
 
 % This is the pipeline script to compare two groups of subjects using connectivity multiplex data and binary undirected graphs at fixed thresholds.
 % 1. It loads a brain atlas from an XLS file (e.g., aal90_atlas.xlsx).
-% 2.1 It loads the connectivity data of two groups of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
-% 2.2 It loads the connectivity data of two groups of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
+% 2. It loads the connectivity data of two groups of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
 % 3. It analyzes the first group using connectivity multiplex analyses (CON_MP) based on binary undirected graphs at fixed thresholds (BUT).
 % 4. It analyzes the second group using the same parameters selected for the first group.
 % 5. It compares the results of the two analyses.