Hello
This is a quite important change, that I only realize it now.
Why to make this change ? I advocate for taking the sform as default mainly because this is the way spm choose :
The choice of 2 orientations matrix on the nifti header, was really a bad choice, that has cause a number “silent” bugs.
The bigger mistake is to not have specified a clear use of those 2 matrix (which one should be taken first) . I did not read the all nifti specification but I can see from the different sorftware uses of those orientation file that there is no common use.
Nifti format has made the multi-software user life much better but this 2 matrix makes it buggy: arggg !!!
spm made the choice to directly modify the sform when you do a coregistration to an other volume. This is a quite unique choice (since fls mrtrix ants freesurfer) have all choosen to write the coregistration in a distinc file and to never touch the nifti orientation. Both solution have pro and cons.
I thing that spm use if coherent with the fact to desing 2 orientation matrix, in this way you can have a view of the current possition of the volume (and of its previous one). if you alway keep the sform qform identical, what is then the need to define 2 orientations in the header ?
I am fine with spm use (and I use spm for coregistration) but then we have to clearly decide which orientation to take into consideration. Why this point is not clearly define in the nifti specification ? why spm is making the assumption that the sform should be taken and why mrtrix change it recently to the qform ???
Sorry for this long mail. on this old topic,