How can I find 26 neighbors of point with coordinates of (i,j,k)?

I have a stack of images in a 3D matrix.

How can I find 26 neighbors of a specific voxel with coordinates of (i,j,k) in Matlab?

Your help is appreciated.

Answer 1

[Image Analyst]

To get a 27 element cube around the voxel, do this:

neighbors = matrix3d(i-1:i+1, j-1:j+1, k-1:k+1);

Then turn it into a column vector like this:

neighbors = neighbors(:);

Then delete the i,j,k element to get the final 26 neighbors, by deleting the middle element of the column vector:

neighbors[14] = [];  % Now we're done!  We have a list of 26 voxel values.

[Sara Salimi]

Dear Image Analyst, Thank you very much for your response. How can I get the indices of neighbors since I want to extract the corresponding rows from a feature set matrix (7485463x138). Each rows relates to a voxel.

to be more clear:

• How to extract the indices of neighbors of a specific voxel?
• How to retrieve the corresponding rows related to obtained indices from the previous step?

Many thanks in advance

[Image Analyst]

It depends on whether you're keeping the neighbors as a 3-D cube, or as a 1-D vector For a vector it will all k-1:k+1 for i=1 and j=1. Then it will be k-1:k+1 for i=1, j=2. Then it will be k-1:k+1 for i=1, j=3. Then it will be k-1:k+1 for i=2, j=2. Then it will be k-1:k+1 for i=1, j=2, and so on.

[Sandhiya Prakash]

what is matrix3d()? I am using this it gives error like neighbors = matrix3d(i-1:i+1, j-1:j+1, k-1:k+1); Undefined function or variable 'matrix3d'.

[Walter Roberson]

matrix3d is the name of the variable your data is stored in.

[Sandhiya Prakash]

yeah thank you sir..its working.I have another doubt.Now i am having 26 scalar values.I need to identify neighbors of these 26 scalar values?how can i perform that?

[Image Analyst]

What does "identify" mean to you? You have the indexes of a voxel and its neighbors, so what else do you need to "identify" them?

[Sandhiya Prakash]

Yes sir.I am having indexes of voxel and its neighbours,so totally i will have 27 scalar values.Now leaving the actual voxel consider only the neighbours(26) and identify its neighbouring voxel values.How to perform this?

Answer 2

[KSSV]

doc knnsearch

Answer 3

[Walter Roberson]

function [idx3d, valid, linidx] = neighbour26(i, j, k, Your3DMatrix)
  %returns the indices of the 26 3-D neighbors of location i, j, k within Your3DMatrix
  %In the first output, indices are returned as a 26 x 3 matrix of row, column, page triples.
  %Since on the border areas neighbours might be outside of the matrix, the
  %second output is a vector indicating which of the rows are valid.
  %The third output is the linear indices -- useful for extracting content

    [rows, cols, pages] = size(Your3DMatrix);

    [R, C, P] = ndgrid(R-1:R+1, C-1:C+1, P-1:P+1);
    idx3d = [R(:), C(:), P(:)];
    idx3d(14,:) = [];     %remove center

    valid = idx(:,1) >= 1 & idx(:,2) >= 1 & idx(:,3) >= 1 & idx(:,1) <= rows & idx(:,2) <= cols & idx(:,3) <= pages;

    linidx = nan(size(valid));
    linidx(valid) = sub2ind( [rows, cols, pages], idx3(valid,1), idx3d(valid,2), idx3d(valid,3) );