Hi, Sondos-
Before getting into these other tracking/viewing issues, there is a more fundamental problem with the network of targets (as uploaded): it is not made of binary numbers. Each region must be defined as being either a 1 or 2 or 27, etc. Central parts of the ROIs appear to be integers, but at the edges that is not the case. I am going to guess that these were warped somehow without applying a "nearest neighbors" (NN) interpolation?
Since there is no history in this file's header, I don't know what command was used to make that file. Also since there is no history, I can only guess it was a non-AFNI program? How did you make it?
This is a fundamental issue to tracking before looking at anything else.
--pt
