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Just my experience: I recently installed FSL under Karmic using the synaptic repositories and all went fine regarding FSL usage. The atlases were not part of the package downloaded by synaptic though - I found out by seeing fslview crashing on me every time when I tried to see the MNI template. So I manually downloaded the fsl-atlases package from the website Michael kindly maintains, and now FSL and fslview are fully functional as in other Ubuntu versions I worked with (8.04 and 8.10). Estephan