Hi,
The easiest way to do that (and the only way if you are applying
any non-linear transformations) is to take the resampled image
(that is now in MNI space) and use the run_first script (as explained
in the docs) but using an identity matrix for the transformation.
Note that this isn't ideal, and if you are only doing affine
transformations
then you are better using the original image and a transformation
matrix which describes the transformation to MNI space, but this
is harder to create from other software outputs if you are not using
flirt.
All the best,
Mark
On 13 Dec 2008, at 20:46, siamak wrote:
> Hi,
>
> I want to test my registration method and measure its effectiveness
> in the
> segmentation stage. I use an affine transformation to the MNI space
> in my
> first stage of registration as FIRST but my second stage of
> registration is
> different from FIRST. So, I have the registered image. Now, I only
> want to
> segment this image. FIRST tool combines registration and
> segmentation. So,
> my question is: How can I use segmentation part of FIRST alone?
>
> Thanks for your time,
> Siamak
>
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