def tensor_metrics_pipeline(self, **name_maps): # @UnusedVariable
"""
Fits the apparrent diffusion tensor (DT) to each voxel of the image
"""
# inputs=[FilesetSpec('tensor', nifti_gz_format),
# FilesetSpec('brain_mask', nifti_gz_format)],
# outputs=[FilesetSpec('fa', nifti_gz_format),
# FilesetSpec('adc', nifti_gz_format)],
pipeline = self.new_pipeline(
name='fa',
desc=("Calculates the FA and ADC from a tensor image"),
references=[],
name_maps=name_maps)
# Create tensor fit node
metrics = pipeline.add(
'metrics',
TensorMetrics(),
requirements=[mrtrix_req.v('3.0rc3')])
metrics.inputs.out_fa = 'fa.nii.gz'
metrics.inputs.out_adc = 'adc.nii.gz'
# Connect to inputs
pipeline.connect_input('tensor', metrics, 'in_file')
pipeline.connect_input('brain_mask', metrics, 'in_mask')
# Connect to outputs
pipeline.connect_output('fa', metrics, 'out_fa')
pipeline.connect_output('adc', metrics, 'out_adc')
# Check inputs/output are connected
return pipeline
def fa_pipeline(self, **kwargs): # @UnusedVariable
"""
Fits the apparrent diffusion tensor (DT) to each voxel of the image
"""
pipeline = self.create_pipeline(
name='fa',
inputs=[
DatasetSpec('tensor', nifti_gz_format),
DatasetSpec('brain_mask', nifti_gz_format)
],
outputs=[
DatasetSpec('fa', nifti_gz_format),
DatasetSpec('adc', nifti_gz_format)
],
desc=("Calculates the FA and ADC from a tensor image"),
version=1,
citations=[],
**kwargs)
# Create tensor fit node
metrics = pipeline.create_node(TensorMetrics(),
name='metrics',
requirements=[mrtrix3_req])
metrics.inputs.out_fa = 'fa.nii.gz'
metrics.inputs.out_adc = 'adc.nii.gz'
# Connect to inputs
pipeline.connect_input('tensor', metrics, 'in_file')
pipeline.connect_input('brain_mask', metrics, 'in_mask')
# Connect to outputs
pipeline.connect_output('fa', metrics, 'out_fa')
pipeline.connect_output('adc', metrics, 'out_adc')
# Check inputs/output are connected
return pipeline
def tensor_metrics_pipeline(self, **name_maps):
"""
Fits the apparrent diffusion tensor (DT) to each voxel of the image
"""
pipeline = self.new_pipeline(
name='fa',
desc=("Calculates the FA and ADC from a tensor image"),
citations=[],
name_maps=name_maps)
# Create tensor fit node
pipeline.add(
'metrics',
TensorMetrics(
out_fa='fa.nii.gz',
out_adc='adc.nii.gz'),
inputs={
'in_file': ('tensor', nifti_gz_format),
'in_mask': (self.brain_mask_spec_name, nifti_gz_format)},
outputs={
'fa': ('out_fa', nifti_gz_format),
'adc': ('out_adc', nifti_gz_format)},
requirements=[mrtrix_req.v('3.0rc3')])
return pipeline
def test_TensorMetrics_outputs():
output_map = dict(out_adc=dict(),
out_eval=dict(),
out_evec=dict(),
out_fa=dict(),
)
outputs = TensorMetrics.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_TensorMetrics_inputs():
input_map = dict(args=dict(argstr='%s',
),
component=dict(argstr='-num %s',
sep=',',
),
environ=dict(nohash=True,
usedefault=True,
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
in_file=dict(argstr='%s',
mandatory=True,
position=-1,
),
in_mask=dict(argstr='-mask %s',
),
modulate=dict(argstr='-modulate %s',
),
out_adc=dict(argstr='-adc %s',
),
out_eval=dict(argstr='-value %s',
),
out_evec=dict(argstr='-vector %s',
),
out_fa=dict(argstr='-fa %s',
),
terminal_output=dict(nohash=True,
),
)
inputs = TensorMetrics.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
def create_mrtrix_recon_flow(config):
'''Create the diffusion reconstruction workflow.
It estimates the tensors or the fiber orientation distribution functions.
