Error in Graphvar analysis

Submitted by James on

Hi, I am receiving multiple errors and am hoping someone can assist me in my queries, thank you for your help:

 

1)      Not including weighted betweenness centrality appears to remove normalization error of "normalization error: some metrics derived from random networks result in zero which cannot be used for normalization". I am slightly confused as I had already removed 1 participant whose network is fragmented at 0.15 but when I include betweenness centrality, the above normalization error appears. Can you kindly explain why and is there anything I can do apart from excluding betweenness centrality

 

 

2) I am keen to include local clustering coefficient to better understand small world properties but received this error. Is there anything I can do to address this please:  

 

Error using plot

Data cannot have more than 2 dimensions.
 
Error in Results_PlotView (line 508)
        tmpID = plot(secVal, STAT, 'LineWidth', 2);
 
Error in Results_OpeningFcn (line 177)
Results_PlotView(hObject,handles);
 
Error in gui_mainfcn (line 220)
    feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});
 
Error in Results (line 34)
    gui_mainfcn(gui_State, varargin{:});
 
Error in GraphVar_corr (line 140)
    Results;
 
Error in GraphVar>Btn_calcCorr_Callback (line 75)
    GraphVar_corr(handles,allTask)
 
Error in gui_mainfcn (line 95)
        feval(varargin{:});
 
Error in GraphVar (line 40)
    gui_mainfcn(gui_State, varargin{:});
 
Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)GraphVar('Btn_calcCorr_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback.
 

  

3) when I included weighted rich club coeff undirected, I received this error. Can I check if it is wise just to omit rich club coeff as a metric to analyse or should I address this error? If I should address this error, what can I do please? This is the error message received:

 

Error using tlstsq
tlstsq dgelsd error

Error in graphvar_glm/RFIT (line 549)
        [B, R] = tlstsq(X, Y);

Error in executeStats (line 289)
                                     ] = RFUN(Y_(:, CHUNK), nRandom_); % originally: SE(:, CHUNK)] = RFUN(Y_(:, CHUNK), nRandom_);

Error in GraphVar_corr (line 86)
[Files, LAB, N] = executeStats(allTasks, ...

Error in GraphVar>Btn_calcCorr_Callback (line 75)
    GraphVar_corr(handles,allTask)

Error in gui_mainfcn (line 95)
        feval(varargin{:});

Error in GraphVar (line 40)
    gui_mainfcn(gui_State, varargin{:});

Error in matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)GraphVar('Btn_calcCorr_Callback',hObject,eventdata,guidata(hObject))
 
Error while evaluating UIControl Callback.

 

4) when I ran my analyses with 1 model, 1 interaction, 1 rep, there was no error but when I did 1000 models, 1 iteration and 100 rep, I received this error, again (I received the same error when I tried with 500 models), I am not sure how to proceed as I am the impression that 1000 models, 1 iteration and 100 rep is the bare minimum to obtain valid results: 

 

Index in position 2 exceeds array bounds (must not exceed 198).
Error in CalcVars (line 779)
                        Result = ResultRandVar(:,i_rand);
Error in GraphVar_calc (line 93)
[res,shuffelFiles] =
CalcVars(dialogData.thresholds,dialogData.thresholdType,dialogData.brainD,dialogData.functionList,handles.vpFiles,'TaskPlaner',allTasks,'MatrixName',dialogData.MatrixName,'FilePos',dialogData.subjectNamePos,
'DoRandom',get(handles.RandomNetwork_check,'Value'), 'nRandom',
dialogData.nRandom, 'RandomFunction' ,randomNetwork_func ,  'RandomIterations' ,
dialogData.randomIter, 'Smallworldness',
get(handles.RandomNetwork_smallWorld,'Value'), 'randomForType',
[get(handles.binary_check,'Value'),get(handles.weighted_check,'Value')],'pValueField',handles.sigField,'TestAgainstRandom',strcmp(dialogData.random_network,'graph_randNW'),'DoShuffelRandom',get(handles.shuffel_check,'Value'),'NShuffelRandom',dialogData.nShuffel,'Normalize',dialogData.normalize,'RandomRaw',dialogData.shuffleRandom,'RandomRawIter',dialogData.RandomRawIter,'NoCorr',noCorr,'InterimResult',InterimResultsID,'weightAdjust_Thr',dialogData.weightAdjust_Thr,'DynamicGraphVar',
dialogData.DynamicGraphVar,'n_multislice', dialogData.n_multislice,'n_alpha',
dialogData.n_alpha);
Error in GraphVar>Btn_calcCorr_Callback (line 73)
[res allTask] = GraphVar_calc(handles);      %%%%%%???????
Error in gui_mainfcn (line 95)
        feval(varargin{:});
Error in GraphVar (line 40)
    gui_mainfcn(gui_State, varargin{:});
Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)GraphVar('Btn_calcCorr_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback.

