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, out_path):
"""
Convert the clinical data of ADNI specified into the file clinical_specifications_adni.xlsx
Args:
clinical_data_dir: path to the clinical data directory
out_path: path to the BIDS directory
"""
from os import path
import os
import pandas as pd
import clinica.iotools.bids_utils as bids
from clinica.utils.stream import cprint
import clinica.iotools.converters.adni_to_bids.adni_utils as adni_utils
clinic_specs_path = path.join(os.path.dirname(os.path.dirname(os.path.dirname(__file__))), 'data',
'clinical_specifications_adni.xlsx')
try:
os.path.exists(out_path)
except IOError:
print('BIDS folder not found.')
raise
bids_ids = bids.get_bids_subjs_list(out_path)
bids_subjs_paths = bids.get_bids_subjs_paths(out_path)
if not bids_ids:
adni_merge_path = path.join(clinical_data_dir, 'ADNIMERGE.csv')
adni_merge = pd.io.parsers.read_csv(adni_merge_path, sep=',')
bids_ids = ['sub-ADNI' + subj.replace('_', '') for subj in list(adni_merge.PTID.unique())]
bids_subjs_paths = [path.join(out_path, subj) for subj in bids_ids]
# -- Creation of participant.tsv --
cprint("Creating participants.tsv...")
participants_df = bids.create_participants_df('ADNI', clinic_specs_path, clinical_data_dir, bids_ids)
# Replace the original values with the standard defined by the AramisTeam
participants_df['sex'] = participants_df['sex'].replace('Male', 'M')
participants_df['sex'] = participants_df['sex'].replace('Female', 'F')
participants_df.to_csv(path.join(out_path, 'participants.tsv'), sep='\t', index=False, encoding='utf-8')
# -- Creation of sessions.tsv --
cprint("Creating sessions files...")
adni_utils.create_adni_sessions_dict(bids_ids, clinic_specs_path, clinical_data_dir, bids_subjs_paths)
# -- Creation of scans files --
cprint('Creating scans files...')
adni_utils.create_adni_scans_files(clinic_specs_path, bids_subjs_paths, bids_ids)
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)
def convert_clinical_data(
self,
clinical_data_dir: str,
out_path: str,
clinical_data_only: bool = False,
subjects_list_path: Optional[str] = None,
):
"""Convert the clinical data of ADNI specified into the file clinical_specifications_adni.xlsx.
Args:
clinical_data_dir: path to the clinical data directory
out_path: path to the BIDS directory
"""
import os
from os import path
import clinica.iotools.bids_utils as bids
import clinica.iotools.converters.adni_to_bids.adni_utils as adni_utils
from clinica.utils.stream import cprint
clinic_specs_path = path.join(
os.path.dirname(os.path.dirname(os.path.dirname(__file__))),
"data",
"clinical_specifications_adni",
)
try:
os.path.exists(out_path)
except IOError:
print("BIDS folder not found.")
raise
conversion_path = path.join(out_path, "conversion_info")
if clinical_data_only:
bids_ids, bids_subjs_paths = get_bids_subjs_info(
clinical_data_dir=clinical_data_dir,
out_path=out_path,
subjects_list_path=subjects_list_path,
)
else:
bids_ids = bids.get_bids_subjs_list(out_path)
bids_subjs_paths = bids.get_bids_subjs_paths(out_path)
# -- Creation of modality agnostic files --
cprint("Creating modality agnostic files...")
bids.write_modality_agnostic_files("ADNI", out_path)
# -- Creation of participant.tsv --
cprint("Creating participants.tsv...")
participants_df = bids.create_participants_df(
"ADNI", clinic_specs_path, clinical_data_dir, bids_ids
)
# Replace the original values with the standard defined by the AramisTeam
participants_df["sex"] = participants_df["sex"].replace("Male", "M")
participants_df["sex"] = participants_df["sex"].replace("Female", "F")
# Correction of diagnosis_sc for ADNI3 participants
participants_df = adni_utils.correct_diagnosis_sc_adni3(
clinical_data_dir, participants_df
)
participants_df.to_csv(
path.join(out_path, "participants.tsv"),
sep="\t",
index=False,
encoding="utf-8",
)
# -- Creation of sessions.tsv --
cprint("Creating sessions files...")
adni_utils.create_adni_sessions_dict(
bids_ids, clinic_specs_path, clinical_data_dir, bids_subjs_paths
)
# -- Creation of scans files --
if os.path.exists(conversion_path):
cprint("Creating scans files...")
adni_utils.create_adni_scans_files(conversion_path, bids_subjs_paths)
def convert_clinical_data(self, clinical_data_dir, out_path):
"""Convert the clinical data of ADNI specified into the file clinical_specifications_adni.xlsx.
Args:
clinical_data_dir: path to the clinical data directory
out_path: path to the BIDS directory
"""
import os
from os import path
import pandas as pd
import clinica.iotools.bids_utils as bids
import clinica.iotools.converters.adni_to_bids.adni_utils as adni_utils
from clinica.utils.stream import cprint
clinic_specs_path = path.join(
os.path.dirname(os.path.dirname(os.path.dirname(__file__))),
"data",
"clinical_specifications_adni.xlsx",
)
try:
os.path.exists(out_path)
except IOError:
print("BIDS folder not found.")
raise
bids_ids = bids.get_bids_subjs_list(out_path)
bids_subjs_paths = bids.get_bids_subjs_paths(out_path)
conversion_path = path.join(out_path, "conversion_info")
if not bids_ids:
adni_merge_path = path.join(clinical_data_dir, "ADNIMERGE.csv")
adni_merge = pd.io.parsers.read_csv(adni_merge_path, sep=",")
bids_ids = [
"sub-ADNI" + subj.replace("_", "")
for subj in list(adni_merge.PTID.unique())
]
bids_subjs_paths = [path.join(out_path, subj) for subj in bids_ids]
# -- Creation of modality agnostic files --
cprint("Creating modality agnostic files...")
bids.write_modality_agnostic_files("ADNI", out_path)
# -- Creation of participant.tsv --
cprint("Creating participants.tsv...")
participants_df = bids.create_participants_df("ADNI",
clinic_specs_path,
clinical_data_dir,
bids_ids)
# Replace the original values with the standard defined by the AramisTeam
participants_df["sex"] = participants_df["sex"].replace("Male", "M")
participants_df["sex"] = participants_df["sex"].replace("Female", "F")
# Correction of diagnosis_sc for ADNI3 participants
participants_df = adni_utils.correct_diagnosis_sc_adni3(
clinical_data_dir, participants_df)
participants_df.to_csv(
path.join(out_path, "participants.tsv"),
sep="\t",
index=False,
encoding="utf-8",
)
# -- Creation of sessions.tsv --
cprint("Creating sessions files...")
adni_utils.create_adni_sessions_dict(bids_ids, clinic_specs_path,
clinical_data_dir,
bids_subjs_paths)
# -- Creation of scans files --
cprint("Creating scans files...")
adni_utils.create_adni_scans_files(
conversion_path,
bids_subjs_paths,
)
