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 purpose_handling(bids_purpose,
bids_intendedfor,
seq_name,
work_nii_fname,
work_json_fname,
bids_nii_fname,
bids_json_fname,
overwrite=False):
"""
Special handling for each image purpose (func, anat, fmap, dwi, etc)
:param bids_purpose: str
:param bids_intendedfor: str
:param seq_name: str
:param work_nii_fname: str
:param work_json_fname: str
:param bids_nii_fname: str
:param bids_json_fname: str
:param overwrite: bool
:return:
"""
# Init DWI sidecars
work_bval_fname = []
work_bvec_fname = []
bids_bval_fname = []
bids_bvec_fname = []
# Load the JSON sidecar
bids_info = bio.read_json(work_json_fname)
if bids_purpose == 'func':
if seq_name == 'EP':
print(' EPI detected')
create_events_template(bids_nii_fname, overwrite)
# Add taskname to BIDS JSON sidecar
bids_keys = bio.parse_bids_fname(bids_nii_fname)
if 'task' in bids_keys:
bids_info['TaskName'] = bids_keys['task']
else:
bids_info['TaskName'] = 'unknown'
elif bids_purpose == 'fmap':
# Add IntendedFor field if requested through protocol translator
if 'UNASSIGNED' not in bids_intendedfor:
bids_info['IntendedFor'] = bids_intendedfor
# Check for MEGE vs SE-EPI fieldmap images
# MEGE will have a 'GR' sequence, SE-EPI will have 'EP'
print(' Identifying fieldmap image type')
if seq_name == 'GR':
print(' GRE detected')
print(' Identifying magnitude and phase images')
# Siemens: Dual gradient echo fieldmaps reconstruct to three series
# (Requires dcm2nixx v1.0.20180404 or later for echo number suffix)
# *--GR--<serno>_e1.<ext> : magnitude image from echo 1
# *--GR--<serno>_e2.<ext> : magnitude image from echo 2
# *--GR--<serno+1>_ph.<ext> : inter-echo phase difference
# Pull dcm2niix filename info
work_info = bio.parse_dcm2niix_fname(work_nii_fname)
if 'e1' in work_info['Suffix']:
print(' Echo 1 magnitude detected')
# Replace existing contrast suffix (if any) with '_magnitude1'
bids_nii_fname = replace_contrast(bids_nii_fname, 'magnitude1')
bids_json_fname = [] # Do not copy sidecar
elif 'e2' in work_info['Suffix']:
print(' Echo 2 magnitude detected')
# Replace existing contrast suffix (if any) with '_magnitude1'
bids_nii_fname = replace_contrast(bids_nii_fname, 'magnitude2')
bids_json_fname = [] # Do not copy sidecar
elif 'ph' in work_info['Suffix']:
print(' Interecho phase difference detected')
# Replace existing contrast suffix (if any) with '_phasediff'
bids_nii_fname = replace_contrast(bids_nii_fname, 'phasediff')
bids_json_fname = replace_contrast(bids_json_fname,
'phasediff')
# Extract TE1 and TE2 from mag and phase JSON sidecars
te1, te2 = fmap_echotimes(work_json_fname)
bids_info['EchoTime1'] = te1
bids_info['EchoTime2'] = te2
else:
print('* Magnitude or phase image not found - skipping')
bids_nii_fname = []
bids_json_fname = []
elif seq_name == 'EP':
print(' EPI detected')
else:
print(' Unrecognized fieldmap detected')
print(' Simply copying image and sidecar to fmap directory')
elif bids_purpose == 'anat':
if seq_name == 'GR_IR':
print(
' IR-prepared GRE detected - likely T1w MP-RAGE or equivalent'
)
elif seq_name == 'SE':
print(' Spin echo detected - likely T1w or T2w anatomic image')
elif seq_name == 'GR':
print(' Gradient echo detected')
elif bids_purpose == 'dwi':
# Fill DWI bval and bvec working and source filenames
# Non-empty filenames trigger the copy below
work_bval_fname = str(work_json_fname.replace('.json', '.bval'))
bids_bval_fname = str(bids_json_fname.replace('dwi.json', 'dwi.bval'))
work_bvec_fname = str(work_json_fname.replace('.json', '.bvec'))
bids_bvec_fname = str(bids_json_fname.replace('dwi.json', 'dwi.bvec'))
# Populate BIDS source directory with Nifti images, JSON and DWI sidecars
print(' Populating BIDS source directory')
if bids_nii_fname:
bio.safe_copy(work_nii_fname, str(bids_nii_fname), overwrite)
if bids_json_fname:
bio.write_json(bids_json_fname, bids_info, overwrite)
if bids_bval_fname:
bio.safe_copy(work_bval_fname, bids_bval_fname, overwrite)
if bids_bvec_fname:
bio.safe_copy(work_bvec_fname, bids_bvec_fname, overwrite)
