3D Free Form Image Registration Toolbox (GUI): recalcvol(sz,dgridx,dgridy,dgridz) - File Exchange

Code covered by the BSD License

Highlights from
3D Free Form Image Registration Toolbox (GUI)

Crop_image(varargin) APPLY_IMAGE M-file for apply_image.fig
Dcoord(varargin) DCOORD M-file for Dcoord.fig
Deform(varargin) DEFORM M-file for Deform.fig
Disocenter(varargin) DISOCENTER M-file for Disocenter.fig
FFD4D(varargin) FFD4D M-file for FFD4D.fig
Registration_Parameters(varar... REGISTRATION_PARAMETERS M-file for Registration_Parameters.fig
auto_segmentation(varargin) AUTO_SEGMENTATION M-file for auto_segmentation.fig
createpatient(varargin) CREATEPATIENT M-file for createpatient.fig
featurep(varargin) FEATUREP M-file for featurep.fig
formatsel(varargin) FORMATSEL M-file for formatsel.fig
formatsel2(varargin) FORMATSEL2 M-file for formatsel2.fig
load_cont(varargin) LOAD_CONT M-file for load_cont.fig
load_patient(varargin) LOAD_PATIENT M-file for load_patient.fig
name_dose(varargin) NAME_DOSE M-file for name_dose.fig
name_image(varargin) NAME_IMAGE M-file for name_image.fig
newimage(varargin) NEWIMAGE M-file for newimage.fig
reg_params(varargin) REG_PARAMS M-file for reg_params.fig
registration(varargin) REGISTRATION M-file for registration.fig
resolution(varargin) RESOLUTION M-file for resolution.fig
validation(varargin) VALIDATION M-file for Validation.fig
RTOGread(fullpath)
Registration_Parameters(varar... REGISTRATION_PARAMETERS M-file for Registration_Parameters.fig
amvd(base,dgridx,dgridy) amvd function outlines bone structures and ensures that deformations are
amvd3D.m
amvold(dgridx,dgridy,dgridz,r... amvold.m applies a formula similar to the maximum volume displacement but
autoseg(image,type)
bspline(u,k) calculates the derivative of kth basis function of a cubic B-spline
bspline2(u,k) calculates the derivative of kth basis function of a cubic B-spline
calcDVH(doses3D,contour,rez) volume introduced from using cubic voxels at the edge of the ROI as opposed to using more precise
calcgrad(base,mask,dgridx,dgr... distance transforms of images.
calcgrad3D(base,distmask,dgri... distance transforms of images.
calcgrad3D2(base,distmask,dgr... distance transforms of images.
dLdPx(base,sz2,sz,m,n,i1,j1) determine the change in deformation in the x direction for the mth by nth
dLdPx3D(sz3,sz2,sz,m,n,p,i1,j... determine the change in deformation in the x direction for the mth by nth
dLdPy(base,sz2,sz,m,n,i1,j1) determine the change in deformation in the y direction for the mth by nth
dLdPy3D(sz3,sz2,sz,m,n,p,i1,j... determine the change in deformation in the y direction for the mth by nth
dLdPz3D(sz3,sz2,sz,m,n,p,i1,j... determine the change in deformation in the y direction for the mth by nth
dLdx(base,dgridx,dgridy) calculate the derivative of the change in the tensor product for a free
dLdx3D(sz,dgridx,dgridy,dgrid... calculate the derivative of the change in the tensor product for a free
dLdy(base,dgridx,dgridy) calculate the derivative of the change in the tensor product for a free
dLdy3D(sz,dgridx,dgridy,dgrid... calculate the derivative of the change in the tensor product for a free
dLdz3D(sz,dgridx,dgridy,dgrid... calculate the derivative of the change in the tensor product for a free
dbspline(u,k); calculates the derivative of kth basis function of a cubic B-spline
dbspline2(u,k); calculates the derivative of kth basis function of a cubic B-spline
ddLdxdPx(base,sz2,sz,m,n,i1,j... determine the change in deformation in the x direction for the mth by nth
ddLdxdPx3D(sz3,sz2,sz,m,n,p,i... determine the change in deformation in the x direction for the mth by nth
ddLdydPy(base,sz2,sz,m,n,i1,j... determine the change in deformation in the x direction for the mth by nth
ddLdydPy2(base,dgrid,m,n) determine the change in deformation in the x direction for the mth by nth
ddLdydPy3D(sz3,sz2,sz,m,n,p,i... determine the change in deformation in the x direction for the mth by nth
ddLdzdPz3D(sz3,sz2,sz,m,n,p,i... determine the change in deformation in the x direction for the mth by nth
dferror3D(fpoints,fpoints2,m,...
disttrans(coords,size)
drawcont(shape,dose) convert contour outline (shape) to 2D dose distribution
eliminateskin(image1)
elocal(base,mask,dgridx,dgrid... distance transforms of images.
elocal3D.m
errormn(base,mask,dgridx,dgri... distsource = bwdist(image);
ferror3D(fpoints,fpoints2,dgr... try
finterp2(x,y,z,xi,yi,uniformF...
finterp3(xInterpV, yInterpV, ...
getRTOGcont(fullpath,segname,...
getRTOGcont2(fullpath,segname...
getRTOGcont3(fullpath,segname... fullpath is the path including filename and extension to the RTOG header
getRTOGstructures(fullpath)
imdeform(image1,image2)
imdeform2(density,image1,imag...
imdeform3D(image1,image2,alph... Imdeform3D
iminterpn(varargin) IMINTERPN Multidimensional interpolation using Image Processing Toolbox functions.
imrecreate3D.m
imrecreate3D2(base,dgridx,dgr... recreate an image based on it's deformation control point grid
imrecreate3D3.m
imrecreate3D_eff.m
interpslice(image1,sz2) this function was created as a method of performing 3 Dimension
irongrid(gridx,gridy) smooth down
irongrid3D(gridx,gridy,gridz) smooth down
loadDICOM(sFolder) LOADDICOM M-file
loadDICOM2(sFolder) LOADDICOM M-file
loadDICOM2(sFolder) LOADDICOM M-file
loadDICOM4(sFolder) LOADDICOM M-file
loadRTOG(filename)
numbername(number,digits)
pathdef PATHDEF Search path defaults.
readRTOGDose(fullPath) READRTOGDOSE M-file
readRTOGDose(fullPath) READRTOGDOSE M-file
recalcvol(sz,dgridx,dgridy,dg... shed padding
refgrid(dgrid,M,N);
slice3DVolOrtho(data3M, xV, y... "slice3DVolOrtho"
DVH_extract.m
NTCP_TCP.m
coefficients.m
copystuff.m
crop.m
dgrid.m
example.m
example2.m
metadata.m
tempf.m
writing.m
View all files

