Here is an example of a subset of the matrix I would like to use:
1 3 5 2 3 6 1 1 1 3 5 4 5 5 5 8 8 0
1 3 5
2 3 6
1 1 1
3 5 4
5 5 5
8 8 0
Here's another way to implement this with bsxfun, slightly different from natan's bsxfun implementation -
bsxfun
t1 = reshape(a,3,[]); %// a is the input matrix out = reshape(bsxfun(@minus,t1,t1(1,:)),[],3); %// Desired output