Error in preprocessing

Submitted by echoqiu77 on

Dear ChaoGan,

Because I don't have the latest version of matlab, so I use the matlab 2011a, spm8 and dpabi4.1 to do the preprocessing, this is the Error:

Warning: File: DPARSFA_run.m Line: 680 Column: 66
The temporary variable SliceOrder 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 SliceOrder is used before it is assigned in
 the parfor loop, a runtime error will occur.
 See Parallel for Loops in MATLAB, "Temporary Variables". 
> In DPARSF_run at 113
  In DPARSF>pushbuttonRun_Callback at 1152
  In gui_mainfcn at 96
  In DPARSF at 52
Warning: File: DPARSFA_run.m Line: 935 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 DPARSF_run at 113
  In DPARSF>pushbuttonRun_Callback at 1152
  In gui_mainfcn at 96
  In DPARSF at 52
Warning: File: DPARSFA_run.m Line: 2683 Column: 24
The temporary variable DirImg 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 DirImg is used before it is assigned in
 the parfor loop, a runtime error will occur.
 See Parallel for Loops in MATLAB, "Temporary Variables". 
> In DPARSF_run at 113
  In DPARSF>pushbuttonRun_Callback at 1152
  In gui_mainfcn at 96
  In DPARSF at 52
Warning: File: DPARSFA_run.m Line: 4389 Column: 32
The temporary variable DirImg 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 DirImg is used before it is assigned in
 the parfor loop, a runtime error will occur.
 See Parallel for Loops in MATLAB, "Temporary Variables". 
> In DPARSF_run at 113
  In DPARSF>pushbuttonRun_Callback at 1152
  In gui_mainfcn at 96
  In DPARSF at 52
Chris Rorden's dcm2nii :: 1 April 2010 
reading preferences file C:\fMRI\DPABI_V2.1_160415\DPARSF\dcm2nii\dcm2nii.ini 
reading preferences file DCM2NII.INI 
0 C:\fMRI\DPABI_V2.1_160415\DPARSF\dcm2nii\dcm2nii.exe ERROR: unable to find Qiu\Desktop\Analysis\FunImg\sub003 C:\Users\Haitang Qiu\Desktop\Analysis\FunRaw\sub003\IM1 
Either drag and drop or specify command line options: 
  dcm2nii <options> <sourcenames> 
OPTIONS: 
-a Anonymize [remove identifying information]: Y,N = Y 
-b load settings from specified inifile, e.g. '-b C:\set\t1.ini'   
-c Collapse input folders: Y,N = N 
-d Date in filename [filename.dcm -> 20061230122032.nii]: Y,N = Y 
-e events (series/acq) in filename [filename.dcm -> s002a003.nii]: Y,N = Y 
-f Source filename [e.g. filename.par -> filename.nii]: Y,N = N 
-g gzip output, filename.nii.gz [ignored if '-n n']: Y,N = N 
-i ID  in filename [filename.dcm -> johndoe.nii]: Y,N = Y 
-n output .nii file [if no, create .hdr/.img pair]: Y,N = Y 
-o Output Directory, e.g. 'C:\TEMP' (if unspecified, source directory is used) 
-p Protocol in filename [filename.dcm -> TFE_T1.nii]: Y,N = Y 
-r Reorient image to nearest orthogonal: Y,N  
-s SPM2/Analyze not SPM5/NIfTI [ignored if '-n y']: Y,N = N 
-v Convert every image in the directory: Y,N = Y 
-x Reorient and crop 3D NIfTI images: Y,N = N 
  You can also set defaults by editing DCM2NII.INI 
EXAMPLE: dcm2nii -a y -o C:\TEMP>> 
 
It seems have some problem with dcm2nii , so I  traslate to NII by MRICORN myself and start in DPARSF from FunImg,
it's work untill Reorienting, the Error is:
 
