I have downloaded HAMMER 1.0.2 and am trying to run the sample data. I used the values in the user manual to set up the project. However, when I run the "Perform Normalization Step", I get an error "Abnormal termination: 1". What does this mean?

I am on Linux, and have Java 1.6.0_01 and FSL 4.1.4. I get the same result whether I select "Use FSL for Linear Transformation" or not.

So the current version of HAMMER was designed with FSL 4.0.. may be that is the issue. Have you tried using the CLI?