def coin_data2bids(dataformat: str, session: Path, bidsmap: dict,
bidsfolder: Path, personals: dict, subprefix: str,
sesprefix: str) -> None:
"""
Converts the session source-files into BIDS-valid nifti-files in the corresponding bidsfolder and
extracts personals (e.g. Age, Sex) from the source header
:param dataformat: The format of the raw input data that is to be coined (e.g. 'DICOM' or 'PAR', see bids.get_dataformat)
:param session: The full-path name of the subject/session source file/folder
:param bidsmap: The full mapping heuristics from the bidsmap YAML-file
:param bidsfolder: The full-path name of the BIDS root-folder
:param personals: The dictionary with the personal information
:param subprefix: The prefix common for all source subject-folders
:param sesprefix: The prefix common for all source session-folders
:return: Nothing
"""
# Get valid BIDS subject/session identifiers from the (first) DICOM- or PAR/XML source file
if dataformat == 'DICOM':
sourcefile = Path()
sources = bids.lsdirs(session)
for source in sources:
sourcefile = bids.get_dicomfile(source)
manufacturer = bids.get_dicomfield('Manufacturer', sourcefile)
if sourcefile.name:
break
elif dataformat == 'PAR':
sources = bids.get_parfiles(session)
manufacturer = 'Philips Medical Systems'
if sources:
sourcefile = sources[0]
else:
LOGGER.error(
f"Unsupported data format: {dataformat}\nPlease report this bug")
return
if not sources:
LOGGER.info(f"No data found for: {session}")
return
subid, sesid = bids.get_subid_sesid(sourcefile,
bidsmap[dataformat]['subject'],
bidsmap[dataformat]['session'],
subprefix, sesprefix)
if subid == subprefix:
LOGGER.error(f"No valid subject identifier found for: {session}")
return
# Create the BIDS session-folder and a scans.tsv file
bidsses = bidsfolder / subid / sesid
if bidsses.is_dir():
LOGGER.warning(
f"Existing BIDS output-directory found, which may result in duplicate data (with increased run-index). Make sure {bidsses} was cleaned-up from old data before (re)running the bidscoiner"
)
bidsses.mkdir(parents=True, exist_ok=True)
scans_tsv = bidsses / f"{subid}{bids.add_prefix('_',sesid)}_scans.tsv"
if scans_tsv.is_file():
scans_table = pd.read_csv(scans_tsv, sep='\t', index_col='filename')
else:
scans_table = pd.DataFrame(columns=['acq_time'], dtype='str')
scans_table.index.name = 'filename'
# Process all the source files or run subfolders
for source in sources:
# Get a source-file
if dataformat == 'DICOM':
sourcefile = bids.get_dicomfile(source)
elif dataformat == 'PAR':
sourcefile = source
if not sourcefile.name:
continue
# Get a matching run from the bidsmap
run, datatype, index = bids.get_matching_run(sourcefile, bidsmap,
dataformat)
# Check if we should ignore this run
if datatype == bids.ignoredatatype:
LOGGER.info(f"Leaving out: {source}")
continue
# Check if we already know this run
if index is None:
LOGGER.error(
f"Skipping unknown '{datatype}' run: {sourcefile}\n-> Re-run the bidsmapper and delete {bidsses} to solve this warning"
)
continue
LOGGER.info(f"Processing: {source}")
# Create the BIDS session/datatype output folder
if run['bids']['suffix'] in bids.get_derivatives(datatype):
outfolder = bidsfolder / 'derivatives' / manufacturer.replace(
' ', '') / subid / sesid / datatype
else:
outfolder = bidsses / datatype
outfolder.mkdir(parents=True, exist_ok=True)
# Compose the BIDS filename using the matched run
bidsname = bids.get_bidsname(subid, sesid, run)
runindex = run['bids'].get('run', '')
if runindex.startswith('<<') and runindex.endswith('>>'):
bidsname = bids.increment_runindex(outfolder, bidsname)
jsonfiles = [
(outfolder / bidsname).with_suffix('.json')
] # List -> Collect the associated json-files (for updating them later) -- possibly > 1
# Check if file already exists (-> e.g. when a static runindex is used)
if (outfolder / bidsname).with_suffix('.json').is_file():
LOGGER.warning(
f"{outfolder/bidsname}.* already exists and will be deleted -- check your results carefully!"
)
for ext in ('.nii.gz', '.nii', '.json', '.bval', '.bvec',
'tsv.gz'):
(outfolder / bidsname).with_suffix(ext).unlink(missing_ok=True)
# Convert physiological log files (dcm2niix can't handle these)
if run['bids']['suffix'] == 'physio':
if bids.get_dicomfile(source, 2).name:
LOGGER.warning(
f"Found > 1 DICOM file in {source}, using: {sourcefile}")
physiodata = physio.readphysio(sourcefile)
physio.physio2tsv(physiodata, outfolder / bidsname)
# Convert the source-files in the run folder to nifti's in the BIDS-folder
else:
command = '{path}dcm2niix {args} -f "{filename}" -o "{outfolder}" "{source}"'.format(
path=bidsmap['Options']['dcm2niix']['path'],
args=bidsmap['Options']['dcm2niix']['args'],
filename=bidsname,
outfolder=outfolder,
source=source)
if not bids.run_command(command):
continue
# Replace uncropped output image with the cropped one
if '-x y' in bidsmap['Options']['dcm2niix']['args']:
for dcm2niixfile in sorted(
outfolder.glob(bidsname +
'*_Crop_*')): # e.g. *_Crop_1.nii.gz
ext = ''.join(dcm2niixfile.suffixes)
newbidsfile = str(dcm2niixfile).rsplit(ext, 1)[0].rsplit(
'_Crop_', 1)[0] + ext
LOGGER.info(
f"Found dcm2niix _Crop_ postfix, replacing original file\n{dcm2niixfile} ->\n{newbidsfile}"
)
dcm2niixfile.replace(newbidsfile)
# Rename all files that got additional postfixes from dcm2niix. See: https://github.com/rordenlab/dcm2niix/blob/master/FILENAMING.md
dcm2niixpostfixes = ('_c', '_i', '_Eq', '_real', '_imaginary',
'_MoCo', '_t', '_Tilt', '_e', '_ph')
dcm2niixfiles = sorted(
set([
dcm2niixfile for dcm2niixpostfix in dcm2niixpostfixes
for dcm2niixfile in outfolder.glob(
f"{bidsname}*{dcm2niixpostfix}*")
]))
for dcm2niixfile in dcm2niixfiles:
ext = ''.join(dcm2niixfile.suffixes)
postfixes = str(dcm2niixfile).split(bidsname)[1].rsplit(
ext)[0].split('_')[1:]
newbidsname = dcm2niixfile.name # Strip the additional postfixes and assign them to bids entities in the for-loop below
for postfix in postfixes: # dcm2niix postfixes _c%d, _e%d and _ph (and any combination of these in that order) are for multi-coil data, multi-echo data and phase data
# Patch the echo entity in the newbidsname with the dcm2niix echo info # NB: We can't rely on the bids-entity info here because manufacturers can e.g. put multiple echos in one series / run-folder
if postfix[0] == 'e' and bids.get_bidsvalue(
newbidsname, 'echo'
): # NB: Check if postfix[0]=='e' uniquely refers to the right dcm2niixpostfix
echonr = f"_{postfix}" # E.g. echonr='_e1' or echonr='_pha'
for dcm2niixpostfix in dcm2niixpostfixes:
echonr = echonr.replace(
dcm2niixpostfix, ''
) # Strip the dcm2niixpostfix to keep the echonr info. E.g. [echonr='_e1' or echonr='_pha'] -> [echonr='1' or echonr='a']
if echonr.isalpha():
echonr = ord(
echonr
) - 95 # dcm2niix adds an alphabetically ordered character if it outputs more than one image with the same name. Convert character to echo-number: '' -> 1, 'a'->2, etc
elif not echonr:
echonr = 1
newbidsname = bids.get_bidsvalue(
newbidsname, 'echo', str(echonr)
) # In contrast to other labels, run and echo labels MUST be integers. Those labels MAY include zero padding, but this is NOT RECOMMENDED to maintain their uniqueness
# Patch fieldmap images (NB: datatype=='fmap' is too broad, see the fmap.yaml file)
elif run['bids']['suffix'] in ('magnitude', 'magnitude1',
'magnitude2', 'phase1',
'phase2', 'phasediff',
'fieldmap'):
if len(dcm2niixfiles) not in (
0, 2, 4, 6, 8
): # Phase / echo data may be stored in the same data source / run folder
LOGGER.warning(
f"Unknown fieldmap {outfolder/bidsname} for '{postfix}'"
)
newbidsname = newbidsname.replace(
'_fieldmap_ph', '_fieldmap')
newbidsname = newbidsname.replace(
'_magnitude_e1', '_magnitude')
newbidsname = newbidsname.replace(
'_magnitude_ph', '_fieldmap')
newbidsname = newbidsname.replace(
'_magnitude1_e1', '_magnitude1')
newbidsname = newbidsname.replace(
'_magnitude2_e1', '_magnitude1'
) # This can happen when the e2 image is stored in the same directory as the e1 image, but with the e2 listed first
newbidsname = newbidsname.replace(
'_magnitude1_e2', '_magnitude2')
if len(dcm2niixfiles) == 8:
newbidsname = newbidsname.replace(
'_magnitude1_ph', '_phase1'
) # Two magnitude + 2 phase images in one folder / datasource
else:
newbidsname = newbidsname.replace(
'_magnitude1_ph', '_phasediff'
) # One or two magnitude + 1 phasediff image
newbidsname = newbidsname.replace(
'_magnitude1a', '_magnitude2')
newbidsname = newbidsname.replace(
'_magnitude1_pha', '_phase2')
newbidsname = newbidsname.replace(
'_magnitude2_e2', '_magnitude2')
newbidsname = newbidsname.replace(
'_magnitude2_ph', '_phase2')
newbidsname = newbidsname.replace(
'_phase1_e1', '_phase1')
newbidsname = newbidsname.replace(
'_phase2_e1', '_phase1'
) # This can happen when the e2 image is stored in the same directory as the e1 image, but with the e2 listed first
newbidsname = newbidsname.replace(
'_phase1_ph', '_phase1')
newbidsname = newbidsname.replace(
'_phase1_e2', '_phase2')
newbidsname = newbidsname.replace(
'_phase2_e2', '_phase2')
newbidsname = newbidsname.replace(
'_phase2_ph', '_phase2')
# Append the dcm2niix info to acq-label, may need to be improved / elaborated for future BIDS standards, supporting multi-coil data
else:
newbidsname = bids.get_bidsvalue(
newbidsname, 'dummy', postfix)
# Remove the added postfix from the new bidsname
newbidsname = newbidsname.replace(f"_{postfix}_",
'_') # If it is not last
newbidsname = newbidsname.replace(f"_{postfix}.",
'.') # If it is last
# Save the file with a new name
if runindex.startswith('<<') and runindex.endswith('>>'):
newbidsname = bids.increment_runindex(
outfolder, newbidsname, ''
) # Update the runindex now that the acq-label has changed
newbidsfile = outfolder / newbidsname
LOGGER.info(
f"Found dcm2niix {postfixes} postfixes, renaming\n{dcm2niixfile} ->\n{newbidsfile}"
)
if newbidsfile.is_file():
LOGGER.warning(
f"Overwriting existing {newbidsfile} file -- check your results carefully!"
