Hi Shady,
Yes, that’s right. If you are using --useReconMNI, you probably don’t need --useScale though, as the MNI space reconstruction will already have removed the effect of head size. Using --useScale will remove any additional scaling of the structure, but you will probably want to keep that variability as it is usually of interest.
Cheers,
Eelke
> On 6 Dec 2016, at 18:26, Shady Rahayel <[log in to unmask]> wrote:
>
> Thank you very much Eelke!
>
> So I understand that the results I would get when using --useReconMNI, --useScale, and --useRigidAlign in first_utils could then be considered as 'shape-only' differences, with the structure's pose and translation removed?
>
> Thank you
>
> Shady
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