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.

Mail list:

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).

• native space - original MRI 
• isotropic scaling - scaling that is the same in all directions

UseScale

• Does rigid body registration
• Resizes each volume to the other - accounts for structure size, not head size
  • Picks up differences in shape but not volume
• 7 DOF - Rigid Align (6 DOF) + isotropic scaling (1 DOF)

Rigid Align

• 6 DOF
• Places the structures in the same place

MNI

• Doesn't change the shape
• Allows us to look at the volume based on the volume of head
• Doesn't make sense to useScale and ReconMNI because MNI distorts the shape and then you're trying to look at the shape

Shape differences - ReconNative, RigidAlign, useScale

Volume differences accounting for head size - ReconMNI, RigidAlign

Volume differences - ReconNative, RigidAlign