def fdg_pet_paths_to_bids(images, bids_dir, dcm2niix="dcm2niix", dcm2nii="dcm2nii", mod_to_update=False):
"""
Args:
images:
bids_dir:
dcm2niix:
dcm2nii:
mod_to_update:
Returns:
"""
from clinica.iotools.converters.adni_to_bids import adni_utils
import os
from os import path
import glob
from clinica.utils.stream import cprint
count = 0
total = images.shape[0]
for row in images.iterrows():
image = row[1]
subject = image.Subject_ID
count += 1
if image.Path == '':
cprint('No path specified for ' + image.Subject_ID + ' in session ' + image.VISCODE)
continue
cprint('Processing subject ' + str(subject) + ' - session ' + image.VISCODE + ', ' + str(count) + ' / ' + str(total))
session = adni_utils.viscode_to_session(image.VISCODE)
image_path = image.Path
# ADDED lines
# ------------------
image_id = image.Image_ID
# If the original image is a DICOM, check if contains two DICOM inside the same folder
if image.Is_Dicom:
image_path = adni_utils.check_two_dcm_folder(image_path, bids_dir, image_id)
# ------------------
bids_subj = subject.replace('_', '')
output_path = path.join(bids_dir, 'sub-ADNI' + bids_subj + '/ses-' + session + '/pet')
output_filename = 'sub-ADNI' + bids_subj + '_ses-' + session + '_task-rest_acq-fdg_pet'
# ADDED lines
# ------------------
# If updated mode is selected, check if an old FDG image is existing and remove it
existing_fdg = glob.glob(path.join(output_path, output_filename + '*'))
if mod_to_update and len(existing_fdg) > 0:
cprint('Removing the old FDG image...')
for fdg in existing_fdg:
os.remove(fdg)
# ------------------
try:
os.makedirs(output_path)
except OSError:
if not path.isdir(output_path):
raise
if not image.Is_Dicom:
adni_utils.center_nifti_origin(image_path, path.join(output_path, output_filename + '.nii.gz'))
else:
command = dcm2niix + ' -b n -z n -o ' + output_path + ' -f ' + output_filename + ' ' + image_path
os.system(command)
nifti_file = path.join(output_path, output_filename + '.nii')
output_image = nifti_file + '.gz'
# Check if conversion worked (output file exists?)
if not path.isfile(nifti_file):
command = dcm2nii + ' -a n -d n -e n -i y -g n -p n -m n -r n -x n -o ' + output_path + ' ' + image_path
os.system(command)
nifti_file = path.join(output_path, subject.replace('_', '') + '.nii')
output_image = path.join(output_path, output_filename + '.nii.gz')
if not path.isfile(nifti_file):
cprint('DICOM to NIFTI conversion error for ' + image_path)
continue
adni_utils.center_nifti_origin(nifti_file, output_image)
os.remove(nifti_file)
adni_utils.remove_tmp_dmc_folder(bids_dir)
def create_file(image, modality, total, bids_dir, mod_to_update):
import subprocess
from colorama import Fore
from clinica.utils.stream import cprint
from clinica.iotools.converters.adni_to_bids import adni_utils
from numpy import nan
import os
from os import path
from glob import glob
modality_specific = {'t1': {'output_path': 'anat',
'output_filename': '_T1w'},
'av45': {'output_path': 'pet',
'output_filename': '_task-rest_acq-av45_pet'},
'fdg': {'output_path': 'pet',
'output_filename': '_task-rest_acq-fdg_pet'}
}
global counter
with counter.get_lock():
counter.value += 1
subject = image.Subject_ID
if image.Path == '':
cprint(Fore.RED + '[' + modality.upper() + '] No path specified for '
+ image.Subject_ID + ' in session '
+ image.VISCODE + ' ' + str(counter.value)
+ ' / ' + str(total) + Fore.RESET)
return nan
cprint('[' + modality.upper() + '] Processing subject ' + str(subject)
+ ' - session ' + image.VISCODE + ', ' + str(counter.value)
+ ' / ' + str(total))
session = adni_utils.viscode_to_session(image.VISCODE)
image_path = image.Path
image_id = image.Image_ID
# If the original image is a DICOM, check if contains two DICOM
# inside the same folder
if image.Is_Dicom:
image_path = adni_utils.check_two_dcm_folder(image_path,
bids_dir,
image_id)
bids_subj = subject.replace('_', '')
output_path = path.join(bids_dir, 'sub-ADNI' + bids_subj, 'ses-'
+ session, modality_specific[modality]['output_path'])
output_filename = 'sub-ADNI' + bids_subj + '_ses-' + session + modality_specific[modality]['output_filename']
# If updated mode is selected, check if an old image is existing and remove it
existing_im = glob(path.join(output_path, output_filename + '*'))
if mod_to_update and len(existing_im) > 0:
print('Removing the old image...')
