From FSL user guide:
-vertexAnalysis : Set mode of operation such that vertex-wise stats are calculated.
--usebvars : Set mode of operation such that it uses the combined mode parameters across the group (this is compulsory for vertex analysis).
-i : concatenated bvars file containing mode parameters from all subjects (created by concat_bvars).
-o : Base name of output meshes.
-d : FSL design matrix (as created by the Glm GUI).
--useReconNative : Reconstructs the meshes in the native space of the image. For vertex-wise stats need to also use --useRigidAlign.
--useReconMNI : Reconstructs the meshes in MNI space (native space of the model). This does not require the flirt matrices.
--useRigidAlign : Uses a 6 Degrees Of Freedom transformation to remove pose from the meshes (see --useScale if you wish to remove size as well). All meshes are aligned to the mean shape from the shape Model. Can be used with either ReconNative or ReconMNI.
--useScale : Used in conjunction with --useRigidAlign, it will remove global scalings when aligning meshes.
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The --useScale option does a 7 DOF registration for the individual meshes. That is, it takes them from the native space and removes all pose (translation and rotation) as well as isotropic scaling (with --useScale). This will naturally be different from removing it based on the size of the head (or ICV), especially if the size of the caudate has changed. It is also different from the MNI space version, as in the MNI space the whole brain has been used to optimise a 12 DOF registration, allowing different scaling on different axes and also skews (or shears).