def main():
# Parse command line arguments
parser = argparse.ArgumentParser(description='Convert DICOM files to BIDS-compliant Nifty structure')
parser.add_argument('-d', '--dataset', default='.', help='BIDS dataset directory containing sourcedata subdirectory')
parser.add_argument('--no-sessions', action='store_true', default=False,
help='Do not use session sub-directories')
parser.add_argument('--overwrite', action='store_true', default=False,
help='Overwrite existing files')
parser.add_argument('--skip_if_pruning', action='store_true', default=False,
help='Skip pruning of nonexistent IntendedFor items in json files')
parser.add_argument('--clean_conv_dir', action='store_true', default=False,
help='Clean up conversion directory')
# Parse command line arguments
args = parser.parse_args()
dataset_dir = os.path.realpath(args.dataset)
no_sessions = args.no_sessions
overwrite = args.overwrite
print('\n------------------------------------------------------------')
print('BIDSKIT %s' % __version__)
print('------------------------------------------------------------')
# Check for minimum dcm2niix version (mostly for multirecon suffix handling)
btr.check_dcm2niix_version('v1.0.20181125')
# Create a BIDS directory tree object to handle file locations
# Creates directory
btree = BIDSTree(dataset_dir, overwrite)
print('\nSource data directory : %s' % btree.sourcedata_dir)
print('Working Directory : %s' % btree.work_dir)
print('Use Session Directories : %s' % ('No' if no_sessions else 'Yes'))
print('Overwrite Existing Files : %s' % ('Yes' if overwrite else 'No'))
# Load protocol translation and exclusion info from derivatives/conversion directory
# If no translator is present, prot_dict is an empty dictionary
# and a template will be created in the derivatives/conversion directory.
# This template should be completed by the user and the conversion rerun.
translator = btree.read_translator()
if translator and os.path.isdir(btree.work_dir):
print('\n------------------------------------------------------------')
print('Pass 2 : Populating BIDS directory')
print('------------------------------------------------------------')
first_pass = False
else:
print('\n------------------------------------------------------------')
print('Pass 1 : DICOM to Nifti conversion and translator creation')
print('------------------------------------------------------------')
first_pass = True
subject_dir_list = []
# Loop over subject directories in DICOM root
for dcm_sub_dir in glob(btree.sourcedata_dir + '/*/'):
sid = os.path.basename(dcm_sub_dir.strip('/'))
# Check that subject ID is legal
btr.check_subject_session(sid)
subject_dir_list.append(dataset_dir + "/sub-" + sid)
print('\n------------------------------------------------------------')
print('Processing subject ' + sid)
print('------------------------------------------------------------')
# Handle subject vs subject/session directory lists
if no_sessions:
dcm_dir_list = [dcm_sub_dir]
else:
dcm_dir_list = glob(dcm_sub_dir + '/*/')
# Loop over source data session directories in subject directory
for dcm_dir in dcm_dir_list:
# BIDS subject, session and conversion directories
sub_prefix = 'sub-' + sid
if no_sessions:
# If session subdirs aren't being used, *_ses_dir = *sub_dir
# Use an empty ses_prefix with os.path.join to achieve this
ses = ''
ses_prefix = ''
else:
ses = os.path.basename(dcm_dir.strip('/'))
# Check that session ID is legal
btr.check_subject_session(ses)
ses_prefix = 'ses-' + ses
print(' Processing session ' + ses)