for im in existing_im:
os.remove(im)
try:
os.makedirs(output_path)
except OSError:
# Folder already created with previous instance
pass
if image.Is_Dicom:
command = 'dcm2niix -b n -z n -o ' + output_path + ' -f ' + output_filename + ' ' + image_path
subprocess.run(command,
shell=True,
stderr=subprocess.DEVNULL,
stdout=subprocess.DEVNULL)
nifti_file = path.join(output_path, output_filename + '.nii')
output_image = nifti_file + '.gz'
# Check if conversion worked (output file exists?)
if not path.isfile(nifti_file):
cprint('\tConversion with dcm2niix failed, trying with dcm2nii')
command = 'dcm2nii -a n -d n -e n -i y -g n -p n -m n -r n -x n -o ' + output_path + ' ' + image_path
subprocess.run(command,
shell=True,
stdout=subprocess.DEVNULL,
stderr=subprocess.DEVNULL)
nifti_file = path.join(output_path,
subject.replace('_', '') + '.nii')
output_image = path.join(output_path,
output_filename + '.nii.gz')
if not path.isfile(nifti_file):
cprint('DICOM to NIFTI conversion error for ' + image_path)
return nan
adni_utils.center_nifti_origin(nifti_file, output_image)
os.remove(nifti_file)
else:
output_image = path.join(output_path, output_filename + '.nii.gz')
adni_utils.center_nifti_origin(image_path, output_image)
# Check if there is still the folder tmp_dcm_folder and remove it
adni_utils.remove_tmp_dmc_folder(bids_dir, image_id)
return output_image
def av45_pet_paths_to_bids(images, bids_dir, dcm2niix="dcm2niix", dcm2nii="dcm2nii", mod_to_update=False):
"""
Read the paths generated by the method compute_av45_pet and convert the original images to the BIDS standard
Args:
images: the dataframe returned by the method compute_av45_pet
bids_dir: path to the BIDS directory
dcm2niix: path to the dcm2niix tool (not useful anymore)
dcm2nii: path to the dcm2nii tool (not useful anymore
"""
import os
import glob
from numpy import nan
from clinica.iotools.converters.adni_to_bids import adni_utils
from clinica.utils.stream import cprint
count = 0
total = images.shape[0]
for row in images.iterrows():
image = row[1]
subject = image.Subject_ID
count += 1
if image.Path is nan:
cprint('No path specified for ' + image.Subject_ID + ' in session ' + image.VISCODE)
continue
cprint('Processing subject ' + str(subject) + ' - session ' + image.VISCODE + ', ' + str(count) + ' / ' + str(total))
session = adni_utils.viscode_to_session(image.VISCODE)
image_path = image.Path
# ADDED lines
# ------------------
image_id = image.Image_ID
# If the original image is a DICOM, check if contains two DICOM inside the same folder
if image.Is_Dicom:
image_path = adni_utils.check_two_dcm_folder(image_path, bids_dir, image_id)
# ------------------
bids_subj = subject.replace('_', '')
output_path = os.path.join(bids_dir, 'sub-ADNI' + bids_subj +'/ses-' + session + '/pet')
output_filename = 'sub-ADNI' + bids_subj + '_ses-' + session + '_task-rest_acq-av45_pet'
# ADDED lines
# ------------------
# If updated mode is selected, check if an old AV45 image is existing and remove it
existing_av45 = glob.glob(os.path.join(output_path, output_filename + '*'))
if mod_to_update and len(existing_av45) > 0:
cprint('Removing the old AV45 image...')
