Thanks Paul. 3dExtrema seems to be the best route - however, am I correct that it kicks out all the maxima within the ROI mask?

The command was: 3dExtrema -volume -closure -mask_file ../mask+tlrc $name_Z+tlrc

Maxima for Volume #0 (Coordinates Order = RAI):
Index Intensity RL[mm] AP[mm] IS[mm] Count Dist[mm]
----- --------- ------ ------ ------ ----- --------
1 0.069 4.50 67.50 11.50 1 6.000
2 0.069 7.50 73.50 5.50 1 6.708
3 0.067 -10.50 70.50 17.50 1 6.708
4 0.066 13.50 73.50 2.50 1 6.708
5 0.065 -7.50 70.50 11.50 1 6.708
6 0.063 -1.50 67.50 11.50 1 6.000
7 0.059 -40.50 58.50 5.50 1 13.748
8 0.057 16.50 70.50 8.50 1 7.348
9 0.056 19.50 64.50 -3.50 1 8.485
10 0.055 -40.50 55.50 -9.50 1 7.348
11 0.053 -10.50 70.50 2.50 1 8.485
12 0.051 -4.50 64.50 2.50 1 8.485
13 0.050 13.50 58.50 -3.50 1 8.485
14 0.047 -46.50 52.50 -6.50 1 7.348
15 0.028 -52.50 52.50 2.50 1 10.817