about extract aal time courses (90)

Submitted by yangth0306 on

Dear professor,

could you tell me how to extract AAl time courses (90) through dpabi? there is no button for this.

I have used the old version of dparsf, but an error occur. could you help me solve this problem? The error is shown below:

Extracting ROI time courses: "E:\aal\FunImgNormalizedSmoothedDetrendedFiltered\p-chensiyu"
Read 3D EPI functional images: "E:\aal\FunImgNormalizedSmoothedDetrendedFiltered\p-chensiyu".
 
ROI time courses retrieving through "D:\FDataanalysis\DATAanalysis\DPARSF_V2.1_120101\DPARSF_V2.1_120101\Templates\CsfMask_07_61x73x61.img".
ROI time courses retrieving through "D:\FDataanalysis\DATAanalysis\DPARSF_V2.1_120101\DPARSF_V2.1_120101\Templates\WhiteMask_09_61x73x61.img".
Extracting ROI time courses over, elapsed time: 4.35938 seconds.
Error using horzcat
Dimensions of matrices being concatenated are not consistent.
 
Error in DPARSF_run (line 1209)
            Covariables=[Covariables,theROITimeCourses];
 
Error in DPARSF>pushbuttonRun_Callback (line 976)
    [Error]=DPARSF_run(handles.Cfg);
 
Error in gui_mainfcn (line 96)
        feval(varargin{:});
 
Error in DPARSF (line 43)
    gui_mainfcn(gui_State, varargin{:});
 
Error while evaluating uicontrol Callback

 

YAN Chao-Gan

Mon, 04/20/2015 - 18:34

Permalink

Hi,

You can do it through DPARSF or DPABI->Utilities->ROI Signal Extractor.

For the error you encountered, you can post a snapshot of your DPARSF settings here.

Best,

Chao-Gan

 

yangth0306

Tue, 04/21/2015 - 14:33

Permalink

Dear Prof. chao-gan,

I want to do graph analysis, and i use dpabi to get functional connectivity of 90 AAL Regions. however, an error happened.

Warning: File: DPARSFA_run.m Line: 671 Column: 83
The temporary variable RefFile will be cleared at the beginning of each iteration of the parfor
loop.
Any value assigned to it before the loop will be lost.  If RefFile is used before it is assigned
in
the parfor loop, a runtime error will occur.
See Parallel for Loops in MATLAB, "Temporary Variables". 
> In DPARSFA>pushbuttonRun_Callback at 1579
  In gui_mainfcn at 96
  In DPARSFA at 33 
Chris Rorden's dcm2nii :: 1 April 2010 
reading preferences file D:\FDataanalysis\DATAanalysis\DPARSF_V2.2_130309\DPARSF_V2.2_130309\dcm2nii\dcm2nii.ini 
reading preferences file DCM2NII.INI 
Validating 205 potential DICOM images. 
Found 205 DICOM images. 
Converting 205/205  205 
0001.dcm->20110318_173402restmriChensiyus017a001.img 
Time elapsed 375ms 
Converting Functional Images:p-chensiyu OK
Removing First 10 Time Points: p-chensiyu OK
Slice Timing Setup:p-chensiyu OK
Warning: Run spm_jobman('initcfg'); beforehand 
> In spm_jobman at 107
  In DPARSFA_run>(parfor body) at 426
  In parallel_function at 484
  In DPARSFA_run at 362
  In DPARSFA>pushbuttonRun_Callback at 1579
  In gui_mainfcn at 96
  In DPARSFA at 33 
 
 
------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Slice Timing'
 
SPM8: spm_slice_timing (v4310)                     22:19:14 - 21/04/2015
========================================================================
Your TR is 2.0
Done    'Slice Timing'
Done
 
Moving Slice Timing Corrected Files:p-chensiyu OK
Realign Setup:p-chensiyu OK
 
 
------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Realign: Estimate & Reslice'
Done    'Realign: Estimate & Reslice'
Done
 
Moving Head Motion Corrected Files:p-chensiyu OK
 
Extracting ROI signals...
Read 3D EPI functional images: "E:\try-aal\FunImgAR\p-chensiyu"........................................
Error using y_ExtractROISignal (line 188)
Wrong ROI definition, please check:
E:\try-aal\Masks\p-chensiyu_CsfMask_07_91x109x91.nii
 
Error in DPARSFA_run>(parfor body) (line 1852)
                y_ExtractROISignal([AutoDataProcessParameter.DataProcessDir,filesep,FunSessionPrefixSet{iFunSession},AutoDataProcessParameter.StartingDirName,filesep,AutoDataProcessParameter.SubjectI
                Error in parallel_function (line 466)
            F(base, limit);
 
Error in DPARSFA_run (line 1753)
        parfor i=1:AutoDataProcessParameter.SubjectNum
 
Error in DPARSFA>pushbuttonRun_Callback (line 1579)
    [Error]=DPARSFA_run(handles.Cfg);
 
Error in gui_mainfcn (line 96)
        feval(varargin{:});
 
Error in DPARSFA (line 33)
    gui_mainfcn(gui_State, varargin{:});
 
Error while evaluating uicontrol Callback
Below is the settings. thanks a lot.

Hi, 

"Wrong ROI definition, please check: E:\try-aal\Masks\p-chensiyu_CsfMask_07_91x109x91.nii"

I will first suggest you to change "-" in path to "_".

If that doesn't work, please try a later version of DPARSFA, in case there is any bug with that version.

Best,

Chao-Gan

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