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Extract 2D slice parallel to an arbitrary plane in 3D image.

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M W
M W 21 Jan 2020
댓글: M W 23 Jan 2020
Hi,
I have a 3D medical image (IM) containing grayvalues. (size: 352 229 277, data type double).
I want slice through the 3D image, parallel to a plane.
The plane is defined by a line.
The line is defined by selecting 2 points in 2D view of the 3D image. (This 2D view is obtained by IM(:,123,:) )
Points:
A=[104,123,111];
B=[253,123,153];
The plane is defined with a normal vector orthogonal to this line.
I want to slice the 3D image with a slice parallel to this plane.
Then I want to view these slices in 2D setting. Like the function sliceViewer. (sliceViewer doesn't support arbitrary angle slices).
I tried to use the slice function, following this example: https://www.mathworks.com/help/releases/R2016b/matlab/ref/slice.html#f33-509125.
Tbh I don't understand much:
Firstly I don't understand how to define a surface with this:
I seems that I can't give a value to the meshgrid indices from my image: slice(x,y,z,V,XI,YI,ZI)
Secondly:
I have 3 points to define the plane.
I have the normal vector.
But I don't know how to use it with the slice function: slice(x,y,z,V,XI,YI,ZI)
Thanks in advance!
%% load
I=Tiff('im','r');
im=read(I);
im=uint8(squeeze(im));
imf=imgaussfilt3(im,0.5);
imf=im2double(imf);
%% isometric
sz_im=size(imf);
average=(sum(sz_im))./3;
imc=imresize3(imf,[average,average,average]);
%% plane equation
% points on slice y=123. Line runs through A and B. http://www2.math.umd.edu/~jmr/241/lines_planes.html
A=[104,123,111];
B=[253,123,153];
%third point for determining the plane
C=[104,124,111];
%normal is cross product
normal = cross(A-B,A-C);
%% meshgrid
[row,col,z] = meshgrid(0:1:average,0:1:average,0:1:average);
v = imc(row,col,z); %ERROR: dimensions
row_slice= %WHAT should I enter here?
col_slice= %WHAT should I enter here?
z_slice= %WHAT should I enter here?
slice(row,col,z,V,row_slice,col_slice,z_slice)

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답변(1개)

KALYAN ACHARJYA
KALYAN ACHARJYA 22 Jan 2020
I want to slice the 3D image with a slice parallel to this plane.
Let suppose image3d is 3D image, which you want to slices
Slice 1
image3d_1= image3d(:,:,1);
Slice 2
image3d_2= image3d(:,:,2);
so on... or you can store the all slices in cell array

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M W
M W 22 Jan 2020
Thank you, but I would like to know what the input for the last 3 variables in the slice function should be:
slice(x,y,z,V,XI,YI,ZI)
KALYAN ACHARJYA
KALYAN ACHARJYA 23 Jan 2020
Have you seen this example in MATLAB documentation?
[X,Y,Z] = meshgrid(-2:.2:2);
V = X.*exp(-X.^2-Y.^2-Z.^2);
xslice = [-1.2,0.8,2];
yslice =0;
zslice = 0;
slice(X,Y,Z,V,xslice,yslice,zslice);
Here xslice,yslice,zslice represents the position of slices with respect to x,y,z axis
xslice = [-1.2,0.8,2] represents the position of slices in the x axis, where yslice =0 (Parellel to y axis) & zslice = 0(Parellel to z axis)
678.png
M W
M W 23 Jan 2020
Yes I did!
But I don't understand how to define an plane that is not parallel to one of the axis, by matrices.
For example a plane that runs through these points:
A=[104,123,111];
B=[253,123,153];
%third point for determining the plane
C=[104,124,111];

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