I have a question regarding the orientation of the BSE output in BrainSuite17a. When I feed in an image that is RPI and use the –norotate specification it throws the warning “the orientation matrix is not proper (i.e., |R|=-1). Please check the output”; when I view the output BSE image in fslview it throws the warning “ERROR: Inconsistent left-right order stored in sform and qform in file … Using sform instead of qform values”, and the image has visually had it’s left/right flipped. Additionally, if I use AFNI’s 3dinfo to get the orientation it reports the orientation as RPI but throws the warning that “*+ WARNING: NIfTI(‘func_example_bse_norotated.nii.gz’): Qform/Sform handedness differ; S wins!”
Has anyone else had any similar issues with the –norotate option in BSE and, if so, what ended up being the solution?
As background, I’ve never had any orientation issues with these images before. Also, if I feed in the same RPI image to BSE without the –norotate specification, none of the above issues come up, but AFNI says the output orientation is LPI (when I’d like to be able to keep the image as RPI for consistency).