def test_MaxImage_outputs():
output_map = dict(out_file=dict(), )
outputs = MaxImage.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_MaxImage_outputs():
output_map = dict(out_file=dict(),
)
outputs = MaxImage.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_MaxImage_inputs():
input_map = dict(
args=dict(argstr='%s', ),
dimension=dict(
argstr='-%smax',
position=4,
usedefault=True,
),
environ=dict(
nohash=True,
usedefault=True,
),
ignore_exception=dict(
nohash=True,
usedefault=True,
),
in_file=dict(
argstr='%s',
mandatory=True,
position=2,
),
internal_datatype=dict(
argstr='-dt %s',
position=1,
),
nan2zeros=dict(
argstr='-nan',
position=3,
),
out_file=dict(
argstr='%s',
genfile=True,
hash_files=False,
position=-2,
),
output_datatype=dict(
argstr='-odt %s',
position=-1,
),
output_type=dict(),
terminal_output=dict(
mandatory=True,
nohash=True,
),
)
inputs = MaxImage.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 test_MaxImage_inputs():
input_map = dict(args=dict(argstr='%s',
),
dimension=dict(argstr='-%smax',
position=4,
usedefault=True,
),
environ=dict(nohash=True,
usedefault=True,
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
in_file=dict(argstr='%s',
mandatory=True,
position=2,
),
internal_datatype=dict(argstr='-dt %s',
position=1,
),
nan2zeros=dict(argstr='-nan',
position=3,
),
out_file=dict(argstr='%s',
genfile=True,
hash_files=False,
position=-2,
),
output_datatype=dict(argstr='-odt %s',
position=-1,
),
output_type=dict(),
terminal_output=dict(mandatory=True,
nohash=True,
),
)
inputs = MaxImage.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_steps_propagation_pipeline(name='steps_propagation',
aligned_templates=False):
workflow = pe.Workflow(name=name)
# Create an input node
input_node = pe.Node(
interface=niu.IdentityInterface(
fields=['in_file',
'database_file']),
name='input_node')
extract_db_info = pe.Node(interface=niu.Function(input_names=['in_db_file'], output_names=['input_template_images',
'input_template_labels'],
function=extract_db_info_function),
name='extract_db_info')
workflow.connect(input_node, 'database_file', extract_db_info, 'in_db_file')
# All the template images are affinely registered to the target image
current_aladin = pe.MapNode(interface=niftyreg.RegAladin(verbosity_off_flag=True),
name='aladin',
iterfield=['flo_file'])
workflow.connect(input_node, 'in_file', current_aladin, 'ref_file')
workflow.connect(extract_db_info, 'input_template_images', current_aladin, 'flo_file')
# Compute the affine TLS if required
current_robust_affine = None
if aligned_templates is True:
current_robust_affine = pe.Node(interface=niftyreg.RegAverage(), name='robust_affine')
workflow.connect(current_aladin, 'aff_file', current_robust_affine, 'avg_lts_files')
current_aff_prop = pe.MapNode(interface=niftyreg.RegResample(verbosity_off_flag=True, inter_val='NN'),
name='resample_aff',
iterfield=['flo_file'])
workflow.connect(current_robust_affine, 'out_file', current_aff_prop, 'trans_file')
else:
current_aff_prop = pe.MapNode(interface=niftyreg.RegResample(verbosity_off_flag=True, inter_val='NN'),
name='resample_aff',
iterfield=['flo_file',
'trans_file'])
workflow.connect(current_aladin, 'aff_file', current_aff_prop, 'trans_file')
workflow.connect(input_node, 'in_file', current_aff_prop, 'ref_file')
workflow.connect(extract_db_info, 'input_template_labels', current_aff_prop, 'flo_file')
# Merge all the affine parcellation into one 4D
current_aff_prop_merge = pe.Node(interface=fsl.Merge(dimension='t'), name='merge_aff_prop')
workflow.connect(current_aff_prop, 'out_file', current_aff_prop_merge, 'in_files')
# Combine all the propagated parcellation into a single image
current_aff_prop_max = pe.Node(interface=MaxImage(dimension='T'), name='max_aff')
workflow.connect(current_aff_prop_merge, 'merged_file', current_aff_prop_max, 'in_file')
