% ---------------------------------------------------------
% 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
4		% Number of pixels per element
6.e3 	        % Elasticity (E)
3.e3 	        % Density x capacity (RhoC)
1		% Image energy scaling (gamma) - sets gradient step size
2		% NumberOfIntegrationPoints
1  		% WidthOfMetricRegion
50		% 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
% ----------------------------------
109	% Nx (image x dimension)
109	% Ny (image y dimension)
58  	% Nz (image z dimension - not used if 2D)
ResampledVolume_RigidRegistered.mha  % ReferenceFileName 
ResampledVolume_Intraop.mha  % 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
FiniteElementRegistrationLandmarks.txt	% LandmarkFileName
DeformableRegistered.mha               % ResultsFileName (prefix only)
0                                     % WriteDisplacementField?
./RatLung_disp                         % DisplacementsFileName (prefix only)
0       % ReadMeshFile?
-       % MeshFileName
END