[Insight-users] Problems with 3D DeformableRegistrationFilter

[Jayme Kosior]

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