We encountered a confusing problem with image coregistration which we ultimately traced to a discrepancy of the qform and sform offsets in nifti files generated with the 3D crop option (-x). Evidently the srow_z value in the header is updated with cropping, but the qoffset_z is not. Some versions of ITK default to the qform transformation when both are present, and we ended up with images aligned in voxel space but not in scanner space. I suggest either updating qoffset_z to match srow_z(4) or setting the qcode value to NIFTI_XFORM_UNKNOWN (0) to indicate that the qform transform no longer matches scanner space.