Bet begin...
Chris Rorden's dcm2nii :: 1 April 2010 
reading preferences file C:\fMRI\DPABI_V2.1_160415\DPARSF\dcm2nii\dcm2nii.ini 
0 C:\fMRI\DPABI_V2.1_160415\DPARSF\dcm2nii\dcm2nii.exe ERROR: unable to find Qiu\Desktop\Analysis\RealignParameter\sub003 C:\Users\Haitang Qiu\Desktop\Analysis\RealignParameter\sub003\Bet_meana20111103_230745ZhaoWenJin07132s002a1001BeforeBet.img 
Either drag and drop or specify command line options: 
  dcm2nii <options> <sourcenames> 
OPTIONS: 
-a Anonymize [remove identifying information]: Y,N = Y 
-b load settings from specified inifile, e.g. '-b C:\set\t1.ini'   
-c Collapse input folders: Y,N = N 
-d Date in filename [filename.dcm -> 20061230122032.nii]: Y,N = Y 
-e events (series/acq) in filename [filename.dcm -> s002a003.nii]: Y,N = Y 
-f Source filename [e.g. filename.par -> filename.nii]: Y,N = N 
-g gzip output, filename.nii.gz [ignored if '-n n']: Y,N = N 
-i ID  in filename [filename.dcm -> johndoe.nii]: Y,N = Y 
-n output .nii file [if no, create .hdr/.img pair]: Y,N = N 
-o Output Directory, e.g. 'C:\TEMP' (if unspecified, source directory is used) 
-p Protocol in filename [filename.dcm -> TFE_T1.nii]: Y,N = Y 
-r Reorient image to nearest orthogonal: Y,N  
-s SPM2/Analyze not SPM5/NIfTI [ignored if '-n y']: Y,N = Y 
-v Convert every image in the directory: Y,N = N 
-x Reorient and crop 3D NIfTI images: Y,N = N 
  You can also set defaults by editing C:\fMRI\DPABI_V2.1_160415\DPARSF\dcm2nii\dcm2nii.ini 
EXAMPLE: dcm2nii -a y -o C:\TEMP C:\DICOM\input1.par C:\input2.par 
Hit <Enter>>> 
 to exit. 
Can't open C:\Users\Haitang.hdr 
??? Error using ==> y_Read at 54
File doesn't exist: C:\Users\Haitang
Qiu\Desktop\Analysis\RealignParameter\sub003\Bet_meana20111103_230745ZhaoWenJin07132s002a1001AfterBet.img
 
Error in ==> y_Call_bet at 46
    Data = y_Read(fullfile(OutPath,[OutFile,'AfterBet.img']));
 
Error in ==> DPARSFA_run>(parfor body) at 1329
                y_Call_bet(MeanFile, OutputFile_Temp, '-f 0.3');
 
Error in ==> parallel_function at 473
            F(base, limit);
 
Error in ==> DPARSFA_run at 1314
    parfor i=1:AutoDataProcessParameter.SubjectNum
 
Error in ==> DPARSF_run at 113
[Error] = DPARSFA_run(Cfg);
 
Error in ==> DPARSF>pushbuttonRun_Callback at 1152
    [Error]=DPARSF_run(handles.Cfg);
 
Error in ==> gui_mainfcn at 96
        feval(varargin{:});
 
Error in ==> DPARSF at 52
    gui_mainfcn(gui_State, varargin{:});
 
??? Error while evaluating uicontrol Callback
 
thanks a lot for your help!!
 
 

you should replace path like "X:\programme files\MATLAB" into path like "X:\programme_files\MATLAB".

-----原始邮件-----
发件人: "The R-fMRI Network" <rfmri.org@gmail.com>
发送时间: 2017年7月12日 星期三
收件人: rfmri.org@rnet.co
抄送:
主题: Re: [RFMRI] Error in preprocessing

[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

Commented by Jamiu Aminu (aminuj)

Hi Prof, I don't quite understand what you mean by space in the path.


Online version of this post: http://rfmri.org/comment/5004#comment-5004






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