[Insight-users] Specifying landmarks in the ThinPlateSplineWarp.cxx example?

[Luis Ibanez]

Hi Motes,

Integrating this into the registration process is straightforward.

The ThinPlateSpline is a Transform, so you just need to connect it
to the RegistrationMethod in the same way that you would have
used an AffineTransform or a BSplineDeformableTransform.

The only caveat is that you should use Optimizers that do not
require derivatives, for example:


   - AmoebaOptimizer or
   - OnePlusOneEvolutionaryOptimizer


This is because the ThinPlateSpline transforms have not
implemented yet the methods that compute Jacobians.


---

Your approach for implementing a BSplineDeformableTransform
that also moves the Nodes, can easily be achieved by combining
two BSplineDeformableTransforms, both of them with the same
number of Nodes. The first transform could be used for representing
the locations of the nodes of the second transform, while the second
transform represents deformation vectors in the usual BSpline context.

You could put these two transforms together inside a new Transform
class, and then plug that larger transform class into the Registration
framework.


      Regards,


              Luis


---------------------------------------------------------------------------------------
On Sun, Aug 16, 2009 at 3:04 PM, motes motes <mort.motes at gmail.com> wrote:

>
>
> On Sun, Aug 16, 2009 at 5:22 PM, Luis Ibanez <luis.ibanez at kitware.com>wrote:
>
>> Hi Motes,
>>
>>
>>           "Glimpsing at the source leaves no doubt"
>>
>>
>> If you look at lines 120-130 of the ThinPlateSplineWarp.cxx file:
>>
>>   while (!infile.eof())
>>     {
>>     infile >>  p1[0] >> p1[1] >> p1[2] >> p2[0] >> p2[1] >> p2[2];
>>
>>     sourceLandMarkContainer->InsertElement( id, p1 );
>>     targetLandMarkContainer->InsertElement( id++, p2 );
>>     }
>>
>> You will see that the first three values of the file are assigned
>> to the X,Y,Z coordinates of the first source landmark, while the
>> second group of three values is assigned to the X,Y,Z coordinates
>> of the first landmark in the group of target landmarks.
>>
>>
>> Note that this is different from how we manage
>> BSplineDeformableTransforms.
>>
>> In this ThinPlateSpline example there are no deformation vectors.  We use
>> a group of landmarks in the Fixed image, that map, one-to-one, to
>> landmarks
>> in the moving image.
>>
>> The triplet ( 180  217  0 )  that you pointed out to in your email,
>> correspond
>> indeed to the coordinates of a point in the space of the fixed image.
>>
>> It is the point with coordinates:   X = 180.0, Y = 217.0,  Z = 0.0
>>
>>
>>      Regards,
>>
>>
>>             Luis
>>
>>
>
>
>
>
> Ok that makes sense, but how would that be used in a registration context
> eg. connecting the ThinplateSpline to an optimizer?
>
> The source and target landmarks are choosen manually in the example but I
> am working on a project where this is not possible and the registration
> process should run automatically.
>
>
>
> I am therefore still pretty interested in using the
> BSplineDeformationTransform, but I am still stuck with how to create a
> non-uniform grid of deformation vectors - if this is even possible with the
> current implementation?
>
>
> Assume that I have defined a 5*5 grid of deformation vectors. Now I want
> the deformation vector at location (2,3) to be located at another location,
> how would that be possible?
>
>
> As I understand the only way to create a non-uniform location of
> deformation vectors is to change the spacing. But that will only result in
> non-uniform spacing arcross dimesions and not within each of the dimesions.
>
> Am I walking down a dark and lonely path trying to make the current
> BSplineDeformationTransform more flexible?
>
>
>
>
>
>
>
>
>
>
>
>
>
>>
>>
>> --------------------------------------------------------------------------------------------
>> On Sun, Aug 16, 2009 at 2:10 AM, motes motes <mort.motes at gmail.com>wrote:
>>
>>> In the ThinPlateSplineWarp.cxx a set of landmarks are read from the file
>>> LandmarkWarping3Landmarks1.txt which contains this:
>>>
>>>   0   0   0        0   0      0
>>> 180   0   0      180   0      0
>>> 180 217   0      180 217      0
>>>   0 217   0        0 217      0
>>>   0   0 180        0   0    180
>>> 180   0 180      180   0    180
>>> 180 217 180      180 217    180
>>>   0 217 180        0 217    180
>>>  90 108  90       90 130     90
>>>
>>>
>>>
>>> As I understand these are 18 landmark points which is actually just
>>> deformation vectors. So the 3 first values in the third row:
>>>
>>> 180  217  0
>>>
>>> corresponds to a vector at some location pointing 180 unit in the
>>> x-direction and 217 units in the y-direction.
>>>
>>> But where in the image is this vector located?
>>>
>>> Or are the above landmarks just 'regular' points that are interpolated by
>>> the ThinPlateSpline and not deformation vectors?
>>>
>>>
>>>
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