Sorry for not keeping up with this.
The only spatial information in this dataset is pixdim which specifies the voxel size, along with the qform_code=4 claim that the coordinates are in MNI space. But there are no actual coordinates specified (e.g. stating where 0,0,0 should actually be), and there is no orientation information (stating which direction is left vs anterior, for example). Right now, the software assumes an identity matrix, scaled by the pixdim values, but that is surely inappropriate.
If your software inputs a NIFTI dataset, it would be good to preserve all of the spatial attributes of that input when writing the output (which could include the sform again).
- rick