)
dcm2niixfile.replace(newbidsfile)
if ext == '.json':
oldjsonfile = (outfolder / bidsname).with_suffix('.json')
if oldjsonfile in jsonfiles and not oldjsonfile.is_file():
jsonfiles.remove(
(outfolder / bidsname).with_suffix('.json'))
jsonfiles.append(newbidsfile)
# Loop over and adapt all the newly produced json files and write to the scans.tsv file (every nifti-file comes with a json-file)
for jsonfile in sorted(set(jsonfiles)):
# Check if dcm2niix behaved as expected
if not jsonfile.is_file():
LOGGER.error(
f"Unexpected file conversion result: {jsonfile} not found")
continue
# Add a dummy b0 bval- and bvec-file for any file without a bval/bvec file (e.g. sbref, b0 scans)
if datatype == 'dwi':
bvecfile = jsonfile.with_suffix('.bvec')
bvalfile = jsonfile.with_suffix('.bval')
if not bvecfile.is_file():
LOGGER.info(f"Adding dummy bvec file: {bvecfile}")
with bvecfile.open('w') as bvec_fid:
bvec_fid.write('0\n0\n0\n')
if not bvalfile.is_file():
LOGGER.info(f"Adding dummy bval file: {bvalfile}")
with bvalfile.open('w') as bval_fid:
bval_fid.write('0\n')
# Add the TaskName to the func json-file
elif datatype == 'func':
with jsonfile.open('r') as json_fid:
data = json.load(json_fid)
if not 'TaskName' in data:
LOGGER.info(f"Adding TaskName to: {jsonfile}")
data['TaskName'] = run['bids']['task']
with jsonfile.open('w') as json_fid:
json.dump(data, json_fid, indent=4)
# Parse the acquisition time from the json file or else from the source header (NB: assuming the source file represents the first acquisition)
niifile = list(
jsonfile.parent.glob(jsonfile.stem + '.nii*')
) # Find the corresponding nifti file (there should be only one, let's not make assumptions about the .gz extension)
if niifile and datatype not in bidsmap['Options']['bidscoin'][
'bidsignore'] and not run['bids'][
'suffix'] in bids.get_derivatives(datatype):
with jsonfile.open('r') as json_fid:
data = json.load(json_fid)
if 'AcquisitionTime' not in data or not data['AcquisitionTime']:
data['AcquisitionTime'] = bids.get_sourcefield(
'AcquisitionTime', sourcefile) # DICOM
if not data['AcquisitionTime']:
data['AcquisitionTime'] = bids.get_sourcefield(
'exam_date', sourcefile) # PAR/XML
try:
acq_time = dateutil.parser.parse(data['AcquisitionTime'])
except:
LOGGER.warning(
f"Could not parse the acquisition time from: '{data['AcquisitionTime']}' in {sourcefile}"
)
acq_time = dateutil.parser.parse('00:00:00')
scanpath = niifile[0].relative_to(bidsses)
scans_table.loc[
scanpath.as_posix(),
'acq_time'] = '1925-01-01T' + acq_time.strftime('%H:%M:%S')
# Write the scans_table to disk
LOGGER.info(f"Writing acquisition time data to: {scans_tsv}")
scans_table.sort_values(by=['acq_time', 'filename'], inplace=True)
scans_table.to_csv(scans_tsv, sep='\t', encoding='utf-8')
# Add IntendedFor and TE1+TE2 meta-data to the fieldmap json-files. This has been postponed untill all datatypes have been processed (i.e. so that all target images are indeed on disk)
if bidsmap[dataformat]['fmap'] is not None:
for fieldmap in bidsmap[dataformat]['fmap']:
bidsname = bids.get_bidsname(subid, sesid, fieldmap)
niifiles = []
intendedfor = fieldmap['bids']['IntendedFor']
# Search for the imaging files that match the IntendedFor search criteria
if intendedfor:
if intendedfor.startswith('<<') and intendedfor.endswith('>>'):
intendedfor = intendedfor[2:-2].split('><')
elif not isinstance(intendedfor, list):
intendedfor = [intendedfor]
for selector in intendedfor:
niifiles.extend(
[
Path(niifile).relative_to(bidsfolder / subid)
for niifile in sorted(
bidsses.rglob(f"*{selector}*.nii*"))
if selector
]
) # Search in all runs using a relative path to the subject folder
else:
intendedfor = []
# Get the set of json-files (account for multiple runs in one data source and dcm2niix postfixes inserted into the acquisition label)
jsonfiles = []
acqlabel = bids.get_bidsvalue(bidsname, 'acq')
patterns = (bidsname.replace('_run-1_', '_run-[0-9]*_').replace(
'_magnitude1',
'_magnitude*').replace('_magnitude2', '_magnitude*').replace(
'_phase1', '_phase*').replace('_phase2', '_phase*'),
bidsname.replace('_run-1_', '_run-[0-9]*_').replace(
'_magnitude1',
'_phase*').replace('_magnitude2', '_phase*'))
for pattern in patterns:
jsonfiles.extend((bidsses / 'fmap').glob(pattern + '.json'))
if acqlabel:
cepattern = bids.get_bidsvalue(pattern, 'acq',
acqlabel + '[CE][0-9]*')
jsonfiles.extend(
list((bidsses / 'fmap').glob(cepattern + '.json')))
# Save the meta-data in the jsonfiles
for jsonfile in sorted(set(jsonfiles)):
# Add the IntendedFor data
with jsonfile.open('r') as json_fid:
data = json.load(json_fid)
if 'IntendedFor' not in data:
if niifiles:
LOGGER.info(f"Adding IntendedFor to: {jsonfile}")
elif intendedfor:
LOGGER.warning(
f"Empty 'IntendedFor' fieldmap value in {jsonfile}: the search for {intendedfor} gave no results"
)
else:
LOGGER.warning(
f"Empty 'IntendedFor' fieldmap value in {jsonfile}: the IntendedFor value of the bidsmap entry was empty"
)
data['IntendedFor'] = [
niifile.as_posix() for niifile in niifiles
] # The path needs to use forward slashes instead of backward slashes
with jsonfile.open('w') as json_fid:
json.dump(data, json_fid, indent=4)
# Extract the echo times from magnitude1 and magnitude2 and add them to the phasediff json-file
if jsonfile.name.endswith('phasediff.json'):
json_magnitude = [None, None]
TE = [None, None]
for n in (0, 1):
json_magnitude[
n] = jsonfile.parent / jsonfile.name.replace(
'_phasediff', f"_magnitude{n+1}")
if not json_magnitude[n].is_file():
LOGGER.error(
f"Could not find expected magnitude{n+1} image associated with: {jsonfile}"
)
else:
with json_magnitude[n].open('r') as json_fid:
data = json.load(json_fid)
TE[n] = data['EchoTime']
if None in TE:
LOGGER.error(
f"Cannot find and add valid EchoTime1={TE[0]} and EchoTime2={TE[1]} data to: {jsonfile}"
)
elif TE[0] > TE[1]:
LOGGER.error(
f"Found invalid EchoTime1={TE[0]} > EchoTime2={TE[1]} for: {jsonfile}"
)
else:
with jsonfile.open('r') as json_fid:
data = json.load(json_fid)
data['EchoTime1'] = TE[0]
data['EchoTime2'] = TE[1]
LOGGER.info(
f"Adding EchoTime1: {TE[0]} and EchoTime2: {TE[1]} to {jsonfile}"
)
with jsonfile.open('w') as json_fid:
json.dump(data, json_fid, indent=4)
# Collect personal data from a source header (PAR/XML does not contain personal info)
if dataformat == 'DICOM' and sourcefile.name:
personals['participant_id'] = subid
if sesid:
if 'session_id' not in personals:
personals['session_id'] = sesid
else:
return # Only take data from the first session -> BIDS specification
age = bids.get_dicomfield(
'PatientAge', sourcefile
) # A string of characters with one of the following formats: nnnD, nnnW, nnnM, nnnY
if age.endswith('D'):
personals['age'] = str(int(float(age.rstrip('D')) / 365.2524))
elif age.endswith('W'):
personals['age'] = str(int(float(age.rstrip('W')) / 52.1775))
elif age.endswith('M'):
personals['age'] = str(int(float(age.rstrip('M')) / 12))
elif age.endswith('Y'):
personals['age'] = str(int(float(age.rstrip('Y'))))
elif age:
personals['age'] = age
personals['sex'] = bids.get_dicomfield('PatientSex', sourcefile)
personals['size'] = bids.get_dicomfield('PatientSize', sourcefile)
personals['weight'] = bids.get_dicomfield('PatientWeight', sourcefile)
def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> None:
"""
The bidscoiner plugin to convert the session DICOM and PAR/REC source-files into BIDS-valid nifti-files in the
corresponding bids session-folder and extract personals (e.g. Age, Sex) from the source header
:param session: The full-path name of the subject/session source folder
:param bidsmap: The full mapping heuristics from the bidsmap YAML-file
:param bidsses: The full-path name of the BIDS output `sub-/ses-` folder
:return: Nothing
"""
# Get the subject identifiers and the BIDS root folder from the bidsses folder
if bidsses.name.startswith('ses-'):
bidsfolder = bidsses.parent.parent
subid = bidsses.parent.name
sesid = bidsses.name
else:
bidsfolder = bidsses.parent
subid = bidsses.name
sesid = ''
# Get started and see what dataformat we have
options = bidsmap['Options']['plugins']['dcm2niix2bids']
datasource = bids.get_datasource(session, {'dcm2niix2bids': options})
dataformat = datasource.dataformat
if not dataformat:
LOGGER.info(f"No {__name__} sourcedata found in: {session}")
return
# Make a list of all the data sources / runs
manufacturer = 'UNKNOWN'
sources = []
if dataformat == 'DICOM':
sources = bidscoin.lsdirs(session)
manufacturer = datasource.attributes('Manufacturer')
elif dataformat == 'PAR':
sources = bids.get_parfiles(session)
manufacturer = 'Philips Medical Systems'
else:
LOGGER.exception(f"Unsupported dataformat '{dataformat}'")
# Read or create a scans_table and tsv-file
scans_tsv = bidsses / f"{subid}{bids.add_prefix('_',sesid)}_scans.tsv"
if scans_tsv.is_file():
scans_table = pd.read_csv(scans_tsv, sep='\t', index_col='filename')
else:
scans_table = pd.DataFrame(columns=['acq_time'], dtype='str')
scans_table.index.name = 'filename'
# Process all the source files or run subfolders
sourcefile = Path()
for source in sources:
# Get a sourcefile
if dataformat == 'DICOM':
sourcefile = bids.get_dicomfile(source)
elif dataformat == 'PAR':
sourcefile = source
if not sourcefile.name:
continue
# Get a matching run from the bidsmap
datasource = bids.DataSource(sourcefile, {'dcm2niix2bids': options},
dataformat)
run, match = bids.get_matching_run(datasource, bidsmap, runtime=True)
# Check if we should ignore this run
if datasource.datatype in bidsmap['Options']['bidscoin'][
'ignoretypes']:
LOGGER.info(f"Leaving out: {source}")
continue
# Check if we already know this run
if not match:
LOGGER.error(
f"Skipping unknown '{datasource.datatype}' run: {sourcefile}\n-> Re-run the bidsmapper and delete {bidsses} to solve this warning"
)
continue
LOGGER.info(f"Processing: {source}")
# Create the BIDS session/datatype output folder
if run['bids']['suffix'] in bids.get_derivatives(datasource.datatype):
outfolder = bidsfolder / 'derivatives' / manufacturer.replace(
' ', '') / subid / sesid / datasource.datatype
else:
outfolder = bidsses / datasource.datatype
outfolder.mkdir(parents=True, exist_ok=True)
# Compose the BIDS filename using the matched run
bidsname = bids.get_bidsname(subid, sesid, run, runtime=True)
runindex = run['bids'].get('run', '')
if runindex.startswith('<<') and runindex.endswith('>>'):
bidsname = bids.increment_runindex(outfolder, bidsname)
jsonfiles = [
(outfolder / bidsname).with_suffix('.json')
] # List -> Collect the associated json-files (for updating them later) -- possibly > 1
# Check if file already exists (-> e.g. when a static runindex is used)
if (outfolder / bidsname).with_suffix('.json').is_file():
LOGGER.warning(
f"{outfolder/bidsname}.* already exists and will be deleted -- check your results carefully!"