# Working conversion directories
work_subj_dir = os.path.join(btree.work_dir, sub_prefix)
work_conv_dir = os.path.join(work_subj_dir, ses_prefix)
# BIDS source directory directories
bids_subj_dir = os.path.join(dataset_dir, sub_prefix)
bids_ses_dir = os.path.join(bids_subj_dir, ses_prefix)
print(' Working subject directory : %s' % work_subj_dir)
if not no_sessions:
print(' Working session directory : %s' % work_conv_dir)
print(' BIDS subject directory : %s' % bids_subj_dir)
if not no_sessions:
print(' BIDS session directory : %s' % bids_ses_dir)
# Safely create working directory for current subject
# Flag for conversion if no working directory existed
if not os.path.isdir(work_conv_dir):
os.makedirs(work_conv_dir)
needs_converting = True
else:
needs_converting = False
if first_pass or needs_converting:
# Run dcm2niix conversion into working conversion directory
print(' Converting all DICOM images in %s' % dcm_dir)
devnull = open(os.devnull, 'w')
subprocess.call(['dcm2niix', '-b', 'y', '-z', 'y', '-f', '%n--%d--%q--%s',
'-o', work_conv_dir, dcm_dir],
stdout=devnull, stderr=subprocess.STDOUT)
if not first_pass:
# Get subject age and sex from representative DICOM header
dcm_info = bio.dcm_info(dcm_dir)
# Add line to participants TSV file
btr.add_participant_record(dataset_dir, sid, dcm_info['Age'], dcm_info['Sex'])
# Organize dcm2niix output into BIDS subject/session directories
organize_series(work_conv_dir, first_pass, translator, bids_ses_dir, sid, ses,
args.clean_conv_dir, overwrite)
if first_pass:
# Create a template protocol dictionary
btree.write_translator(translator)
if not args.skip_if_pruning:
print("\nSubject directories to prune: " + ", ".join(subject_dir_list))
for bids_subj_dir in subject_dir_list:
btr.prune_intendedfors(bids_subj_dir, True)
# Finally validate that all is well with the BIDS dataset
if not first_pass:
btree.validate()
# Clean exit
sys.exit(0)
def main():
# Parse command line arguments
parser = argparse.ArgumentParser(description='Convert DICOM files to BIDS-compliant Nifty structure')
parser.add_argument('-d', '--dataset', default='.', help='BIDS dataset directory containing sourcedata subdirectory')
parser.add_argument('--no-sessions', action='store_true', default=False,
help='Do not use session sub-directories')
parser.add_argument('--overwrite', action='store_true', default=False,
help='Overwrite existing files')
parser.add_argument('--skip_if_pruning', action='store_true', default=False,
help='Skip pruning of nonexistent IntendedFor items in json files')
parser.add_argument('--clean_conv_dir', action='store_true', default=False,
help='Clean up conversion directory')
# Parse command line arguments
args = parser.parse_args()
dataset_dir = os.path.realpath(args.dataset)
no_sessions = args.no_sessions
overwrite = args.overwrite
print('\n------------------------------------------------------------')
print('BIDSKIT %s' % __version__)
print('------------------------------------------------------------')
# Check for minimum dcm2niix version (mostly for multirecon suffix handling)
btr.check_dcm2niix_version('v1.0.20181125')
# Create a BIDS directory tree object to handle file locations
# Creates directory
btree = BIDSTree(dataset_dir, overwrite)
print('\nSource data directory : %s' % btree.sourcedata_dir)
print('Working Directory : %s' % btree.work_dir)
print('Use Session Directories : %s' % ('No' if no_sessions else 'Yes'))
print('Overwrite Existing Files : %s' % ('Yes' if overwrite else 'No'))
