% 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
% ---------------------------------------------------------
3	% Number of levels in the multi-res pyramid (1 = single-res)
3	% Highest level to use in the pyramid
 1 1 1   	% Scaling at lowest level of pyramid
 16 8 4 		% Number of pixels per element
 3.e5 6.e6 8.e7 	        % Elasticity (E)
 1.e2 1.e2 1.e2                 % Density x capacity (RhoC)
 1 1 1          % Image energy scaling (gamma) - sets gradient step size
 3 3 3          % NumberOfIntegrationPoints
 3 3 3                  % WidthOfMetricRegion
 15 30 45          % MaximumIterations
% -------------------------------
% Parameters for the registration
% -------------------------------
0 0.99  % Similarity metric (0=mean sq, 1 = ncc, 2=pattern int, 3=MI, 5=demons)
1.0	% Alpha
0	% DescentDirection (1 = max, 0 = min)
0	% 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
% ----------------------------------
70	% Nx (image x dimension)
80	% Ny (image y dimension)
70 % Nz (image z dimension - not used if 2D)
Brain165Cropped.mhd  % ReferenceFileName 
Brain165DeformedByTPS.mhd  % TargetFileName
% -------------------------------------------------------------------
% 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
FiniteElementRegistrationLandmarks3.txt	% LandmarkFileName
Brain3D_result                       % ResultsFileName (prefix only)
1       % WriteDisplacementField?
Brain3D_disp                         % DisplacementsFileName (prefix only)
0       % ReadMeshFile?
%MeshFileName
END