Hi,
My suggestion is that you resample your AAL NIfTI to the same dimmension as the functional NIfTI's (with a nearest neigbour aproximation, to maintain the AAL ROI numbers), and then you call for each ROI the temporal dimension of the functional NIfTI in the voxels that coincide with the AAL ROI number. You can do with just one "for" in any programming language, if you use R you can easily open the NIfTI's with the package oro.nifti.

Cheers.
Z.