Howdy Jodene,
Looks like you 've got to go the way of the Draw ROI plugin. Make sure you have a recent distribution of AFNI because the Draw ROI plugin has been improved.
You will be drawing a lot of ROIs, I suggest you consider the Cintiq drawing tablet which works well with Linux and speeds up ROI drawing considerably. Drawing with a stylus on the screen sure beats using a mouse. Let us know if you need more info on that.
You will be using integers to label the different ROIs. There are many AFNI programs that can be used to extract information from these ROIs, including volume measures.
cheers,
-z