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 purpose_handling(bids_purpose, bids_intendedfor, seq_name,
work_nii_fname, work_json_fname, bids_nii_fname, bids_json_fname,
overwrite=False):
"""
Special handling for each image purpose (func, anat, fmap, dwi, etc)
:param bids_purpose: str
:param bids_intendedfor: str
:param seq_name: str
:param work_nii_fname: str
:param work_json_fname: str
:param bids_nii_fname: str
:param bids_json_fname: str
:param overwrite: bool
:return:
"""
# Init DWI sidecars
work_bval_fname = []
work_bvec_fname = []
bids_bval_fname = []
bids_bvec_fname = []
# Load the JSON sidecar
bids_info = bio.read_json(work_json_fname)
if bids_purpose == 'func':
if seq_name == 'EP':
print(' EPI detected')
create_events_template(bids_nii_fname, overwrite)
# Add taskname to BIDS JSON sidecar
bids_keys = bio.parse_bids_fname(bids_nii_fname)
if 'task' in bids_keys:
bids_info['TaskName'] = bids_keys['task']
else:
bids_info['TaskName'] = 'unknown'
elif bids_purpose == 'fmap':
# Add IntendedFor field if requested through protocol translator
if 'UNASSIGNED' not in bids_intendedfor:
bids_info['IntendedFor'] = bids_intendedfor
# Check for MEGE vs SE-EPI fieldmap images
# MEGE will have a 'GR' sequence, SE-EPI will have 'EP'
print(' Identifying fieldmap image type')
if seq_name == 'GR':
print(' GRE detected')
print(' Identifying magnitude and phase images')
# Siemens: Dual gradient echo fieldmaps reconstruct to three series
# (Requires dcm2nixx v1.0.20180404 or later for echo number suffix)
# *--GR--<serno>_e1.<ext> : magnitude image from echo 1
# *--GR--<serno>_e2.<ext> : magnitude image from echo 2
# *--GR--<serno+1>_ph.<ext> : inter-echo phase difference
# Pull dcm2niix filename info
work_info = bio.parse_dcm2niix_fname(work_nii_fname)
if 'e1' in work_info['Suffix']:
print(' Echo 1 magnitude detected')
# Replace existing contrast suffix (if any) with '_magnitude1'
bids_nii_fname = replace_contrast(bids_nii_fname, 'magnitude1')
bids_json_fname = [] # Do not copy sidecar
elif 'e2' in work_info['Suffix']:
print(' Echo 2 magnitude detected')
# Replace existing contrast suffix (if any) with '_magnitude1'
bids_nii_fname = replace_contrast(bids_nii_fname, 'magnitude2')
bids_json_fname = [] # Do not copy sidecar
elif 'ph' in work_info['Suffix']:
print(' Interecho phase difference detected')
# Replace existing contrast suffix (if any) with '_phasediff'
bids_nii_fname = replace_contrast(bids_nii_fname, 'phasediff')
bids_json_fname = replace_contrast(bids_json_fname, 'phasediff')
# Extract TE1 and TE2 from mag and phase JSON sidecars
te1, te2 = fmap_echotimes(work_json_fname)
bids_info['EchoTime1'] = te1
bids_info['EchoTime2'] = te2
else:
print('* Magnitude or phase image not found - skipping')
bids_nii_fname = []
bids_json_fname = []
elif seq_name == 'EP':
print(' EPI detected')
else:
print(' Unrecognized fieldmap detected')
print(' Simply copying image and sidecar to fmap directory')
elif bids_purpose == 'anat':
if seq_name == 'GR_IR':
print(' IR-prepared GRE detected - likely T1w MP-RAGE or equivalent')
elif seq_name == 'SE':
print(' Spin echo detected - likely T1w or T2w anatomic image')
elif seq_name == 'GR':
print(' Gradient echo detected')
elif bids_purpose == 'dwi':
# Fill DWI bval and bvec working and source filenames
# Non-empty filenames trigger the copy below
work_bval_fname = str(work_json_fname.replace('.json', '.bval'))
bids_bval_fname = str(bids_json_fname.replace('dwi.json', 'dwi.bval'))
work_bvec_fname = str(work_json_fname.replace('.json', '.bvec'))
bids_bvec_fname = str(bids_json_fname.replace('dwi.json', 'dwi.bvec'))
# Populate BIDS source directory with Nifti images, JSON and DWI sidecars
print(' Populating BIDS source directory')
if bids_nii_fname:
bio.safe_copy(work_nii_fname, str(bids_nii_fname), overwrite)
if bids_json_fname:
bio.write_json(bids_json_fname, bids_info, overwrite)
if bids_bval_fname:
bio.safe_copy(work_bval_fname, bids_bval_fname, overwrite)
if bids_bvec_fname:
bio.safe_copy(work_bvec_fname, bids_bvec_fname, overwrite)