Error with DPARSF

Submitted by ShengChe on Thu, 02/11/2016 - 20:32

Dear all, 

I got the following error messages when I run the DPARSF advanced mode.

I am using SPM12 and Matlab 2014b.

Could someone help me for this?

Thank you!

Alex

-------

Error using DPARSFA_run>(parfor body) (line 571)
Index exceeds matrix dimensions.
 
Error in DPARSFA_run (line 546)
        parfor i=1:AutoDataProcessParameter.SubjectNum
 
 
Error in DPARSFA>pushbuttonRun_Callback (line 1761)
    [Error]=DPARSFA_run(handles.Cfg);
 
 
Error in gui_mainfcn (line 95)
        feval(varargin{:});
 
Error in DPARSFA (line 30)
    gui_mainfcn(gui_State, varargin{:});
 
 
Error using drawnow
Error while evaluating UIControl Callback

Forums:

YAN Chao-Gan

Mon, 02/15/2016 - 02:27

Hi Alex,

Please make sure all the subjects have the correct number of time points in FunImg.

Best,

Chao-Gan

ShengChe

Mon, 02/15/2016 - 04:08

Dear Chao-Gan,

Thank you. I found my error.

However, when I continued, there were some new error messages.

 

---

Error using DPARSFA_run>(parfor body) (line 4722)
/bin/mv: Argument list too long.
 
Error in DPARSFA_run (line 4719)
        parfor iMeasure=1:length(MeasureSet)
 
 
Error in DPARSFA>pushbuttonRun_Callback (line 1761)
    [Error]=DPARSFA_run(handles.Cfg);
 
 
Error in gui_mainfcn (line 95)
        feval(varargin{:});
 
Error in DPARSFA (line 30)
    gui_mainfcn(gui_State, varargin{:});
 
 
Error while evaluating UIControl Callback
---
 
Was the long path of the working folder too long?
 
Thanks a lot!
Alex

YAN Chao-Gan

Mon, 02/15/2016 - 05:00

Seems there were too many files need to move. How many subjects do you have?

Best,

ShengChe

Mon, 02/15/2016 - 18:17

I only tried one subject (9000 files in total)

Best,

Alex

YAN Chao-Gan

Tue, 02/16/2016 - 07:44

There were 9000 time points for that subject? It should be ok.

Could you reduce the number of time points and retry, to see what happens?

Best,

Chao-Gan

ShengChe

Tue, 02/16/2016 - 19:51

Dear Chao-Gan, 

Only 200 time points for that subject.

I tried again using another subject and still encountered the same error.

This error happened after moving the degree of centrality.

Best,

Alex

-----

Moving Smoothed Files:ReHo_FunImgARCWDF OK
Moving Smoothed Files:DegreeCentrality_FunImgARCWDF OKMoving Smoothed Files:ALFF_FunImgARCWD OKMoving Smoothed Files:VMHC_FunImgARCWDFsymS OKMoving Smoothed Files:fALFF_FunImgARCWD OK
Error using DPARSFA_run>(parfor body) (line 4722)
/bin/mv: Argument list too long.
 
Error in DPARSFA_run (line 4719)
        parfor iMeasure=1:length(MeasureSet)
 
 
Error in DPARSFA>pushbuttonRun_Callback (line 1761)
    [Error]=DPARSFA_run(handles.Cfg);
 
 
Error in gui_mainfcn (line 95)
        feval(varargin{:});
 
Error in DPARSFA (line 30)
    gui_mainfcn(gui_State, varargin{:});
 
 
Error using drawnow
Error while evaluating UIControl Callback
-----

 

YAN Chao-Gan

Wed, 02/17/2016 - 00:20

Hi,

Could you check what do you have under "fALFF_FunImgARCWD".

ShengChe

Thu, 03/03/2016 - 20:40

Hi Chao-Gan,
I have checked the folder.
In the folder of 'Results\fALFF_FunImgARCW\", it has fALFFMAP, mfALFFMap, zfALFFMap of all subjects.
In the folder of 'ResultsS\fALFF_FunImgARCW\", it has sfALFFMAP, smfALFF, szfALFFMap of all subjects.

The folder after fALFF_FunImgARCW is FC_FunImgARCWF, which contains 75,300 files of 1568 ROIs.

Is this problem due to I didn't give predefined ROIs?

Sheng-Che


2016-02-16 19:20 GMT-05:00 The R-fMRI Network <rfmri.org@gmail.com>:

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Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi,

Could you check what do you have under "fALFF_FunImgARCWD".

ShengChe

Fri, 03/04/2016 - 01:00

But even I unchecked the options of "functional connectivity" and "Extract ROI time courses", there were still some other error messages.
----
Computing VMHC...
Reading images from "/Users/schung/analysis/Disconnection/FunImgARCFWsymS/sub40_pre/ssym_wFiltered_4DVolume.nii" etc.
Error using y_VMHC (line 75)
To RESHAPE the number of elements must not change.

