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I don't think FSL automatically correct the 'error'. As long as input images have the same dimensions, you can run through the commands without encountering any error messages. On Thu, Mar 23, 2017 at 8:57 PM, Athanasia Metoki < [log in to unmask]> wrote: > Hello, > > You are right according to the header of the fsl_paths image: > qform_xorient Left-to-Right > qform_yorient Posterior-to-Anterior > qform_zorient Inferior-to-Superior > sform_name Aligned Anat > > while for the MNI standard brain and the several atlases images: > qform_xorient Right-to-Left > qform_yorient Posterior-to-Anterior > qform_zorient Inferior-to-Superior > sform_name MNI_152 > > But the fsl_paths image is not in native space. It's in standard space > (you could see for yourself by opening the file on fsl). > And fslview does a good job interpreting this orientation issue, so when I > overlay the fdt_paths on the MNI_2mm brain they are displayed in the right > side as they should. > > So is it a mistake on the coding of the command "atlasquery" the fact that > I am getting left side structures when I run it? Shouldn't the atlasquery > command be able to "interpret" that my fdt_paths mask is on the right side > and give me right side structures as results? >