def test_study_config_fs(self): freesurfer_config = "/i2bm/local/freesurfer/SetUpFreeSurfer.sh" if not os.path.exists(freesurfer_config) \ or not sys.platform.startswith('linux'): # skip this test if FS is not available, or not running # on linux (other systems may see this directory but cannot use it) return study_config = StudyConfig(modules=['FreeSurferConfig'], freesurfer_config = freesurfer_config) study_config.use_fs = True for varname in ["FREESURFER_HOME", "FSF_OUTPUT_FORMAT", "MNI_DIR", "FSFAST_HOME", "FMRI_ANALYSIS_DIR", "FUNCTIONALS_DIR", "MINC_BIN_DIR", "MNI_DATAPATH"]: self.assertTrue(os.environ.get(varname) is not None, msg='%s environment variable not set' % varname)