[Insight-users] multi-modality with FEM or with Demons ? :
BSplineTransform
Luis Ibanez
luis.ibanez@kitware.com
Thu May 13 05:04:19 EDT 2004
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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>>>
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>>
>>
>
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