When you type 'DTIPrep --help' you can get the full description of the options for this program. 

The flag you want to use is '-c' when you don't want to use the graphical user interface. 

Something like, 

./DTIPrep_build/bin/DTIPrep.app/Contents/MacOS/DTIPrep -w sub5621/data/01+dti_64dir_3x3x3/sub5621_a.nhdr -d -f working_projects/sub5621/sub5621_QC/ -c

Best, 

Juan