DPARSF not finding files

Submitted by cogsci on

I have attempted to use DPRASF with my data and with the unzipped contents of ProcessingDemoData.zip .  The "participants" folder is empty.  Drilling down further into the FunRaw folder, does not solve the problem.

 

When I go into Quality Control, I can see the subject directories, but not act upon the files contained within (see "error dialog").

 

We are using Matlab R2014a and I have spm8 in my path with these tool boxes installed 

No errors have been displayed in my Matlab Command window.

Thank you!

YAN Chao-Gan

Wed, 01/14/2015 - 22:18

Permalink

Hi,

For DPARSF, please set up the starting directory name at the bottom right, then DPARSF will start to detect the subjects.

Best,

Chao-Gan

 

Thanks,
That improved the situation, sorry if it should have been obvious to me. The demo data now loads and I accept the defualts. Now I get this error bellow in red.
 
 
Citing Information:
If you think DPARSFA is useful for your work, citing it in your paper would be greatly appreciated.
Something like "... The preprocessing was carried out by using Data Processing Assistant for Resting-State fMRI (DPARSF) (Yan & Zang, 2010, http://rfmri.org/DPARSF) which is based on Statistical Parametric Mapping (SPM8) (http://www.fil.ion.ucl.ac.uk/spm) and the toolbox for Data Processing & Analysis of Brain Imaging (DPABI, http://rfmri.org/DPABI)..."
Reference: Yan C and Zang Y (2010) DPARSF: a MATLAB toolbox for "pipeline" data analysis of resting-state fMRI. Front. Syst. Neurosci. 4:13. doi:10.3389/fnsys.2010.00013
Warning: matlabpool will be removed in a future release.
To query the size of an already started parallel pool,
query the 'NumWorkers' property of the pool.
To check if a pool is already started use
'isempty(gcp('nocreate'))'. 
Warning: Directory already exists.
> In DPARSFA_run>(parfor body) at 209
  In parallel_function>make_general_channel/channel_general at 929
  In remoteParallelFunction at 38 
Chris Rorden's dcm2nii :: 1 April 2010
reading preferences file ./dcm2nii_linux.ini
Validating 240 potential DICOM images.
Found 240 DICOM images.
Chris Rorden's dcm2nii :: 1 April 2010
reading preferences file ./dcm2nii_linux.ini
Validating 241 potential DICOM images.
Found 240 DICOM images.
Warning: Directory already exists.
> In DPARSFA_run>(parfor body) at 209
  In parallel_function>make_general_channel/channel_general at 929
  In remoteParallelFunction at 38 
Chris Rorden's dcm2nii :: 1 April 2010
reading preferences file ./dcm2nii_linux.ini
Validating 240 potential DICOM images.
Found 240 DICOM images.
Converting 240/240  240
0000001.dcm->gefunc31x31x30240RSA.nii
Saving /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/FunImg/Sub_002/gefunc31x31x30240RSA.nii
Converting 240/240  240
0000001.dcm->gefunc31x31x30240RSA.nii
Saving /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/FunImg/Sub_001/gefunc31x31x30240RSA.nii
Converting 240/240  240
0000001.dcm->gefunc31x31x30240RS.nii
Saving /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/FunImg/Sub_003/gefunc31x31x30240RS.nii
Converting Functional Images:Sub_002 OK
Converting Functional Images:Sub_003 OK
Converting Functional Images:Sub_001 OK
 
Chris Rorden's dcm2nii :: 1 April 2010
reading preferences file ./dcm2nii_linux.ini
Validating 131 potential DICOM images.
Found 128 DICOM images.
Converting 128/128  1
0000001.dcm->t1mpragesag.nii
Saving /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/T1Img/Sub_002/t1mpragesag.nii
Reorienting as /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/T1Img/Sub_002/ot1mpragesag.nii
Saving /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/T1Img/Sub_002/ot1mpragesag.nii
Chris Rorden's dcm2nii :: 1 April 2010
reading preferences file ./dcm2nii_linux.ini
Validating 131 potential DICOM images.
Found 128 DICOM images.
Converting 128/128  1
0000001.dcm->t1mpragesag.nii
Saving /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/T1Img/Sub_003/t1mpragesag.nii
Reorienting as /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/T1Img/Sub_003/ot1mpragesag.nii
Saving /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/T1Img/Sub_003/ot1mpragesag.nii
Cropping NIfTI/Analyze image /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/T1Img/Sub_003/ot1mpragesag.nii
Saving /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/T1Img/Sub_003/cot1mpragesag.nii
Warning: Directory already exists.
> In DPARSFA_run>(parfor body) at 234
  In parallel_function>make_general_channel/channel_general at 929
  In remoteParallelFunction at 38 
Chris Rorden's dcm2nii :: 1 April 2010
reading preferences file ./dcm2nii_linux.ini
Validating 128 potential DICOM images.
Found 128 DICOM images.
Converting 128/128  1
0000001.dcm->t1mpragesagA.nii
Saving /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/T1Img/Sub_001/t1mpragesagA.nii
Reorienting as /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/T1Img/Sub_001/ot1mpragesagA.nii
Saving /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/T1Img/Sub_001/ot1mpragesagA.nii
Cropping NIfTI/Analyze image /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/T1Img/Sub_001/ot1mpragesagA.nii
Saving /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/T1Img/Sub_001/cot1mpragesagA.nii
Cropping NIfTI/Analyze image /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/T1Img/Sub_002/ot1mpragesag.nii
Saving /scratch/lfs/rlts/cam/working/cam_scratch/rsfmri_ot/dpabi/ProcessingDemoData/T1Img/Sub_002/cot1mpragesag.nii
Converting T1 Images:Sub_002 OK
Converting T1 Images:Sub_003 OK
Converting T1 Images:Sub_001 OK
 
Error using DPARSFA_run>(parfor body) (line 565)
Index exceeds matrix dimensions.
 
Error in DPARSFA_run (line 540)
        parfor i=1:AutoDataProcessParameter.SubjectNum
 
 
Error in DPARSFA>pushbuttonRun_Callback (line 1670)
    [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,

Please have a check on the data structure. You can paste a snapshot of the data and your settings here.

Best,

Chao-Gan

cogsci

Thu, 01/15/2015 - 03:54

Permalink

Directory structure

[xxxx@gui1 dpabi]$ tree -d ProcessingDemoData
ProcessingDemoData
├── DemoResults
│   ├── ALFF
│   ├── fALFF
│   ├── FC
│   └── ReHo
├── FunImg
│   ├── Sub_001
│   ├── Sub_002
│   └── Sub_003
├── FunRaw
│   ├── Sub_001
│   ├── Sub_002
│   └── Sub_003
├── StatisticalDemo
│   ├── AD_MCI_NC
│   │   ├── AD
│   │   │   ├── ALFF
│   │   │   ├── fALFF
│   │   │   └── ReHo
│   │   ├── MCI
│   │   │   ├── ALFF
│   │   │   ├── fALFF
│   │   │   └── ReHo
│   │   └── NC
│   │       ├── ALFF
│   │       ├── fALFF
│   │       └── ReHo
│   └── EC_EO
│       ├── EC
│       │   ├── ALFF
│       │   ├── fALFF
│       │   └── ReHo
│       └── EO
│           ├── ALFF
│           ├── fALFF
│           └── ReHo
├── T1Img
│   ├── Sub_001
│   ├── Sub_002
│   └── Sub_003
└── T1Raw
    ├── Sub_001
    ├── Sub_002
    └── Sub_003
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