Dear Buyean,

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).

What you should use is a tricky question, and that's why
we have the different options available as there is no single
"correct" answer.  If you want to normalise by TICV then
the third option is best.  If you want to adjust for global size
and shape differences of the whole brain, including anisotropic
scaling and skews, then use MNI.  If you want to eliminate the
overall size changes in the structure of interest, and just look
at shape changes on top of this, then use the first option.
Or there is the fourth option of doing it in native space without
any correction for brain size or structure size.  It is possible
that this might be interesting in some cases too, especially
if you are concerned that the normalisation is not well estimated
and creating additional noise in the measurements.

I'm afraid that's the best I can do for guidance on this issue.
I hope it helps.
All the best,
	Mark


On 25 Nov 2009, at 05:42, Buyean Lee wrote:

> Hi Mark and Brian,
>
> I compared size-and-volume of Caudate between two groups and got the  
> following three output files (*.vtk).
>
> 1. Native*.vtk generated with --useScale (is it the same as Native  
> with 7 dof?).
> 2. MNI*.vtk generated without --useScale and without covariate  
> (i.e., TICV)
> 3. Native*.vtk generated with the design matrix that has TICV as a  
> covariate; I didn't use  '--useScale' option.
>
> I used the command lines in the FIRST website.
>
> To me, the output images should be similar because the three vertex  
> analyses correct for global size difference (actually, I am not  
> positive if --useScale corrects for head size or size of caudate  
> differences).  But, the output images look quite different,  
> especially between Native*.vtk and MNI*.vtk.
>
> I wonder if there is any guideline which output images one should use.
>
> Or, does MNI*.vtk include only shape difference after correcting for  
> head size?
>
> Thank you,
>
> Buyean Lee
>
>