def __init__(self, dataset_dir, overwrite=False):
print('Initializing BIDS dataset directory tree in %s' % dataset_dir)
self.bids_dir = dataset_dir
self.derivatives_dir = os.path.join(dataset_dir, 'derivatives')
self.sourcedata_dir = os.path.join(dataset_dir, 'sourcedata')
self.code_dir = os.path.join(dataset_dir, 'code')
self.work_dir = os.path.join(dataset_dir, 'work')
bio.safe_mkdir(self.derivatives_dir)
bio.safe_mkdir(self.sourcedata_dir)
bio.safe_mkdir(self.code_dir)
bio.safe_mkdir(self.work_dir)
self.translator_file = os.path.join(self.code_dir, 'Protocol_Translator.json')
print('Creating required file templates')
# README file
self.readme_file = os.path.join(dataset_dir, 'README')
with open(self.readme_file, 'w') as fd:
fd.writelines('Useful information about this dataset\n')
# CHANGES changelog file
self.changes_file = os.path.join(dataset_dir, 'CHANGES')
with open(self.changes_file, 'w') as fd:
fd.writelines(['1.0.0 YYYY-MM-DD\n', ' - Initial release\n'])
# Create template JSON dataset description (must comply with BIDS 1.2 spec)
self.datadesc_json = os.path.join(self.bids_dir, 'dataset_description.json')
meta_dict = dict({
'Name': 'Descriptive name for this dataset',
'BIDSVersion': '1.2',
'License': 'This data is made available under the Creative Commons BY-SA 4.0 International License.',
'Authors': ['First Author', 'Second Author'],
'Acknowledgments': 'Thanks to everyone for all your help',
'HowToAcknowledge': 'Please cite: Author AB, Seminal Paper Title, High Impact Journal, 2019',
'Funding': ['First Grant', 'Second Grant'],
'ReferencesAndLinks': ['A Reference', 'Another Reference', 'A Link'],
'DatasetDOI': '10.0.1.2/abcd.10'
})
bio.write_json(self.datadesc_json, meta_dict, overwrite)
# Create participants JSON file defining columns in participants.tsv
# See
self.participants_json = os.path.join(self.bids_dir, 'participants.json')
meta_dict = dict({
'age': {
'Description': 'Age of participant',
'Units': 'years'
},
'sex': {
'Description': 'Sex of participant',
'Levels': {
'M': 'male',
'F': 'female',
'T': 'transgender'
}
},
'group': {
'Description': 'participant group assignment'
},
})
bio.write_json(self.participants_json, meta_dict, overwrite)
# Create .bidsignore file to skip work/ during validation
self.ignore_file = os.path.join(dataset_dir, '.bidsignore')
with open(self.ignore_file, 'w') as fd:
fd.writelines('work/\n')
def organize_series(conv_dir,
first_pass,
prot_dict,
src_dir,
sid,
ses,
clean_conv_dir,
overwrite=False):
"""
Organize dcm2niix output into BIDS subject/session directory
:param conv_dir: string
Working conversion directory
:param first_pass: boolean
Flag for first pass conversion
:param prot_dict: dictionary
Protocol translation dictionary
:param src_dir: string
BIDS source output subj or subj/session directory
:param sid: string
subject ID
:param ses: string
session name or number
:param clean_conv_dir: bool
clean up conversion directory
:param overwrite: bool
overwrite flag
:return:
"""
# Flag for working conversion directory cleanup
do_cleanup = clean_conv_dir
# Proceed if conversion directory exists
if os.path.isdir(conv_dir):
# Get Nifti file list ordered by acquisition time
nii_list, json_list, acq_times = btr.ordered_file_list(conv_dir)