 

5. when I created raw matrix to use NBS, I received this error if I selected r to z, no change in weights or when I selected negative weights to 0. I read that z transformation is recommended, can I check what I can do in order to use r to z please :  

Error using CalcCorrMatrix (line 157)

The connectivity values cannot be Fisher r-to-z transformed, as they are not scaled correctly (-1 < r < 1).

Error in GraphVar_calc (line 107)
    calcCorrMatrixResult =
    CalcCorrMatrix(handles.vpFiles,dialogData.MatrixName,dialogData.brainD,1,dialogData.subjectNamePos,handles.sigField,dialogData.ConnectivityThr_bool,dialogData.ConnectivityThr,0,InterimResultsID,dialogData.weightAdjust_Raw,
    dialogData.R2Z, dialogData.DynamicGraphVar2,outputName);

Error in GraphVar>Btn_calcCorr_Callback (line 73)
[res allTask] = GraphVar_calc(handles);      %%%%%%???????

Error in gui_mainfcn (line 95)
        feval(varargin{:});

Error in GraphVar (line 40)
    gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)GraphVar('Btn_calcCorr_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback.


 
6. when I included small world properties, I received this message, can you kindly advise how to proceed please: 
 
Error using graphalgs
There was an error in Johnson's algorithm.

Error in graphallshortestpaths (line 89)
    dist = graphalgs('all',debug_level,directed,G);

Error in small_world_propensity>avg_path_matrix (line 154)
D = graphallshortestpaths(M);

Error in small_world_propensity (line 73)
rand_path = avg_path_matrix(1./W_rand);    %path of the random netowork

Error in CalcVars (line 682)
                                        Result{i_dyn,i_sub} = eval([functionList{i_func} '(VPData{i_sub,i_dyn})']);

Error in GraphVar_calc (line 93)
[res,shuffelFiles] =
CalcVars(dialogData.thresholds,dialogData.thresholdType,dialogData.brainD,dialogData.functionList,handles.vpFiles,'TaskPlaner',allTasks,'MatrixName',dialogData.MatrixName,'FilePos',dialogData.subjectNamePos,
'DoRandom',get(handles.RandomNetwork_check,'Value'), 'nRandom', dialogData.nRandom, 'RandomFunction' ,randomNetwork_func ,
'RandomIterations' , dialogData.randomIter, 'Smallworldness', get(handles.RandomNetwork_smallWorld,'Value'), 'randomForType',
[get(handles.binary_check,'Value'),get(handles.weighted_check,'Value')],'pValueField',handles.sigField,'TestAgainstRandom',strcmp(dialogData.random_network,'graph_randNW'),'DoShuffelRandom',get(handles.shuffel_check,'Value'),'NShuffelRandom',dialogData.nShuffel,'Normalize',dialogData.normalize,'RandomRaw',dialogData.shuffleRandom,'RandomRawIter',dialogData.RandomRawIter,'NoCorr',noCorr,'InterimResult',InterimResultsID,'weightAdjust_Thr',dialogData.weightAdjust_Thr,'DynamicGraphVar',
dialogData.DynamicGraphVar,'n_multislice', dialogData.n_multislice,'n_alpha', dialogData.n_alpha);

Error in GraphVar>Btn_calcCorr_Callback (line 73)
[res allTask] = GraphVar_calc(handles);      %%%%%%???????

Error in gui_mainfcn (line 95)
        feval(varargin{:});

Error in GraphVar (line 40)
    gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)GraphVar('Btn_calcCorr_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback.

 

 

 
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