Hi Pete,
Actually, 3dttest++ can indeed handle this, but there has to be the same number of values per location (the datasets themselves cannot be sparse). For locations with missing data, specify the value as zero. Then use 3dttest++ -zskip to skip those zero values (so each location would have varying degrees of freedom, hence the automatic application of -toz).
As Paul noted, 3dMEMA is a possibility, but then you would need the first level t-stats, if you have them.
- rick