Here's a snippet from the output log from a previous participant:

Chris Rorden's dcm2nii :: 2MAY2016 64bit BSD License  :: (upgrade to dcm2niix suggested)
reading preferences file /home/USER/.dcm2nii/dcm2nii.ini
Data will be exported to /outdir/
Validating 1328 potential DICOM images.
Found 1319 DICOM images.

.....

Converting 123/1017  volumes: 1
file.dcm->MPRAGETRAT1.nii
For slice timing correction: the slice order is Siemens-even interleaved ascending (2,4..,1,3...)
 brightest voxel was 1253: data will be saved as 16-bit signed integer.
Saving /outdir/MPRAGETRAT1.nii
Reorienting as /outdir/oMPRAGETRAT1.nii
Saving /outdir/oMPRAGETRAT1.nii
Cropping NIfTI/Analyze image /outdir2/oMPRAGETRAT1.nii
Saving /outdir/coMPRAGETRAT1.nii

.....

Where the command calling dcm2nii (older version from an older script) was:

subprocess.call('dcm2nii -d N -e N -f N -i N -4 Y -g N -n Y -o '+ExpLoc+' -v Y '+glob(Folder[Day])[0]+' > '+ExpLoc+'/conversion.txt', shell=True).

dcm2nii was updated to dcm2niix, but calling dcm2niix with:

subprocess.call(["dcm2niix", "-f", "%p", "-x", "y", "-o", ExpLoc, glob(Folder[Day])[0]])

doesn't seem to crop or rotate the .dcm file. The main issue is that only one file is not being cropped and reoriented. I've run the above dcm2niix command in the terminal on the single file and it prompts the error mentioned in my earlier post.


EDIT: Ignore this post, I've since resolved the issue.