[Insight-users] Extract slice but keep orientation

[Matt McCormick]

PS.  This IJ article may be of interest:

    http://hdl.handle.net/10380/3264

On Tue, May 7, 2013 at 2:28 PM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> 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