GraphVar

Submitted by James on

Hi everyone, 

I know that this thread is for DPABI but I am hoping to post here in case anyone can help with my query as I have not received any responses from the GraphVar thread,will appreciate any inputs, 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.

 

Thank you, 

James

 

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