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what I meat is the -m option :) On Wed, Mar 22, 2017 at 3:08 PM, Athanasia Metoki < [log in to unmask]> wrote: > Dear FSL experts, > > I ran probabilistic tractography between the right amygdala and the right > superior temporal sulcus. The resulting probability map is on the right > hemisphere when I display it on fslview, as it is supposed to be. > > But when I run the atlasquery command the probabilities I get for each of > the atlas structures are for the left side. This happens with every atlas > on FSL. For example: > > atlasquery -a "JHU White-Matter Tractography Atlas" -m fdt_paths.nii.gz > > Anterior thalamic radiation L:0.201337 <-- > Anterior thalamic radiation R:0.000251848 > Corticospinal tract L:2.44528 <-- > Cingulum (cingulate gyrus) L:0.000941523 > Cingulum (hippocampus) L:0.000877592 > Forceps major:0.00613346 > Forceps minor:0.0370836 > Inferior fronto-occipital fasciculus L:0.702578 <-- > Inferior fronto-occipital fasciculus R:0.000209227 > Inferior longitudinal fasciculus L:0.156926 <-- > Superior longitudinal fasciculus L:6.33462 <-- > Superior longitudinal fasciculus R:1.16237e-05 > Uncinate fasciculus L:0.558532 <-- > Uncinate fasciculus R:0.000581187 > Superior longitudinal fasciculus (temporal part) L:2.93717 <-- > Superior longitudinal fasciculus (temporal part) R:3.48712e-05 > > Shouldn't these results be flipped? Shouldn't I be getting mostly R > structures since my probability map is on the right hemisphere? I have > attached the right amygdala-right superior temporal sulcus probability map > (fdt_paths.nii.gz). > > I would appreciate any insight! > Thanks! >