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)
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)
