def args(self):
for fmri, meta in zip(self.config.get_bids('func'),
self.config.get_bids('func_metadata')):
# set ts parameters
self.kwargs['fmritcs'] = fmri
self.kwargs['fmriname'] = get_fmriname(fmri)
self.kwargs['fmriscout'] = None # not implemented
if self.kwargs['dcmethod'] == 'TOPUP':
self.kwargs['seunwarpdir'] = ijk_to_xyz(
meta['PhaseEncodingDirection'])
self.kwargs['sephasepos'], self.kwargs['sephaseneg'] = \
self._get_intended_sefmaps()
else:
self.kwargs['sephasepos'] = self.kwargs['sephaseneg'] = None
# None to NONE
kw = {
k: (v if v is not None else "NONE")
for k, v in self.kwargs.items()
}
yield self.spec.format(**kw)
def __init__(self, bids_data, output_directory):
"""
Specification to run pipeline on a single subject session.
:param bids_data: yielded spec from read_bids_dataset
:param output_directory: output directory for pipeline
"""
# input bids data struct
self.bids_data = bids_data
# @ parameters read from bids @ #
self.t1w = self.bids_data['t1w']
self.t1samplespacing = get_realdwelltime(
self.bids_data['t1w_metadata'])
if 'T2w' in self.bids_data['types']:
self.useT2 = 'true'
self.t2w = self.bids_data['t2w']
self.t2samplespacing = get_realdwelltime(
self.bids_data['t2w_metadata'])
else:
self.useT2 = 'false'
self.t2w = []
self.t2samplespacing = None
# distortion correction method: TOPUP, FIELDMAP, or NONE, inferred
# from files, defaults to spin echo (topup) if both field maps exist
self.unwarpdir = get_readoutdir(self.bids_data['t1w_metadata'])
if 'epi' in self.bids_data['types']:
self.dcmethod = 'TOPUP'
# spin echo field map spacing @TODO read during volume per fmap?
self.echospacing = self.bids_data['fmap_metadata']['positive'][0][
'EffectiveEchoSpacing']
self.echospacing = ('%.12f' % self.echospacing).rstrip('0')
# distortion correction phase encoding direction
if self.bids_data['func']:
self.seunwarpdir = ijk_to_xyz(
self.bids_data['func_metadata']['PhaseEncodingDirection'])
else:
# if no functional data is provided, use positive spin echo
self.seunwarpdir = ijk_to_xyz(
self.bids_data['fmap_metadata']['positive'][0]
['PhaseEncodingDirection'])
# set unused fmap parameters to none
self.fmapmag = self.fmapphase = self.fmapgeneralelectric = \
self.echodiff = self.gdcoeffs = None
elif 'magnitude' in self.bids_data['types']:
self.dcmethod = 'FIELDMAP'
# gradient field map delta TE
self.echodiff = None # @TODO
# set unused spin echo parameters to none
self.seunwarpdir = None
else:
# all distortion correction parameters set to none
self.fmapmag = self.fmapphase = self.fmapgeneralelectric = \
self.echodiff = self.gdcoeffs = self.dcmethod = \
self.seunwarpdir = self.echospacing = None
if not hasattr(self, 'fmribfcmethod'):
self.fmribfcmethod = None # this parameter has not been validated
# dwi parameters
if 'dwi' in self.bids_data['types']:
pass
# @TODO handle bids formatted physio data
self.physio = None
# intermediate template defaults
self.usestudytemplate = "false"
self.studytemplate = None
self.studytemplatebrain = None
# @ output files @ #
self.path = os.path.join(output_directory, 'files')
self.logs = os.path.join(output_directory, 'logs')
self.subject = self.bids_data['subject']
self.session = self.bids_data['session']
# Exec summ doesn't need this anymore. KJS 11/6/18
#deriv_root = self.path.split('/')[:-3]
#self.deriv = '/'.join(deriv_root)
# @ input files @ #
session_root = '/'.join(self.t1w[0].split('/')[:-2])
self.unproc = os.path.join(session_root, 'func')
bids_input_root = '/'.join(session_root.split('/')[:-2])
self.sourcedata_root = os.path.join(bids_input_root, 'sourcedata')
# print command for HCP
self.printcom = ''