def fmap_echotimes(src_phase_json_fname):
"""
Extract TE1 and TE2 from mag and phase MEGE fieldmap pairs
:param src_phase_json_fname: str
:return:
"""
# Init returned TEs
te1, te2 = 0.0, 0.0
if os.path.isfile(src_phase_json_fname):
# Read phase image metadata
phase_dict = bio.read_json(src_phase_json_fname)
# Populate series info dictionary from dcm2niix output filename
info = bio.parse_dcm2niix_fname(src_phase_json_fname)
# Siemens: Magnitude 1 series number is one less than phasediff series number
mag1_ser_no = str(int(info['SerNo']) - 1)
# Construct dcm2niix mag1 JSON filename
# Requires dicm2niix v1.0.20180404 or later for echo number suffix '_e1'
src_mag1_json_fname = info['SubjName'] + '--' + info['SerDesc'] + '--' + \
info['SeqName'] + '--' + mag1_ser_no + '_e1.json'
src_mag1_json_path = os.path.join(
os.path.dirname(src_phase_json_fname), src_mag1_json_fname)
# Read mag1 metadata
mag1_dict = bio.read_json(src_mag1_json_path)
# Add te1 key and rename TE2 key
if mag1_dict:
te1 = mag1_dict['EchoTime']
te2 = phase_dict['EchoTime']
else:
print(
'*** Could not determine echo times multiecho fieldmap - using 0.0 '
)
else:
print('* Fieldmap phase difference sidecar not found : ' +
src_phase_json_fname)
return te1, te2
def get_acq_time(json_file):
"""
Extract acquisition time from JSON sidecar of Nifti file
:param json_file: str, JSON sidecar filename
:return: acq_time: int, integer datetime
"""
info = bio.read_json(json_file)
return info['AcquisitionTime']
def fmap_echotimes(src_phase_json_fname):
"""
Extract TE1 and TE2 from mag and phase MEGE fieldmap pairs
:param src_phase_json_fname: str
:return:
"""
# Init returned TEs
te1, te2 = 0.0, 0.0
if os.path.isfile(src_phase_json_fname):
# Read phase image metadata
phase_dict = bio.read_json(src_phase_json_fname)
# Populate series info dictionary from dcm2niix output filename
info = bio.parse_dcm2niix_fname(src_phase_json_fname)
# Siemens: Magnitude 1 series number is one less than phasediff series number
mag1_ser_no = str(int(info['SerNo']) - 1)
# Construct dcm2niix mag1 JSON filename
# Requires dicm2niix v1.0.20180404 or later for echo number suffix '_e1'
src_mag1_json_fname = info['SubjName'] + '--' + info['SerDesc'] + '--' + \
info['SeqName'] + '--' + mag1_ser_no + '_e1.json'
src_mag1_json_path = os.path.join(os.path.dirname(src_phase_json_fname), src_mag1_json_fname)
# Read mag1 metadata
mag1_dict = bio.read_json(src_mag1_json_path)
# Add te1 key and rename TE2 key
if mag1_dict:
te1 = mag1_dict['EchoTime']
te2 = phase_dict['EchoTime']
else:
print('*** Could not determine echo times multiecho fieldmap - using 0.0 ')
else:
print('* Fieldmap phase difference sidecar not found : ' + src_phase_json_fname)
return te1, te2
def get_acq_time(json_file):
"""
Extract acquisition time from JSON sidecar of Nifti file
:param json_file: str, JSON sidecar filename
:return: acq_time: int, integer datetime
"""
info = bio.read_json(json_file)
return info['AcquisitionTime']
def get_acq_time(json_file):
"""
Extract acquisition time from JSON sidecar of Nifti file
:param json_file: str, JSON sidecar filename
:return: acq_time: int, integer datetime
"""
info = bio.read_json(json_file)
if 'AcquisitionTime' in info:
acq_time = info['AcquisitionTime']
else:
print('* AcquisitionTime not found in {}'.format(json_file))
acq_time = "00:00:00.00"
return acq_time
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 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)