You haven't given us a lot to go on there, but the form of assignment you mention is only valid if qWaypoints is a parfor "temporary" variable. In other words, you must have a full (non-indexed) assignment inside the loop to that variable, like this:
parfor i = 1:N
qWaypoints = zeros(3, 5); % or whatever size is appropriate
[qWaypoints(2,:), solutionInfo] = gik_Pick(q0, fixOrientation);
end
I doubt this is actually what you want though. Could you update your question please to give us a minimal reproduction of what you're trying to achieve.
