DPARSF error

Submitted by djo155 on Thu, 09/13/2012 - 23:26

Hi Guys,

Preprocessed (detrend) my data outside of your toolbox but wanted to use DPARSF to smooth and calculate ALFF, fALFF, etc.  I created the proper folders in FunRaw, put my data in the FunImgNormalized folder, and tried to run just these steps that I wanted.  I checked smooth, use with smooth, no mask, checked everything on the ALFF line, regress out CSF.  I get the following error:

------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Smooth'
Done    'Smooth'
Done

Moving Smoothed Files:gad_c029 OKMoving Smoothed Files:gad_c031 OK
Undefined function 'alff' for input arguments of type 'char'.

Error in DPARSF_run (line 1100)
        alff(
        [AutoDataProcessParameter.DataProcessDir,filesep,FunImgDir,filesep,AutoDataProcessParameter.SubjectID{i}],
        ...

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

Any suggestions would be appreciated.  Thank you!

Desmond
Stanford Psychiatry Dept.

Submitted by YAN Chao-Gan on Sat, 09/15/2012 - 00:40

 Hi,

Have you also install the REST toolbox?

Best,

Chao-Gan

Submitted by djo155 on Sat, 09/15/2012 - 03:00

Thank you, Chao-Gan. I needed to add REST to my path. I have a new problem now that I think relates to where my data are kept. To get them to show up in the dialogue, I've been putting them in FunImgNormalized and get the following error:

------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Smooth'
Done 'Smooth'
Done

Moving Smoothed Files:gad_c029 OKMoving Smoothed Files:gad_c031 OK

Computing ALFF with: "/Volumes/EtkinLab_Data/Imaging/ctr_gad_mdd_cmd_pts/resting_state/D.Oathes/Temp/FunRaw/FunImgNormalizedSmoothedDetrendedFiltered/gad_c029"
Read 3D EPI functional images: "/Volumes/EtkinLab_Data/Imaging/ctr_gad_mdd_cmd_pts/resting_state/D.Oathes/Temp/FunRaw/FunImgNormalizedSmoothedDetrendedFiltered/gad_c029".Index exceeds matrix dimensions.

Error in rest_to4d (line 50)
rest_waitbar(0.001, ...

Error in alff (line 34)
[AllVolume,vsize,theImgFileList, Header,nVolumn] =rest_to4d(ADataDir);

Error in DPARSF_run (line 1100)
alff(
[AutoDataProcessParameter.DataProcessDir,filesep,FunImgDir,filesep,AutoDataProcessParameter.SubjectID{i}],
...

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

===================================

Is there a different folder I should put the images into if I want to calculate ALFF, fALFF, etc. in native space?

Thanks much,
Desmond

Submitted by YAN Chao-Gan on Tue, 09/18/2012 - 02:48

Hi Desmond,

The basic edition need you to put the data under FunImgNormalizedSmoothedDetrendedFiltered other than FunImgNormalized.

I suggest you use DPARSF advanced edition by type in DPARSFA. It's much more flexible and you can use any Starting Directory name.

Best,

Chao-Gan