)
for ext in ('.nii.gz', '.nii', '.json', '.tsv', '.tsv.gz', '.bval',
'.bvec'):
(outfolder / bidsname).with_suffix(ext).unlink(missing_ok=True)
# Convert physiological log files (dcm2niix can't handle these)
if run['bids']['suffix'] == 'physio':
if bids.get_dicomfile(
source, 2).name: # TODO: issue warning or support PAR
LOGGER.warning(
f"Found > 1 DICOM file in {source}, using: {sourcefile}")
physiodata = physio.readphysio(sourcefile)
physio.physio2tsv(physiodata, outfolder / bidsname)
# Convert the source-files in the run folder to nifti's in the BIDS-folder
else:
command = '{command} {args} -f "{filename}" -o "{outfolder}" "{source}"'.format(
command=options['command'],
args=options.get('args', ''),
filename=bidsname,
outfolder=outfolder,
source=source)
if not bidscoin.run_command(command):
if not list(outfolder.glob(f"{bidsname}.nii*")): continue
if list(outfolder.glob(f"{bidsname}a.nii*")):
LOGGER.warning(
f"Unexpected variants of {outfolder/bidsname}* were produced by dcm2niix. Possibly this can be remedied by using the dcm2niix -i option (to ignore derived, localizer and 2D images)"
)
# Replace uncropped output image with the cropped one
if '-x y' in options.get('args', ''):
for dcm2niixfile in sorted(
outfolder.glob(bidsname +
'*_Crop_*')): # e.g. *_Crop_1.nii.gz
ext = ''.join(dcm2niixfile.suffixes)
newbidsfile = str(dcm2niixfile).rsplit(ext, 1)[0].rsplit(
'_Crop_', 1)[0] + ext
LOGGER.info(
f"Found dcm2niix _Crop_ postfix, replacing original file\n{dcm2niixfile} ->\n{newbidsfile}"
)
dcm2niixfile.replace(newbidsfile)
# Rename all files that got additional postfixes from dcm2niix. See: https://github.com/rordenlab/dcm2niix/blob/master/FILENAMING.md
dcm2niixpostfixes = ('_c', '_i', '_Eq', '_real', '_imaginary',
'_MoCo', '_t', '_Tilt', '_e', '_ph', '_ADC',
'_fieldmaphz')
dcm2niixfiles = sorted(
set([
dcm2niixfile for dcm2niixpostfix in dcm2niixpostfixes
for dcm2niixfile in outfolder.glob(
f"{bidsname}*{dcm2niixpostfix}*.nii*")
]))
if not jsonfiles[0].is_file(
) and dcm2niixfiles: # Possibly renamed by dcm2niix, e.g. with multi-echo data (but not always for the first echo)
jsonfiles.pop(0)
for dcm2niixfile in dcm2niixfiles:
ext = ''.join(dcm2niixfile.suffixes)
postfixes = str(dcm2niixfile).split(bidsname)[1].rsplit(
ext)[0].split('_')[1:]
newbidsname = dcm2niixfile.name # Strip the additional postfixes and assign them to bids entities in the for-loop below
for postfix in postfixes: # dcm2niix postfixes _c%d, _e%d and _ph (and any combination of these in that order) are for multi-coil data, multi-echo data and phase data
# Patch the echo entity in the newbidsname with the dcm2niix echo info # NB: We can't rely on the bids-entity info here because manufacturers can e.g. put multiple echos in one series / run-folder
if 'echo' in run['bids'] and postfix.startswith('e'):
echonr = f"_{postfix}".replace('_e',
'') # E.g. postfix='e1'
if not echonr:
echonr = '1'
if echonr.isnumeric():
newbidsname = bids.insert_bidskeyval(
newbidsname, 'echo', echonr.lstrip('0')
) # In contrast to other labels, run and echo labels MUST be integers. Those labels MAY include zero padding, but this is NOT RECOMMENDED to maintain their uniqueness
else:
LOGGER.error(
f"Unexpected postix '{postfix}' found in {dcm2niixfile}"
)
newbidsname = bids.get_bidsvalue(
newbidsname, 'dummy', postfix
) # Append the unknown postfix to the acq-label
# Patch the phase entity in the newbidsname with the dcm2niix mag/phase info
elif 'part' in run['bids'] and postfix in (
'ph', 'real', 'imaginary'
): # e.g. part: ['', 'mag', 'phase', 'real', 'imag', 0]
if postfix == 'ph':
newbidsname = bids.insert_bidskeyval(
newbidsname, 'part', 'phase')
if postfix == 'real':
newbidsname = bids.insert_bidskeyval(
newbidsname, 'part', 'real')
if postfix == 'imaginary':
newbidsname = bids.insert_bidskeyval(
newbidsname, 'part', 'imag')
# Patch fieldmap images (NB: datatype=='fmap' is too broad, see the fmap.yaml file)
elif run['bids']['suffix'] in bids.bidsdatatypes['fmap'][0][
'suffixes']: # i.e. in ('magnitude','magnitude1','magnitude2','phase1','phase2','phasediff','fieldmap'). TODO: Make this robust for future BIDS versions
if len(dcm2niixfiles) not in (
1, 2, 3, 4
): # Phase / echo data may be stored in the same data source / run folder
LOGGER.debug(
f"Unknown fieldmap {outfolder/bidsname} for '{postfix}'"
)
newbidsname = newbidsname.replace(
'_magnitude1a', '_magnitude2'
) # First catch this potential weird / rare case
newbidsname = newbidsname.replace(
'_magnitude1_pha', '_phase2'
) # First catch this potential weird / rare case
newbidsname = newbidsname.replace(
'_magnitude1_e1', '_magnitude1'
) # Case 2 = Two phase and magnitude images
newbidsname = newbidsname.replace(
'_magnitude1_e2', '_magnitude2'
) # Case 2: This can happen when the e2 image is stored in the same directory as the e1 image, but with the e2 listed first
newbidsname = newbidsname.replace(
'_magnitude2_e1', '_magnitude1'
) # Case 2: This can happen when the e2 image is stored in the same directory as the e1 image, but with the e2 listed first
newbidsname = newbidsname.replace(
'_magnitude2_e2', '_magnitude2') # Case 2
if len(dcm2niixfiles) in (
2, 3
): # Case 1 = One or two magnitude + one phasediff image
newbidsname = newbidsname.replace(
'_magnitude1_ph', '_phasediff')
newbidsname = newbidsname.replace(
'_magnitude2_ph', '_phasediff')
newbidsname = newbidsname.replace(
'_phasediff_e1', '_phasediff') # Case 1
newbidsname = newbidsname.replace(
'_phasediff_e2', '_phasediff') # Case 1
newbidsname = newbidsname.replace(
'_phasediff_ph', '_phasediff') # Case 1
newbidsname = newbidsname.replace(
'_magnitude1_ph', '_phase1'
) # Case 2: One or two magnitude and phase images in one folder / datasource
newbidsname = newbidsname.replace(
'_magnitude2_ph', '_phase2'
) # Case 2: Two magnitude + two phase images in one folder / datasource
newbidsname = newbidsname.replace(
'_phase1_e1', '_phase1') # Case 2
newbidsname = newbidsname.replace(
'_phase1_e2', '_phase2'
) # Case 2: This can happen when the e2 image is stored in the same directory as the e1 image, but with the e2 listed first
newbidsname = newbidsname.replace(
'_phase2_e1', '_phase1'
) # Case 2: This can happen when the e2 image is stored in the same directory as the e1 image, but with the e2 listed first
newbidsname = newbidsname.replace(
'_phase2_e2', '_phase2') # Case 2
newbidsname = newbidsname.replace(
'_phase1_ph', '_phase1'
) # Case 2: One or two magnitude and phase images in one folder / datasource
newbidsname = newbidsname.replace(
'_phase2_ph', '_phase2'
) # Case 2: Two magnitude + two phase images in one folder / datasource
newbidsname = newbidsname.replace(
'_magnitude_e1', '_magnitude'
) # Case 3 = One magnitude + one fieldmap image
if len(dcm2niixfiles) == 2:
newbidsname = newbidsname.replace(
'_fieldmap_e1', '_magnitude'
) # Case 3: One magnitude + one fieldmap image in one folder / datasource
newbidsname = newbidsname.replace(
'_fieldmap_e1', '_fieldmap') # Case 3
newbidsname = newbidsname.replace(
'_magnitude_ph', '_fieldmap'
) # Case 3: One magnitude + one fieldmap image in one folder / datasource
newbidsname = newbidsname.replace(
'_fieldmap_ph', '_fieldmap') # Case 3
# Append the dcm2niix info to acq-label, may need to be improved / elaborated for future BIDS standards, supporting multi-coil data
else:
newbidsname = bids.get_bidsvalue(
newbidsname, 'dummy', postfix)
# Remove the added postfix from the new bidsname
newbidsname = newbidsname.replace(f"_{postfix}_",
'_') # If it is not last
newbidsname = newbidsname.replace(f"_{postfix}.",
'.') # If it is last
# The ADC images are not BIDS compliant
if postfix == 'ADC':
LOGGER.warning(
f"The {newbidsname} image is most likely not BIDS-compliant -- you can probably delete it safely and update the scants.tsv file"
)
# Save the nifti file with a new name
if runindex.startswith('<<') and runindex.endswith('>>'):
newbidsname = bids.increment_runindex(
outfolder, newbidsname, ''
) # Update the runindex now that the acq-label has changed
newbidsfile = outfolder / newbidsname
LOGGER.info(
f"Found dcm2niix {postfixes} postfixes, renaming\n{dcm2niixfile} ->\n{newbidsfile}"
)
if newbidsfile.is_file():
LOGGER.warning(
f"Overwriting existing {newbidsfile} file -- check your results carefully!"
