Some alternatives:
One more choice is to use a 3dmaskdump command which will dump out values by sub-brik not by time, but the data can all be read fairly easily with something like Matlab. It also offers the nice options of restricting the voxels to a mask, range or a box.
For a specific ROI, there are lots of choices; you could use the plug-ins ROI_Plot, ROI Average.
For graphing the time course of many voxels, you can use the graphing function for up to 21x21 sub-graphs, and this can be done across datasets with the plugin, Dataset #N.