Parameters
----------
config '''
# TODO: Add AD and RD maps
flow = pe.Workflow(name="reconstruction")
inputnode = pe.Node(
interface=util.IdentityInterface(
fields=["diffusion", "diffusion_resampled", "wm_mask_resampled", "grad"]),
name="inputnode")
outputnode = pe.Node(interface=util.IdentityInterface(fields=["DWI", "FA", "ADC", "tensor", "eigVec", "RF", "grad"],
mandatory_inputs=True), name="outputnode")
# Flip gradient table
flip_table = pe.Node(interface=flipTable(), name='flip_table')
flip_table.inputs.flipping_axis = config.flip_table_axis
flip_table.inputs.delimiter = ' '
flip_table.inputs.header_lines = 0
flip_table.inputs.orientation = 'v'
flow.connect([
(inputnode, flip_table, [("grad", "table")]),
(flip_table, outputnode, [("table", "grad")])
])
# flow.connect([
# (inputnode,outputnode,[("grad","grad")])
# ])
# Tensor
mrtrix_tensor = pe.Node(interface=DWI2Tensor(), name='mrtrix_make_tensor')
flow.connect([
(inputnode, mrtrix_tensor, [('diffusion_resampled', 'in_file')]),
(flip_table, mrtrix_tensor, [("table", "encoding_file")]),
])
# Tensor -> FA map
mrtrix_tensor_metrics = pe.Node(interface=TensorMetrics(out_fa='FA.mif', out_adc='ADC.mif'),
name='mrtrix_tensor_metrics')
convert_Tensor = pe.Node(interface=MRConvert(
out_filename="dwi_tensor.nii.gz"), name='convert_tensor')
convert_FA = pe.Node(interface=MRConvert(
out_filename="FA.nii.gz"), name='convert_FA')
convert_ADC = pe.Node(interface=MRConvert(
out_filename="ADC.nii.gz"), name='convert_ADC')
flow.connect([
(mrtrix_tensor, convert_Tensor, [('tensor', 'in_file')]),
(mrtrix_tensor, mrtrix_tensor_metrics, [('tensor', 'in_file')]),
(mrtrix_tensor_metrics, convert_FA, [('out_fa', 'in_file')]),
(mrtrix_tensor_metrics, convert_ADC, [('out_adc', 'in_file')]),
(convert_Tensor, outputnode, [("converted", "tensor")]),
(convert_FA, outputnode, [("converted", "FA")]),
(convert_ADC, outputnode, [("converted", "ADC")])
])
# Tensor -> Eigenvectors
mrtrix_eigVectors = pe.Node(
interface=Tensor2Vector(), name='mrtrix_eigenvectors')
flow.connect([
(mrtrix_tensor, mrtrix_eigVectors, [('tensor', 'in_file')]),
(mrtrix_eigVectors, outputnode, [('vector', 'eigVec')])
])
# Constrained Spherical Deconvolution
if config.local_model:
print("CSD true")
# Compute single fiber voxel mask
mrtrix_erode = pe.Node(interface=Erode(
out_filename='wm_mask_res_eroded.nii.gz'), name='mrtrix_erode')
mrtrix_erode.inputs.number_of_passes = 1
mrtrix_erode.inputs.filtertype = 'erode'
mrtrix_mul_eroded_FA = pe.Node(
interface=MRtrix_mul(), name='mrtrix_mul_eroded_FA')
mrtrix_mul_eroded_FA.inputs.out_filename = "diffusion_resampled_tensor_FA_masked.mif"
mrtrix_thr_FA = pe.Node(interface=MRThreshold(
out_file='FA_th.mif'), name='mrtrix_thr')
mrtrix_thr_FA.inputs.abs_value = config.single_fib_thr
flow.connect([
(inputnode, mrtrix_erode, [("wm_mask_resampled", 'in_file')]),
(mrtrix_erode, mrtrix_mul_eroded_FA, [('out_file', 'input2')]),
(mrtrix_tensor_metrics, mrtrix_mul_eroded_FA,
[('out_fa', 'input1')]),
(mrtrix_mul_eroded_FA, mrtrix_thr_FA, [('out_file', 'in_file')])
])
# Compute single fiber response function
mrtrix_rf = pe.Node(