# Infer run numbers accounting for duplicates.
# Only used if run-* not present in translator BIDS filename stub
if not first_pass:
run_no = btr.auto_run_no(nii_list, prot_dict)
# Loop over all Nifti files (*.nii, *.nii.gz) for this subject
for fc, src_nii_fname in enumerate(nii_list):
# Parse image filename into fields
info = bio.parse_dcm2niix_fname(src_nii_fname)
# Check if we're creating new protocol dictionary
if first_pass:
print(' Adding protocol %s to dictionary template' %
info['SerDesc'])
# Add current protocol to protocol dictionary
# Use default EXCLUDE_* values which can be changed (or not) by the user
prot_dict[info['SerDesc']] = [
"EXCLUDE_BIDS_Directory", "EXCLUDE_BIDS_Name", "UNASSIGNED"
]
else:
# JSON sidecar for this image
src_json_fname = json_list[fc]
# Warn if not found and continue
if not os.path.isfile(src_json_fname):
print('* WARNING: JSON sidecar %s not found' %
src_json_fname)
continue
if info['SerDesc'] in prot_dict.keys():
if prot_dict[info['SerDesc']][0].startswith('EXCLUDE'):
# Skip excluded protocols
print('* Excluding protocol ' + str(info['SerDesc']))
else:
print(' Organizing ' + str(info['SerDesc']))
# Use protocol dictionary to determine purpose folder, BIDS filename suffix and fmap linking
bids_purpose, bids_suffix, bids_intendedfor = prot_dict[
info['SerDesc']]
# Safely add run-* key to BIDS suffix
bids_suffix = btr.add_run_number(
bids_suffix, run_no[fc])
# Assume the IntendedFor field should aslo have a run- added
prot_dict = btr.add_intended_run(
prot_dict, info, run_no[fc])
# Create BIDS purpose directory
bids_purpose_dir = os.path.join(src_dir, bids_purpose)
bio.safe_mkdir(bids_purpose_dir)
# Complete BIDS filenames for image and sidecar
if ses:
bids_prefix = 'sub-' + sid + '_ses-' + ses + '_'
else:
bids_prefix = 'sub-' + sid + '_'
# Construct BIDS source Nifti and JSON filenames
bids_nii_fname = os.path.join(
bids_purpose_dir,
bids_prefix + bids_suffix + '.nii.gz')
bids_json_fname = bids_nii_fname.replace(
'.nii.gz', '.json')
# Add prefix and suffix to IntendedFor values
if 'UNASSIGNED' not in bids_intendedfor:
if isinstance(bids_intendedfor, str):
# Single linked image
bids_intendedfor = btr.build_intendedfor(
sid, ses, bids_intendedfor)
else:
# Loop over all linked images
for ifc, ifstr in enumerate(bids_intendedfor):
# Avoid multiple substitutions
if '.nii.gz' not in ifstr:
bids_intendedfor[
ifc] = btr.build_intendedfor(
sid, ses, ifstr)
# Special handling for specific purposes (anat, func, fmap, etc)
# This function populates BIDS structure with the image and adjusted sidecar
btr.purpose_handling(bids_purpose, bids_intendedfor,
info['SeqName'], src_nii_fname,
src_json_fname, bids_nii_fname,
bids_json_fname, overwrite)
else:
# Skip protocols not in the dictionary
print('* Protocol ' + str(info['SerDesc']) +
' is not in the dictionary, did not convert.')
if not first_pass:
# Optional working directory cleanup after Pass 2
if do_cleanup:
print(' Cleaning up temporary files')
shutil.rmtree(conv_dir)
else:
print(' Preserving conversion directory')
def __init__(self, dataset_dir, overwrite=False):
print('Initializing BIDS dataset directory tree in %s' % dataset_dir)
self.bids_dir = dataset_dir
self.derivatives_dir = os.path.join(dataset_dir, 'derivatives')
self.sourcedata_dir = os.path.join(dataset_dir, 'sourcedata')
self.code_dir = os.path.join(dataset_dir, 'code')
self.work_dir = os.path.join(dataset_dir, 'work')
bio.safe_mkdir(self.derivatives_dir)
bio.safe_mkdir(self.sourcedata_dir)
bio.safe_mkdir(self.code_dir)
bio.safe_mkdir(self.work_dir)
self.translator_file = os.path.join(self.code_dir,
'Protocol_Translator.json')
print('Creating required file templates')
# README file
self.readme_file = os.path.join(dataset_dir, 'README')
with open(self.readme_file, 'w') as fd:
fd.writelines('Useful information about this dataset\n')
# CHANGES changelog file
self.changes_file = os.path.join(dataset_dir, 'CHANGES')
with open(self.changes_file, 'w') as fd:
fd.writelines(['1.0.0 YYYY-MM-DD\n', ' - Initial release\n'])
# Create template JSON dataset description (must comply with BIDS 1.2 spec)
self.datadesc_json = os.path.join(self.bids_dir,
'dataset_description.json')
meta_dict = dict({
'Name':
'Descriptive name for this dataset',
'BIDSVersion':
'1.2',
'License':
'This data is made available under the Creative Commons BY-SA 4.0 International License.',
'Authors': ['First Author', 'Second Author'],
'Acknowledgments':
'Thanks to everyone for all your help',
'HowToAcknowledge':
'Please cite: Author AB, Seminal Paper Title, High Impact Journal, 2019',
'Funding': ['First Grant', 'Second Grant'],
'ReferencesAndLinks':
['A Reference', 'Another Reference', 'A Link'],
'DatasetDOI':
'10.0.1.2/abcd.10'
})
bio.write_json(self.datadesc_json, meta_dict, overwrite)
# Create participants JSON file defining columns in participants.tsv
# See
self.participants_json = os.path.join(self.bids_dir,
'participants.json')
meta_dict = dict({
'age': {
'Description': 'Age of participant',
'Units': 'years'
},
'sex': {
'Description': 'Sex of participant',
'Levels': {
'M': 'male',
'F': 'female',
'T': 'transgender'
}
},
'group': {
'Description': 'participant group assignment'
},
})
bio.write_json(self.participants_json, meta_dict, overwrite)
# Create .bidsignore file to skip work/ during validation
self.ignore_file = os.path.join(dataset_dir, '.bidsignore')
with open(self.ignore_file, 'w') as fd:
fd.writelines('work/\n')
def organize_series(conv_dir, first_pass, prot_dict, src_dir, sid, ses, clean_conv_dir, overwrite=False):
"""
Organize dcm2niix output into BIDS subject/session directory
:param conv_dir: string
Working conversion directory
:param first_pass: boolean
Flag for first pass conversion
:param prot_dict: dictionary
Protocol translation dictionary
:param src_dir: string
BIDS source output subj or subj/session directory
:param sid: string
subject ID
:param ses: string
session name or number
:param clean_conv_dir: bool
clean up conversion directory
:param overwrite: bool
overwrite flag
:return:
"""
# Flag for working conversion directory cleanup
do_cleanup = clean_conv_dir
# Proceed if conversion directory exists
if os.path.isdir(conv_dir):
# Get Nifti file list ordered by acquisition time
nii_list, json_list, acq_times = btr.ordered_file_list(conv_dir)
