Error using copyfile

Dear experts

All files were in NIfTI format (FunImg and T1Img)

From the error message:

Removing First 10 Time Points: Sub_001 OKRemoving First 10 Time Points: Sub_002 OKRemoving First 10 Time Points: Sub_003 OK

    'Error in Removing First 10Time Points: Sub_002'
    'Error in Removing First 10Time Points: Sub_003'
Error using copyfile
No matching files were found.
Error in DPARSFA_RerunWithGSR (line 84)
        copyfile([Cfg.DataProcessDir,filesep,FunSessionPrefixSet{iFunSession},StartingDirName],[Cfg.DataProcessDir,filesep,FunSessionPrefixSet{iFunSession},StartingDirName,'global']);
       
Error in DPARSFA>pushbuttonRun_Callback (line 1789)
        [Error]=DPARSFA_RerunWithGSR(handles.Cfg);

 

Thanks for considering my request!

 

Cheers

Larry

AttachmentSize
1.png75.83 KB
folder.png22.51 KB

Forums:

Dear experts

All subjects had different time points. So, I managed to run the subjects with different time points now.

However, the new error message are:

Apply Reorient Mats to functional images for Sub_003: OK
Apply Reorient Mats to functional images for Sub_002: OK
Bet begin...
Chris Rorden's dcm2nii :: 1 April 2010
reading preferences file C:\DPABI_V2.3_170105\DPARSF\dcm2nii\dcm2nii.ini
Adjusting NIfTI/Analyze image E:\dpabi\RealignParameter\Sub_003\Bet_LT_MoCoSeriesBeforeBet.hdr
Changing subformat of E:\dpabi\RealignParameter\Sub_003\Bet_LT_MoCoSeriesBeforeBet.hdr
Image data-type is SHORTS
Image min/max is 0 1872
bas = 0, range = 1872
Image voxel size: 1.000000 1.000000 1.000000
Image dimensions: 70 70 40
hist_min=0.000000 thresh2=1.000000 thresh=18.000000 thresh98=164.000000 hist_max=255.000000
CofG (33.686818,43.091489,20.885342) mm
RADIUS 23.801655
MEDIANVAL 87.000000
Pass 1, iteration 0
Pass 1, iteration 50
Pass 1, iteration 100
Pass 1, iteration 150
Pass 1, iteration 200
Pass 1, iteration 250
Pass 1, iteration 300
Pass 1, iteration 350
Pass 1, iteration 400
Pass 1, iteration 450
Pass 1, iteration 500
Pass 1, iteration 550
Pass 1, iteration 600
Pass 1, iteration 650
Pass 1, iteration 700
Pass 1, iteration 750
Pass 1, iteration 800
Pass 1, iteration 850
Pass 1, iteration 900
Pass 1, iteration 950
self-intersection total = 18.393887 (threshold=4000.000000)
1.512921 secs
 
0.023008 for pre-processing
0.236988 for normal computation
0.979221 for search along normal
0.157314 for checking self-intersection
0.013732 for output
Chris Rorden's dcm2nii :: 1 April 2010
reading preferences file C:\DPABI_V2.3_170105\DPARSF\dcm2nii\dcm2nii.ini
Adjusting NIfTI/Analyze image E:\dpabi\RealignParameter\Sub_002\Bet_RT_MoCoSeriesBeforeBet.hdr
Changing subformat of E:\dpabi\RealignParameter\Sub_002\Bet_RT_MoCoSeriesBeforeBet.hdr
Image data-type is SHORTS
Image min/max is 0 1885
bas = 0, range = 1885
Image voxel size: 1.000000 1.000000 1.000000
Image dimensions: 70 70 40
hist_min=0.000000 thresh2=1.000000 thresh=17.000000 thresh98=162.000000 hist_max=254.000000
CofG (33.666305,43.013038,20.672851) mm
RADIUS 23.897210
MEDIANVAL 85.000000
Pass 1, iteration 0
Pass 1, iteration 50
Pass 1, iteration 100
Pass 1, iteration 150
Pass 1, iteration 200
Pass 1, iteration 250
Pass 1, iteration 300
Pass 1, iteration 350
Pass 1, iteration 400
Pass 1, iteration 450
Pass 1, iteration 500
Pass 1, iteration 550
Pass 1, iteration 600
Pass 1, iteration 650
Pass 1, iteration 700
Pass 1, iteration 750
Pass 1, iteration 800
Pass 1, iteration 850
Pass 1, iteration 900
Pass 1, iteration 950
self-intersection total = 13.982716 (threshold=4000.000000)
1.441349 secs
 
