Hi,

Thanks Juan it works. The difference was in the step 4. I was doing ccmake rather than make.

But now when i am running the command line, it opens the GUI. I do not want to use GUI. I need to use it from command line.

./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/

Any idea how to make it run via command line?