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?
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