mriconvert: mcverter outputs are not the same as MRI Convert outputs

[Justin Chang]

Hi,

I have been comparing .nii outputs from mcverter and MRI Convert and I am unable to get mcverter outputs to match those produced using the MRI Convert GUI. It appears that mcverter is flipping the alignment .

The configurations I have been using for DICOM data (T1, T2 and DTI)

T1 GUI Configuration:
- Save each subject in a separate directory (unchecked)
- Save each series in a separate directory (unchecked)
- Save multivolume series as 4D files (unchecked)
- Skip volumes for multivolume series (0)
- Apply rescale slope and intercept to data (unchecked)
- save as .nii file (checked)

T1 Terminal
$ mcverter -o ~/Desktop/DICOM/T1 -f nifti -n ~/Desktop/NIFTI/

T2 GUI Configuration:
- Save each subject in a separate directory (unchecked)
- Save each series in a separate directory (unchecked)
- Save multivolume series as 4D files (checked)
- Skip volumes for multivolume series (0)
- Apply rescale slope and intercept to data (unchecked)
- save as .nii file (checked)

T2 Terminal
$ mcverter -o ~/Desktop/DICOM/T2 -f nifti -n -d ~/Desktop/NIFTI/

DTI GUI Configuration:
- Save each subject in a separate directory (unchecked)
- Save each series in a separate directory (unchecked)
- Save multivolume series as 4D files (checked)
- Skip volumes for multivolume series (0)
- Apply rescale slope and intercept to data (unchecked)
- save as .nii file (checked)

T2 Terminal
$ mcverter -o ~/Desktop/DICOM/DTI -f nifti -n -d –s 7 ~/Desktop/NIFTI/

Is there any errors in my terminal argument that could be causing this issue?

Kind regards
Justin

JUSTIN CHANG | Business Portfolio Manager Research
Information and Communications Technology

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