)
dcm2niixfile.replace(newbidsfile)
# Rename all associated files (i.e. the json-, bval- and bvec-files)
oldjsonfile = dcm2niixfile.with_suffix('').with_suffix('.json')
newjsonfile = newbidsfile.with_suffix('').with_suffix('.json')
if not oldjsonfile.is_file():
LOGGER.warning(
f"Unexpected file conversion result: {oldjsonfile} not found"
)
else:
if oldjsonfile in jsonfiles:
jsonfiles.remove(oldjsonfile)
if newjsonfile not in jsonfiles:
jsonfiles.append(newjsonfile)
for oldfile in outfolder.glob(
dcm2niixfile.with_suffix('').stem + '.*'):
oldfile.replace(
newjsonfile.with_suffix(''.join(oldfile.suffixes)))
# Copy over the source meta-data
metadata = bids.copymetadata(sourcefile, outfolder / bidsname,
options.get('meta', []))
# Loop over and adapt all the newly produced json sidecar-files and write to the scans.tsv file (NB: assumes every nifti-file comes with a json-file)
for jsonfile in sorted(set(jsonfiles)):
# Load the json meta-data
with jsonfile.open('r') as json_fid:
jsondata = json.load(json_fid)
# Add all the source meta data to the meta-data
for metakey, metaval in metadata.items():
if jsondata.get(metakey) == metaval:
LOGGER.warning(
f"Replacing {metakey} values in {jsonfile}: {jsondata[metakey]} -> {metaval}"
)
jsondata[metakey] = metaval
# Add all the run meta data to the meta-data. NB: the dynamic `IntendedFor` value is handled separately later
for metakey, metaval in run['meta'].items():
if metakey != 'IntendedFor':
metaval = datasource.dynamicvalue(metaval,
cleanup=False,
runtime=True)
try:
metaval = ast.literal_eval(str(metaval))
except (ValueError, SyntaxError):
pass
LOGGER.info(
f"Adding '{metakey}: {metaval}' to: {jsonfile}")
if not metaval:
metaval = None
jsondata[metakey] = metaval
# Remove unused (but added from the template) B0FieldIdentifiers/Sources
if not jsondata.get('B0FieldSource'):
jsondata.pop('B0FieldSource', None)
if not jsondata.get('B0FieldIdentifier'):
jsondata.pop('B0FieldIdentifier', None)
# Save the meta-data to the json sidecar-file
with jsonfile.open('w') as json_fid:
json.dump(jsondata, json_fid, indent=4)
# Parse the acquisition time from the source header or else from the json file (NB: assuming the source file represents the first acquisition)
outputfile = [
file for file in jsonfile.parent.glob(jsonfile.stem + '.*')
if file.suffix in ('.nii', '.gz')
] # Find the corresponding nifti/tsv.gz file (there should be only one, let's not make assumptions about the .gz extension)
if not outputfile:
LOGGER.exception(
f"No data-file found with {jsonfile} when updating {scans_tsv}"
)
elif datasource.datatype not in bidsmap['Options']['bidscoin'][
'bidsignore'] and not run['bids'][
'suffix'] in bids.get_derivatives(datasource.datatype):
acq_time = ''
if dataformat == 'DICOM':
acq_time = f"{datasource.attributes('AcquisitionDate')}T{datasource.attributes('AcquisitionTime')}"
elif dataformat == 'PAR':
acq_time = datasource.attributes('exam_date')
if not acq_time or acq_time == 'T':
acq_time = f"1925-01-01T{jsondata.get('AcquisitionTime','')}"
try:
acq_time = dateutil.parser.parse(acq_time)
if options.get('anon', 'y') in ('y', 'yes'):
acq_time = acq_time.replace(
year=1925, month=1, day=1
) # Privacy protection (see BIDS specification)
acq_time = acq_time.isoformat()
except Exception as jsonerror:
LOGGER.warning(
f"Could not parse the acquisition time from: {sourcefile}\n{jsonerror}"
)
acq_time = 'n/a'
scanpath = outputfile[0].relative_to(bidsses)
scans_table.loc[scanpath.as_posix(), 'acq_time'] = acq_time
# Write the scans_table to disk
LOGGER.info(f"Writing acquisition time data to: {scans_tsv}")
scans_table.sort_values(by=['acq_time', 'filename'], inplace=True)
scans_table.replace('', 'n/a').to_csv(scans_tsv,
sep='\t',
encoding='utf-8',
na_rep='n/a')
# Collect personal data from a source header (PAR/XML does not contain personal info)
personals = {}
if sesid and 'session_id' not in personals:
personals['session_id'] = sesid
personals['age'] = ''
if dataformat == 'DICOM':
age = datasource.attributes(
'PatientAge'
) # A string of characters with one of the following formats: nnnD, nnnW, nnnM, nnnY
if age.endswith('D'): age = float(age.rstrip('D')) / 365.2524
elif age.endswith('W'): age = float(age.rstrip('W')) / 52.1775
elif age.endswith('M'): age = float(age.rstrip('M')) / 12
elif age.endswith('Y'): age = float(age.rstrip('Y'))
if age:
if options.get('anon', 'y') in ('y', 'yes'):
age = int(float(age))
personals['age'] = str(age)
personals['sex'] = datasource.attributes('PatientSex')
personals['size'] = datasource.attributes('PatientSize')
personals['weight'] = datasource.attributes('PatientWeight')
# Store the collected personals in the participants_table
participants_tsv = bidsfolder / 'participants.tsv'
if participants_tsv.is_file():
participants_table = pd.read_csv(participants_tsv, sep='\t', dtype=str)
participants_table.set_index(['participant_id'],
verify_integrity=True,
inplace=True)
else:
participants_table = pd.DataFrame()
participants_table.index.name = 'participant_id'
if subid in participants_table.index and 'session_id' in participants_table.keys(
) and participants_table.loc[subid, 'session_id']:
return # Only take data from the first session -> BIDS specification
for key in personals: # TODO: Check that only values that are consistent over sessions go in the participants.tsv file, otherwise put them in a sessions.tsv file
if key not in participants_table or participants_table[key].isnull(
).get(subid, True) or participants_table[key].get(subid) == 'n/a':
participants_table.loc[subid, key] = personals[key]
# Write the collected data to the participants tsv-file
LOGGER.info(f"Writing {subid} subject data to: {participants_tsv}")
participants_table.replace('', 'n/a').to_csv(participants_tsv,
sep='\t',
encoding='utf-8',
na_rep='n/a')
def coin_dicom(session: str, bidsmap: dict, bidsfolder: str, personals: dict,
subprefix: str, sesprefix: str) -> None:
"""
Converts the session dicom-files into BIDS-valid nifti-files in the corresponding bidsfolder and
extracts personals (e.g. Age, Sex) from the dicom header
:param session: The full-path name of the subject/session source folder
:param bidsmap: The full mapping heuristics from the bidsmap YAML-file
:param bidsfolder: The full-path name of the BIDS root-folder
:param personals: The dictionary with the personal information
:param subprefix: The prefix common for all source subject-folders
:param sesprefix: The prefix common for all source session-folders
:return: Nothing
"""
if not bids.lsdirs(session):
logger.warning('No series subfolder(s) found in: ' + session)
return
TE = [None, None]
# Get a valid BIDS subject identifier from the (first) dicom-header or from the session source folder
if bidsmap['DICOM']['participant_label'] and bidsmap['DICOM'][
'participant_label'].startswith(
'<<') and bidsmap['DICOM']['participant_label'].endswith('>>'):
subid = bids.get_dicomfield(
bidsmap['DICOM']['participant_label'][2:-2],
bids.get_dicomfile(bids.lsdirs(session)[0]))
elif bidsmap['DICOM']['participant_label']:
subid = bidsmap['DICOM']['participant_label']
else:
subid = session.rsplit(os.sep + subprefix,
1)[1].split(os.sep + sesprefix, 1)[0]
subid = 'sub-' + bids.cleanup_label(subid.lstrip(subprefix))
if subid == subprefix:
logger.error('Error: No valid subject identifier found for: ' +
session)
return
# Get a valid or empty BIDS session identifier from the (first) dicom-header or from the session source folder
if bidsmap['DICOM']['session_label'] and bidsmap['DICOM'][
'session_label'].startswith(
'<<') and bidsmap['DICOM']['session_label'].endswith('>>'):
sesid = bids.get_dicomfield(
bidsmap['DICOM']['session_label'][2:-2],
bids.get_dicomfile(bids.lsdirs(session)[0]))
elif bidsmap['DICOM']['session_label']:
sesid = bidsmap['DICOM']['session_label']
elif os.sep + sesprefix in session:
sesid = session.rsplit(os.sep + sesprefix)[1]
else:
sesid = ''
if sesid:
sesid = 'ses-' + bids.cleanup_label(sesid.lstrip(sesprefix))
# Create the BIDS session-folder and a scans.tsv file
bidsses = os.path.join(
bidsfolder, subid, sesid
) # NB: This gives a trailing '/' if ses=='', but that should be ok
os.makedirs(bidsses, exist_ok=True)
scans_tsv = os.path.join(bidsses,
f'{subid}{bids.add_prefix("_",sesid)}_scans.tsv')
if os.path.exists(scans_tsv):
scans_table = pd.read_csv(scans_tsv, sep='\t', index_col='filename')
else:
scans_table = pd.DataFrame(columns=['acq_time'], dtype='str')
scans_table.index.name = 'filename'
# Process all the dicom series subfolders
for series in bids.lsdirs(session):
if series.startswith('.'):
logger.info('Ignoring hidden dicom-folder: ' + series)
continue
else:
logger.info('Processing dicom-folder: ' + series)
# Get the cleaned-up bids labels from a dicom-file and bidsmap
dicomfile = bids.get_dicomfile(series)
if not dicomfile: continue
result = bids.get_matching_dicomseries(dicomfile, bidsmap)
series_ = result['series']
modality = result['modality']
# Create the BIDS session/modality folder
bidsmodality = os.path.join(bidsses, modality)
os.makedirs(bidsmodality, exist_ok=True)
# Compose the BIDS filename using the bids labels and run-index
runindex = series_['bids']['run_index']
if runindex.startswith('<<') and runindex.endswith('>>'):
bidsname = bids.get_bidsname(subid, sesid, modality, series_,
runindex[2:-2])
bidsname = bids.increment_runindex(bidsmodality, bidsname)
else:
bidsname = bids.get_bidsname(subid, sesid, modality, series_,
runindex)
# Convert the dicom-files in the series folder to nifti's in the BIDS-folder
command = '{path}dcm2niix {args} -f "{filename}" -o "{outfolder}" "{infolder}"'.format(
path=bidsmap['Options']['dcm2niix']['path'],
args=bidsmap['Options']['dcm2niix']['args'],
filename=bidsname,
outfolder=bidsmodality,
infolder=series)
logger.info('$ ' + command)
process = subprocess.run(
command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT
) # TODO: investigate shell=False and capture_output=True
logger.info(process.stdout.decode('utf-8'))
if process.returncode != 0:
errormsg = f'Error: Failed to process {series} (errorcode {process.returncode})'
logger.error(errormsg)
continue
# Replace uncropped output image with the cropped one
if '-x y' in bidsmap['Options']['dcm2niix']['args']:
for filename in sorted(
glob.glob(os.path.join(
bidsmodality,
bidsname + '*_Crop_*'))): # e.g. *_Crop_1.nii.gz
basepath, ext1 = os.path.splitext(filename)
basepath, ext2 = os.path.splitext(
basepath) # Account for .nii.gz files
basepath = basepath.rsplit('_Crop_', 1)[0]
newfilename = basepath + ext2 + ext1
logger.info(
f'Found dcm2niix _Crop_ suffix, replacing original file\n{filename} ->\n{newfilename}'
)
os.replace(filename, newfilename)
# Rename all files ending with _c%d, _e%d and _ph (and any combination of these): These are produced by dcm2niix for multi-coil data, multi-echo data and phase data, respectively
jsonfiles = [
] # Collect the associated json-files (for updating them later) -- possibly > 1
for suffix in ('_c', '_e', '_ph', '_i'):
for filename in sorted(
glob.glob(
os.path.join(bidsmodality,
bidsname + suffix + '[0-9]*'))):
basepath, ext1 = os.path.splitext(filename)
basepath, ext2 = os.path.splitext(
basepath) # Account for .nii.gz files
basepath, index = basepath.rsplit(suffix, 1)
index = index.split('_')[0].zfill(
2
