qform=2 on testing data

[jcohenadad]

On the data_testing/sub-unf01/anat/sub-unf01_T1w.nii.gz data, fslhd gives:

qform_code	0
qto_xyz:1	1.000000 0.000000 0.000069 -64.129700 
qto_xyz:2	-0.000011 0.986856 0.161602 -59.711037 
qto_xyz:3	-0.000068 -0.161602 0.986856 -2.379487 
qto_xyz:4	0.000000 0.000000 0.000000 1.000000 
qform_xorient	Left-to-Right
qform_yorient	Posterior-to-Anterior
qform_zorient	Inferior-to-Superior
sform_name	Unknown
sform_code	2
sto_xyz:1	1.000000 0.000000 0.000069 -64.129700 
sto_xyz:2	-0.000011 0.986856 0.161602 -59.711037 
sto_xyz:3	-0.000068 -0.161602 0.986856 -2.379487 
sto_xyz:4	0.000000 0.000000 0.000000 1.000000 

qform_code=0 means that the physical coordinate system is should not be considered (see "METHOD 1" in nifti doc), and that some software will consider the sform instead.

I think we should set the qform_code=1 for our testing data, because this is how we expect NIFTI header to be presented to SCT's functions.

Related to:

• qform=2 on t2 data spinalcordtoolbox/sct_testing_data#5
• General discussion about qform/sform matrices and codes spinalcordtoolbox/spinalcordtoolbox#3283