Use PDIST2 and get points within a distance smaller (or equal) to the center (node) than the radius.
EDIT : here is a quick example, where we have 4 nodes and we are interested in building a cell array of nodes (IDs) that are within in radius 2 of two centers:
>> dNodes2Centers = pdist2( [1,0,0; 0,2,0; 0,0,3; 1,1,0], [0,0,0; 0,1,0] )
dNodes2Centers =
1.0000 1.4142
2.0000 1.0000
3.0000 3.1623
1.4142 1.0000
>> [r, c] = find( dNodes2Centers < 2 ) ; % R = 2, exclude boundary (<).
>> nodeIdsPerCenter = accumarray( c, r, [], @(x){x} ) ; % Group per center.
which builds:
>> celldisp( nodeIdsPerCenter )
nodeIdsPerCenter{1} =
1
4
nodeIdsPerCenter{2} =
1
2
4
