[Insight-users] multi-modality with FEM or with Demons ? : BSplineTransform
Hari Sundar
hsundar@gmail.com
Thu May 13 14:55:07 EDT 2004
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
On Thu, 13 May 2004 00:04:19 -0400, Luis Ibanez <luis.ibanez@kitware.com> wrote:
>
>
> Hi Hari,
>
> A) Then only change that you have to make in
>
> Insight/Examples/Registration
> DeformableRegistration4.cxx
>
> in order to make it run in 3D, is to change
> line 125 from
>
> const unsigned int ImageDimension = 2;
>
> to
>
> const unsigned int ImageDimension = 3;
>
> B) What makes you suspect that there
> is no Z component in your results ?
>
> C) Did you let it run until convergence ?
> a couple of iteration certainly will not
> be enough for solving the displacements.
>
> It takes hundreds of iterations to solve
> a simple ridig body registration problem.
>
> You will need more than that in order to
> solve for a parametric space with a high
> dimension as is the case of the BSpline
> transform.
>
> If you really plan to do this in 3D, you must
> consider using Multi-Resolution.
>
> Regards,
>
> Luis
>
> -------------------
> Hari Sundar wrote:
>
> > Thanks Luis,
> >
> > Yes it is slow, but seems to work, at least kind of ...
> >
> > I have 2 problems ....
> >
> > 1. The deformations do not seem to have a Z component. Am I doing
> > something wrong ? What all changes are required to make the code work
> > for 3D ?
> >
> > 2. The deformations in certain parts seem to be smaller than what
> > would be expected. Is this just a matter of the number of iterations
> > or do I have to do something different ?
> >
> > thanks,
> > -Hari
> >
> > On Tue, 11 May 2004 16:05:08 -0400, Luis Ibanez <luis.ibanez@kitware.com> wrote:
> >
> >>
> >>Hi Hari,
> >>
> >>Deformable registration is a highly time-consuming task.
> >>
> >>Just to give you an idea of performance here is a
> >>typical configuration for a 3D registration problem:
> >>
> >>Registering two brainweb images of size
> >>
> >> 181 x 217 x 181 pixels,
> >>
> >>Using a BSpline grid of size 5 x 5 x 5, requires to
> >>optimize 625 parameters. That is, the x,y,z coordinates
> >>of the 125 nodes in the BSpline grid.
> >>
> >>Running a gradient descent optimizer in a parametric
> >>space of dimension 625 is certainly not going to be
> >>fast... :-/
> >>
> >>One iteration of the registration framework using
> >>this configuration takes
> >>
> >> 3 minutes 32 seconds
> >>
> >>with a Pentium 4 at 2.4 Ghz, This is for the program
> >>DeformableRegistration4.cxx modified for 3D, compiled
> >>for release (-O3) with gcc 3.3 under Debian Linux.
> >>
> >>As you can see from this example, it is certainly quite
> >>interesting to perform this task on a Parallel Cluster
> >>rather than a single PC :-)
> >>
> >>Of course an alternative is to run the deformable
> >>registration in a Multi-Resolution framework.
> >>
> >>Regards,
> >>
> >> Luis
> >>
> >>-----------------
> >>
> >>Hari Sundar wrote:
> >>
> >>
> >>>Hi Luis,
> >>>
> >>>I am trying to use the bSpline Transform based deformable registration
> >>>in 3D. It seems to take a long time and is not getting anywhere.
> >>>Basically what happens is that it prints out the initial parameters
> >>>(all zeros) and then says "Starting Registration" .. however it does
> >>>not proceed ... I mean shouldn't the observer at least report the
> >>>iteration number ?
> >>>
> >>>Any estimates on how long it is supposed to take when working in 3D ..
> >>>say trying to register 2 256^3 images.
> >>>
> >>>thanks,
> >>>-Hari
> >>>
> >>>
> >>>
> >>>>Hi Eduard,
> >>>>
> >>>>An example on how to perform deformable registration
> >>>>using the BSpline transform has been added under
> >>>>
> >>>> Insight/Examples/Registration/
> >>>> DeformableRegistration4.cxx
> >>>>
> >>>>You may have to update your CVS checkout in order to
> >>>>get this example.
> >>>>
> >>>>Regards,
> >>>>
> >>>> Luis
> >>>>
> >>>>---------------------------
> >>>>Eduard Schreibmann wrote:
> >>>>
> >>>>
> >>>>
> >>>>>Hi Luis,
> >>>>>
> >>>>>As you suggested in your previous e-mail, the Demons did not work so nice
> >>>>>for the images I have, FEM needs more cofee and patience, so thinking of
> >>>>>following your second advice on using BSpline.
> >>>>>
> >>>>>Have problems understanding the code and how it works, mainly I can not
> >>>>>understand how BSplineDeformableTransform (or it's coeficients ?) are
> >>>>>connected to an optimizer. Yes, users still ask such dull questions.
> >>>>>
> >>>>>Is there any simple BSline example/demo available somewhere ? Some code in
> >>>>>testing section is even more confusing for beginers.
> >>>>>
> >>>>>Thank you in advance,
> >>>>>Edi
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>>Hi Edi,
> >>>>>>Along those lines of reasoning, you may want to look
> >>>>>>at the BSpline transform for managing deformable
> >>>>>>registration. In this method, a BSpline is used to
> >>>>>>interpolate deformations over a coarse grid overlapped
> >>>>>>on top of the image. you control the deformation by
> >>>>>>initializing the nodes of the grid.
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>Regards,
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> Luis
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>---------------------------
> >>>>>>Schreibmann Eduard wrote:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>>Hello everybody,
> >>>>>>>
> >>>>>>>Question 1 :
> >>>>>>>I want to use FEM to register some CT and MRI images,
> >>>>>>>using the DeformableRegistration1.exe. With the
> >>>>>>>demo images, it works great but...
> >>>>>>>
> >>>>>>>When using some CT and MRI images that came with ITK (
> >>>>>>>BrainT1Slice and BrainProtonDensitySlice.png ), and
> >>>>>>>with setting the metric to 3 (MI) in the configuration
> >>>>>>>file, the application finishes after 2-3 iterations
> >>>>>>>without doing something visible to the input image.
> >>>>>>>Basically, the only thing changed in the parameter
> >>>>>>>file was file names and metric type.
> >>>>>>>
> >>>>>>>What parameters control this behavior ?
> >>>>>>>What settings are appropriate for this job ?
> >>>>>>>
> >>>>>>>Question 2: Is it true that demons can not be used for
> >>>>>>>multi-modality registration ?
> >>>>>>>
> >>>>>>>Question 3: The "viscous fluid landmark" registration
> >>>>>>>has anything to do with demons or FEM ?
> >>>>>>>
> >>>>>>>Thank you in advance,
> >>>>>>>
> >>>>>>>A nice day,
> >>>>>>>Edi
> >>>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>_______________________________________________
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> >>>>Insight-users@itk.org
> >>>>http://www.itk.org/mailman/listinfo/insight-users
> >>>>
> >>>
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> >>
> >>
> >
>
>
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