[Insight-users] Extract slice but keep orientation

[Matt McCormick]

Hi Emma, (CCing the list-- please reply-to-all),

> I need however do do some deformable registration on a single slice
> extracted from a volume and then use this 2D displacement field (pasted into
> 3D image) on the full 3D volume; in essence to just warp one particular
> slice of that volume
>
>   Deformable registration however requires 4 voxels in the third dimension
> to operate which I believe from memory is because the deformable
> registration uses a Gaussian filter during it's operation.

This seems like a bug.  Which RegistrationMethod class are you using?
Is it possible to turn off the Gaussian filtering?

> This is why I am
> using just a 2D slice with zero dimensions in the third plane and then
> attempting to recast this as a 3D volume dispalcement field.  Would it be
> adequate to resample my initial volume to get x4 the voxels in the in slice
> direction and then perform deformable registration on this now 3D chunk of
> data?

Possibly.  But, adding additional degrees of freedom associated with
the third dimension could make the registration perform worse.  The
SetWeights method on the v4 Optimizer's can be used to prevent this.

HTH,
Matt