# Load protocol translation and exclusion info from derivatives/conversion directory
# If no translator is present, prot_dict is an empty dictionary
# and a template will be created in the derivatives/conversion directory.
# This template should be completed by the user and the conversion rerun.
translator = btree.read_translator()
if translator and os.path.isdir(btree.work_dir):
print('\n------------------------------------------------------------')
print('Pass 2 : Populating BIDS directory')
print('------------------------------------------------------------')
first_pass = False
else:
print('\n------------------------------------------------------------')
print('Pass 1 : DICOM to Nifti conversion and translator creation')
print('------------------------------------------------------------')
first_pass = True
subject_dir_list = []
# Loop over subject directories in DICOM root
for dcm_sub_dir in glob(btree.sourcedata_dir + '/*/'):
sid = os.path.basename(dcm_sub_dir.strip('/'))
# Check that subject ID is legal
btr.check_subject_session(sid)
subject_dir_list.append(dataset_dir + "/sub-" + sid)
print('\n------------------------------------------------------------')
print('Processing subject ' + sid)
print('------------------------------------------------------------')
# Handle subject vs subject/session directory lists
if no_sessions:
dcm_dir_list = [dcm_sub_dir]
else:
dcm_dir_list = glob(dcm_sub_dir + '/*/')
# Loop over source data session directories in subject directory
for dcm_dir in dcm_dir_list:
# BIDS subject, session and conversion directories
sub_prefix = 'sub-' + sid
if no_sessions:
# If session subdirs aren't being used, *_ses_dir = *sub_dir
# Use an empty ses_prefix with os.path.join to achieve this
ses = ''
ses_prefix = ''
else:
ses = os.path.basename(dcm_dir.strip('/'))
# Check that session ID is legal
btr.check_subject_session(ses)
ses_prefix = 'ses-' + ses
print(' Processing session ' + ses)
# Working conversion directories
work_subj_dir = os.path.join(btree.work_dir, sub_prefix)
work_conv_dir = os.path.join(work_subj_dir, ses_prefix)
# BIDS source directory directories
bids_subj_dir = os.path.join(dataset_dir, sub_prefix)
bids_ses_dir = os.path.join(bids_subj_dir, ses_prefix)
print(' Working subject directory : %s' % work_subj_dir)
if not no_sessions:
print(' Working session directory : %s' % work_conv_dir)
print(' BIDS subject directory : %s' % bids_subj_dir)
if not no_sessions:
print(' BIDS session directory : %s' % bids_ses_dir)
# Safely create working directory for current subject
# Flag for conversion if no working directory existed
if not os.path.isdir(work_conv_dir):
os.makedirs(work_conv_dir)
needs_converting = True
else:
needs_converting = False
if first_pass or needs_converting:
# Run dcm2niix conversion into working conversion directory
print(' Converting all DICOM images in %s' % dcm_dir)
devnull = open(os.devnull, 'w')
subprocess.call(['dcm2niix', '-b', 'y', '-z', 'y', '-f', '%n--%d--%q--%s',
'-o', work_conv_dir, dcm_dir],
stdout=devnull, stderr=subprocess.STDOUT)
if not first_pass:
# Get subject age and sex from representative DICOM header
dcm_info = bio.dcm_info(dcm_dir)
# Add line to participants TSV file
btr.add_participant_record(dataset_dir, sid, dcm_info['Age'], dcm_info['Sex'])
# Organize dcm2niix output into BIDS subject/session directories
organize_series(work_conv_dir, first_pass, translator, bids_ses_dir, sid, ses,
args.clean_conv_dir, overwrite)
if first_pass:
# Create a template protocol dictionary
btree.write_translator(translator)
if not args.skip_if_pruning:
print("\nSubject directories to prune: " + ", ".join(subject_dir_list))
for bids_subj_dir in subject_dir_list:
btr.prune_intendedfors(bids_subj_dir, True)
# Finally validate that all is well with the BIDS dataset
if not first_pass:
btree.validate()
# Clean exit
sys.exit(0)
def main():
# Parse command line arguments
parser = argparse.ArgumentParser(
description='Convert DICOM files to BIDS-compliant Nifty structure')
parser.add_argument(
'-d',
'--dataset',
default='.',
help='BIDS dataset directory containing sourcedata subdirectory')
parser.add_argument(
'-s',
'--subjects',
nargs='+',
default=[],
help=
'List of subject IDs to convert (eg --subjects alpha bravo charlie)')
parser.add_argument('--no-sessions',
action='store_true',
default=False,
help='Do not use session sub-directories')
parser.add_argument(
'--no-anon',
action='store_true',
default=False,
help='Do not anonymize BIDS output (eg for phantom data)')
