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Dear Guangyu, Thank you for your email. I don't think I made myself clear in my initial email. I want to use the altasquery command to get the (average) probability of my mask (in my case: fdt_paths) being a member of the different labelled regions within the atlas I choose. I have attached the binarized version of my probability map (fdt_paths_bin.nii.gz). So what I need to know is the probability of fdt_paths_bin.nii.gz being a member of the different labelled regions within the atlas I choose. So the command "altlasquery -a "JHU White-Matter Tractography Atlas" -m fdt_paths_bin.nii.gz" is correct. What I do not understand is why since my mask in on the RIGHT hemisphere the structures I am getting from the atlasquery output are LEFT. It's a mistake but I do not understand why it happens. Any thoughts?