I've got a few followup questions, and I'm going out of town for the weekend, so I'll just leave them here:

1)The program works fine unless "show segmentation" is checked. If you check that box, the program seems to go on indefinitely. Also, in this mode a [pause, resume] dialogue box will not appear.

2) Does the image have to be an 8bit image? Will 16bitunsigned work?

3) Why does it look like the whole volume is not being addressed in the seganno algorithm? (see attached)

4) When I try to use my own atlas.apo file, I get "Error in calling do_AtlasGuidedSAnno()." A few lines from my .apo file look like this:

1, 1, ADAL, , 0.04846648871898651,-3.2340502738952637,0.048466488718986510.000,0.000,0.000,50.000,0.000,,,,255,0,0
2, 2, ADAR, , 0.04777468740940094,-3.2340495586395264,0.047774687409400940.000,0.000,0.000,50.000,0.000,,,,255,0,0
3, 3, ADEL, , 0.041304811835289,-3.2615060806274414,0.0413048118352890.000,0.000,0.000,50.000,0.000,,,,255,0,0

Thanks for working with me on this.
-Chris