afni.nimh.nih.gov

Sure, you could use 3dROIstats. If you want multiple
ROIs, then you could try the generic:

3dROIstats -mask ROI+orig time_series+orig

If you want a 1D time series for a single ROI,
without extra headers and such, you could try:

3dROIstats -mask ROI+orig -quiet time_series+orig

- rick