def main():
global DRYRUN, PARALLEL, LOG_DIR
arguments = docopt(__doc__)
study = arguments['<study>']
use_server = arguments['--log-to-server']
scanid = arguments['--subject']
debug = arguments['--debug']
resubmit = arguments['--resubmit']
PARALLEL = arguments['--parallel']
DRYRUN = arguments['--dry-run']
# If you add an option/argument that needs to be propagated to subject jobs
# after a batch submit make sure to add it to create_command()
# If it needs to be propagated to recon-all add it to
# get_freesurfer_arguments()
config = load_config(study)
if use_server:
add_server_handler(config)
if debug:
logger.setLevel(logging.DEBUG)
logger.info('Starting')
check_input_paths(config)
#Get subject QC status, whether they've been inducted into blacklist or not if empty value to subject key
qc_subjects = utils.get_subject_metadata(config)
fs_path = config.get_path('freesurfer')
LOG_DIR = make_error_log_dir(fs_path)
if scanid:
# single subject mode
blacklisted_series = get_blacklist(qc_subjects, scanid)
subject = dm_scan.Scan(scanid, config)
if subject.is_phantom:
sys.exit(
'Subject {} is a phantom, cannot be analyzed'.format(scanid))
run_freesurfer(subject, blacklisted_series, config, resubmit)
return
# batch mode
update_aggregate_stats(config)
destination = os.path.join(fs_path, 'freesurfer_aggregate_log.csv')
update_aggregate_log(config, qc_subjects, destination)
fs_subjects = get_new_subjects(config, qc_subjects)
logger.info("Submitting {} new subjects".format(len(fs_subjects)))
if resubmit:
# Filter out subjects that were just submitted to reduce search space
remaining_subjects = filter(lambda x: x not in fs_subjects,
qc_subjects)
halted_subjects = get_halted_subjects(fs_path, remaining_subjects)
logger.info("Resubmitting {} subjects".format(len(halted_subjects)))
fs_subjects.extend(halted_subjects)
submit_proc_freesurfer(fs_path, fs_subjects, arguments, config)
def process_subject(subject, cfg, be, bids_dir, rewrite):
"""
Convert subject in DATMAN folder to BIDS-style
"""
ident = scanid.parse(subject)
subscan = scan.Scan(subject, cfg)
bids_sub = ident.get_bids_name()
bids_ses = ident.timepoint
exp_path = make_bids_template(bids_dir, "sub-" + bids_sub,
"ses-" + bids_ses)
dm_to_bids = []
if dashboard.dash_found:
db_subject = dashboard.get_subject(subject)
db_subject.add_bids(bids_sub, bids_ses)
# Construct initial BIDS transformation info
scan_list = list(sort_by_series(subscan.niftis))
for i, series in enumerate(scan_list):
# Construct bids name
logger.info("Processing {}".format(series))
bids_dict = get_tag_bids_spec(cfg, series.tag, series.site)
if not bids_dict:
continue
bids_dict.update({"sub": bids_sub, "ses": bids_ses})
# Deal with reference scans
if bids_dict.get('is_ref', False):
target_dict = get_tag_bids_spec(cfg, scan_list[i + 1].tag,
series.site)
bids_dict.update({'task': target_dict['task']})
bids_prefix = be.construct_bids_name(bids_dict)
class_path = os.path.join(exp_path, bids_dict["class"])
# Make dm2bids transformation file, update source if applicable
bidsfiles = BIDSFile(bids_sub, bids_ses, series, class_path,
bids_prefix, bids_dict).update_source(cfg, be)
if bidsfiles is None:
logger.error("Cannot find derivative of {}".format(series))
logger.warning("Skipping!")
continue
if isinstance(bidsfiles, list):
dm_to_bids.extend(bidsfiles)
else:
dm_to_bids.append(bidsfiles)
# Apply prioritization calls
dm_to_bids = prioritize_scans(dm_to_bids)
# Prepare fieldmap information (requires knowledge about all scans)
dm_to_bids = prepare_fieldmaps(dm_to_bids)
# Transfer files over
for k in dm_to_bids:
if os.path.exists(k.dest_nii) and not rewrite:
logger.info("Output file {} already exists!".format(k.dest_nii))
continue
k.transfer_files()
if dashboard.dash_found:
db_series = dashboard.get_scan(k.series.path)
db_series.add_bids(str(k))
return