interface=EstimateResponseForSH(), name='mrtrix_rf')
# if config.lmax_order != 'Auto':
mrtrix_rf.inputs.maximum_harmonic_order = int(config.lmax_order)
mrtrix_rf.inputs.algorithm = 'tournier'
# mrtrix_rf.inputs.normalise = config.normalize_to_B0
flow.connect([
(inputnode, mrtrix_rf, [("diffusion_resampled", "in_file")]),
(mrtrix_thr_FA, mrtrix_rf, [("thresholded", "mask_image")]),
(flip_table, mrtrix_rf, [("table", "encoding_file")]),
])
# Perform spherical deconvolution
mrtrix_CSD = pe.Node(
interface=ConstrainedSphericalDeconvolution(), name='mrtrix_CSD')
mrtrix_CSD.inputs.algorithm = 'csd'
mrtrix_CSD.inputs.maximum_harmonic_order = int(config.lmax_order)
# mrtrix_CSD.inputs.normalise = config.normalize_to_B0
convert_CSD = pe.Node(interface=MRConvert(
out_filename="spherical_harmonics_image.nii.gz"), name='convert_CSD')
flow.connect([
(inputnode, mrtrix_CSD, [('diffusion_resampled', 'in_file')]),
(mrtrix_rf, mrtrix_CSD, [('response', 'response_file')]),
(mrtrix_rf, outputnode, [('response', 'RF')]),
(inputnode, mrtrix_CSD, [("wm_mask_resampled", 'mask_image')]),
(flip_table, mrtrix_CSD, [("table", "encoding_file")]),
(mrtrix_CSD, convert_CSD, [('spherical_harmonics_image', 'in_file')]),
(convert_CSD, outputnode, [("converted", "DWI")])
# (mrtrix_CSD,outputnode,[('spherical_harmonics_image','DWI')])
])
else:
flow.connect([
(inputnode, outputnode, [('diffusion_resampled', 'DWI')])
])
return flow
def create_mrtrix_recon_flow(config):
"""Create the reconstruction sub-workflow of the `DiffusionStage` using MRtrix3.
Parameters
----------
config : DipyReconConfig
Workflow configuration
Returns
-------
flow : nipype.pipeline.engine.Workflow
Built reconstruction sub-workflow
"""
# TODO: Add AD and RD maps
flow = pe.Workflow(name="reconstruction")
inputnode = pe.Node(
interface=util.IdentityInterface(fields=[
"diffusion", "diffusion_resampled", "wm_mask_resampled", "grad"
]),
name="inputnode",
)
outputnode = pe.Node(
interface=util.IdentityInterface(
fields=["DWI", "FA", "ADC", "tensor", "eigVec", "RF", "grad"],
mandatory_inputs=True,
),
name="outputnode",
)
# Flip gradient table
flip_table = pe.Node(interface=FlipTable(), name="flip_table")
flip_table.inputs.flipping_axis = config.flip_table_axis
flip_table.inputs.delimiter = " "
flip_table.inputs.header_lines = 0
flip_table.inputs.orientation = "v"
# fmt:off
flow.connect([
(inputnode, flip_table, [("grad", "table")]),
(flip_table, outputnode, [("table", "grad")]),
])
# fmt:on
# Tensor
mrtrix_tensor = pe.Node(interface=DWI2Tensor(), name="mrtrix_make_tensor")
# fmt:off
flow.connect([
(inputnode, mrtrix_tensor, [("diffusion_resampled", "in_file")]),
(flip_table, mrtrix_tensor, [("table", "encoding_file")]),
])
# fmt:on
# Tensor -> FA map
mrtrix_tensor_metrics = pe.Node(
interface=TensorMetrics(out_fa="FA.mif", out_adc="ADC.mif"),
name="mrtrix_tensor_metrics",
)
convert_Tensor = pe.Node(
interface=MRConvert(out_filename="dwi_tensor.nii.gz"),
name="convert_tensor")
convert_FA = pe.Node(interface=MRConvert(out_filename="FA.nii.gz"),
name="convert_FA")
convert_ADC = pe.Node(interface=MRConvert(out_filename="ADC.nii.gz"),
name="convert_ADC")