from 3D Free Form Image Registration Toolbox (GUI) by Daniel Markel
A toolbox for performing image registrations on 4D RTOG files or any other volumetric image.

recalcvol(sz,dgridx,dgridy,dgridz)

function volume = recalcvol(sz,dgridx,dgridy,dgridz)

%shed padding
dgridx(1,:,:)=[]; dgridx(end,:,:) =[]; dgridx(:,1,:) = []; dgridx(:,end,:) = []; dgridx(:,:,1) = []; dgridx(:,:,end) =[];
dgridy(1,:,:)=[]; dgridy(end,:,:) =[]; dgridy(:,1,:) = []; dgridy(:,end,:) = []; dgridy(:,:,1) = []; dgridy(:,:,end) =[];
dgridz(1,:,:)=[]; dgridz(end,:,:) =[]; dgridz(:,1,:) = []; dgridz(:,end,:) = []; dgridz(:,:,1) = []; dgridz(:,:,end) =[];

%calculate P 
sz = sz+1;
res1 = size(dgridx);
zarray1 = zeros(1,1,res1(3));
zarray2 = zeros(1,1,sz(3));
zarray1(:) = 1:res1(3);
zarray2(:) = 1:(res1(3)-1)/(sz(3)-1):res1(3);

dgridx = interp3(repmat(1:res1(2),[res1(1),1,res1(3)]),repmat((1:res1(1))',[1,res1(2),res1(3)]),repmat(zarray1,[res1(1),res1(2),1]),dgridx,repmat(1:(res1(2)-1)/(sz(2)-1):res1(2),[sz(1),1,sz(3)]),repmat((1:(res1(1)-1)/(sz(1)-1):res1(1))',[1,sz(2),sz(3)]),repmat(zarray2,[sz(1),sz(2),1]),'linear');
dgridy = interp3(repmat(1:res1(2),[res1(1),1,res1(3)]),repmat((1:res1(1))',[1,res1(2),res1(3)]),repmat(zarray1,[res1(1),res1(2),1]),dgridy,repmat(1:(res1(2)-1)/(sz(2)-1):res1(2),[sz(1),1,sz(3)]),repmat((1:(res1(1)-1)/(sz(1)-1):res1(1))',[1,sz(2),sz(3)]),repmat(zarray2,[sz(1),sz(2),1]),'linear');
dgridz = interp3(repmat(1:res1(2),[res1(1),1,res1(3)]),repmat((1:res1(1))',[1,res1(2),res1(3)]),repmat(zarray1,[res1(1),res1(2),1]),dgridz,repmat(1:(res1(2)-1)/(sz(2)-1):res1(2),[sz(1),1,sz(3)]),repmat((1:(res1(1)-1)/(sz(1)-1):res1(1))',[1,sz(2),sz(3)]),repmat(zarray2,[sz(1),sz(2),1]),'linear');

