def convert_clinical_data(self, clinical_data_dir, bids_dir):
"""
Convert the clinical data defined inside the clinical_specifications.xlx into BIDS
Args:
clinical_data_dir: path to the folder with the original clinical data
bids_dir: path to the bids directory
"""
import clinica.iotools.bids_utils as bids
from os import path
import os
import numpy as np
print('Converting clinical data...')
bids_ids = bids.get_bids_subjs_list(bids_dir)
iotools_folder = os.path.dirname(
os.path.dirname(os.path.dirname(__file__)))
clinic_specs_path = path.join(iotools_folder, 'data',
'clinical_specifications.xlsx')
# --Create participants.tsv--
participants_df = bids.create_participants_df('OASIS',
clinic_specs_path,
clinical_data_dir,
bids_ids)
# Replace the values of the diagnosis_bl column
participants_df['diagnosis_bl'].replace([0.0, np.nan],
'CN',
inplace=True)
participants_df['diagnosis_bl'].replace([0.5, 1.0, 1.5, 2.0],
'AD',
inplace=True)
# Following line has no sense
# participants_df['diagnosis_bl'].replace(participants_df['diagnosis_bl']>0.0, 'AD', inplace=True)
participants_df.to_csv(path.join(bids_dir, 'participants.tsv'),
sep='\t',
index=False,
encoding='utf-8')
# --Create sessions files--
sessions_dict = bids.create_sessions_dict(clinical_data_dir, 'OASIS',
clinic_specs_path, bids_ids,
'ID')
for y in bids_ids:
if sessions_dict[y]['M00']['diagnosis'] > 0:
sessions_dict[y]['M00']['diagnosis'] = 'AD'
else:
sessions_dict[y]['M00']['diagnosis'] = 'CN'
bids.write_sessions_tsv(bids_dir, sessions_dict)
# --Create scans files--
# Note: We have no scans information for OASIS
scans_dict = bids.create_scans_dict(clinical_data_dir, 'OASIS',
clinic_specs_path, bids_ids, 'ID')
bids.write_scans_tsv(bids_dir, bids_ids, scans_dict)
def convert_clinical_data(self, clinical_data_dir, bids_dir):
"""Convert the clinical data defined inside the clinical_specifications.xlx into BIDS.
Args:
clinical_data_dir: path to the folder with the original clinical data
bids_dir: path to the BIDS directory
"""
import os
from os import path
import numpy as np
import clinica.iotools.bids_utils as bids
from clinica.utils.stream import cprint
cprint("Converting clinical data...")
bids_ids = bids.get_bids_subjs_list(bids_dir)
iotools_folder = os.path.dirname(
os.path.dirname(os.path.dirname(__file__)))
clinic_specs_path = path.join(iotools_folder, "data",
"clinical_specifications")
# -- Creation of modality agnostic files --
bids.write_modality_agnostic_files("OASIS-1", bids_dir)
# --Create participants.tsv--
participants_df = bids.create_participants_df("OASIS",
clinic_specs_path,
clinical_data_dir,
bids_ids)
# Replace the values of the diagnosis_bl column
participants_df["diagnosis_bl"].replace([0.0, np.nan],
"CN",
inplace=True)
participants_df["diagnosis_bl"].replace([0.5, 1.0, 1.5, 2.0],
"AD",
inplace=True)
# Following line has no sense
# participants_df['diagnosis_bl'].replace(participants_df['diagnosis_bl']>0.0, 'AD', inplace=True)
participants_df = participants_df.fillna("n/a")
participants_df.to_csv(
path.join(bids_dir, "participants.tsv"),
sep="\t",
index=False,
encoding="utf-8",
)
# --Create sessions files--
sessions_dict = bids.create_sessions_dict_OASIS(
clinical_data_dir, bids_dir, "OASIS", clinic_specs_path, bids_ids,
"ID")
for y in bids_ids:
if sessions_dict[y]["M00"]["diagnosis"] > 0:
sessions_dict[y]["M00"]["diagnosis"] = "AD"
else:
sessions_dict[y]["M00"]["diagnosis"] = "CN"
bids.write_sessions_tsv(bids_dir, sessions_dict)
# --Create scans files--
# Note: We have no scans information for OASIS
scans_dict = bids.create_scans_dict(
clinical_data_dir,
"OASIS",
clinic_specs_path,
bids_ids,
"ID",
"",
sessions_dict,
)
bids.write_scans_tsv(bids_dir, bids_ids, scans_dict)