[Insight-users] multi-modality with FEM or with Demons ? : BSplineTransform

[Luis Ibanez]

Hi Hari,

What version of ParaView are you using ?

Could you please do the following test:

1) Load in ParaView the MetaImage containing
    the Deformation field.

2) Then click on the icon that has Calculator,
    (or select Filter -- >  Calculator).

    When it appears, the GUI of the calculator
    will have a menu-choice on the bottom left
    that says "Scalars".  Please click on it
    and let us know what it shows.

    If the loaded dataset has three components,
    this menu-choice will display:

          ImageFile_0
          ImageFile_1
          ImageFile_2

     if the field only has two components, you
     will only see

          ImageFile_0
          ImageFile_1


    Please let us know what you find.


--

About your question:

The physical extent of the deformation is
defined by the BSpline grid. If you are
observing that it is limited to a restricted
region of the image, that means that your
configuration of the BSpline grid need some
adjustment.  Note that the BSpline grid also
has an spacing. For example if you want the
BSpline grid to be such that there are N
image pixels between two BSpline grid points,
then you must set the spacing of the BSpline
grid to be N * image_pixel_spacing.

Note also that this flexibility of the BSpline
is sometimes desirable, since it lets you
focus on a small region of the image that
is the only place where you expect deformations
to occur.  However this is not an efficient
way of working, given that you still compute
the registration over *all* the pixels of the
fixed image, not just those over the BSpline
grid.  For this reduction to make sense, you
should sync the extent of the FixedImageRegion
with the physical extent of the Bspline grid.



To put it short: please check the physical
extent of the BSpline grid and compare it to
the physical extent of your fixed image.


    Regards,


      Luis


--------------------
Hari Sundar wrote:

> Hi Luis,
> 
> The deformation field has 3 components per pixel. The glyphis set to
> use the vector for orientation. I have attached 2 images to show you
> what I mean.
> 
> Also another small question. Why is the deformation field limited to a
> smaller section of the actual volume dimensions (Bounding box vs.
> where the deformation field != 0 ).
> 
> The parameters are obtained from the fixedImage, so shouldn't it cover
> the whole volume ?
> 
> thanks,
> -Hari
> 
> On Thu, 13 May 2004 10:05:26 -0400, Luis Ibanez <luis.ibanez@kitware.com> wrote:
> 
>>
>>Hi Hari,
>>
>>Please check the content of the MetaImage header to
>>see if the deformable registration program is actually
>>writing 3 components per pixel.
>>
>>Note that in Paraview you have to make sure that the
>>Glyph filter, on its Orient/Scale frame has the
>>Orientation option is set to "Vector".
>>
>>--
>>
>>Multi-res will imply to subsample your original image.
>>The evaluations of the metric are still done over *all*
>>the pixels of the original image. The BSpline transform
>>is used here as any other basic transform.
>>
>>Please read the Chapter on image registration in the
>>SoftwareGuide, There is a full section on how to setup
>>the Multi-Resolution framwork.
>>
>>
>>
>>   Regards,
>>
>>      Luis
>>
>>---------------------
>>Hari Sundar wrote:
>>
>>
>>>Hi Luis,
>>>
>>>I ran it for 50 iterations. It did not converge, but should have
>>>reached somewhere. I'll try and run it till convergence anyway. I
>>>visualized the resulting deformation field in paraview and all the
>>>vectors seem to be parallel to the XY plane. That's why I am saying
>>>that there is no Z component.
>>>
>>>Multi res in this case would be the number of nodes in the bSpline
>>>grid, right ? But then even the 5x5x5 grid seems to take forever. How
>>>do I structure the multi-res approach ?
>>>
>>>thanks,
>>>-Hari
>>>