old line 20: I removed the -verbose option from the TODO list as this was already implemented.
new line 53: Do we really want to specify all numbers as doubles and not integers in the arguments section, even if sometimes decimal numbers are not possible? (e.g. in the case of -dof)
new line 99: I did not know how FSL calculates the index number for the middle volume. Thus, I went with an if statement such that when -refvol is not set, the -refvol option will not be added to the command and FSL will use the default option. Is that ok?
closes #6