How to nest multiple parfor loops

MrAzzman already pointed out how to linearise nested loops. Here is a general solution to linearise n nested loops.

1) Assuming you have a simple nested loop structure like this:

%dummy function for demonstration purposes
f=@(a,b,c)([a,b,c]);

%three loops
X=cell(4,5,6);
for a=1:size(X,1);
    for b=1:size(X,2);
        for c=1:size(X,3);
            X{a,b,c}=f(a,b,c);
        end
    end
end

2) Basic linearisation using a for loop:

%linearized conventional loop
X=cell(4,5,6);
iterations=size(X);
for ix=1:prod(iterations)
    [a,b,c]=ind2sub(iterations,ix);
    X{a,b,c}=f(a,b,c);
end   

3) Linearisation using a parfor loop.

%linearized parfor loop
X=cell(4,5,6);
iterations=size(X);
parfor ix=1:prod(iterations)
    [a,b,c]=ind2sub(iterations,ix);
    X{ix}=f(a,b,c);
end

4) Using the second version with a conventional for loop, the order in which the iterations are executed is altered. If anything relies on this you have to reverse the order of the indices.

%linearized conventional loop
X=cell(4,5,6);
iterations=fliplr(size(X));
for ix=1:prod(iterations)
    [c,b,a]=ind2sub(iterations,ix);
    X{a,b,c}=f(a,b,c);
end

Reversing the order when using a parfor loop is irrelevant. You can not rely on the order of execution at all. If you think it makes a difference, you can not use parfor.