) # Zero padd as specified in the BIDS-standard (assuming two digits is sufficient); strip following suffices (fieldmaps produce *_e2_ph files)
# This is a special hack: dcm2niix does not always add a _c/_e suffix for the first(?) coil/echo image -> add it when we encounter a **_e2/_c2 file
if suffix in (
'_c', '_e'
) and int(index) == 2 and basepath.rsplit(
'_', 1
)[1] != 'magnitude1': # For fieldmaps: *_magnitude1_e[index] -> *_magnitude[index] (This is handled below)
filename_ce = basepath + ext2 + ext1 # The file without the _c1/_e1 suffix
if suffix == '_e' and bids.set_bidslabel(basepath, 'echo'):
newbasepath_ce = bids.set_bidslabel(
basepath, 'echo', '1')
else:
newbasepath_ce = bids.set_bidslabel(
basepath, 'dummy',
suffix.upper() + '1'.zfill(len(index))
) # --> append to acq-label, may need to be elaborated for future BIDS standards, supporting multi-coil data
newfilename_ce = newbasepath_ce + ext2 + ext1 # The file as it should have been
if os.path.isfile(filename_ce):
if filename_ce != newfilename_ce:
logger.info(
f'Found no dcm2niix {suffix} suffix for image instance 1, renaming\n{filename_ce} ->\n{newfilename_ce}'
)
os.rename(filename_ce, newfilename_ce)
if ext1 == '.json':
jsonfiles.append(newbasepath_ce + '.json')
# Patch the basepath with the suffix info
if suffix == '_e' and bids.set_bidslabel(basepath,
'echo') and index:
basepath = bids.set_bidslabel(
basepath, 'echo', str(int(index))
) # In contrast to other labels, run and echo labels MUST be integers. Those labels MAY include zero padding, but this is NOT RECOMMENDED to maintain their uniqueness
elif suffix == '_e' and basepath.rsplit('_', 1)[1] in (
'magnitude1',
'magnitude2') and index: # i.e. modality == 'fmap'
basepath = basepath[0:-1] + str(
int(index)
) # basepath: *_magnitude1_e[index] -> *_magnitude[index]
# Read the echo times that need to be added to the json-file (see below)
if os.path.splitext(filename)[1] == '.json':
with open(filename, 'r') as json_fid:
data = json.load(json_fid)
TE[int(index) - 1] = data['EchoTime']
logger.info(
f"Reading EchoTime{index} = {data['EchoTime']} from: {filename}"
)
elif suffix == '_e' and basepath.rsplit(
'_', 1
)[1] == 'phasediff' and index: # i.e. modality == 'fmap'
pass
elif suffix == '_ph' and basepath.rsplit('_', 1)[1] in [
'phase1', 'phase2'
] and index: # i.e. modality == 'fmap' (TODO: untested)
basepath = basepath[0:-1] + str(
int(index
)) # basepath: *_phase1_e[index] -> *_phase[index]
logger.warning('Untested dcm2niix "_ph"-filetype: ' +
basepath)
else:
basepath = bids.set_bidslabel(
basepath, 'dummy',
suffix.upper() + index
) # --> append to acq-label, may need to be elaborated for future BIDS standards, supporting multi-coil data
# Save the file with a new name
if runindex.startswith('<<') and runindex.endswith('>>'):
newbidsname = bids.increment_runindex(
bidsmodality, os.path.basename(basepath), ext2 + ext1
) # Update the runindex now that the acq-label has changed
else:
newbidsname = os.path.basename(basepath)
newfilename = os.path.join(bidsmodality,
newbidsname + ext2 + ext1)
logger.info(
f'Found dcm2niix {suffix} suffix, renaming\n{filename} ->\n{newfilename}'
)
os.rename(filename, newfilename)
if ext1 == '.json':
jsonfiles.append(
os.path.join(bidsmodality, newbidsname + '.json'))
# Loop over and adapt all the newly produced json files and write to the scans.tsv file (every nifti-file comes with a json-file)
if not jsonfiles:
jsonfiles = [os.path.join(bidsmodality, bidsname + '.json')]
for jsonfile in set(jsonfiles):
# Check if dcm2niix behaved as expected
if not os.path.isfile(jsonfile):
logger.warning(
f'Unexpected file conbids.version result: {jsonfile} not found'
)
continue
# Add a dummy b0 bval- and bvec-file for any file without a bval/bvec file (e.g. sbref, b0 scans)
if modality == 'dwi':
bvecfile = os.path.splitext(jsonfile)[0] + '.bvec'
bvalfile = os.path.splitext(jsonfile)[0] + '.bval'
if not os.path.isfile(bvecfile):
logger.info('Adding dummy bvec file: ' + bvecfile)
with open(bvecfile, 'w') as bvec_fid:
bvec_fid.write('0\n0\n0\n')
if not os.path.isfile(bvalfile):
logger.info('Adding dummy bval file: ' + bvalfile)
with open(bvalfile, 'w') as bval_fid:
bval_fid.write('0\n')
# Add the TaskName to the func json-file
elif modality == 'func':
with open(jsonfile, 'r') as json_fid:
data = json.load(json_fid)
if not 'TaskName' in data:
logger.info('Adding TaskName to: ' + jsonfile)
data['TaskName'] = series_['bids']['task_label']
with open(jsonfile, 'w') as json_fid:
json.dump(data, json_fid, indent=4)
# Add the EchoTime(s) used to create the difference image to the fmap json-file. NB: This assumes the magnitude series have already been parsed (i.e. their nifti's had an _e suffix) -- This is normally the case for Siemens (phase-series being saved after the magnitude series
elif modality == 'fmap':
if series_['bids']['suffix'] == 'phasediff':
logger.info('Adding EchoTime1 and EchoTime2 to: ' +
jsonfile)
with open(jsonfile, 'r') as json_fid:
data = json.load(json_fid)
data['EchoTime1'] = TE[0]
data['EchoTime2'] = TE[1]
with open(jsonfile, 'w') as json_fid:
json.dump(data, json_fid, indent=4)
if TE[0] > TE[1]:
logger.warning('EchoTime1 > EchoTime2 in: ' + jsonfile)
# Parse the acquisition time from the json file
with open(jsonfile, 'r') as json_fid:
data = json.load(json_fid)
acq_time = dateutil.parser.parse(data['AcquisitionTime'])
niipath = glob.glob(
os.path.splitext(jsonfile)[0] + '.nii*'
)[0] # Find the corresponding nifti file (there should be only one, let's not make assumptions about the .gz extension)
niipath = niipath.replace(
bidsses + os.sep, ''
) # Use a relative path. Somehow .strip(bidsses) instead of replace(bidsses,'') does not work properly
scans_table.loc[
niipath,
'acq_time'] = '1900-01-01T' + acq_time.strftime('%H:%M:%S')
# Write the scans_table to disk
logger.info('Writing acquisition time data to: ' + scans_tsv)
scans_table.to_csv(scans_tsv, sep='\t', encoding='utf-8')
# Search for the IntendedFor images and add them to the json-files. This has been postponed untill all modalities have been processed (i.e. so that all target images are indeed on disk)
if bidsmap['DICOM']['fmap'] is not None:
for fieldmap in bidsmap['DICOM']['fmap']:
if 'IntendedFor' in fieldmap['bids'] and fieldmap['bids'][
'IntendedFor']:
bidsname = bids.get_bidsname(subid, sesid, 'fmap', fieldmap,
'1')
acqlabel = bids.set_bidslabel(bidsname, 'acq')
for jsonfile in glob.glob(
os.path.join(
bidsses, 'fmap',
bidsname.replace(
'_run-1_', '_run-[0-9]*_').replace(
acqlabel, acqlabel + '[CE][0-9]*') +
'.json')
): # Account for multiple runs and dcm2niix suffixes inserted into the acquisition label
intendedfor = fieldmap['bids']['IntendedFor']
if intendedfor.startswith('<<') and intendedfor.endswith(
'>>'):
intendedfor = intendedfor[2:-2].split('><')
else:
intendedfor = [intendedfor]
niifiles = []
for selector in intendedfor:
niifiles.extend([
niifile.split(os.sep + subid + os.sep,
1)[1].replace('\\', '/')
for niifile in sorted(
glob.glob(
os.path.join(
bidsses,
f'**{os.sep}*{selector}*.nii*')))
]) # Search in all series using a relative path
with open(jsonfile, 'r') as json_fid:
data = json.load(json_fid)
data['IntendedFor'] = niifiles
logger.info('Adding IntendedFor to: ' + jsonfile)
with open(jsonfile, 'w') as json_fid:
json.dump(data, json_fid, indent=4)
# Catch magnitude2 files produced by dcm2niix (i.e. magnitude1 & magnitude2 both in the same seriesfolder)
if jsonfile.endswith('magnitude1.json'):
jsonfile2 = jsonfile.rsplit('1.json', 1)[0] + '2.json'
if os.path.isfile(jsonfile2):
with open(jsonfile2, 'r') as json_fid:
data = json.load(json_fid)
if 'IntendedFor' not in data:
data['IntendedFor'] = niifiles
logger.info('Adding IntendedFor to: ' + jsonfile2)
with open(jsonfile2, 'w') as json_fid:
json.dump(data, json_fid, indent=4)
# Collect personal data from the DICOM header
dicomfile = bids.get_dicomfile(series)
personals['participant_id'] = subid
if sesid:
personals['session_id'] = sesid
personals['age'] = bids.get_dicomfield('PatientAge', dicomfile)
personals['sex'] = bids.get_dicomfield('PatientSex', dicomfile)
personals['size'] = bids.get_dicomfield('PatientSize', dicomfile)
personals['weight'] = bids.get_dicomfield('PatientWeight', dicomfile)
def coin_dicom(session: Path, bidsmap: dict, bidsfolder: Path, personals: dict,
subprefix: str, sesprefix: str) -> None:
"""
Converts the session dicom-files into BIDS-valid nifti-files in the corresponding bidsfolder and
extracts personals (e.g. Age, Sex) from the dicom header
:param session: The full-path name of the subject/session source folder
:param bidsmap: The full mapping heuristics from the bidsmap YAML-file
:param bidsfolder: The full-path name of the BIDS root-folder
:param personals: The dictionary with the personal information
:param subprefix: The prefix common for all source subject-folders
:param sesprefix: The prefix common for all source session-folders
:return: Nothing
"""
if not bids.lsdirs(session):
LOGGER.warning(f"No run subfolder(s) found in: {session}")
return
TE = [None, None]
# Get valid BIDS subject/session identifiers from the (first) dicom-header or from the session source folder
subid, sesid = bids.get_subid_sesid(
bids.get_dicomfile(bids.lsdirs(session)[0]),
bidsmap['DICOM']['subject'], bidsmap['DICOM']['session'], subprefix,
sesprefix)
if subid == subprefix:
LOGGER.error(f"No valid subject identifier found for: {session}")
return
# Create the BIDS session-folder and a scans.tsv file
bidsses = bidsfolder / subid / sesid
if bidsses.is_dir():
LOGGER.warning(
f"Existing BIDS output-directory found, which may result in duplicate data (with increased run-index). Make sure {bidsses} was cleaned-up from old data before (re)running the bidscoiner"
)
bidsses.mkdir(parents=True, exist_ok=True)
scans_tsv = bidsses / f"{subid}{bids.add_prefix('_',sesid)}_scans.tsv"
if scans_tsv.is_file():
scans_table = pd.read_csv(scans_tsv, sep='\t', index_col='filename')
else:
scans_table = pd.DataFrame(columns=['acq_time'], dtype='str')
scans_table.index.name = 'filename'
# Process all the dicom run subfolders
for runfolder in bids.lsdirs(session):
# Get a dicom-file
dicomfile = bids.get_dicomfile(runfolder)
if not dicomfile.name: continue
# Get a matching run from the bidsmap
run, modality, index = bids.get_matching_run(dicomfile, bidsmap)
# Check if we should ignore this run
if modality == bids.ignoremodality:
LOGGER.info(f"Leaving out: {runfolder}")
continue
# Check if we already know this run
if index is None:
LOGGER.warning(
f"Skipping unknown '{modality}': {dicomfile}\n-> re-run the bidsmapper and delete {session} to solve this warning"
)
continue
LOGGER.info(f"Processing: {runfolder}")
# Create the BIDS session/modality folder
bidsmodality = bidsses / modality
bidsmodality.mkdir(parents=True, exist_ok=True)
# Compose the BIDS filename using the matched run
bidsname = bids.get_bidsname(subid, sesid, modality, run)
runindex = run['bids']['run']
if runindex.startswith('<<') and runindex.endswith('>>'):
bidsname = bids.increment_runindex(bidsmodality, bidsname)
# Check if file already exists (-> e.g. when a static runindex is used)
if (bidsmodality / bidsname).with_suffix('.json').is_file():
LOGGER.warning(
f"{bidsmodality/bidsname}.* already exists -- check your results carefully!"
