Dear Amir,
was very interested to read your post but was disappointed not to see any response :)
I was encouraged to learn that in principle gpu version of FLS works on Ubuntu 14.04 (despite the fact that according to the FSL (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation#Running_bedpostX_on_a_GPU_or_GPU_cluster) it requires Linux CentOS 6 or CentOS 6.5.
Did you solve the problem yourself?
Did you find any other irregularities with GPU FSL on Ubuntu?
Best wishes
Alexander
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