Default qform/sform combination not according to NIFTI spec

[gdevenyi]

According to the NIFTI spec:
https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html

#define NIFTI_XFORM_UNKNOWN      0 /! Arbitrary coordinates (Method 1). /
#define NIFTI_XFORM_SCANNER_ANAT 1 /! Scanner-based anatomical coordinates /
#define NIFTI_XFORM_ALIGNED_ANAT 2 /! Coordinates aligned to another file's, or to anatomical "truth".            /
#define NIFTI_XFORM_TALAIRACH    3 /! Coordinates aligned to Talairach-Tournoux Atlas; (0,0,0)=AC, etc. /
#define NIFTI_XFORM_MNI_152      4 /! MNI 152 normalized coordinates. /

Given that bruker2nifti is converting from a scanner, I believe the default qform/sform code should both be 1.

[SebastianoF]

Thanks, I admit that the choice for a default is a bit arbitrary.

It could also be qform_code = 1 and sform_code = 0, as we may not want to repeat the same information twice.

Although having sform_code < 1 may lead to issues in some registration software considering the sform as initialisation, and applying coarse initialisation if the sform_code = 0. This was the reason why, as the images are converted, the scanner reference and the template reference coincides, considering the scanner origin as the template, which provided a good initialisation.

I'll keep this issue open open to further suggestions from users, and in mind for a next major release.