Hi there,

I am trying to reorient my image (screenshot attached) so that FSLView displays my image the same way as the standard templates (MNI152). Following the instructions here http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained, I did the following to my image.

fslswapdim brain.nii.gz RL PA IS reorient.nii.gz

fslorient -forceradiological reorient.nii.gz

I expect that after the reorientation, the same RAS coordinates should give me the same intensity value. However, they don’t.

Before reorientation: Intensity @ (50mm, 40mm, 28mm) = 74
After reorientation: Intensity @ (50mm, 40mm, 28mm) = 100

What further confuse me are:

- Visually, the two coordinates correspond to two points that are rather close (both right, superior, posterior). Close but not the same.

- When opened in FreeView, same coordinates always report the same intensity value before and after the reorientation!

Am I missing anything? Why is it so?

Thank you very much for your help in advance!

Best regards,

Xiuming ZHANG (Eric)

Xiuming ZHANG (Mr.) :: Department of Electrical & Computer Engineering (ECE) :: National University of Singapore (NUS)