how can we get coordinates of non zero pixel in 3D image

I have a stack of 249 images (image of the skeleton of the aorta) it appears like points in some slices and like lines in another slices. I want to get for each slice the coordinates of the non zero value in the image (my images are binary). I tried the command Find but it gives me just the coordinates and i don't know at which slice it corresponds.

Answer 1

[KSSV]

find gives you row and col position along with the value you asked to seek. You can run a loop on each matrix and use find as

[row,col,v] = find(I(:,:,1)~=0)

Or alternatively you can try find on 3D matrix using:

[r,c,v] = ind2sub(size(I),find(I ~= 0));

Note that the above command is taken from the link: https://in.mathworks.com/matlabcentral/answers/789-using-find-in-a-3d-matrix-in-matlab

[Sayan Bhattacharya]

KSSV code is okay. But how to find the co-ordinate of that point?

[Image Analyst]

Of WHAT point? You have the coordinates of all the points. If you want one certain special point, you're going to have to identify it somehow so we know which one it is.

[Sayan Bhattacharya]

Image Analyst,

Like in the following figure, let's say its size is 100x100 that's rows & columns.

If we are moving lets say from 1st row to the last row in a loop can you please help me get the code for identifying the co-ordinates of that point where there is 1st non zero pixel encountered?

Answer 2

[IKRAM jebali]

Thank you for your answer. I tried these two commands but it doesn't give me what I want to get. And when I use a loop it gives no value for r,c and v (an empty scalar).

For i=1:249
[r c v]=find (I (:,:,i))
end

This is the loop I've tried.

[KSSV]

[r,c,v] = find(I(:,:,i))

should work....what is class(I) ?

[IKRAM jebali]

this is my code skel = load_nii('CT10seg_skel.img'); skel=skel.img; for i=1:249 [x y v]=find(skel(:,:,i)==0); end

[IKRAM jebali]

Thank you for your answer, I think maybe the problem is with my image.