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Hi, It looks like you are running the old version of FSL - we not recommend using version 5, which works differently. Either way, it is possible for the majority of the change to be swamped by a positional shift. If that is the case then you should use the --useRigidAlign option in first_utils to remove the global translational and rotational changes. All the best, Mark On 23 Jan 2013, at 01:13, Kyoo H. Cho <[log in to unmask]> wrote: > Dear experts, > I think this as a silly, but basic question.. > > I analyzed a disease group (n=10) vs. control group (n=30) on FSL-FIRST. > With FSL-FIRST volumetric analysis, I found volume of caudate and thalamus are smaller in disease group with statistical significance. > In vertex shape analysis, I imagined that this would show region of focal atrophy in each structure, but I found only "global" displacement (in case of caudate nucleus, upward and laterally) in visualization of the outcome *_mni1.vtk file , whose vectors (arrows) are mainly aligned in one ways in every part of the structure. > > My pictures and vtk files are here : > > http://doremifafa.egloos.com/1035750 > > In this respect, I think that region of higher F statistics cannot be told to have more severe atrophy. > > Thanks in advance, > Cho