Dear Arash,
There is a difference between these options, as the useScale option removes
all average scaling information from that structure. Hence if it does not scale
exactly with brain size then the two scalings will be different. Particularly, if you
had a diffuse atrophy (scaling) of one structure, independent of brain size, then
the --useScale option would tend to remove that atrophy. Hence it is much more
common to want to normalize by the brain size instead, and therefore to use the
--useReconMNI option.
Hope this is clear.
All the best,
Mark
On 14 Jun 2011, at 14:22, Arash Nazeri wrote:
> Dear Mark,
>
> Thank you very much. Could this be resolved by accounting for global thalamic changes across subjects with adding --useScale option to --useReconNative? As brain size most likely affect global measures of sucortical nuclei.
>
> Many thanks,
> Arash
>
> On Tue, Jun 14, 2011 at 3:51 AM, Mark Jenkinson <[log in to unmask]> wrote:
> Dear Arash,
>
> I hope you only used the --useRigidAlign with the --useReconNative option.
> They should be used together but the --useReconMNI should be used on its own.
>
> As the MNI-space reconstruction puts the image into MNI space, it normalizes
> for brain size as part of the process, whereas the native-space reconstruction
> does not. So the most likely thing is that you are seeing a difference due to
> brain size changes which is being normalized away in the --useReconMNI
> option.
>
> It might be worth checking to see if there is a systematic brain size change
> amongst your subjects which would support this interpretation.
>
> All the best,
> Mark
>
>
> On 14 Jun 2011, at 04:46, Arash Nazeri wrote:
>
> > Dear Mark,
> >
> > As it has been recommended on FIRST's documentation webpage, we tried FSL vertex analysis using both --useReconNative and --useReconMNI flags along with --useRigidAlign. However, --useReconNative yielded a lot of significant regions on both left thalamus and left pallidum while --useReconMNI yielded none.
> > Does this mean that our findings are in fact spurious?
> >
> > Thanks,
> > Arash
>
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