Hi Dr. Rorden,

I am using a commercial software called 'Vivoquant' to view the data. I, however, tried your data on both SPM and MRIcroGL and for both instances, the images still appears to be flipped. I've attached a screen capture of the images viewed through MRIcroGL.

Regarding your concerns about the images being 3D, I've tested dcm2niix binary on both 3D (pre-clinical) and 2D (clinical) images and for both attempts, I get a flipped image on the same axis. 

As for the rotations, I will have to read more into the source of your code to see what actually is happening in the internals. Do you recommend a particular excerpt in the source?

I will be investigating the affine mapping from voxel space to subject-scanner reference space soon to see if the affines are accurate to the voxel space flip.

Anyways, thank you so much for replying. I really appreciate the help.

Regards,
Anderson