)
# Convert the dicom-files in the run folder to nifti's in the BIDS-folder
command = '{path}dcm2niix {args} -f "{filename}" -o "{outfolder}" "{infolder}"'.format(
path=bidsmap['Options']['dcm2niix']['path'],
args=bidsmap['Options']['dcm2niix']['args'],
filename=bidsname,
outfolder=bidsmodality,
infolder=runfolder)
if not bids.run_command(command):
continue
# Replace uncropped output image with the cropped one
if '-x y' in bidsmap['Options']['dcm2niix']['args']:
for filename in sorted(
bidsmodality.glob(bidsname +
'*_Crop_*')): # e.g. *_Crop_1.nii.gz
ext = ''.join(filename.suffixes)
newfilename = str(filename).rsplit(ext, 1)[0].rsplit(
'_Crop_', 1)[0] + ext
LOGGER.info(
f"Found dcm2niix _Crop_ suffix, replacing original file\n{filename} ->\n{newfilename}"
)
filename.replace(newfilename)
# Rename all files ending with _c%d, _e%d and _ph (and any combination of these): These are produced by dcm2niix for multi-coil data, multi-echo data and phase data, respectively
jsonfiles = [
] # Collect the associated json-files (for updating them later) -- possibly > 1
for dcm2niisuffix in ('_c', '_e', '_ph', '_i'):
for filename in sorted(
bidsmodality.glob(bidsname + dcm2niisuffix + '*')):
ext = ''.join(filename.suffixes)
basepath, index = str(filename).rsplit(ext, 1)[0].rsplit(
dcm2niisuffix, 1
) # basepath = the name without the added stuff (i.e. bidsmodality/bidsname), index = added dcm2niix index (e.g. _c1 -> index=1)
basesuffix = basepath.rsplit(
'_', 1
)[1] # The BIDS suffix, e.g. basepath = *_magnitude1 -> basesuffix=magnitude1
index = index.split('_')[0].zfill(
2
) # Zero padd as specified in the BIDS-standard (assuming two digits is sufficient); strip following suffices (fieldmaps produce *_e2_ph files)
# This is a special hack: dcm2niix does not always add a _c/_e suffix for the first(?) coil/echo image -> add it when we encounter a **_e2/_c2 file
if dcm2niisuffix in (
'_c', '_e'
) and int(index) == 2 and basesuffix not in [
'magnitude1', 'phase1'
]: # For fieldmaps: *_magnitude1_e[index] -> *_magnitude[index] (This is handled below)
filename_ce = Path(
basepath + ext) # The file without the _c1/_e1 suffix
if dcm2niisuffix == '_e' and bids.get_bidsvalue(
basepath, 'echo'):
newbasepath_ce = Path(
bids.get_bidsvalue(basepath, 'echo', '1'))
else:
newbasepath_ce = Path(
bids.get_bidsvalue(
basepath, 'dummy',
dcm2niisuffix.upper() + '1'.zfill(len(index)))
) # --> append to acq-label, may need to be elaborated for future BIDS standards, supporting multi-coil data
newfilename_ce = newbasepath_ce.with_suffix(
ext) # The file as it should have been
if filename_ce.is_file():
if filename_ce != newfilename_ce:
LOGGER.info(
f"Found no dcm2niix {dcm2niisuffix} suffix for image instance 1, renaming\n{filename_ce} ->\n{newfilename_ce}"
)
filename_ce.replace(newfilename_ce)
if ext == '.json':
jsonfiles.append(
newbasepath_ce.with_suffix('.json'))
# Patch the basepath with the dcm2niix suffix info (we can't rely on the basepath info here because Siemens can e.g. put multiple echos in one series / run-folder)
if dcm2niisuffix == '_e' and bids.get_bidsvalue(
basepath, 'echo') and index:
basepath = bids.get_bidsvalue(
basepath, 'echo', str(int(index))
) # In contrast to other labels, run and echo labels MUST be integers. Those labels MAY include zero padding, but this is NOT RECOMMENDED to maintain their uniqueness
elif dcm2niisuffix == '_e' and basesuffix in (
'magnitude1',
'magnitude2') and index: # i.e. modality == 'fmap'
basepath = basepath[0:-1] + str(
int(index)
) # basepath: *_magnitude1_e[index] -> *_magnitude[index]
# Collect the echo times that need to be added to the json-file (see below)
if filename.suffix == '.json':
with filename.open('r') as json_fid:
data = json.load(json_fid)
TE[int(index) - 1] = data['EchoTime']
LOGGER.info(
f"Collected EchoTime{index} = {data['EchoTime']} from: {filename}"
)
elif dcm2niisuffix == '_e' and basesuffix == 'phasediff' and index: # i.e. modality == 'fmap'
pass
elif dcm2niisuffix == '_e' and basesuffix in [
'phase1', 'phase2'
] and index: # i.e. modality == 'fmap'
basepath = basepath[0:-1] + str(
int(index)
) # basepath: *_phase1_e[index]_ph -> *_phase[index]
else:
basepath = bids.get_bidsvalue(
basepath, 'dummy',
dcm2niisuffix.upper() + index
) # --> append to acq-label, may need to be elaborated for future BIDS standards, supporting multi-coil data
# Save the file with a new name
newbidsname = str(Path(basepath).name)
if runindex.startswith('<<') and runindex.endswith('>>'):
newbidsname = bids.increment_runindex(
bidsmodality, newbidsname, ext
) # Update the runindex now that the acq-label has changed
newfilename = (bidsmodality / newbidsname).with_suffix(ext)
LOGGER.info(
f"Found dcm2niix {dcm2niisuffix} suffix, renaming\n{filename} ->\n{newfilename}"
)
filename.replace(newfilename)
if ext == '.json':
jsonfiles.append(
(bidsmodality / newbidsname).with_suffix('.json'))
# Loop over and adapt all the newly produced json files and write to the scans.tsv file (every nifti-file comes with a json-file)
if not jsonfiles:
jsonfiles = [(bidsmodality / bidsname).with_suffix('.json')]
for jsonfile in set(jsonfiles):
# Check if dcm2niix behaved as expected
if not jsonfile.is_file():
LOGGER.error(
f"Unexpected file conversion result: {jsonfile} not found")
continue
# Add a dummy b0 bval- and bvec-file for any file without a bval/bvec file (e.g. sbref, b0 scans)
if modality == 'dwi':
bvecfile = jsonfile.with_suffix('.bvec')
bvalfile = jsonfile.with_suffix('.bval')
if not bvecfile.is_file():
LOGGER.info(f"Adding dummy bvec file: {bvecfile}")
with bvecfile.open('w') as bvec_fid:
bvec_fid.write('0\n0\n0\n')
if not bvalfile.is_file():
LOGGER.info(f"Adding dummy bval file: {bvalfile}")
with bvalfile.open('w') as bval_fid:
bval_fid.write('0\n')
# Add the TaskName to the func json-file
elif modality == 'func':
with jsonfile.open('r') as json_fid:
data = json.load(json_fid)
if not 'TaskName' in data:
LOGGER.info(f"Adding TaskName to: {jsonfile}")
data['TaskName'] = run['bids']['task']
with jsonfile.open('w') as json_fid:
json.dump(data, json_fid, indent=4)
# Add the EchoTime(s) used to create the difference image to the fmap json-file. NB: This assumes the magnitude runs have already been parsed (i.e. their nifti's had an _e suffix) -- This is normally the case for Siemens (phase-runs being saved after the magnitude runs
elif modality == 'fmap':
if run['bids']['suffix'] == 'phasediff':
LOGGER.info(
f"Adding EchoTime1: {TE[0]} and EchoTime2: {TE[1]} to {jsonfile}"
)
if TE[0] is None or TE[1] is None:
LOGGER.warning(
f"Missing Echo-Time data for: {jsonfile}")
elif TE[0] > TE[1]:
LOGGER.warning(
f"EchoTime1 > EchoTime2 for: {jsonfile}")
with jsonfile.open('r') as json_fid:
data = json.load(json_fid)
data['EchoTime1'] = TE[0]
data['EchoTime2'] = TE[1]
with jsonfile.open('w') as json_fid:
json.dump(data, json_fid, indent=4)
# Parse the acquisition time from the json file or else from the dicom header (NB: assuming the dicom file represents the first aqcuisition)
with jsonfile.open('r') as json_fid:
data = json.load(json_fid)
if 'AcquisitionTime' not in data:
data['AcquisitionTime'] = bids.get_dicomfield(
'AcquisitionTime', dicomfile)
acq_time = dateutil.parser.parse(data['AcquisitionTime'])
scanpath = list(
jsonfile.parent.glob(jsonfile.stem + '.nii*')
)[0].relative_to(
bidsses
) # Find the corresponding nifti file (there should be only one, let's not make assumptions about the .gz extension)
scans_table.loc[
scanpath.as_posix(),
'acq_time'] = '1900-01-01T' + acq_time.strftime('%H:%M:%S')
# Write the scans_table to disk
LOGGER.info(f"Writing acquisition time data to: {scans_tsv}")
scans_table.sort_values(by=['acq_time', 'filename'], inplace=True)
scans_table.to_csv(scans_tsv, sep='\t', encoding='utf-8')
# Search for the IntendedFor images and add them to the json-files. This has been postponed untill all modalities have been processed (i.e. so that all target images are indeed on disk)
if bidsmap['DICOM']['fmap'] is not None:
for fieldmap in bidsmap['DICOM']['fmap']:
bidsname = bids.get_bidsname(subid, sesid, 'fmap', fieldmap)
niifiles = []
intendedfor = fieldmap['bids']['IntendedFor']
# Search for the imaging files that match the IntendedFor search criteria
if intendedfor:
if intendedfor.startswith('<<') and intendedfor.endswith('>>'):
intendedfor = intendedfor[2:-2].split('><')
elif not isinstance(intendedfor, list):
intendedfor = [intendedfor]
for selector in intendedfor:
niifiles.extend(
[
Path(niifile).relative_to(bidsfolder / subid)
for niifile in sorted(
bidsses.rglob(f"*{selector}*.nii*"))
if selector
]
) # Search in all runs using a relative path to the subject folder
else:
intendedfor = []
# Save the IntendedFor data in the json-files (account for multiple runs and dcm2niix suffixes inserted into the acquisition label)
acqlabel = bids.get_bidsvalue(bidsname, 'acq')
for jsonfile in list((bidsses/'fmap').glob(bidsname.replace('_run-1_', '_run-[0-9]*_') + '.json')) + \
list((bidsses/'fmap').glob(bidsname.replace('_run-1_', '_run-[0-9]*_').replace(acqlabel, acqlabel+'[CE][0-9]*') + '.json')):
if niifiles:
LOGGER.info(f"Adding IntendedFor to: {jsonfile}")
elif intendedfor:
LOGGER.warning(
f"Empty 'IntendedFor' fieldmap value in {jsonfile}: the search for {intendedfor} gave no results"
)
else:
LOGGER.warning(
f"Empty 'IntendedFor' fieldmap value in {jsonfile}: the IntendedFor value of the bidsmap entry was empty"
)
with jsonfile.open('r') as json_fid:
data = json.load(json_fid)
data['IntendedFor'] = [
niifile.as_posix() for niifile in niifiles
] # The path needs to use forward slashes instead of backward slashes
with jsonfile.open('w') as json_fid:
json.dump(data, json_fid, indent=4)
# Catch magnitude2 and phase2 files produced by dcm2niix (i.e. magnitude1 & magnitude2 both in the same runfolder)
if jsonfile.name.endswith(
'magnitude1.json') or jsonfile.name.endswith(
'phase1.json'):
jsonfile2 = jsonfile.with_name(
jsonfile.name.rsplit('1.json', 1)[0] + '2.json')
if jsonfile2.is_file():
with jsonfile2.open('r') as json_fid:
data = json.load(json_fid)
if 'IntendedFor' not in data:
if niifiles:
LOGGER.info(
f"Adding IntendedFor to: {jsonfile2}")
else:
LOGGER.warning(
f"Empty 'IntendedFor' fieldmap value in {jsonfile2}: the search for {intendedfor} gave no results"
)
data['IntendedFor'] = [
niifile.as_posix() for niifile in niifiles
] # The path needs to use forward slashes instead of backward slashes
with jsonfile2.open('w') as json_fid:
json.dump(data, json_fid, indent=4)
# Collect personal data from the DICOM header: only from the first session (-> BIDS specification)
if 'runfolder' in locals():
dicomfile = bids.get_dicomfile(runfolder)
personals['participant_id'] = subid
if sesid:
if 'session_id' not in personals:
personals['session_id'] = sesid
else:
return
age = bids.get_dicomfield(
'PatientAge', dicomfile
) # A string of characters with one of the following formats: nnnD, nnnW, nnnM, nnnY
if age.endswith('D'):
personals['age'] = str(int(float(age.rstrip('D')) / 365.2524))
elif age.endswith('W'):
personals['age'] = str(int(float(age.rstrip('W')) / 52.1775))
elif age.endswith('M'):
personals['age'] = str(int(float(age.rstrip('M')) / 12))
elif age.endswith('Y'):
personals['age'] = str(int(float(age.rstrip('Y'))))
elif age:
personals['age'] = age
personals['sex'] = bids.get_dicomfield('PatientSex', dicomfile)
personals['size'] = bids.get_dicomfield('PatientSize', dicomfile)
personals['weight'] = bids.get_dicomfield('PatientWeight', dicomfile)
def coin_dicom(session, bidsmap, bidsfolder, personals):
"""
Converts the session dicom-files into BIDS-valid nifti-files in the corresponding bidsfolder and
extracts personals (e.g. Age, Sex) from the dicom header
:param str session: The full-path name of the subject/session source folder
:param dict bidsmap: The full mapping heuristics from the bidsmap YAML-file
:param str bidsfolder: The full-path name of the BIDS root-folder
:param dict personals: The dictionary with the personal information
:return: Nothing
:rtype: NoneType
"""
global logfile
