ROI signals

Submitted by toronto on

Hello.

I was wondering if I can generate ROI signals using either fsl or AFNI for GraphVar.

 

Thanks,

Yuko

Johann Kruschwitz

Tue, 08/11/2015 - 08:11

Permalink

Sorry for the delay - yes, you can use fsl or AFNI for extraction of ROI signals (the only thing GraphVar needs is a vector of time points for each ROI, i.e. a matrix with n columns representing the ROIs, whereas the number of rows represent number of time points). Please have a look at the sample data folder "Signals" that comes along with GraphVar to see how the data has to be organized.

Best,
Johann

Hi Johann,

Thanks very much for response. To follow up on that, compared with the numbers in the ROISignals files in the SampleWorkspace, mine are a lot larger. Is there specifc range in the number?

Also, I created a covariance matrix from the signals and selected SICE for the threshold. When I clicked on Calculate variables and export, I got the following message. 

???  Index of element to remove exceeds matrix dimensions.
 
Error in ==> CalcVars at 299
                R(del,:) = [];
 
Error in ==> GraphVar_calc at 85
[res,shuffelFiles] =
CalcVars(dialogData.thresholds,dialogData.thresholdType,dialogData.brainD,dialogData.functionList,handles.vpFiles,'TaskPlaner',allTasks,'MatrixName',dialogData.MatrixName,'FilePo
Error in ==> GraphVar_CalcExport_Callback at 42
[res allTasks] = GraphVar_calc(handles,1);
 
Error in ==> gui_mainfcn at 96
        feval(varargin{:});
 
Error in ==> GraphVar at 40
    gui_mainfcn(gui_State, varargin{:});
 
Error in ==>
@(hObject,eventdata)GraphVar('GraphVar_CalcExport_Callback',hObject,eventdata,guidata(hObject))
 
 

 

??? Error while evaluating uicontrol Callback
 
I appreciate your help in advance.

Hi Johann,

Thanks very much for your response. To follow up on that, compared with the numbers in the ROISignals files in the SampleWorkspace, mine are a lot larger. Is there specifc range in the number?

Also, I created a covariance matrix from the signals and selected SICE for the threshold. When I clicked on Calculate variables and export, I got the following message. 

???  Index of element to remove exceeds matrix dimensions.
 
Error in ==> CalcVars at 299
                R(del,:) = [];
 
Error in ==> GraphVar_calc at 85
[res,shuffelFiles] =
CalcVars(dialogData.thresholds,dialogData.thresholdType,dialogData.brainD,dialogData.functionList,handles.vpFiles,'TaskPlaner',allTasks,'MatrixName',dialogData.MatrixName,'FilePo
Error in ==> GraphVar_CalcExport_Callback at 42
[res allTasks] = GraphVar_calc(handles,1);
 
Error in ==> gui_mainfcn at 96
        feval(varargin{:});
 
Error in ==> GraphVar at 40
    gui_mainfcn(gui_State, varargin{:});
 
Error in ==>
@(hObject,eventdata)GraphVar('GraphVar_CalcExport_Callback',hObject,eventdata,guidata(hObject))
 
 

 

??? Error while evaluating uicontrol Callback
 
I appreciate your help in advance.

Just to follow up on my previous post, signals in my data rage from around -100 to around 100. I did preprocessing using afni proc.py and extracted signals using the coordinates of Dosenbach brain regions with the radius of 5mm for each subject.  

 

Thanks. 

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