Hello Hunter,

Thank you for taking the time to contribute to the discussion.

I'm not very well-versed in the world of image orientations to be honest, and this is the first time I encounter such an issue, so please bear with me...


So, using fslhd, the nifti file going in has the following orientation:

qform_name Scanner Anat
qform_code 1
qto_xyz:1 -2.018740 -0.000000 0.044033 103.536331
qto_xyz:2 -0.010218 1.965173 -0.459562 -75.819267
qto_xyz:3 0.043266 0.464093 1.945987 -87.045891
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -2.018740 0.000000 0.044034 103.536331
sto_xyz:2 -0.010218 1.965174 -0.459562 -75.819267
sto_xyz:3 0.043267 0.464093 1.945987 -87.045891
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior



And checking the file header for the DKE fa output, first I got this message:


ERROR: Inconsistent left-right order stored in sform and qform in file fa
Using sform instead of qform values 



Followed by the usual header info:


qform_name Aligned Anat
qform_code 2
qto_xyz:1 1.000000 0.000000 -0.000000 -104.393929
qto_xyz:2 0.000000 1.000000 -0.000000 -106.743248
qto_xyz:3 0.000000 0.000000 -1.000000 -87.045891
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Superior-to-Inferior
sform_name Aligned Anat
sform_code 2
sto_xyz:1 1.000000 0.000000 0.000000 -104.393929
sto_xyz:2 0.000000 1.000000 0.000000 -106.743248
sto_xyz:3 0.000000 0.000000 1.000000 -87.045891
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Left-to-Right
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior


There seems to be some obvious changes in the image orientation, e.g from Right-to-Left  to Left-to-Right and "Scanner Anat" to "Aligned Anat" etc.

Any idea why this is happening? Can it be rectified somehow? 

Thanks again for the help!

Cheers,
Shereif