TE = [None, None]
# Get a valid BIDS subject identifier from the (first) dicom-header or from the session source folder
if bidsmap['DICOM']['participant_label'] and bidsmap['DICOM'][
'participant_label'].startswith(
'<<') and bidsmap['DICOM']['participant_label'].endswith('>>'):
subid = 'sub-' + bids.get_dicomfield(
bidsmap['DICOM']['participant_label'][2:-2],
bids.get_dicomfile(bids.lsdirs(session)[0]))
elif bidsmap['DICOM']['participant_label']:
subid = 'sub-' + bidsmap['DICOM']['participant_label']
else:
subid = 'sub-' + session.rsplit(os.sep + 'sub-', 1)[1].split(
os.sep + 'ses-', 1)[0]
if subid == 'sub-':
bids.printlog(
'Error: No valid subject identifier found for: ' + session,
logfile)
return
# Get a BIDS session identifier from the (first) dicom-header or from the session source folder
if bidsmap['DICOM']['session_label'] and bidsmap['DICOM'][
'session_label'].startswith(
'<<') and bidsmap['DICOM']['session_label'].endswith('>>'):
sesid = 'ses-' + bids.get_dicomfield(
bidsmap['DICOM']['session_label'][2:-2],
bids.get_dicomfile(bids.lsdirs(session)[0]))
elif bidsmap['DICOM']['session_label']:
sesid = 'ses-' + bidsmap['DICOM']['session_label']
elif os.sep + 'ses-' in session:
sesid = 'ses-' + session.rsplit(os.sep + 'ses-')[1]
else:
sesid = ''
# Create the BIDS session-folder
bidsses = os.path.join(
bidsfolder, subid, sesid
) # NB: This gives a trailing '/' if ses=='', but that should be ok
os.makedirs(bidsses, exist_ok=True)
# Process all the dicom series subfolders
for series in bids.lsdirs(session):
bids.printlog('Processing dicom-folder: ' + series, logfile)
# Get the cleaned-up bids labels from a dicom-file and bidsmap
dicomfile = bids.get_dicomfile(series)
result = bids.get_matching_dicomseries(dicomfile, bidsmap)
series_ = result['series']
modality = result['modality']
# Create the BIDS session/modality folder
bidsmodality = os.path.join(bidsses, modality)
os.makedirs(bidsmodality, exist_ok=True)
# Compose the BIDS filename using the bids labels and run-index
runindex = series_['run_index']
if runindex.startswith('<<') and runindex.endswith('>>'):
bidsname = bids.get_bidsname(subid, sesid, modality, series_,
runindex[2:-2])
bidsname = bids.increment_runindex(bidsmodality, bidsname)
else:
bidsname = bids.get_bidsname(subid, sesid, modality, series_,
runindex)
# Convert the dicom-files in the series folder to nifti's in the BIDS-folder
command = '{path}dcm2niix {args} -f "{filename}" -o "{outfolder}" "{infolder}"'.format(
path=bidsmap['Options']['dcm2niix']['path'],
args=bidsmap['Options']['dcm2niix']['args'],
filename=bidsname,
outfolder=bidsmodality,
infolder=series)
bids.printlog('$ ' + command, logfile)
process = subprocess.run(
command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT
) # TODO: investigate shell=False and capture_output=True
bids.printlog(process.stdout.decode('utf-8'), logfile)
if process.returncode != 0:
errormsg = 'Error: Failed to process {} (errorcode {})'.format(
series, process.returncode)
bids.printlog(errormsg, logfile)
continue
# Rename all files ending with _c%d, _e%d and _ph: These are produced by dcm2niix for multi-coil data, multi-echo data and phase data, respectively
jsonfiles = [
] # Collect the associated json-files (for updating them later)
for suffix in ('_c', '_e', '_ph'):
for filename in sorted(
glob.glob(
os.path.join(bidsmodality, bidsname + suffix + '*'))):
basepath, ext1 = os.path.splitext(filename)
basepath, ext2 = os.path.splitext(
basepath) # Account for .nii.gz files
basepath, index = basepath.rsplit(suffix, 1)
if suffix == '_e' and bids.set_bidslabel(basepath,
'echo') and index:
basepath = bids.set_bidslabel(basepath, 'echo', index)
elif suffix == '_e' and basepath.rsplit('_', 1)[1] in [
'magnitude1', 'magnitude2'
] and index: # i.e. modality == 'fmap'
basepath = basepath[0:-1] + index
# Read the echo times that need to be added to the json-file (see below)
if os.path.splitext(filename)[1] == '.json':
with open(filename, 'r') as json_fid:
data = json.load(json_fid)
TE[int(index) - 1] = data['EchoTime']
bids.printlog(
'Reading EchoTime{} = {} from: {}'.format(
index, data['EchoTime'], filename), logfile)
elif suffix == '_e' and basepath.rsplit(
'_', 1
)[1] == 'phasediff' and index: # i.e. modality == 'fmap'
pass
elif suffix == '_ph' and basepath.rsplit('_', 1)[1] in [
'phase1', 'phase2'
] and index: # i.e. modality == 'fmap' (TODO: untested)
basepath = basepath[0:-1] + index
bids.printlog(
'WARNING: Untested dcm2niix "_ph"-filetype: ' +
basepath, logfile)
else:
basepath = bids.set_bidslabel(
basepath, 'dummy',
suffix.upper() + index
) # --> append to acq-label, may need to be elaborated for future BIDS standards, supporting multi-coil data
if runindex.startswith('<<') and runindex.endswith('>>'):
newbidsname = bids.increment_runindex(
bidsmodality, os.path.basename(basepath), ext2 + ext1
) # Update the runindex now that the acq-label has changed
else:
newbidsname = os.path.basename(basepath)
newfilename = os.path.join(bidsmodality,
newbidsname + ext2 + ext1)
bids.printlog(
'Found dcm2niix {} suffix, renaming\n{} ->\n{}'.format(
suffix, filename, newfilename), logfile)
os.rename(filename, newfilename)
if ext1 == '.json':
jsonfiles.append(
os.path.join(bidsmodality, newbidsname + '.json'))
# Loop over and adapt all the newly produced json files (every nifti file comes with a json file)
if not jsonfiles:
jsonfiles = [os.path.join(bidsmodality, bidsname + '.json')]
for jsonfile in jsonfiles:
# Add a dummy b0 bval- and bvec-file for any file without a bval/bvec file (e.g. sbref, b0 scans)
if modality == 'dwi':
bvecfile = os.path.splitext(jsonfile)[0] + '.bvec'
bvalfile = os.path.splitext(jsonfile)[0] + '.bval'
if not os.path.isfile(bvecfile):
with open(bvecfile, 'w') as bvec_fid:
bids.printlog('Adding dummy bvec file: ' + bvecfile,
logfile)
bvec_fid.write('0\n0\n0\n')
if not os.path.isfile(bvalfile):
with open(bvalfile, 'w') as bval_fid:
bids.printlog('Adding dummy bval file: ' + bvalfile,
logfile)
bval_fid.write('0\n')
# Add the TaskName to the func json-file
elif modality == 'func':
with open(jsonfile, 'r') as json_fid:
data = json.load(json_fid)
if not 'TaskName' in data:
bids.printlog('Adding TaskName to: ' + jsonfile, logfile)
with open(jsonfile, 'w') as json_fid:
data['TaskName'] = series_['task_label']
json.dump(data, json_fid, indent=4)
# Add the EchoTime(s) used to create the difference image to the fmap json-file. NB: This assumes the magnitude series have already been parsed (i.e. their nifti's had an _e suffix) -- This is normally the case for Siemens (phase-series being saved after the magnitude series
elif modality == 'fmap':
if series_['suffix'] == 'phasediff':
bids.printlog(
'Adding EchoTime1 and EchoTime2 to: ' + jsonfile,
logfile)
with open(jsonfile, 'r') as json_fid:
data = json.load(json_fid)
data['EchoTime1'] = TE[0]
data['EchoTime2'] = TE[1]
with open(jsonfile, 'w') as json_fid:
json.dump(data, json_fid, indent=4)
if TE[0] > TE[1]:
bids.printlog(
'WARNING: EchoTime1 > EchoTime2 in: ' + jsonfile,
logfile)
# Search for the IntendedFor images and add them to the json-files. This has been postponed untill all modalities have been processed (i.e. so that all target images are indeed on disk)
if bidsmap['DICOM']['fmap'] is not None:
for fieldmap in bidsmap['DICOM']['fmap']:
if 'IntendedFor' in fieldmap and fieldmap['IntendedFor']:
jsonfile = os.path.join(
bidsses, 'fmap',
bids.get_bidsname(subid, sesid, 'fmap', fieldmap, '1') +
'.json'
) # TODO: Assumes that there is only 1 fieldmap acquired for each bidsmap entry / series
if not os.path.isfile(jsonfile):
continue
intendedfor = fieldmap['IntendedFor']
if intendedfor.startswith('<<') and intendedfor.endswith('>>'):
intendedfor = intendedfor[2:-2].split('><')
else:
intendedfor = [intendedfor]
with open(jsonfile, 'r') as json_fid:
data = json.load(json_fid)
niifiles = [
niifile.split(os.sep + subid + os.sep, 1)[1]
for niifile in sorted(
glob.glob(
os.path.join(
bidsses, '**' + os.sep + '*' +
'*'.join(intendedfor) + '*.nii*')))
] # Use a relative path
data['IntendedFor'] = niifiles
bids.printlog('Adding IntendedFor to: ' + jsonfile, logfile)
with open(jsonfile, 'w') as json_fid:
json.dump(data, json_fid, indent=4)
# Catch magnitude2 files produced by dcm2niix
if jsonfile.endswith('magnitude1.json'):
jsonfile2 = jsonfile.rsplit('1.json', 1)[0] + '2.json'
if os.path.isfile(jsonfile2):
with open(jsonfile2, 'r') as json_fid:
data = json.load(json_fid)
data['IntendedFor'] = niifiles
bids.printlog('Adding IntendedFor to: ' + jsonfile2,
logfile)
with open(jsonfile2, 'w') as json_fid:
json.dump(data, json_fid, indent=4)
# Collect personal data from the DICOM header
dicomfile = bids.get_dicomfile(series)
personals['participant_id'] = subid
if sesid:
personals[
'session_id'] = sesid # TODO: Check if this can be in the participants.tsv file according to BIDS
personals['age'] = bids.get_dicomfield('PatientAge', dicomfile)
personals['sex'] = bids.get_dicomfield('PatientSex', dicomfile)
personals['size'] = bids.get_dicomfield('PatientSize', dicomfile)
personals['weight'] = bids.get_dicomfield('PatientWeight', dicomfile)
def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> None:
"""
This wrapper funtion around spec2nii converts the MRS data in the session folder and saves it in the bidsfolder.
Each saved datafile should be accompanied with a json sidecar file. The bidsmap options for this plugin can be found in:
bidsmap_new['Options']['plugins']['spec2nii2bids']
:param session: The full-path name of the subject/session raw data source folder
:param bidsmap: The full mapping heuristics from the bidsmap YAML-file
:param bidsses: The full-path name of the BIDS output `sub-/ses-` folder
:return: Nothing
"""
# Get the subject identifiers and the BIDS root folder from the bidsses folder
if bidsses.name.startswith('ses-'):
bidsfolder = bidsses.parent.parent
subid = bidsses.parent.name
sesid = bidsses.name
else:
bidsfolder = bidsses.parent
subid = bidsses.name
sesid = ''
# Get started and see what dataformat we have
options = bidsmap['Options']['plugins']['spec2nii2bids']
datasource = bids.get_datasource(session, {'spec2nii2bids': options})
dataformat = datasource.dataformat
sourcefiles = [file for file in session.rglob('*') if is_sourcefile(file)]
if not sourcefiles:
LOGGER.info(f"No {__name__} sourcedata found in: {session}")
return
# Read or create a scans_table and tsv-file
scans_tsv = bidsses / f"{subid}{bids.add_prefix('_',sesid)}_scans.tsv"
if scans_tsv.is_file():
scans_table = pd.read_csv(scans_tsv, sep='\t', index_col='filename')
else:
scans_table = pd.DataFrame(columns=['acq_time'], dtype='str')
scans_table.index.name = 'filename'
# Loop over all MRS source data files and convert them to BIDS
for sourcefile in sourcefiles:
# Get a data source, a matching run from the bidsmap
datasource = bids.DataSource(sourcefile, {'spec2nii2bids': options})
run, index = bids.get_matching_run(datasource, bidsmap, runtime=True)
# Check if we should ignore this run
if datasource.datatype in bidsmap['Options']['bidscoin'][
'ignoretypes']:
LOGGER.info(f"Leaving out: {sourcefile}")
continue
# Check that we know this run
if index is None:
LOGGER.error(
f"Skipping unknown '{datasource.datatype}' run: {sourcefile}\n-> Re-run the bidsmapper and delete the MRS output data in {bidsses} to solve this warning"
)
continue
LOGGER.info(f"Processing: {sourcefile}")
# Create the BIDS session/datatype output folder
outfolder = bidsses / datasource.datatype
outfolder.mkdir(parents=True, exist_ok=True)
# Compose the BIDS filename using the matched run
bidsname = bids.get_bidsname(subid, sesid, run, runtime=True)
runindex = run['bids'].get('run', '')
if runindex.startswith('<<') and runindex.endswith('>>'):
bidsname = bids.increment_runindex(outfolder, bidsname)
jsonfile = (outfolder / bidsname).with_suffix('.json')
# Check if file already exists (-> e.g. when a static runindex is used)
if jsonfile.is_file():
LOGGER.warning(
f"{outfolder/bidsname}.* already exists and will be deleted -- check your results carefully!"
