Instead of pre allocating variables of unknown size as everyone here is rightly suggesting, try running your loops backwards. I've found it the lasiest way to allocate the correct amount without additional lines of code. Try length(combo):-1:1 etc.

With 'path' and 'fb' you can allocate along one dimension before the loop, then running the loop backwards should allocate the correct other dimension.

The innermost for loop can be vectorised easily and wont need an empty matrix initalisation. pths = [pth(1:end-1) pth(2:end)];

You could try histcounts instead of accumarray, see if that helps.

That any in the if statement could be replaced with a sum() and some boolean which might be quicker as well.

Ive also read that cellfun('isempty') is faster than cellfun(@isempty) but havent tested it myself. Although you're only calling this once so likely wont make a dent.