Dear experts,

I'm converting T1 images from a 3T Siemens TIM Trio MRI scanner (acquired 2014) with dcm2niix in MRIcroGL (Version from February, 12, 2016). I want to further process these images in SPM12/CAT12 for voxel-based morphometry analyzes. 
Thereby, a question regarding the conversion of dicom to niftis came up: When I compare the nifti-images converted with dcm2niix, they look the same on a superficial level as niftis converted with the spm12 dicom import function or the older version of dcm2nii (the image without cropping and without reorientation). However, when I more closely compare the images, I see several differences: 

- the origin is not the same
- the voxel size is -1 1 1 for the images converted with dcm2niix (as compared to 1 1 1 for the two other conversion versions)
- the image dimension is 192x256x256 for the images converted with dcm2niix (as compared to 256x256x192 for the other two conversion versions)
- the rotation matrix is not the same

I'm wondering whether these differences are relevant and whether the images converted with dcm2niix are correctly read by SPM12. As I am working with SPM12/CAT12, should I use the SPM12 dicom import function? Or are the images converted with dicom2niix usable with these differences (I will not use different conversions for the same study, but preferably I would want to convert all images with the dicom2niix function)?

I would appreciate very much some insights on this matter.

Greetings,
Julia