print(
"Please refer to the output directory for a template of the file "
"and, after customizing to your analysis, add the flag"
"\n\n"
" --group_file {0}"
"\n\n"
"to your `docker run` command"
"\n".format(output_group))
sys.exit(1)
else:
import CPAC.pipeline.cpac_group_runner as cgr
print("Starting group level analysis of data in {0} using {1}".format(
args.bids_dir, args.group_file))
cgr.run(args.group_file)
sys.exit(0)
elif args.analysis_level in ["test_config", "participant"]:
# check to make sure that the input directory exists
if not args.data_config_file and \
not args.bids_dir.lower().startswith("s3://") and \
not os.path.exists(args.bids_dir):
print("Error! Could not find {0}".format(args.bids_dir))
sys.exit(1)
# check to make sure that the output directory exists
if not args.output_dir.lower().startswith("s3://") and \
print()
else:
print(
"Please refer to the output directory for a template of the file "
"and, after customizing to your analysis, add the flag\n\n"
" --group_file %s"
"\n\nto your `docker run` command\n"
% output_group
)
sys.exit(1)
else:
import CPAC.pipeline.cpac_group_runner as cgr
print("Starting group level analysis of data in {0} using {1}".format(args.bids_dir, args.group_file))
cgr.run(args.group_file)
sys.exit(0)
# otherwise we move on to conforming the data configuration
if not args.data_config_file:
from bids_utils import collect_bids_files_configs, bids_gen_cpac_sublist
(file_paths, config) = collect_bids_files_configs(args.bids_dir, args.aws_input_creds)
if args.participant_label:
pt_file_paths = []
for pt in args.participant_label: