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Hi, The use of the "--useScale" option really depends on what you're asking. Strictly speaking if you use "--useScale" its "shape analysis" , if not it's "size-and-shape analysis" . Assuming you're using native space surfaces, then the removal of scale allows you to look at "shape" changes. In other words, local atrophy within the structure and omitting any isotropic global scaling. If you do not remove scale, you include global scaling when looking at differences. However, you still get surface maps showing where the largest differences were observed. In practice, I typically have not seen major differences when looking at "shape" versus "size-and-shape" differences in the subcortical structures. Assumedly, this has been because there has not a large isotropic scaling in the structures. As an aside, if you were to transform the surface into a standard space (such as MNI) prior to analysis, you could remove scale related to brain/head size, then by not removing scale in the alignment will retain global scaling for an individual structure after controlling for brain/head size (depend how the transformation is calculated). Alternatively, ou could also use head size as an EV in your design matrix. Hopefully this clears things up a bit? cheers, brian > Hi, > > in Brian's thesis it says (page 177-178): > "In neuroanatomy, variation in the global scale of a structure may be of > interest as it may correspond to variations in grey matter volume due to > pathology. Thus strictly speaking we are usually interested in > investigating > the variation in size-and-shape of the deep grey structures.." > > on the FIRST website: > http://www.fmrib.ox.ac.uk/fsl/first/index.html > > it says: > *"--useScale* : Used in conjunction with *--useRigidAlign*, it will remove > global scalings when aligning meshes." > > "Also note that the --useScale option will not be used. Without the > --useScale option, changes in both local shape and size can be found in > shape analysis. This type of finding can be interpreted, for example, as > local atrophy. With the --useScale option, overall changes in size are > lost." > > i'm not sure i understand. No --useScale means that my metric does not > separate size from shape, i.e. it is a size-and-shape analysis. i do not > see > how my finding can then be interpreted as local atrophy (size). > including --useScale or some kind of size variable in my statistical model > assures, at least, that my metric is interpretable as shape, i.e. it is a > shape analysis. > > -joost >