% for t = 2:res1(3)-1
%     [dgridx(:,:,t-1:t+1),dgridy(:,:,t-1:t+1),dgridz(:,:,t-1:t+1)] = amvd3D(sz,res1,[sz(1),sz(2),3],dgridx(:,:,t-1:t+1),dgridy(:,:,t-1:t+1),dgridz(:,:,t-1:t+1));
% end 



zarray = zeros(1,1,sz(3));
zarray(:) = 1:sz(3);
X = repmat(1:sz(2),[sz(1),1,sz(3)])+ dgridx -0.5;
Y = repmat((1:sz(1))',[1,sz(2),sz(3)])+ dgridy -0.5;
Z = repmat(zarray,[sz(1),sz(2),1])+ dgridz -0.5;

% [X,Y,Z] = irongrid3D(X,Y,Z);
clear dgridx dgridy dgridz;
%Voxels centre coordinates
sz = sz-1;
zarray = zeros(1,1,sz(3));
zarray(:) = 1:sz(3);
centerx = repmat(1:sz(2),[sz(1),1,sz(3)]);
centery = repmat((1:sz(1))',[1,sz(2),sz(3)]);
centerz = repmat(zarray,[sz(1),sz(2),1]);

volume = zeros(sz(1),sz(2),sz(3));
%going layer by layer in the Z-axis
for n = 1:sz(3)