parser.add_argument('--overwrite',
action='store_true',
default=False,
help='Overwrite existing files')
parser.add_argument(
'--skip-if-pruning',
action='store_true',
default=False,
help='Skip pruning of nonexistent IntendedFor items in json files')
parser.add_argument('--clean-conv-dir',
action='store_true',
default=False,
help='Clean up conversion directory')
parser.add_argument(
'--bind-fmaps',
action='store_true',
default=False,
help='Bind fieldmaps to fMRI series using IntendedFor field')
parser.add_argument('-V',
'--version',
action='store_true',
default=False,
help='Display bidskit version number and exit')
# Parse command line arguments
args = parser.parse_args()
dataset_dir = os.path.realpath(args.dataset)
subject_list = args.subjects
no_sessions = args.no_sessions
no_anon = args.no_anon
overwrite = args.overwrite
bind_fmaps = args.bind_fmaps
# Read version from setup.py
ver = pkg_resources.get_distribution('bidskit').version
if args.version:
print('BIDSKIT {}'.format(ver))
sys.exit(1)
print('')
print('------------------------------------------------------------')
print('BIDSKIT {}'.format(ver))
print('------------------------------------------------------------')
# Check for minimum dcm2niix version (mostly for multirecon suffix handling)
btr.check_dcm2niix_version('v1.0.20181125')
# Create a BIDS directory tree object to handle file locations
# Creates directory
btree = BIDSTree(dataset_dir, overwrite)
if len(subject_list) > 1:
subj_to_convert = ' '.join(subject_list)
else:
subj_to_convert = 'All'
print('')
print('Subjects to convert : {}'.format(subj_to_convert))
print('Source data directory : {}'.format(btree.sourcedata_dir))
print('Working Directory : {}'.format(btree.work_dir))
print('Use Session Directories : {}'.format(
'No' if no_sessions else 'Yes'))
print(
'Overwrite Existing Files : {}'.format('Yes' if overwrite else 'No'))
print('Anonymize BIDS Output : {}'.format('No' if no_anon else 'Yes'))
print('Bind fieldmaps : {}'.format(
'Yes' if bind_fmaps else 'No'))
# Load protocol translation and exclusion info from derivatives/conversion directory
# If no translator is present, prot_dict is an empty dictionary
# and a template will be created in the derivatives/conversion directory.
# This template should be completed by the user and the conversion rerun.
translator = btree.read_translator()
if translator and os.path.isdir(btree.work_dir):
print('')
print('------------------------------------------------------------')
print('Pass 2 : Populating BIDS directory')
print('------------------------------------------------------------')
first_pass = False
else:
print('')
print('------------------------------------------------------------')
print('Pass 1 : DICOM to Nifti conversion and translator creation')
print('------------------------------------------------------------')
first_pass = True
# Init list of output subject directories
out_subj_dir_list = []
# Init list of source subject directories from sourcedata contents if no subjects provided in command line
if len(subject_list) < 1:
print(' Creating subject list from sourcedata contents')
subject_list = []
for it in os.scandir(btree.sourcedata_dir):
if it.is_dir():
subject_list.append(it.name)
print(' Found {:d} subjects in sourcedata folder'.format(
len(subject_list)))
# Loop over subject list (either from sourcedata contents or command line)
for sid in subject_list:
print('')
print('------------------------------------------------------------')
print('Processing subject {}'.format(sid))
print('------------------------------------------------------------')
# Full path to subject directory in sourcedata/
src_subj_dir = os.path.realpath(os.path.join(btree.sourcedata_dir,
sid))
# BIDS subject ID with prefix
subj_prefix = 'sub-{:s}'.format(sid)
# Add full path to subject output directory to running list
out_subj_dir_list.append(os.path.join(dataset_dir, subj_prefix))
# Create list of DICOM directories to convert
# This will be either a session or series folder list depending on no-sessions command line flag
if no_sessions:
dcm_dir_list = [src_subj_dir]
else:
dcm_dir_list = glob(os.path.join(src_subj_dir, '*'))
# Loop over DICOM directories in subject directory
for dcm_dir in dcm_dir_list:
if no_sessions:
# If session subdirs aren't being used, *_ses_dir = *sub_dir
# Use an empty ses_prefix with os.path.join to achieve this
ses = ''
ses_prefix = ''
else:
ses = os.path.basename(os.path.normpath(dcm_dir))
ses_prefix = 'ses-{:s}'.format(ses)
