def update_sub_scans_file(output_dir,
bids_sub,
bids_ses,
bids_modality,
out_filename,
par_file,
public_output=True):
"""
one file per subject with
-ses id
-filename
-if not public: date of acquisition
"""
general_info, image_defs = read_par(par_file)
acq_time = parse_acq_time(general_info)
scans_file = os.path.join(output_dir, bids_sub, bids_sub + "_scans.tsv")
if os.path.exists(scans_file):
scans = read_tsv(scans_file)
else:
scans = pd.DataFrame([])
scans = scans.append(
{
"participant_id": bids_sub,
"session_id": bids_ses,
"filename":
bids_ses + "/" + bids_modality + "/" + out_filename + ".nii.gz",
"acq_time": acq_time
},
ignore_index=True)
if not public_output:
scans = scans[["participant_id", "session_id", "filename", "acq_time"]]
else:
scans = scans[["participant_id", "session_id", "filename"]]
to_tsv(scans, scans_file)
def reduce_sub_files(bids_dir, output_file, sub_file):
df = pd.DataFrame([])
layout = BIDSLayout(bids_dir)
files = layout.get(extensions=sub_file)
for file in [f.filename for f in files]:
print(file)
df_ = read_tsv(file)
df = pd.concat((df, df_))
to_tsv(df, os.path.join(bids_dir, output_file))
def get_acq_dates(info_out_dir):
df = pd.DataFrame()
info_out_dir = Path(info_out_dir)
acq_dir = info_out_dir / "acq_time_PRIVATE"
acq_files = list(acq_dir.glob("sub-*"))
for file in acq_files:
df_ = read_tsv(file)
df_["acq_date"] = pd.to_datetime(df_.acq_time).dt.date
subject, session, *_ = file.name.split("_")
df = df.append(
pd.DataFrame(
{
"participant_id": subject,
"session_id": session,
"acq_date": df_.iloc[0].acq_date
},
index=[0]))
df = df.sort_values(by=["participant_id", "session_id"])
df = df.reset_index(drop=True)
return df
type=int,
default=120,
help=
"Checks if session duration is smaller x minutes (default: 120). If set to 0, "
"don't check session duration")
args = parser.parse_args()
do_deface = True if args.public_output else False
info_list_v2 = get_info_list_v2(do_deface)
###
if args.analysis_level == "participant":
if args.participant_label:
old_sub_id_list = [s.strip() for s in args.participant_label]
else:
old_sub_id_list = read_tsv(args.subject_list_file,
no_header=False).iloc[:, 0].to_list()
elif args.analysis_level == "group":
# participants automatically derived
old_sub_id_list = []
else:
raise RuntimeError(f"Analysis level unknown {args.analysis_level}")
run_conversion(args.raw_dir, args.output_base_dir, args.analysis_level,
args.info_out_dir, old_sub_id_list, args.session_label,
args.public_output, args.use_new_ids, args.ds_version,
info_list_v2, dataset_description_v2, args.new_id_lut_file,
args.bvecs_from_scanner_file, args.tp6_raw_lut,
args.dry_run, args.demo_file, args.session_duration_min)