def create_workflow(self, flow, inputnode, outputnode):
#conflow = pe.Workflow(name='MRTRix_connectome_pipeline')
#connectome_inputnode = pe.Node(interface=util.IdentityInterface(fields=['intck','fod_file','roi_volumes']),name='inputnode')
#connectome_outputnode = pe.Node(interface=util.IdentityInterface(fields=['connectome']),name='outputnode')
def get_first(output):
return output[0]
# Additional maps
map_merge = pe.Node(interface=util.Merge(4),
name="merge_additional_maps")
flow.connect([
(inputnode, map_merge, [('gFA', 'in1'), ('skewness', 'in2'),
('kurtosis', 'in3'), ('P0', 'in4')])
#(map_merge,cmtk_mrtrixcmat, [('out','additional_maps')]),
])
#print "INTCK : ",intck
if self.config.fiber_filter:
fibers_filter = pe.Node(
interface=FilterTractogram(out_file='streamlines_weights.txt'),
name='fibers_filter')
flow.connect([(inputnode, fibers_filter, [('track_file',
'in_tracks')])])
# if inputnode.inputs.diffusion_model == 'Deterministic':
# flow.connect([
# (inputnode,fibers_filter,[('track_file','in_tracks')])
# ])
# else:
# flow.connect([
# (inputnode,fibers_filter,[(('track_file',get_first),'in_tracks')]),
# ])
flow.connect([(inputnode, fibers_filter, [('fod_file', 'in_fod')])
])
connectome_builder = pe.Node(interface=BuildConnectome(),
name='connectome_builder')
#connectome_builder.inputs.zero_diagonal = True
#Test if trackfile is a list of tracks filename (Probabilistic tracking) or only a filename (Deterministic tracking)
flow.connect([(inputnode, connectome_builder, [('track_file',
'in_file')])])
# if inputnode.inputs.diffusion_model == 'Deterministic':
# print "Deterministic"
# flow.connect([
# (inputnode,connectome_builder,[('track_file','in_file')])
# ])
# else:
# print "Probabilistic"
# flow.connect([
# (inputnode,connectome_builder,[(('track_file',get_first),'in_file')])
# ])
flow.connect([
(inputnode, connectome_builder, [(('roi_volumes_registered',
get_first), 'in_parc')]),
])
if self.config.fiber_filter:
flow.connect([(fibers_filter, connectome_builder,
[('out_weights', 'in_weights')])])
flow.connect([(inputnode, outputnode, [('track_file',
'streamline_final_file')]),
(connectome_builder, outputnode,
[('out_file', 'connectivity_matrices')])])
