sigmasPositive = zeros(1,4);
for j = 1:size(y2D,2)
idxOfInterest = y2D(:,j) > 0;
sigmasPositive(j) = std(y2D(idxOfInterest,j));
end
or you can avoid the loop using
z = mat2cell(y2D,size(y2D,1),ones(1,size(y2D,2)));
sigmasPositiveNoLoop = cellfun(@(c)std(c(c>0)),z);