class IQMFileSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
subject_id = Str(mandatory=True, desc='the subject id')
modality = Str(mandatory=True, desc='the qc type')
session_id = traits.Either(None, Str, usedefault=True)
task_id = traits.Either(None, Str, usedefault=True)
acq_id = traits.Either(None, Str, usedefault=True)
rec_id = traits.Either(None, Str, usedefault=True)
run_id = traits.Either(None, Str, usedefault=True)
metadata = traits.Dict()
provenance = traits.Dict()
root = traits.Dict(desc='output root dictionary')
out_dir = File(desc='the output directory')
_outputs = traits.Dict(value={}, usedefault=True)
def __setattr__(self, key, value):
if key not in self.copyable_trait_names():
if not isdefined(value):
super(IQMFileSinkInputSpec, self).__setattr__(key, value)
self._outputs[key] = value
else:
if key in self._outputs:
self._outputs[key] = value
super(IQMFileSinkInputSpec, self).__setattr__(key, value)
if key == 'subject_id':
#I can not find where it is set from bids ... dirty fix
if str(value) == '<undefined>':
self.subject_id = 'TODO'
class FunctionalQCOutputSpec(TraitedSpec):
fber = traits.Float
efc = traits.Float
snr = traits.Float
gsr = traits.Dict
tsnr = traits.Float
dvars = traits.Dict
fd = traits.Dict
fwhm = traits.Dict(desc='full width half-maximum measure')
size = traits.Dict
spacing = traits.Dict
summary = traits.Dict
out_qc = traits.Dict(desc='output flattened dictionary with all measures')
class BIDSDataGrabberOutputSpec(TraitedSpec):
out_dict = traits.Dict(desc='output data structure')
fmap = OutputMultiPath(desc='output fieldmaps')
bold = OutputMultiPath(desc='output functional images')
sbref = OutputMultiPath(desc='output sbrefs')
t1w = OutputMultiPath(desc='output T1w images')
t2w = OutputMultiPath(desc='output T2w images')
class BIDSDataGrabberOutputSpec(TraitedSpec):
out_dict = traits.Dict(desc='output data structure')
preproc = OutputMultiPath(desc='output preproc functional images')
mask = OutputMultiPath(desc='output masks for functional images')
MELODICmix = OutputMultiPath(desc='output MELODICmix')
AROMAnoiseICs = OutputMultiPath(desc='output AROMAnoiseICs')
confounds = OutputMultiPath(desc='output confounds')
class ReadSidecarJSONOutputSpec(TraitedSpec):
subject_id = traits.Str()
session_id = traits.Str()
task_id = traits.Str()
acq_id = traits.Str()
rec_id = traits.Str()
run_id = traits.Str()
out_dict = traits.Dict()
class StructuralQCOutputSpec(TraitedSpec):
summary = traits.Dict(desc='summary statistics per tissue')
icvs = traits.Dict(desc='intracranial volume (ICV) fractions')
rpve = traits.Dict(desc='partial volume fractions')
size = traits.Dict(desc='image sizes')
spacing = traits.Dict(desc='image sizes')
fwhm = traits.Dict(desc='full width half-maximum measure')
inu = traits.Dict(desc='summary statistics of the bias field')
snr = traits.Dict
snrd = traits.Dict
cnr = traits.Float
fber = traits.Float
efc = traits.Float
qi_1 = traits.Float
wm2max = traits.Float
cjv = traits.Float
out_qc = traits.Dict(desc='output flattened dictionary with all measures')
out_noisefit = File(exists=True,
desc='plot of background noise and chi fitting')
tpm_overlap = traits.Dict
class BIDSDataGrabberInputSpec(BaseInterfaceInputSpec):
subject_data = traits.Dict(Str, traits.Any)
subject_id = Str()
class Phasediff2FieldmapInputSpec(BaseInterfaceInputSpec):
in_file = File(exists=True, mandatory=True, desc='input fieldmap')
metadata = traits.Dict(mandatory=True, desc='BIDS metadata dictionary')