Error in DPARSFA_run>(parfor body) (line 4327)
            [VMHCBrain, Header] =
            y_VMHC([AutoDataProcessParameter.DataProcessDir,filesep,FunSessionPrefixSet{iFunSession},AutoDataProcessParameter.StartingDirName,filesep,AutoDataProcessParameter.SubjectID{i}],
            ...


Error in DPARSFA_run (line 4324)
        parfor i=1:AutoDataProcessParameter.SubjectNum


Error in DPARSFA>pushbuttonRun_Callback (line 1761)
    [Error]=DPARSFA_run(handles.Cfg);


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

Error in DPARSFA (line 30)
    gui_mainfcn(gui_State, varargin{:});

 
Error while evaluating UIControl Callback
----



2016-03-03 15:40 GMT-05:00 The R-fMRI Network <rfmri.org@gmail.com>:

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Commented by Sheng-Che Hung (ShengChe)

Hi Chao-Gan,
I have checked the folder.
In the folder of 'Results\fALFF_FunImgARCW\", it has fALFFMAP, mfALFFMap, zfALFFMap of all subjects.
In the folder of 'ResultsS\fALFF_FunImgARCW\", it has sfALFFMAP, smfALFF, szfALFFMap of all subjects.

The folder after fALFF_FunImgARCW is FC_FunImgARCWF, which contains 75,300 files of 1568 ROIs.

Is this problem due to I didn't give predefined ROIs?

Sheng-Che




2016-02-16 19:20 GMT-05:00 The R-fMRI Network <rfmri.org@gmail.com>:

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Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi,

Could you check what do you have under "fALFF_FunImgARCWD".
Online version of this post: http://rfmri.org/comment/4167#comment-4167





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YAN Chao-Gan

Sun, 03/06/2016 - 05:44

Hi, 

According to the error message "To RESHAPE the number of elements must not change", could you check the dimension and voxel size of the mask and your functional data?

Best,

Chao-Gan

ShengChe

Mon, 03/07/2016 - 04:40

The voxel size of my data is 3.5 x 3.5 x 3.5
I used FWHM as 6 x 6 x 6 and default mask.
Sheng-Che


2016-03-06 0:44 GMT-05:00 The R-fMRI Network <rfmri.org@gmail.com>:

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Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi, 

According to the error message "To RESHAPE the number of elements must not change", could you check the dimension and voxel size of the mask and your functional data?

Best,

Chao-Gan


Online version of this post: http://rfmri.org/comment/4171#comment-4171





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YAN Chao-Gan

Mon, 03/07/2016 - 05:00

I am not sure if resampling the data to 3.5x3.5x3.5 is the cause. You can try to set to the default 3x3x3 in Normalization.

Best,

ShengChe

Mon, 03/07/2016 - 12:40

Yes. It works after I used 3 x 3 x 3.
But the problem with functional connectivity still persisted.
Moving Smoothed Files:ReHo_FunImgARCFW OK
Moving Smoothed Files:DegreeCentrality_FunImgARCFW OKMoving Smoothed Files:ALFF_FunImgARCFW OKMoving Smoothed Files:VMHC_FunImgARCFWsymS OKMoving Smoothed Files:fALFF_FunImgARCFW OK
Error using DPARSFA_run>(parfor body) (line 4722)
Home: Undefined variable.

Error in DPARSFA_run (line 4719)
        parfor iMeasure=1:length(MeasureSet)


Error in DPARSFA>pushbuttonRun_Callback (line 1761)
    [Error]=DPARSFA_run(handles.Cfg);


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

Error in DPARSFA (line 30)
    gui_mainfcn(gui_State, varargin{:});

 
Error while evaluating UIControl Callback

------
I have checked the folder.
In the folder of 'Results\fALFF_FunImgARCW\", it has fALFFMAP, mfALFFMap, zfALFFMap of all subjects.
In the folder of 'ResultsS\fALFF_FunImgARCW\", it has sfALFFMAP, smfALFF, szfALFFMap of all subjects.

The folder after fALFF_FunImgARCW is FC_FunImgARCWF, which contains 75,300 files of 1568 ROIs.

I have chosen AAL ROIs in template\aal.nii

Sheng-Che


2016-03-07 0:00 GMT-05:00 The R-fMRI Network <rfmri.org@gmail.com>:

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Commented by YAN Chao-Gan (YAN Chao-Gan)

I am not sure if resampling the data to 3.5x3.5x3.5 is the cause. You can try to set to the default 3x3x3 in Normalization.

Best,
Online version of this post: http://rfmri.org/comment/4184#comment-4184





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YAN Chao-Gan

Mon, 03/07/2016 - 22:20

"Home: Undefined variable."
What's your path? Do you have space in the path?

Best,

Chao-Gan


ShengChe

Tue, 03/08/2016 - 00:40

Hi Chao-Gan,

Here is my path

ShengChe

Tue, 03/08/2016 - 01:00

The path is 
/user/schung/Disconnection/FunRaw
No space in the path


2016-03-07 19:40 GMT-05:00 The R-fMRI Network <rfmri.org@gmail.com>:

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Commented by Sheng-Che Hung (ShengChe)

Hi Chao-Gan,

Here is my path


Online version of this post: http://rfmri.org/comment/4190#comment-4190





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