0.021403 for pre-processing
0.230148 for normal computation
0.974684 for search along normal
0.097135 for checking self-intersection
0.024130 for output
Chris Rorden's dcm2nii :: 1 April 2010
reading preferences file C:\DPABI_V2.3_170105\DPARSF\dcm2nii\dcm2nii.ini
Adjusting NIfTI/Analyze image E:\dpabi\T1ImgBet\Sub_003\Bet__traBeforeBet.hdr
Changing subformat of E:\dpabi\T1ImgBet\Sub_003\Bet__traBeforeBet.hdr
Not enough data in E:\dpabi\T1ImgBet\Sub_003\fBet_traBeforeBet.img
Actually read 0
Error using y_Read (line 54)
File doesn't exist:
E:\dpabi\T1ImgBet\Sub_003\Bet_traAfterBet.img

Error in y_Call_bet (line 46)
    Data = y_Read(fullfile(OutPath,[OutFile,'AfterBet.img']));
Error in DPARSFA_run (line 1411)
        parfor i=1:AutoDataProcessParameter.SubjectNum
Error in DPARSFA>pushbuttonRun_Callback (line 1786)
    [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.

 

Hi there,

Please make sure all subjects' names in FunImg and T1Img are exactly same (e.g. no spaces or any other unexpecting characters).

Best,

Xiao

 

Hi Xiao

Thanks for your reply.

I found out "BET" (compiled by Dr. Chris Rorden) can not process those subjects.

 

Best regards

Larry

Are you working on a mac? Then you should install fsl

Hi

FYI.

Removing First 10 Time Points: Sub_001 OK

Slice Timing Setup:Sub_001 OK
Initialising batch system... done.


------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Slice Timing'

SPM12: spm_slice_timing (v6130)                    07:50:20 - 15/11/2017
========================================================================
Number of slices is...                  :                             40
Time to Repeat (TR) is...               :                              2
Parameters are specified as...          :                  slice indices
Completed                               :          07:50:29 - 15/11/2017
Done    'Slice Timing'
Done

Moving Slice Timing Corrected Files:Sub_001 OK

Realign Setup:Sub_001 OK


------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Realign: Estimate & Reslice'

SPM12: spm_realign (v6070)                         07:50:30 - 15/11/2017
========================================================================
Completed                               :          07:50:37 - 15/11/2017

SPM12: spm_reslice (v5929)                         07:50:37 - 15/11/2017
========================================================================
Completed                               :          07:50:48 - 15/11/2017
Done    'Realign: Estimate & Reslice'
Done

Moving Head Motion Corrected Files:Sub_001 OK

Reorienting T1 Image Interactively for Sub_001:

Reorienting T1 Image Interactively for Sub_001: OK
Reorienting Functional Images Interactively for Sub_001:

Reorienting Functional Images Interactively for Sub_001: OK
Warning: Directory already exists.
> In DPARSFA_run (line 1194)
  In DPARSFA>pushbuttonRun_Callback (line 1786)
  In gui_mainfcn (line 95)
  In DPARSFA (line 30)
Apply Reorient Mats to functional images for Sub_001: OK
Bet begin...

Error: input image /home/larry/New not valid


Error: input image /home/larry/New not valid

Bet finished
Copying T1 image Files:Sub_001 OK

Error using DPARSFA_run (line 1587)
Index exceeds matrix dimensions.

Error in DPARSFA>pushbuttonRun_Callback (line 1786)
    [Error]=DPARSFA_run(handles.Cfg);

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

Hi Xiao

Here you are.

The "Bet" issue has been fixed (Win 10).

Chris Roden's dcm2niiX v1.0.20170624 (Siemens DICOM)-> OK

MRIConvert v.21 -> failed.

In addition, I'm trying to figure out how to run "Bet" from Matlab in Linux.

 

 

 

 

 

 

Although I don't know details, you may try to start matlab with terminal.

LD_PRELOAD="/usr/lib/x86_64-linux-gnu/libstdc++.so.6" matlab

This command line may help.

Hi Xiao

Add the following lines to ~/bashrc.

FSLDIR=/usr/local/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH

Thanks for your suggestion.

Best wishes

Larry