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

[Luis Ibanez]

Hi Hari,


Thanks for the details on ParaView.

Yeap 1.2 is fine, that's the release version.


Did you check if the Glyph filter had the option
"Orient/Scale"

          Orient Mode = Vector

You can check also the content of the third component
of your deformation field by selecting ImageFile_2 in
the calculator, and clicking in the red "Accept" button.


This will create an image whose pixels have the values
of the third component in the input image.

If the image comes out with an uniform color... then
we will have to conclude that the third component is
actually null....


Please let us know what you find,



    Thanks


      Luis




-------------------

Hari Sundar wrote:

> Hi Luis,
> 
> I am using Paraview 1.2 on linux.
> Yes, it shows three scalar components, ImageFile_0, ImageFile_1 and ImageFile_2
> 
> thanks,
> -Hari
> 
> On Thu, 13 May 2004 14:23:04 -0400, Luis Ibanez <luis.ibanez@kitware.com> wrote:
> 
>>
>>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
>>>>>
>>
>>
>