[Insight-users] Problems with 3D DeformableRegistrationFilter

[Luis Ibanez]

Hi Jayme,

At first sight this looks like you forgot to switch
some of the FEM components from 2D to 3D.

Could you please post your modified version of the
DeformableRegistration1.cxx example.

Once we debug it, we will actually like to add it
as an extra example in the same directory.


   Thanks


     Luis


--------------------------
Jayme Kosior wrote:

> Hello.
> 
> I can successfully run DeformableRegistration1 to register 2D images.  I 
> have modified DeformableRegistration1 and the parameter file accordingly 
> to perform 3D deformable registration.  After performing the 
> registration, only the first image in the 3D dataset is deformed.  The 
> rest of the images are not modified.  The only change in the rest of the 
> registered data set is that it is now in the fixed image coordinate space.
> 
> I'm not sure if the registration is not warping the images properly, or 
> if maybe it is not writing them correctly.  Of course, maybe I'm not 
> doing something correctly. :)
> 
> Here is the parameter file that I am using.
> 
> Thank you in advance for your help.
> 
> Jayme
> 
> Setup Info: 700 Mhz Athlon, Red Hat Linux 9.0, ITK version 1.6 release, 
> 2 8-bit 3D data sets in Analyze format at input.
> 
> 
> % Configuration file #1 for DeformableRegistration1.cxx
> %
> % This example demonstrates the setup of a basic registration
> % problem that does NOT use multi-resolution strategies.  As a
> % result, only one value for the parameters between
> % (# of pixels per element) and (maximum iterations) is necessary.
> % If you were using multi-resolution, you would have to specify
> % values for those parameters at each level of the pyramid.
> %
> % Note: the paths in the parameters assume you have the traditional
> % ITK file hierarchy as shown below:
> %
> % ITK/Insight/Examples/Registration/DeformableRegistration1.cxx
> % ITK/Insight/Examples/Data/RatLungSlice*
> % ITK/Insight-Bin/bin/DeformableRegistration1
> %
> % ---------------------------------------------------------
> % Parameters for the single- or multi-resolution techniques
> % ---------------------------------------------------------
> 1    % Number of levels in the multi-res pyramid (1 = single-res)
> 1    % Highest level to use in the pyramid
>  1 1 1       % Scaling at lowest level of pyramid
>  8        % Number of pixels per element
>  1.e4             % Elasticity (E)
>  1.e3             % Density x capacity (RhoC)
>  1        % Image energy scaling (gamma) - sets gradient step size
>  6        % NumberOfIntegrationPoints
>  4          % WidthOfMetricRegion
>  50        % MaximumIterations
> % -------------------------------
> % Parameters for the registration
> % -------------------------------
> 4 1.0  % Similarity metric (0=mean sq, 1 = ncc, 2=pattern int, 3=MI, 
> 5=demons) 2nd num changes NormalizeGradient
> 0.5    % Alpha
> 0    % DescentDirection (1 = max, 0 = min)
> 2    % DoLineSearch (0=never, 1=always, 2=if needed)
> 1.e1    % TimeStep
> 0.5     % Landmark variance
> 0       % Employ regridding / enforce diffeomorphism ( >= 1 -> true)
> % ----------------------------------
> % Information about the image inputs
> % ----------------------------------
> 256    % Nx (image x dimension)
> 256    % Ny (image y dimension)
> 12      % Nz (image z dimension - not used if 2D)
> ./images-8bit/CFLAIR30m.hdr        % moving image
> ./images-8bit/CPWI0d_brain3.hdr    % fixed image
> % -------------------------------------------------------------------
> % The actions below depend on the values of the flags preceding them.
> % For example, to write out the displacement fields, you have to set
> % the value of WriteDisplacementField to 1.
> % -------------------------------------------------------------------
> 0    % UseLandmarks? - read the file name below if this is true
> -    % LandmarkFileName
> ./results/PatientC-FtoP-8bit                       % ResultsFileName 
> (prefix only)
> 1       % WriteDisplacementField?
> ./results/OtherPatientC-FtoP_disp                         % 
> DisplacementsFileName (prefix only)
> 0       % ReadMeshFile?
> -                                      % MeshFileName
> END
> 
>                
> 
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