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added code to specify the session from command line #5

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10 changes: 8 additions & 2 deletions processing/pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@

"""


import argparse
import os
import json
import glob
Expand All @@ -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 """
Expand Down Expand Up @@ -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
Expand Down