That ordering is not changeable. (It frustrates me, too, since it is different from the normal linear index ordering!)
I think this function will do the conversion for you:
% The size of the matrix
M = 3;
N = 4;
% The index according to your preferred ordering (column-wise)
i_colwise = 4;
% Conversion function
[jj,ii] = ind2sub([N,M],i_colwise);
i_rowwise = sub2ind([M,N],ii,jj); % This is the ordering MATLAB expects (row-wise)
