B-spline Grid, Image and Point based Registration: [I,T]=bspline_transform(O,I,Spacing,mode) - File Exchange

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Highlights from
B-spline Grid, Image and Point based Registration

manually_warp_images(varargin) MANUALLY_WARP_IMAGES, is a GUI which shows the controlpoint grid used
showcs3(varargin) Function showcs3(V) will display x,y,z cross sections of the volume V
A=imresize3d(V,scale,tsize,nt... This function resizes a 3D image volume to new dimensions
Dlocal=jacobiandet_transform_... Determinant of the Jacobian of the transformation grid
E=strain(Ux,Uy,Uz) Calculate the Eulerian strain from displacement images
F=backwards2forwards(B) This function will turn a backward transformation field in to a
I3=movepixels(I1,T,mode) This function movepixels, will (backwards) translate the pixels
I=affine_registration_image(p... This function affine_registration_image, uses affine transfomation of the
I=imgaussian(I,sigma,siz) IMGAUSSIAN filters an 1D, 2D color/greyscale or 3D image with an
Igrid=make_grid_image(Spacing... This function creates a uniform 2d or 3D image of grid
Iout=affine_transform(Iin,M,m... Function affine_transform, is a wrapper of the (mex) functions
Iout=affine_transform_2d_doub... Affine transformation function (Rotation, Translation, Resize)
Iout=movepixels_2d_double(Iin... This function movepixels, will translate the pixels of an image
M=make_transformation_matrix(... This function make_transformation_matrix.m creates an affine
O_error=bspline_registration_... Function Registration_image. This function will create
O_trans=bspline_grid_fitting(... calculate which is the closest point on the lattic to the top-left
O_trans=make_init_grid(Spacin... This function creates a uniform 2d or 3D b-spline control grid
W=bspline_coefficients(u,v,w) Calculate influences of all neighborh b-spline knots
[Fx,Fy]=backwards2forwards_2d... This function will turn a backwards transformation field into
[I,T]=bspline_transform(O,I,S... Function bspline_transform, is a wrapper of the mex
[Iout,Tx,Ty]=bspline_transfor... Bspline transformation grid function
[O_error, O_grad]=bspline_reg... Function registration_gradient. This function will calculate a registration
[O_error, O_grad]=jacobiandet... Convert Grid vector to grid matrix
[O_error, O_grad]=jacobiandet... Gradient and error of the Jacobian of the transformation grid
[O_new,Spacing]=refine_grid(O... Refine image transformation grid of 1D b-splines with use of spliting matrix
[O_penalty, O_grad]=penalties... This function calculates the 2D or 3D equivalent of the 2D
[O_trans,Spacing,Xreg]=point_... This function creates a 2D or 3D b-spline grid, which transform space to
[O_trans,Spacing]=MakeDiffeom... This function MakeDiffeomorphic will make the b-spline grid diffeomorphic
[O_trans2,Spacing2]=inversegr... Calculates the (numeric) inverse of the current b-spline grid
[Tlocal,Dlocal]=bspline_trans... If Spacing and points are not an integer, we can not use fast look up tables,
[V1,V2]=get_example_data get_example_data is used to make some rigid and nonrigid transformed
[e,egrad]=affine_registration... This function affine_registration_error, uses affine transfomation of the
[hist12, hist1, hist2]=mutual... This function makes a 2D joint histogram of 1D,2D...ND images
[s_Trans, s_Rotation, s_Scale... This function gives scaling values for different parameters, such as
[t,I]=image_difference(V,U,ty... This function gives a registration error and error image I between the two
[x,fval,exitflag,output,grad]... FMINLBFGS finds a local minimum of a function of several variables.
addpaths.m add all needed function paths
err=squared_difference_double...
image_interpolation(Iin,Tloca... This function is used to transform an 2D image, in a backwards way with an
image_registration(Imoving,Is... This function image_registration is the most easy way to register two
maxNumCompThreads(varargin) maxNumCompThreads returns the number of available CPU cores, works with
compile_c_files.m
example_2d_affine.m
example_2d_nonrigid_1.m
example_2d_nonrigid_2.m
example_2d_nonrigid_3.m
example_3d_affine.m
example_3d_nonrigid.m
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from B-spline Grid, Image and Point based Registration by Dirk-Jan Kroon
B-spline registration of two 2D / 3D images or corrsp. points, affine and with smooth b-spline grid.

[I,T]=bspline_transform(O,I,Spacing,mode)

function [I,T]=bspline_transform(O,I,Spacing,mode)
% Function bspline_transform, is a wrapper of the mex 
% bspline_transform_2d_double and bspline_transform_3d mex functions
%
% [Iout,T] = bspline_transform(O,Iin,Spacing,mode)
%
% inputs,
%   Iin :  Input image.
%   O  : Transformation grid of control points
%   Spacing : Are the b-spline grid knot spacings.
%   mode: If 0: linear interpolation and outside pixels set to nearest pixel
%            1: linear interpolation and outside pixels set to zero
%            2: cubic interpolation and outsite pixels set to nearest pixel
%            3: cubic interpolation and outside pixels set to zero
%
% outputs,
%   Iout : The Rueckert transformed image
%   T : The transformation images (in 2D Tx=T(:,:,1)), describing the
%             (backwards) translation of every pixel in x,y and z direction.
%
% Function is written by D.Kroon University of Twente (February 2009)

% Check if spacing has integer values
if(sum(Spacing-floor(Spacing))>0), error('Spacing must be a integer'); end
if(~exist('mode','var')), mode=0; end

if(size(I,3)<4)
    if(~isa(I,'double')), I=im2double(I); end
    if(nargout > 1 )
        [I,Tx,Ty]=bspline_transform_2d_double(double(O(:,:,1)),double(O(:,:,2)),I,double(Spacing(1)),double(Spacing(2)),double(mode));
        T(:,:,1)=Tx; 
        T(:,:,2)=Ty;
    else
        I=bspline_transform_2d_double(double(O(:,:,1)),double(O(:,:,2)),I,double(Spacing(1)),double(Spacing(2)),double(mode));
        T=0;
    end
else
    if(isa(I,'double'))
        if(nargout > 1 )
            [I,Tx,Ty,Tz]=bspline_transform_3d_double(double(O(:,:,:,1)),double(O(:,:,:,2)),double(O(:,:,:,3)),double(I),double(Spacing(1)),double(Spacing(2)),double(Spacing(3)),double(mode));
            T(:,:,:,1)=Tx; T(:,:,:,2)=Ty; T(:,:,:,3)=Tz;
        else
            I=bspline_transform_3d_double(double(O(:,:,:,1)),double(O(:,:,:,2)),double(O(:,:,:,3)),double(I),double(Spacing(1)),double(Spacing(2)),double(Spacing(3)),double(mode));
            T=0;
        end
    else
        if(nargout > 1 )
             [I,Tx,Ty,Tz]=bspline_transform_3d_single(single(O(:,:,:,1)),single(O(:,:,:,2)),single(O(:,:,:,3)),single(I),single(Spacing(1)),single(Spacing(2)),single(Spacing(3)),single(mode));
             T(:,:,:,1)=Tx; T(:,:,:,2)=Ty; T(:,:,:,3)=Tz;
        else
             I=bspline_transform_3d_single(single(O(:,:,:,1)),single(O(:,:,:,2)),single(O(:,:,:,3)),single(I),single(Spacing(1)),single(Spacing(2)),single(Spacing(3)),single(mode));
             T=0;
        end
   end
end

Highlights from B-spline Grid, Image and Point based Registration

Highlights from
B-spline Grid, Image and Point based Registration