%calculating tetrahedron vectors
vectorsx = -cat(3,X(2:end,1:end-1,n)-centerx(:,:,n),X(2:end,1:end-1,n+1)-centerx(:,:,n),X(2:end,2:end,n+1)-centerx(:,:,n),...
            X(2:end,2:end,n)-centerx(:,:,n),X(1:end-1,1:end-1,n)-centerx(:,:,n),X(1:end-1,1:end-1,n+1)-centerx(:,:,n),...
            X(1:end-1,2:end,n+1)-centerx(:,:,n),X(1:end-1,2:end,n)-centerx(:,:,n));
vectorsy = -cat(3,Y(2:end,1:end-1,n)-centery(:,:,n),Y(2:end,1:end-1,n+1)-centery(:,:,n),Y(2:end,2:end,n+1)-centery(:,:,n),...
            Y(2:end,2:end,n)-centery(:,:,n),Y(1:end-1,1:end-1,n)-centery(:,:,n),Y(1:end-1,1:end-1,n+1)-centery(:,:,n),...
            Y(1:end-1,2:end,n+1)-centery(:,:,n),Y(1:end-1,2:end,n)-centery(:,:,n));
vectorsz = -cat(3,Z(2:end,1:end-1,n)-centerz(:,:,n),Z(2:end,1:end-1,n+1)-centerz(:,:,n),Z(2:end,2:end,n+1)-centerz(:,:,n),...
            Z(2:end,2:end,n)-centerz(:,:,n),Z(1:end-1,1:end-1,n)-centerz(:,:,n),Z(1:end-1,1:end-1,n+1)-centerz(:,:,n),...
            Z(1:end-1,2:end,n+1)-centerz(:,:,n),Z(1:end-1,2:end,n)-centerz(:,:,n));
%calculate the 12 tetrahedron volumes for each voxel.        
volumes = (1/6)*cat(3,vectorsx(:,:,4).*(vectorsy(:,:,2).*vectorsz(:,:,1) - vectorsy(:,:,1).*vectorsz(:,:,2)) - vectorsy(:,:,4).*(vectorsx(:,:,2).*vectorsz(:,:,1) - vectorsx(:,:,1).*vectorsz(:,:,2)) + vectorsz(:,:,4).*(vectorsx(:,:,2).*vectorsy(:,:,1) - vectorsx(:,:,1).*vectorsy(:,:,2)),...
                      vectorsx(:,:,3).*(vectorsy(:,:,4).*vectorsz(:,:,2) - vectorsy(:,:,2).*vectorsz(:,:,4)) - vectorsy(:,:,3).*(vectorsx(:,:,4).*vectorsz(:,:,2) - vectorsx(:,:,2).*vectorsz(:,:,4)) + vectorsz(:,:,3).*(vectorsx(:,:,4).*vectorsy(:,:,2) - vectorsx(:,:,2).*vectorsy(:,:,4)),...
                      vectorsx(:,:,4).*(vectorsy(:,:,8).*vectorsz(:,:,1) - vectorsy(:,:,1).*vectorsz(:,:,8)) - vectorsy(:,:,4).*(vectorsx(:,:,8).*vectorsz(:,:,1) - vectorsx(:,:,1).*vectorsz(:,:,8)) + vectorsz(:,:,4).*(vectorsx(:,:,8).*vectorsy(:,:,1) - vectorsx(:,:,1).*vectorsy(:,:,8)),...
                      vectorsx(:,:,8).*(vectorsy(:,:,5).*vectorsz(:,:,1) - vectorsy(:,:,1).*vectorsz(:,:,5)) - vectorsy(:,:,8).*(vectorsx(:,:,5).*vectorsz(:,:,1) - vectorsx(:,:,1).*vectorsz(:,:,5)) + vectorsz(:,:,8).*(vectorsx(:,:,5).*vectorsy(:,:,1) - vectorsx(:,:,1).*vectorsy(:,:,5)),...
                      vectorsx(:,:,3).*(vectorsy(:,:,4).*vectorsz(:,:,8) - vectorsy(:,:,8).*vectorsz(:,:,4)) - vectorsy(:,:,3).*(vectorsx(:,:,4).*vectorsz(:,:,8) - vectorsx(:,:,8).*vectorsz(:,:,4)) + vectorsz(:,:,3).*(vectorsx(:,:,4).*vectorsy(:,:,8) - vectorsx(:,:,8).*vectorsy(:,:,4)),...
                      vectorsx(:,:,3).*(vectorsy(:,:,7).*vectorsz(:,:,8) - vectorsy(:,:,8).*vectorsz(:,:,7)) - vectorsy(:,:,3).*(vectorsx(:,:,7).*vectorsz(:,:,8) - vectorsx(:,:,8).*vectorsz(:,:,7)) + vectorsz(:,:,3).*(vectorsx(:,:,7).*vectorsy(:,:,8) - vectorsx(:,:,8).*vectorsy(:,:,7)),...
                      vectorsx(:,:,7).*(vectorsy(:,:,8).*vectorsz(:,:,5) - vectorsy(:,:,5).*vectorsz(:,:,8)) - vectorsy(:,:,7).*(vectorsx(:,:,8).*vectorsz(:,:,5) - vectorsx(:,:,5).*vectorsz(:,:,8)) + vectorsz(:,:,7).*(vectorsx(:,:,8).*vectorsy(:,:,5) - vectorsx(:,:,5).*vectorsy(:,:,8)),...
                      vectorsx(:,:,7).*(vectorsy(:,:,6).*vectorsz(:,:,5) - vectorsy(:,:,5).*vectorsz(:,:,6)) - vectorsy(:,:,7).*(vectorsx(:,:,6).*vectorsz(:,:,5) - vectorsx(:,:,5).*vectorsz(:,:,6)) + vectorsz(:,:,7).*(vectorsx(:,:,6).*vectorsy(:,:,5) - vectorsx(:,:,5).*vectorsy(:,:,6)),...
                      vectorsx(:,:,3).*(vectorsy(:,:,7).*vectorsz(:,:,6) - vectorsy(:,:,6).*vectorsz(:,:,7)) - vectorsy(:,:,3).*(vectorsx(:,:,7).*vectorsz(:,:,6) - vectorsx(:,:,6).*vectorsz(:,:,7)) + vectorsz(:,:,3).*(vectorsx(:,:,7).*vectorsy(:,:,6) - vectorsx(:,:,6).*vectorsy(:,:,7)),...
                      vectorsx(:,:,3).*(vectorsy(:,:,2).*vectorsz(:,:,6) - vectorsy(:,:,6).*vectorsz(:,:,2)) - vectorsy(:,:,3).*(vectorsx(:,:,2).*vectorsz(:,:,6) - vectorsx(:,:,6).*vectorsz(:,:,2)) + vectorsz(:,:,3).*(vectorsx(:,:,2).*vectorsy(:,:,6) - vectorsx(:,:,6).*vectorsy(:,:,2)),...
                      vectorsx(:,:,6).*(vectorsy(:,:,2).*vectorsz(:,:,1) - vectorsy(:,:,1).*vectorsz(:,:,2)) - vectorsy(:,:,6).*(vectorsx(:,:,2).*vectorsz(:,:,1) - vectorsx(:,:,1).*vectorsz(:,:,2)) + vectorsz(:,:,6).*(vectorsx(:,:,2).*vectorsy(:,:,1) - vectorsx(:,:,1).*vectorsy(:,:,2)),...
                      vectorsx(:,:,6).*(vectorsy(:,:,5).*vectorsz(:,:,1) - vectorsy(:,:,1).*vectorsz(:,:,5)) - vectorsy(:,:,6).*(vectorsx(:,:,5).*vectorsz(:,:,1) - vectorsx(:,:,1).*vectorsz(:,:,5)) + vectorsz(:,:,6).*(vectorsx(:,:,5).*vectorsy(:,:,1) - vectorsx(:,:,1).*vectorsy(:,:,5)));
%sum for total voxel volume
volumes = sum(abs(volumes),3);
volume(:,:,n) = volumes;
end

Highlights from 3D Free Form Image Registration Toolbox (GUI)

Highlights from
3D Free Form Image Registration Toolbox (GUI)