Yes, that is why it is experimental. 

However, global atrophy will affect the ventricles (they are growing) which is an effect in the opposite direction, so maybe it cancels out to some extend. 

Best, Martin

On 12 Apr 2017, at 23:55, Arman Eshaghi <arman.eshaghi@gmail.com> wrote:

Thanks Martin. Should I be worried about affine transform masking out the global atrophy if I am using the whole brain (no skull stripping)?

Arman

On Wed, Apr 12, 2017 at 9:36 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:
Hi Arman,

should be possible by passing the - - affine flag. I think I also experimented around with a -base-affine flag to recon-all for that (instead of -base). It is experimental!

Best, Martin


> On 07 Apr 2017, at 13:34, Arman Eshaghi <arman.eshaghi@gmail.com> wrote:
>
> Hi,
>
> I wonder if there is a way for mri_robust_template to perform iterative registration with 9 DOF rather than 6-7 default. The rational is to allow for a bit of scaling to adjust for potential scanner drifts in a longitudinal study over years.
>
> Thanks,
> Arman
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