diff --git a/processing/pipeline.py b/processing/pipeline.py index e3369421..2ec84ebb 100755 --- a/processing/pipeline.py +++ b/processing/pipeline.py @@ -6,7 +6,7 @@ """ - +import argparse import os import json import glob @@ -19,6 +19,12 @@ from ibc_public.utils_data import get_subject_session from script_resample_normalized_data import resample_func_and_anat +parser = argparse.ArgumentParser(description='Parameters for the logfiles') +parser.add_argument('-s', '--session', metavar='SessionLabel', type=str, + help="Session label, should be compliand with the " + "ini files names.") +args = parser.parse_args() + def clean_anatomical_images(main_dir): """ Removed NaNs from SPM12-supplied images """ @@ -211,7 +217,7 @@ def run_subject_preproc(jobfile, subject, session=None): cache_dir = '/neurospin/tmp/ibc' prepare_derivatives(main_dir) do_topup = True - protocol = 'lpp1' + protocol = args.session subject_session = sorted(get_subject_session([protocol])) if do_topup: acq = None