DPARSF/dcm2nii

Submitted by ladansh on

Hi all.
I'm kind of new in DPARSF and I'm having trouble doing normalization with T1 image unified segmentation. after reorienting the images. somehow dcm2nii is called, I have  my nifti T1 images and I unchecked T1 dicom to nifti. here's my workspace:

Apply Reorient Mats to functional images for Subject002: OK
Apply Reorient Mats to functional images for Subject001: OK
Bet begin...
Chris Rorden's dcm2nii :: 1 April 2010 
reading preferences file E:\Program Files\MATLAB\R2013a\bin\Analysis\DPABI_V1.3_150710\DPARSF_V3.2_150710\dcm2nii\dcm2nii.ini 
0 E:\Program Files\MATLAB\R2013a\bin\Analysis\DPABI_V1.3_150710\DPARSF_V3.2_150710\dcm2nii\dcm2nii.exe ERROR: unable to find Files\MATLAB\R2013a\bin\Analysis\Pre Process DPARSF\RealignParameter\Subject008 E:\Program Files\MATLAB\R2013a\bin\Analysis\Pre Process DPARSF\RealignParameter\Subject008\Bet_meanNSEPILEPSY_NL0028_20100820_3681_005_Q_EPILEPSY_NEW1_4_fMRI_Rest_Open_006BeforeBet.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 E:\Program Files\MATLAB\R2013a\bin\Analysis\DPABI_V1.3_150710\DPARSF_>> 
 
thanks

YAN Chao-Gan

Fri, 09/18/2015 - 03:22

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Hi, 
 
The bet step in windows depends on Dr. Chris Rorden's compiled version of bet, which only works on ANALYZE files. Here dcm2nii was called to convert the file format.
 
I think the problem in your case is that there were spaces in your path, i.e., "Pre Process DPARSF". You can remove the spaces in the path and see how it works.
 
Best,
 
Chao-Gan
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