I got it working. I actually took advantage of what the fitnesse TestRunner can do. In groovy one can call .execute() on a string and any command in that string will be execute against the shell so i fired off FitNesse tests like this.
def process = "cmd /c java -jar fitnesse.jar -c \"MyTestPage?test&format=text\"".execute()
this process is the groovy implementation of a java process, API found here,
http://groovy.codehaus.org/groovy-jdk/java/lang/Process.html so to my purpose i used the waitForProcessOutput method to get the output in a stream after the process finishes.
ByteArrayOutputStream outStream = new ByteArrayOutputStream()
process.waitForProcessOutput(outStream, new ByteArrayOutputStream())
now this outStream contains the entire console ouput from the command execution so you can parse it at will. For example this line will print every line in the stream to your log.
outStream.toString().eachLine{line -> log.info line }
Hope this helps someone out there trying to get something similar done. Thank you for your suggestion.