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

[Luis Ibanez]

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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