def run_command(self, args):
from clinica.iotools.converters.oasis_to_bids.oasis_to_bids import OasisToBids
oasis_to_bids = OasisToBids()
oasis_to_bids.convert_images(args.dataset_directory,
args.bids_directory)
oasis_to_bids.convert_clinical_data(args.clinical_data_directory,
args.bids_directory)
def run_oasis2bids(input_dir: PathLike, output_dir: PathLike,
ref_dir: PathLike) -> None:
from clinica.iotools.converters.oasis_to_bids.oasis_to_bids import OasisToBids
# Arrange
clinical_data_directory = input_dir / "clinical_data"
# Act
oasis_to_bids = OasisToBids()
oasis_to_bids.convert_images(input_dir / "unorganized",
output_dir / "bids")
oasis_to_bids.convert_clinical_data(clinical_data_directory,
output_dir / "bids")
# Assert
compare_folders(output_dir / "bids", ref_dir / "bids", output_dir)
def cli(
dataset_directory: str,
clinical_data_directory: str,
bids_directory: str,
) -> None:
"""OASIS to BIDS converter.
Convert the imaging and clinical data of OASIS (http://oasis-brains.org/), located in DATASET_DIRECTORY and
CLINICAL_DATA_DIRECTORY respectively, to a BIDS dataset in the target BIDS_DIRECTORY.
"""
from clinica.iotools.converters.oasis_to_bids.oasis_to_bids import OasisToBids
oasis_to_bids = OasisToBids()
oasis_to_bids.convert_images(dataset_directory, bids_directory)
oasis_to_bids.convert_clinical_data(clinical_data_directory,
bids_directory)
def run_command(self, args):
from clinica.iotools.converters.oasis_to_bids.oasis_to_bids import OasisToBids
from clinica.iotools.converter_utils import check_bin
from clinica.utils.stream import cprint
from colorama import Fore
import sys
missing_bin = check_bin('mri_convert')
if missing_bin:
cprint(Fore.RED + 'mri_convert from FreeSurfer is required.'
+ ' Install it and re-run the converter.' + Fore.RESET)
cprint('Exiting clinica...')
sys.exit()
oasis_to_bids = OasisToBids()
oasis_to_bids.convert_images(args.dataset_directory, args.bids_directory)
oasis_to_bids.convert_clinical_data(args.clinical_data_directory, args.bids_directory)
def test_run_Oasis2Bids(cmdopt):
from os.path import abspath, dirname, join
from clinica.iotools.converters.oasis_to_bids.oasis_to_bids import OasisToBids
root = join(dirname(abspath(__file__)), pardir, 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_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)