print(' Processing session ' + ses)
# Working conversion directories
work_subj_dir = os.path.join(btree.work_dir, subj_prefix)
work_conv_dir = os.path.join(work_subj_dir, ses_prefix)
# BIDS source directory directories
bids_subj_dir = os.path.join(dataset_dir, subj_prefix)
bids_ses_dir = os.path.join(bids_subj_dir, ses_prefix)
print(' Working subject directory : %s' % work_subj_dir)
if not no_sessions:
print(' Working session directory : %s' % work_conv_dir)
print(' BIDS subject directory : %s' % bids_subj_dir)
if not no_sessions:
print(' BIDS session directory : %s' % bids_ses_dir)
# Safely create working directory for current subject
# Flag for conversion if no working directory exists
if not os.path.isdir(work_conv_dir):
os.makedirs(work_conv_dir)
needs_converting = True
else:
needs_converting = False
if first_pass or needs_converting:
# Run dcm2niix conversion into working conversion directory
print(' Converting all DICOM images in %s' % dcm_dir)
devnull = open(os.devnull, 'w')
# BIDS anonymization flag - default 'y'
anon = 'n' if no_anon else 'y'
# Compose command
cmd = [
'dcm2niix', '-b', 'y', '-ba', anon, '-z', 'y', '-f',
'%n--%d--%q--%s', '-o', work_conv_dir, dcm_dir
]
with open(os.devnull, 'w') as devnull:
subprocess.run(cmd, stdout=devnull, stderr=devnull)
if not first_pass:
# Get subject age and sex from representative DICOM header
dcm_info = bio.dcm_info(dcm_dir)
# Add line to participants TSV file
btr.add_participant_record(dataset_dir, sid, dcm_info['Age'],
dcm_info['Sex'])
# Organize dcm2niix output into BIDS subject/session directories
organize_series(work_conv_dir, first_pass, translator,
bids_ses_dir, sid, ses, args.clean_conv_dir,
overwrite)
if first_pass:
# Create a template protocol dictionary
btree.write_translator(translator)
if not args.skip_if_pruning:
print('')
print('Subject directories to prune: ' + ', '.join(out_subj_dir_list))
for bids_subj_dir in out_subj_dir_list:
btr.prune_intendedfors(bids_subj_dir, True)
if not first_pass:
if args.bind_fmaps:
print('')
print('Binding nearest fieldmap to each functional series')
for bids_subj_dir in out_subj_dir_list:
btr.bind_fmaps(bids_subj_dir)
# Finally validate that all is well with the BIDS dataset
if not first_pass:
btree.validate()
# Clean exit
sys.exit(0)
def main():
# Parse command line arguments
parser = argparse.ArgumentParser(
description='Convert DICOM files to BIDS-compliant Nifty structure')
parser.add_argument(
'-d',
'--dataset',
default='.',
help='BIDS dataset directory containing sourcedata subdirectory')
parser.add_argument('--no-sessions',
action='store_true',
default=False,
help='Do not use session sub-directories')
parser.add_argument(
'--no-anon',
action='store_true',
default=False,
help='Do not anonymize BIDS output (eg for phantom data)')
parser.add_argument('--overwrite',
action='store_true',
default=False,
help='Overwrite existing files')
parser.add_argument(
'--skip_if_pruning',
action='store_true',
default=False,
help='Skip pruning of nonexistent IntendedFor items in json files')
parser.add_argument('--clean_conv_dir',
action='store_true',
default=False,
help='Clean up conversion directory')
# TODO: Implement option for linking nearest fieldmap in time to BOLD series via IntendedFor field
# parser.add_argument('--nearest_fmap', action='store_true', default=False,
# help='Associate BOLD series with nearest fieldmap in time to series start')
# Parse command line arguments
args = parser.parse_args()
dataset_dir = os.path.realpath(args.dataset)
no_sessions = args.no_sessions
no_anon = args.no_anon
overwrite = args.overwrite
# nearest_fmap = args.nearest_fmap
# Read version from setup.py
ver = pkg_resources.get_distribution('bidskit').version
print('')
print('------------------------------------------------------------')
print('BIDSKIT {}'.format(ver))
print('------------------------------------------------------------')
# Check for minimum dcm2niix version (mostly for multirecon suffix handling)
btr.check_dcm2niix_version('v1.0.20181125')
# Create a BIDS directory tree object to handle file locations
# Creates directory
btree = BIDSTree(dataset_dir, overwrite)
print('')
print('Source data directory : {}'.format(btree.sourcedata_dir))
print('Working Directory : {}'.format(btree.work_dir))
print('Use Session Directories : {}'.format(
'No' if no_sessions else 'Yes'))
print(
'Overwrite Existing Files : {}'.format('Yes' if overwrite else 'No'))
print('Anonymize BIDS Output : {}'.format('No' if no_anon else 'Yes'))
