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

[Hari Sundar]

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
> >>>
> 
>