def test_run_Adni2Bids(cmdopt):
from clinica.iotools.converters.adni_to_bids.adni_to_bids import AdniToBids
from os.path import dirname, join, abspath
root = join(dirname(abspath(__file__)), pardir, 'data', 'Adni2Bids')
clean_folder(join(root, 'out', 'bids'), recreate=True)
adni_to_bids = AdniToBids()
adni_to_bids.check_adni_dependencies()
dataset_directory = join(root, 'in', 'unorganized_data')
clinical_data_directory = join(root, 'in', 'clinical_data_25-04-19')
bids_directory = join(root, 'out', 'bids')
subjects_list = join(root, 'in', 'subjects.txt')
modalities = [
'T1', 'PET_FDG', 'PET_AMYLOID', 'PET_TAU', 'DWI', 'FLAIR', 'fMRI'
]
adni_to_bids.convert_images(dataset_directory, clinical_data_directory,
bids_directory, subjects_list, modalities)
adni_to_bids.convert_clinical_data(clinical_data_directory, bids_directory)
# Generate tree of output files
compare_folders(join(root, 'out'),
join(root, 'ref'),
shared_folder_name='bids')
clean_folder(join(root, 'out', 'bids'), recreate=True)
def test_run_Oasis2Bids(cmdopt):
from clinica.iotools.converters.oasis_to_bids.oasis_to_bids import OasisToBids
from os.path import dirname, join, abspath
root = join(dirname(abspath(__file__)), pardir, 'data', 'Oasis2Bids')
clean_folder(join(root, 'out', 'bids'), recreate=True)
# Data location
dataset_directory = join(root, 'in', 'unorganized')
bids_directory = join(root, 'out', 'bids')
clinical_data_directory = join(root, 'in', 'clinical_data')
oasis_to_bids = OasisToBids()
oasis_to_bids.convert_images(dataset_directory, bids_directory)
oasis_to_bids.convert_clinical_data(clinical_data_directory, bids_directory)
compare_folders(join(root, 'out'), join(root, 'ref'),
shared_folder_name='bids')
clean_folder(join(root, 'out', 'bids'), recreate=True)
def test_run_Aibl2Bids(cmdopt):
from clinica.iotools.converters.aibl_to_bids.aibl_to_bids import convert_clinical_data, convert_images
from os.path import dirname, join, abspath
root = dirname(abspath(join(abspath(__file__), pardir)))
root = join(root, 'data', 'Aibl2Bids')
dataset_directory = join(root, 'in', 'unorganized_data')
clinical_data_directory = join(root, 'in', 'Data_extract_3.2.5')
bids_directory = join(root, 'out', 'bids')
clean_folder(join(root, 'out', 'bids'), recreate=True)
# Perform conversion of dataset
convert_images(dataset_directory, clinical_data_directory, bids_directory)
convert_clinical_data(bids_directory, clinical_data_directory)
# Evaluate difference between ref and out
compare_folders(join(root, 'out'), join(root, 'ref'),
shared_folder_name='bids')
clean_folder(join(root, 'out', 'bids'), recreate=True)