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

[Hari Sundar]

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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> >>
> >
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