# print('Use Nearest Fieldmap : {}'.format('Yes' if nearest_fmap else 'No'))
# Load protocol translation and exclusion info from derivatives/conversion directory
# If no translator is present, prot_dict is an empty dictionary
# and a template will be created in the derivatives/conversion directory.
# This template should be completed by the user and the conversion rerun.
translator = btree.read_translator()
if translator and os.path.isdir(btree.work_dir):
print('')
print('------------------------------------------------------------')
print('Pass 2 : Populating BIDS directory')
print('------------------------------------------------------------')
first_pass = False
else:
print('')
print('------------------------------------------------------------')
print('Pass 1 : DICOM to Nifti conversion and translator creation')
print('------------------------------------------------------------')
first_pass = True
# Init list of output subject directories
subject_dir_list = []
# Loop over list of subject directories in sourcedata directory
for dcm_sub_dir in glob(btree.sourcedata_dir + os.sep + '*' + os.sep):
sid = os.path.basename(os.path.normpath(dcm_sub_dir))
subject_dir_list.append(os.path.join(dataset_dir, 'sub-' + sid))
print('')
print('------------------------------------------------------------')
print('Processing subject ' + sid)
print('------------------------------------------------------------')
# Handle subject vs subject/session directory lists
if no_sessions:
dcm_dir_list = [dcm_sub_dir]
else:
dcm_dir_list = glob(dcm_sub_dir + os.sep + '*' + os.sep)
# Loop over source data session directories in subject directory
for dcm_dir in dcm_dir_list:
# BIDS subject, session and conversion directories
sub_prefix = 'sub-' + sid
if no_sessions:
# If session subdirs aren't being used, *_ses_dir = *sub_dir
# Use an empty ses_prefix with os.path.join to achieve this
ses = ''
ses_prefix = ''
else:
ses = os.path.basename(os.path.normpath(dcm_dir))
ses_prefix = 'ses-' + ses
print(' Processing session ' + ses)
# Working conversion directories
work_subj_dir = os.path.join(btree.work_dir, sub_prefix)
work_conv_dir = os.path.join(work_subj_dir, ses_prefix)
# BIDS source directory directories
bids_subj_dir = os.path.join(dataset_dir, sub_prefix)
bids_ses_dir = os.path.join(bids_subj_dir, ses_prefix)
print(' Working subject directory : %s' % work_subj_dir)
if not no_sessions:
print(' Working session directory : %s' % work_conv_dir)
print(' BIDS subject directory : %s' % bids_subj_dir)
if not no_sessions:
print(' BIDS session directory : %s' % bids_ses_dir)
# Safely create working directory for current subject
# Flag for conversion if no working directory existed
if not os.path.isdir(work_conv_dir):
os.makedirs(work_conv_dir)
needs_converting = True
else:
needs_converting = False
if first_pass or needs_converting:
# Run dcm2niix conversion into working conversion directory
print(' Converting all DICOM images in %s' % dcm_dir)
devnull = open(os.devnull, 'w')
# BIDS anonymization flag - default 'y'
anon = 'n' if no_anon else 'y'
# Compose command
cmd = [
'dcm2niix', '-b', 'y', '-ba', anon, '-z', 'y', '-f',
'%n--%d--%q--%s', '-o', work_conv_dir, dcm_dir
]
with open(os.devnull, 'w') as devnull:
subprocess.run(cmd, stdout=devnull, stderr=devnull)
if not first_pass:
# Get subject age and sex from representative DICOM header
dcm_info = bio.dcm_info(dcm_dir)
# Add line to participants TSV file
btr.add_participant_record(dataset_dir, sid, dcm_info['Age'],
dcm_info['Sex'])
# Organize dcm2niix output into BIDS subject/session directories
organize_series(work_conv_dir, first_pass, translator,
bids_ses_dir, sid, ses, args.clean_conv_dir,
overwrite)
if first_pass:
# Create a template protocol dictionary
btree.write_translator(translator)
if not args.skip_if_pruning:
print('')
print('Subject directories to prune: ' + ', '.join(subject_dir_list))
for bids_subj_dir in subject_dir_list:
btr.prune_intendedfors(bids_subj_dir, True)
# if not first_pass:
#
# if args.nearest_fmap:
#
# print('')
# print('Assigning nearest fieldmap to each BOLD series')
# btr.intendedfor_nearest_fieldmap(bids_subj_dir)
# Finally validate that all is well with the BIDS dataset
if not first_pass:
btree.validate()
# Clean exit
sys.exit(0)