Hi Dr. Rorden,

Thank you so much. Such orientation difference really does explain the difference in affine matrices. I derived my dicom image's affine based-off the following dicom attributes:

(0010,2210) Anatomical Orientation
(7FE0,0010) Pixel Data
(0028,0030) Pixel Spacing
(0020,0032) Image Position Patient
(0020,0032) Image Orientation Patient 

and I was able to derive my dcm2niix-converted image's affine matrix from a permutation matrix multiplied to the affine. 

Bottom line is your software, dcm2niix, is flawless and I just did not pay enough attention to details.

Thank you so much Dr. Rorden. I really appreciate your help.

Regards,
Anderson