# Infer run numbers accounting for duplicates.
# Only used if run-* not present in translator BIDS filename stub
if not first_pass:
run_no = btr.auto_run_no(nii_list, prot_dict)
# Loop over all Nifti files (*.nii, *.nii.gz) for this subject
for fc, src_nii_fname in enumerate(nii_list):
# Parse image filename into fields
info = bio.parse_dcm2niix_fname(src_nii_fname)
# Check if we're creating new protocol dictionary
if first_pass:
print(' Adding protocol %s to dictionary template' % info['SerDesc'])
# Add current protocol to protocol dictionary
# Use default EXCLUDE_* values which can be changed (or not) by the user
prot_dict[info['SerDesc']] = ["EXCLUDE_BIDS_Directory", "EXCLUDE_BIDS_Name", "UNASSIGNED"]
else:
# JSON sidecar for this image
src_json_fname = json_list[fc]
# Warn if not found and continue
if not os.path.isfile(src_json_fname):
print('* WARNING: JSON sidecar %s not found' % src_json_fname)
continue
if info['SerDesc'] in prot_dict.keys():
if prot_dict[info['SerDesc']][0].startswith('EXCLUDE'):
# Skip excluded protocols
print('* Excluding protocol ' + str(info['SerDesc']))
else:
print(' Organizing ' + str(info['SerDesc']))
# Use protocol dictionary to determine purpose folder, BIDS filename suffix and fmap linking
bids_purpose, bids_suffix, bids_intendedfor = prot_dict[info['SerDesc']]
# Safely add run-* key to BIDS suffix
bids_suffix = btr.add_run_number(bids_suffix, run_no[fc])
# Assume the IntendedFor field should aslo have a run- added
prot_dict = btr.add_intended_run(prot_dict, info, run_no[fc])
# Create BIDS purpose directory
bids_purpose_dir = os.path.join(src_dir, bids_purpose)
bio.safe_mkdir(bids_purpose_dir)
# Complete BIDS filenames for image and sidecar
if ses:
bids_prefix = 'sub-' + sid + '_ses-' + ses + '_'
else:
bids_prefix = 'sub-' + sid + '_'
# Construct BIDS source Nifti and JSON filenames
bids_nii_fname = os.path.join(bids_purpose_dir, bids_prefix + bids_suffix + '.nii.gz')
bids_json_fname = bids_nii_fname.replace('.nii.gz', '.json')
# Add prefix and suffix to IntendedFor values
if 'UNASSIGNED' not in bids_intendedfor:
if isinstance(bids_intendedfor, str):
# Single linked image
bids_intendedfor = btr.build_intendedfor(sid, ses, bids_intendedfor)
else:
# Loop over all linked images
for ifc, ifstr in enumerate(bids_intendedfor):
# Avoid multiple substitutions
if '.nii.gz' not in ifstr:
bids_intendedfor[ifc] = btr.build_intendedfor(sid, ses, ifstr)
# Special handling for specific purposes (anat, func, fmap, etc)
# This function populates BIDS structure with the image and adjusted sidecar
btr.purpose_handling(bids_purpose, bids_intendedfor, info['SeqName'],
src_nii_fname, src_json_fname,
bids_nii_fname, bids_json_fname,
overwrite)
else:
# Skip protocols not in the dictionary
print('* Protocol ' + str(info['SerDesc']) + ' is not in the dictionary, did not convert.')
if not first_pass:
# Optional working directory cleanup after Pass 2
if do_cleanup:
print(' Cleaning up temporary files')
shutil.rmtree(conv_dir)
else:
print(' Preserving conversion directory')