for av45 in existing_av45:
os.remove(av45)
# ------------------
try:
os.makedirs(output_path)
except OSError:
if not os.path.isdir(output_path):
raise
if not image.Is_Dicom:
adni_utils.center_nifti_origin(image_path, os.path.join(output_path, output_filename + '.nii.gz'))
else:
command = dcm2niix + ' -b n -z n -o ' + output_path + ' -f ' + output_filename + ' ' + image_path
os.system(command)
nifti_file = os.path.join(output_path, output_filename + '.nii')
output_image = nifti_file + '.gz'
# Check if conversion worked (output file exists?)
if not os.path.isfile(nifti_file):
cprint('Conversion with dcm2niix failed, trying with dcm2nii')
command = dcm2nii + ' -a n -d n -e n -i y -g n -p n -m n -r n -x n -o ' + output_path + ' ' + image_path
os.system(command)
nifti_file = os.path.join(output_path, subject.replace('_', '') + '.nii')
output_image = os.path.join(output_path, output_filename + '.nii.gz')
if not os.path.isfile(nifti_file):
cprint('DICOM to NIFTI conversion error for ' + image_path)
continue
adni_utils.center_nifti_origin(nifti_file, output_image)
os.remove(nifti_file)
adni_utils.remove_tmp_dmc_folder(bids_dir)
def t1_paths_to_bids(images,
bids_dir,
dcm2niix="dcm2niix",
dcm2nii="dcm2nii",
mod_to_update=False):
import os
from os import path
from numpy import nan
from clinica.iotools.converters.adni_to_bids import adni_utils
from glob import glob
from clinica.utils.stream import cprint
count = 0
total = images.shape[0]
for row in images.iterrows():
image = row[1]
subject = image.Subject_ID
count += 1
if image.Path is nan:
cprint('No path specified for ' + image.Subject_ID +
' in session ' + image.VISCODE)
continue
cprint('Processing subject ' + str(subject) + ' - session ' +
image.VISCODE + ', ' + str(count) + ' / ' + str(total))
session = adni_utils.viscode_to_session(image.VISCODE)
image_path = image.Path
# ADDED lines
# ------------------
image_id = image.Image_ID
# If the original image is a DICOM, check if contains two DICOM inside the same folder
if image.Is_Dicom:
image_path = adni_utils.check_two_dcm_folder(
image_path, bids_dir, image_id)
# ------------------
bids_subj = subject.replace('_', '')
output_path = path.join(bids_dir, 'sub-ADNI' + bids_subj,
'ses-' + session, 'anat')
output_filename = 'sub-ADNI' + bids_subj + '_ses-' + session + '_T1w'
# ADDED lines
# ------------------
# If updated mode is selected, check if an old T1 image is existing and remove it
existing_t1 = glob(path.join(output_path, output_filename + '*'))
if mod_to_update and len(existing_t1) > 0:
print 'Removing the old T1 image...'
for t1 in existing_t1:
os.remove(t1)
# ------------------
try:
os.makedirs(output_path)
except OSError:
if not path.isdir(output_path):
raise
if image.Is_Dicom:
command = dcm2niix + ' -b n -z n -o ' + output_path + ' -f ' + output_filename + ' ' + image_path
os.system(command)
nifti_file = path.join(output_path, output_filename + '.nii')
output_image = nifti_file + '.gz'
# Check if conversion worked (output file exists?)
if not path.isfile(nifti_file):
cprint('Conversion with dcm2niix failed, trying with dcm2nii')
command = dcm2nii + ' -a n -d n -e n -i y -g n -p n -m n -r n -x n -o ' + output_path + ' ' + image_path
os.system(command)
nifti_file = path.join(output_path,
subject.replace('_', '') + '.nii')
output_image = path.join(output_path,
output_filename + '.nii.gz')
if not path.isfile(nifti_file):
# TODO - LOG THIS
cprint('DICOM to NIFTI conversion error for ' + image_path)
continue
adni_utils.center_nifti_origin(nifti_file, output_image)
os.remove(nifti_file)
else:
output_image = path.join(output_path, output_filename + '.nii.gz')
adni_utils.center_nifti_origin(image_path, output_image)
# Check if there is still the folder tmp_dcm_folder and remove it
adni_utils.remove_tmp_dmc_folder(bids_dir)