)
for ext in ('.nii.gz', '.nii', '.json', '.bval', '.bvec',
'.tsv.gz'):
(outfolder / bidsname).with_suffix(ext).unlink(missing_ok=True)
# Run spec2nii to convert the source-files in the run folder to nifti's in the BIDS-folder
arg = ''
args = options.get('args', OPTIONS['args'])
if args is None:
args = ''
if dataformat == 'SPAR':
dformat = 'philips'
arg = f'"{sourcefile.with_suffix(".SDAT")}"'
elif dataformat == 'Twix':
dformat = 'twix'
arg = '-e image'
elif dataformat == 'Pfile':
dformat = 'ge'
else:
LOGGER.exception(f"Unsupported dataformat: {dataformat}")
command = options.get("command", "spec2nii")
if not bidscoin.run_command(
f'{command} {dformat} -j -f "{bidsname}" -o "{outfolder}" {args} {arg} "{sourcefile}"'
):
if not list(outfolder.glob(f"{bidsname}.nii*")): continue
# Load and adapt the newly produced json sidecar-file (NB: assumes every nifti-file comes with a json-file)
with jsonfile.open('r') as json_fid:
jsondata = json.load(json_fid)
# Copy over the source meta-data
metadata = bids.copymetadata(sourcefile, outfolder / bidsname,
options.get('meta', []))
for metakey, metaval in metadata.items():
if jsondata.get(metakey) == metaval:
LOGGER.warning(
f"Replacing {metakey} values in {jsonfile}: {jsondata[metakey]} -> {metaval}"
)
jsondata[metakey] = metaval
# Add all the meta data to the json-file
for metakey, metaval in run['meta'].items():
metaval = datasource.dynamicvalue(metaval,
cleanup=False,
runtime=True)
try:
metaval = ast.literal_eval(str(metaval))
except (ValueError, SyntaxError):
pass
LOGGER.info(f"Adding '{metakey}: {metaval}' to: {jsonfile}")
if not metaval:
metaval = None
jsondata[metakey] = metaval
# Save the meta data to disk
with jsonfile.open('w') as json_fid:
json.dump(jsondata, json_fid, indent=4)
# Parse the acquisition time from the source header or else from the json file (NB: assuming the source file represents the first acquisition)
if datasource.datatype not in bidsmap['Options']['bidscoin'][
'bidsignore'] and not run['bids'][
'suffix'] in bids.get_derivatives(datasource.datatype):
acq_time = ''
if dataformat == 'SPAR':
acq_time = datasource.attributes('scan_date')
elif dataformat == 'Twix':
acq_time = f"{datasource.attributes('AcquisitionDate')}T{datasource.attributes('AcquisitionTime')}"
elif dataformat == 'Pfile':
acq_time = f"{datasource.attributes('rhr_rh_scan_date')}T{datasource.attributes('rhr_rh_scan_time')}"
if not acq_time or acq_time == 'T':
acq_time = f"1925-01-01T{jsondata.get('AcquisitionTime','')}"
try:
acq_time = dateutil.parser.parse(acq_time)
if options.get('anon', OPTIONS['anon']) in ('y', 'yes'):
acq_time = acq_time.replace(
year=1925, month=1,
day=1) # Privacy protection (see BIDS specification)
acq_time = acq_time.isoformat()
except Exception as jsonerror:
LOGGER.warning(
f"Could not parse the acquisition time from: {sourcefile}\n{jsonerror}"
)
acq_time = 'n/a'
scans_table.loc[jsonfile.with_suffix('.nii.gz').
relative_to(bidsses).as_posix(),
'acq_time'] = acq_time
# Write the scans_table to disk
LOGGER.info(f"Writing acquisition time data to: {scans_tsv}")
scans_table.sort_values(by=['acq_time', 'filename'], inplace=True)
scans_table.replace('', 'n/a').to_csv(scans_tsv,
sep='\t',
encoding='utf-8',
na_rep='n/a')
# Collect personal data from a source header
personals = {}
if sesid and 'session_id' not in personals:
personals['session_id'] = sesid
age = ''
if sesid and 'session_id' not in personals:
personals['session_id'] = sesid
if dataformat == 'Twix':
personals['sex'] = datasource.attributes('PatientSex')
personals['size'] = datasource.attributes('PatientSize')
personals['weight'] = datasource.attributes('PatientWeight')
age = datasource.attributes(
'PatientAge'
) # A string of characters with one of the following formats: nnnD, nnnW, nnnM, nnnY
elif dataformat == 'Pfile':
sex = datasource.attributes('rhe_patsex')
if sex == '0': personals['sex'] = 'O'
elif sex == '1': personals['sex'] = 'M'
elif sex == '2': personals['sex'] = 'F'
age = dateutil.parser.parse(
datasource.attributes('rhr_rh_scan_date')) - dateutil.parser.parse(
datasource.attributes('rhe_dateofbirth'))
age = str(age.days) + 'D'
if age.endswith('D'): age = float(age.rstrip('D')) / 365.2524
elif age.endswith('W'): age = float(age.rstrip('W')) / 52.1775
elif age.endswith('M'): age = float(age.rstrip('M')) / 12
elif age.endswith('Y'): age = float(age.rstrip('Y'))
if age and options.get('anon', OPTIONS['anon']) in ('y', 'yes'):
age = int(float(age))
personals['age'] = str(age)
# Store the collected personals in the participants_table
participants_tsv = bidsfolder / 'participants.tsv'
if participants_tsv.is_file():
participants_table = pd.read_csv(participants_tsv, sep='\t', dtype=str)
participants_table.set_index(['participant_id'],
verify_integrity=True,
inplace=True)
else:
participants_table = pd.DataFrame()
participants_table.index.name = 'participant_id'
if subid in participants_table.index and 'session_id' in participants_table.keys(
) and participants_table.loc[subid, 'session_id']:
return # Only take data from the first session -> BIDS specification
for key in personals: # TODO: Check that only values that are consistent over sessions go in the participants.tsv file, otherwise put them in a sessions.tsv file
if key not in participants_table or participants_table[key].isnull(
).get(subid, True) or participants_table[key].get(subid) == 'n/a':
participants_table.loc[subid, key] = personals[key]
# Write the collected data to the participants tsv-file
LOGGER.info(f"Writing {subid} subject data to: {participants_tsv}")
participants_table.replace('', 'n/a').to_csv(participants_tsv,
sep='\t',
encoding='utf-8',
na_rep='n/a')
def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> None:
"""
The bidscoiner plugin to convert the session Nibabel source-files into BIDS-valid nifti-files in the
corresponding bids session-folder
:param session: The full-path name of the subject/session source folder
:param bidsmap: The full mapping heuristics from the bidsmap YAML-file
:param bidsses: The full-path name of the BIDS output `sub-/ses-` folder
:return: Nothing
"""
# Get the subject identifiers and the BIDS root folder from the bidsses folder
if bidsses.name.startswith('ses-'):
bidsfolder = bidsses.parent.parent
subid = bidsses.parent.name
sesid = bidsses.name
else:
bidsfolder = bidsses.parent
subid = bidsses.name
sesid = ''
# Get started
options = bidsmap['Options']['plugins']['nibabel2bids']
ext = options.get('ext', OPTIONS['ext'])
meta = options.get('meta', [])
sourcefiles = [file for file in session.rglob('*') if is_sourcefile(file)]
if not sourcefiles:
LOGGER.info(f"No {__name__} sourcedata found in: {session}")
return
# Read or create a scans_table and tsv-file
scans_tsv = bidsses / f"{subid}{bids.add_prefix('_', sesid)}_scans.tsv"
if scans_tsv.is_file():
scans_table = pd.read_csv(scans_tsv, sep='\t', index_col='filename')
else:
scans_table = pd.DataFrame(columns=['acq_time'], dtype='str')
scans_table.index.name = 'filename'
# Collect the different Nibabel source files for all files in the session
for sourcefile in sourcefiles:
datasource = bids.DataSource(sourcefile, {'nibabel2bids': options})
run, match = bids.get_matching_run(datasource, bidsmap, runtime=True)
# Check if we should ignore this run
if datasource.datatype in bidsmap['Options']['bidscoin'][
'ignoretypes']:
LOGGER.info(f"Leaving out: {sourcefile}")
continue
# Check if we already know this run
if not match:
LOGGER.error(
f"Skipping unknown '{datasource.datatype}' run: {sourcefile}\n-> Re-run the bidsmapper and delete {bidsses} to solve this warning"
)
continue
LOGGER.info(f"Processing: {sourcefile}")
# Create the BIDS session/datatype output folder
outfolder = bidsses / datasource.datatype
outfolder.mkdir(parents=True, exist_ok=True)
# Compose the BIDS filename using the matched run
bidsname = bids.get_bidsname(subid, sesid, run, runtime=True)
runindex = run['bids'].get('run', '')
if runindex.startswith('<<') and runindex.endswith('>>'):
bidsname = bids.increment_runindex(outfolder, bidsname)
bidsfile = (outfolder / bidsname).with_suffix(ext)
# Check if file already exists (-> e.g. when a static runindex is used)
if bidsfile.is_file():
LOGGER.warning(
f"{bidsfile}.* already exists and will be deleted -- check your results carefully!"
)
bidsfile.with_suffix('').with_suffix(ext).unlink()
# Save the sourcefile as a BIDS nifti file
nib.save(nib.load(sourcefile), bidsfile)
# Copy over the source meta-data
jsonfile = bidsfile.with_suffix('').with_suffix('.json')
jsondata = bids.copymetadata(sourcefile, bidsfile, meta)
# Add all the meta data to the meta-data. NB: the dynamic `IntendedFor` value is handled separately later
for metakey, metaval in run['meta'].items():
if metakey != 'IntendedFor':
metaval = datasource.dynamicvalue(metaval,
cleanup=False,
runtime=True)
try:
metaval = ast.literal_eval(str(metaval))
except (ValueError, SyntaxError):
pass
LOGGER.info(f"Adding '{metakey}: {metaval}' to: {jsonfile}")
if not metaval:
metaval = None
jsondata[metakey] = metaval
# Remove unused (but added from the template) B0FieldIdentifiers/Sources
if not jsondata.get('B0FieldSource'):
jsondata.pop('B0FieldSource', None)
if not jsondata.get('B0FieldIdentifier'):
jsondata.pop('B0FieldIdentifier', None)
# Save the meta-data to the json sidecar-file
with jsonfile.open('w') as json_fid:
json.dump(jsondata, json_fid, indent=4)
# Add an entry to the scans_table (we typically don't have useful data to put there)
acq_time = dateutil.parser.parse(
f"1925-01-01T{jsondata.get('AcquisitionTime', '')}")
scans_table.loc[bidsfile.relative_to(bidsses).as_posix(),
'acq_time'] = acq_time.isoformat()
# Write the scans_table to disk
LOGGER.info(f"Writing data to: {scans_tsv}")
scans_table.replace('', 'n/a').to_csv(scans_tsv,
sep='\t',
encoding='utf-8',
na_rep='n/a')
# Add an (empty) entry to the participants_table (we don't have useful data to put there)
participants_tsv = bidsfolder / 'participants.tsv'
if participants_tsv.is_file():
participants_table = pd.read_csv(participants_tsv, sep='\t', dtype=str)
participants_table.set_index(['participant_id'],
verify_integrity=True,
inplace=True)
else:
participants_table = pd.DataFrame()
participants_table.index.name = 'participant_id'
if subid in participants_table.index and 'session_id' in participants_table.keys(
) and participants_table.loc[subid, 'session_id']:
return # Only take data from the first session -> BIDS specification
participants_table.loc[subid, 'session_id'] = sesid if sesid else None
# Write the collected data to the participants tsv-file
LOGGER.info(f"Writing {subid} subject data to: {participants_tsv}")
participants_table.replace('', 'n/a').to_csv(participants_tsv,
sep='\t',
encoding='utf-8',
na_rep='n/a')