# Binarise the obtained mask
current_aff_prop_bin = pe.Node(interface=niftyseg.UnaryMaths(operation='bin'), name='bin_aff')
workflow.connect(current_aff_prop_max, 'out_file', current_aff_prop_bin, 'in_file')
# Dilate the obtained mask
current_aff_prop_dil = pe.Node(interface=niftyseg.BinaryMathsInteger(operation='dil', operand_value=10),
name='dil_aff')
workflow.connect(current_aff_prop_bin, 'out_file', current_aff_prop_dil, 'in_file')
# Fill the obtained mask
current_aff_prop_fill = pe.Node(interface=niftyseg.UnaryMaths(operation='fill'), name='fill_aff')
workflow.connect(current_aff_prop_dil, 'out_file', current_aff_prop_fill, 'in_file')
# Crop the target image to speed up the process
current_crop_target = pe.Node(interface=CropImage(), name='crop_target')
workflow.connect(input_node, 'in_file', current_crop_target, 'in_file')
workflow.connect(current_aff_prop_fill, 'out_file', current_crop_target, 'mask_file')
# Crop the mask image to speed up the process
current_crop_mask = pe.Node(interface=CropImage(), name='crop_mask')
workflow.connect(current_aff_prop_fill, 'out_file', current_crop_mask, 'in_file')
workflow.connect(current_aff_prop_fill, 'out_file', current_crop_mask, 'mask_file')
# Perform all the non-linear registration
if aligned_templates is True:
current_f3d = pe.MapNode(interface=niftyreg.RegF3D(sx_val=-2.5, be_val=0.01, verbosity_off_flag=True),
name='f3d',
iterfield=['flo_file'])
workflow.connect(current_robust_affine, 'out_file', current_f3d, 'aff_file')
else:
current_f3d = pe.MapNode(interface=niftyreg.RegF3D(),
name='f3d',
iterfield=['flo_file',
'aff_file'])
workflow.connect(current_aladin, 'aff_file', current_f3d, 'aff_file')
workflow.connect(current_crop_target, 'out_file', current_f3d, 'ref_file')
workflow.connect(current_crop_mask, 'out_file', current_f3d, 'rmask_file')
workflow.connect(extract_db_info, 'input_template_images', current_f3d, 'flo_file')
# Merge all the non-linear warped images into one 4D
current_f3d_temp_merge = pe.Node(interface=fsl.Merge(dimension='t'), name='merge_f3d_temp')
workflow.connect(current_f3d, 'res_file', current_f3d_temp_merge, 'in_files')
# Propagate the obtained mask
current_f3d_prop = pe.MapNode(interface=niftyreg.RegResample(inter_val='NN', verbosity_off_flag=True),
name='f3d_prop',
iterfield=['flo_file',
'trans_file'])
workflow.connect(current_crop_target, 'out_file', current_f3d_prop, 'ref_file')
workflow.connect(extract_db_info, 'input_template_labels', current_f3d_prop, 'flo_file')
workflow.connect(current_f3d, 'cpp_file', current_f3d_prop, 'trans_file')
# Merge all the non-linear warped labels into one 4D
current_f3d_prop_merge = pe.Node(interface=fsl.Merge(dimension='t'), name='merge_f3d_prop')
workflow.connect(current_f3d_prop, 'out_file', current_f3d_prop_merge, 'in_files')
# Extract the consensus parcellation using steps
current_fusion = pe.Node(interface=niftyseg.STEPS(template_num=15, kernel_size=1.5, mrf_value=0.15),
name='fusion')
workflow.connect(current_crop_target, 'out_file', current_fusion, 'in_file')
workflow.connect(current_f3d_temp_merge, 'merged_file', current_fusion, 'warped_img_file')
workflow.connect(current_f3d_prop_merge, 'merged_file', current_fusion, 'warped_seg_file')
workflow.connect(current_aff_prop_fill, 'out_file', current_fusion, 'mask_file')
# Resample the obtained consensus label into the original image space
current_prop_orig_res = pe.MapNode(interface=niftyreg.RegResample(inter_val='NN', verbosity_off_flag=True),
name='prop_orig_res',
iterfield=['flo_file'])
workflow.connect(input_node, 'in_file', current_prop_orig_res, 'ref_file')
workflow.connect(current_fusion, 'out_file', current_prop_orig_res, 'flo_file')
# Connect the output to the output node
output_node = pe.Node(
interface=niu.IdentityInterface(
fields=['parcellated_file']),
name='output_node')
workflow.connect(current_prop_orig_res, 'out_file', output_node, 'parcellated_file')
return workflow