# fmt:off
flow.connect([
(mrtrix_tensor, convert_Tensor, [("tensor", "in_file")]),
(mrtrix_tensor, mrtrix_tensor_metrics, [("tensor", "in_file")]),
(mrtrix_tensor_metrics, convert_FA, [("out_fa", "in_file")]),
(mrtrix_tensor_metrics, convert_ADC, [("out_adc", "in_file")]),
(convert_Tensor, outputnode, [("converted", "tensor")]),
(convert_FA, outputnode, [("converted", "FA")]),
(convert_ADC, outputnode, [("converted", "ADC")]),
])
# fmt:on
# Tensor -> Eigenvectors
mrtrix_eigVectors = pe.Node(interface=Tensor2Vector(),
name="mrtrix_eigenvectors")
# fmt:off
flow.connect([
(mrtrix_tensor, mrtrix_eigVectors, [("tensor", "in_file")]),
(mrtrix_eigVectors, outputnode, [("vector", "eigVec")]),
])
# fmt:on
# Constrained Spherical Deconvolution
if config.local_model:
print("CSD true")
# Compute single fiber voxel mask
mrtrix_erode = pe.Node(
interface=Erode(out_filename="wm_mask_res_eroded.nii.gz"),
name="mrtrix_erode",
)
mrtrix_erode.inputs.number_of_passes = 1
mrtrix_erode.inputs.filtertype = "erode"
mrtrix_mul_eroded_FA = pe.Node(interface=MRtrix_mul(),
name="mrtrix_mul_eroded_FA")
mrtrix_mul_eroded_FA.inputs.out_filename = "diffusion_resampled_tensor_FA_masked.mif"
mrtrix_thr_FA = pe.Node(interface=MRThreshold(out_file="FA_th.mif"),
name="mrtrix_thr")
mrtrix_thr_FA.inputs.abs_value = config.single_fib_thr
# fmt:off
flow.connect([
(inputnode, mrtrix_erode, [("wm_mask_resampled", "in_file")]),
(mrtrix_erode, mrtrix_mul_eroded_FA, [("out_file", "input2")]),
(mrtrix_tensor_metrics, mrtrix_mul_eroded_FA, [("out_fa", "input1")
]),
(mrtrix_mul_eroded_FA, mrtrix_thr_FA, [("out_file", "in_file")]),
])
# fmt:on
# Compute single fiber response function
mrtrix_rf = pe.Node(interface=EstimateResponseForSH(),
name="mrtrix_rf")
mrtrix_rf.inputs.maximum_harmonic_order = int(config.lmax_order)
mrtrix_rf.inputs.algorithm = "tournier"
# mrtrix_rf.inputs.normalise = config.normalize_to_B0
# fmt:off
flow.connect([
(inputnode, mrtrix_rf, [("diffusion_resampled", "in_file")]),
(mrtrix_thr_FA, mrtrix_rf, [("thresholded", "mask_image")]),
(flip_table, mrtrix_rf, [("table", "encoding_file")]),
])
# fmt:on
# Perform spherical deconvolution
mrtrix_CSD = pe.Node(interface=ConstrainedSphericalDeconvolution(),
name="mrtrix_CSD")
mrtrix_CSD.inputs.algorithm = "csd"
mrtrix_CSD.inputs.maximum_harmonic_order = int(config.lmax_order)
# mrtrix_CSD.inputs.normalise = config.normalize_to_B0
convert_CSD = pe.Node(
interface=MRConvert(
out_filename="spherical_harmonics_image.nii.gz"),
name="convert_CSD",
)
# fmt:off
flow.connect([
(inputnode, mrtrix_CSD, [("diffusion_resampled", "in_file")]),
(mrtrix_rf, mrtrix_CSD, [("response", "response_file")]),
(mrtrix_rf, outputnode, [("response", "RF")]),
(inputnode, mrtrix_CSD, [("wm_mask_resampled", "mask_image")]),
(flip_table, mrtrix_CSD, [("table", "encoding_file")]),
(mrtrix_CSD, convert_CSD, [("spherical_harmonics_image", "in_file")
]),
(convert_CSD, outputnode, [("converted", "DWI")])
# (mrtrix_CSD,outputnode,[('spherical_harmonics_image','DWI')])
])
# fmt:on
else:
# fmt:off
flow.connect([(inputnode, outputnode, [("diffusion_resampled", "DWI")])
])
# fmt:on
return flow