interfaces.dtitk.registration¶
AffineTask¶
Wraps command dti_affine_reg
Performs affine registration between two tensor volumes
>>> import nipype.interfaces.dtitk as dtitk >>> node = dtitk.AffineTask() >>> node.inputs.fixed_file = 'diffusion.nii.gz' >>> node.inputs.moving_file = 'diffusion2.nii.gz' >>> node.inputs.similarity_metric = 'EDS' >>> node.inputs.samplingX = 4 >>> node.inputs.samplingY = 4 >>> node.inputs.samplingZ = 4 >>> node.inputs.ftol = 0.01 >>> node.inputs.useInTrans = 1 >>> node.run()
Inputs:
[Mandatory]
fixed_file: (a unicode string)
fixed diffusion tensor image
flag: %s, position: 0
ftol: (a float)
cost function tolerance
flag: %s, position: 6
moving_file: (a unicode string)
diffusion tensor image path
flag: %s, position: 1
samplingX: (a float)
dist between samp points (mm)
flag: %s, position: 3
samplingY: (a float)
dist between samp points (mm)
flag: %s, position: 4
samplingZ: (a float)
dist between samp points (mm)
flag: %s, position: 5
similarity_metric: ('EDS' or 'GDS' or 'DDS' or 'NMI')
similarity metric
flag: %s, position: 2
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a value
of class 'str', nipype default value: {})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
useInTrans: (a float)
to initialize with existing xfm set as 1
flag: %s, position: 7
Outputs:
out_file: (a file name)
out_file_xfm: (a file name)
ComposeXfmTask¶
Wraps command dfRightComposeAffine
Combines diffeomorphic and affine transforms
>>> import nipype.interfaces.dtitk as dtitk >>> node = dtitk.ComposeXfmTask() >>> node.inputs.in_df = 'ants_Warp.nii.gz' >>> node.inputs.in_aff= 'ants_Affine.txt' >>> node.run()
Inputs:
[Mandatory]
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a value
of class 'str', nipype default value: {})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
in_aff: (a unicode string)
affine file.aff
flag: -aff %s, position: 0
in_df: (a unicode string)
diffeomorphic file.df.nii.gz
flag: -df %s, position: 1
out_file: (a unicode string)
output_path
flag: -out %s, position: 2
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (a file name)
cheese
DiffeoTask¶
Wraps command dti_diffeomorphic_reg
Performs diffeomorphic registration between two tensor volumes
>>> import nipype.interfaces.dtitk as dtitk >>> node = dtitk.DiffeoTask() >>> node.inputs.fixed_file = 'diffusion.nii.gz' >>> node.inputs.moving_file = 'diffusion2.nii.gz' >>> node.inputs.mask = 'mask.nii.gz' >>> node.inputs.legacy = 1 >>> node.inputs.n_iters = 6 >>> node.inputs.ftol = 0.002 >>> node.run()
Inputs:
[Mandatory]
ftol: (a float)
iteration for the optimization to stop
flag: %s, position: 5
legacy: (a float)
legacy parameter; always set to 1
flag: %s, position: 3
n_iters: (a float)
number of iterations
flag: %s, position: 4
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a value
of class 'str', nipype default value: {})
Environment variables
fixed_file: (a unicode string)
fixed diffusion tensor image
flag: %s, position: 0
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
mask: (a unicode string)
mask
flag: %s, position: 2
moving_file: (a unicode string)
moving diffusion tensor image
flag: %s, position: 1
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (a file name)
out_file_xfm: (a file name)
RigidTask¶
Wraps command dti_rigid_reg
Performs rigid registration between two tensor volumes
>>> import nipype.interfaces.dtitk as dtitk >>> node = dtitk.RigidTask() >>> node.inputs.fixed_file = 'diffusion.nii.gz' >>> node.inputs.moving_file = 'diffusion2.nii.gz' >>> node.inputs.similarity_metric = 'EDS' >>> node.inputs.samplingX = 4 >>> node.inputs.samplingY = 4 >>> node.inputs.samplingZ = 4 >>> node.inputs.ftol = 0.01 >>> node.inputs.useInTrans = 1 >>> node.run()
Inputs:
[Mandatory]
fixed_file: (a unicode string)
fixed diffusion tensor image
flag: %s, position: 0
ftol: (a float)
cost function tolerance
flag: %s, position: 6
moving_file: (a unicode string)
diffusion tensor image path
flag: %s, position: 1
samplingX: (a float)
dist between samp points (mm)
flag: %s, position: 3
samplingY: (a float)
dist between samp points (mm)
flag: %s, position: 4
samplingZ: (a float)
dist between samp points (mm)
flag: %s, position: 5
similarity_metric: ('EDS' or 'GDS' or 'DDS' or 'NMI')
similarity metric
flag: %s, position: 2
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a value
of class 'str', nipype default value: {})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
useInTrans: (a float)
to initialize with existing xfm set as 1
flag: %s, position: 7
Outputs:
out_file: (a file name)
out_file_xfm: (a file name)
affScalarVolTask¶
Wraps command affineScalarVolume
Applies affine transform to a scalar volume
>>> import nipype.interfaces.dtitk as dtitk >>> node = dtitk.affScalarVolTask() >>> node.inputs.in_volume = 'fa.nii.gz' >>> node.inputs.in_xfm = 'ants_Affine.txt' >>> node.run()
Inputs:
[Mandatory]
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a value
of class 'str', nipype default value: {})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
in_target: (a unicode string)
flag: -target %s, position: 2
in_volume: (a unicode string)
moving volume
flag: -in %s, position: 0
in_xfm: (a unicode string)
transform to apply
flag: -trans %s, position: 1
out_file: (a unicode string)
flag: -out %s, position: 3
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (a file name)
moved volume
affSymTensor3DVolTask¶
Wraps command affineSymTensor3DVolume
Applies affine transform to a tensor volume
>>> import nipype.interfaces.dtitk as dtitk >>> node = dtitk.affSymTensor3DVolTask() >>> node.inputs.in_tensor = 'diffusion.nii' >>> node.inputs.in_xfm = 'ants_Affine.txt' >>> node.run()
Inputs:
[Mandatory]
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a value
of class 'str', nipype default value: {})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
in_target: (a unicode string)
flag: -target %s, position: 2
in_tensor: (a unicode string)
moving tensor
flag: -in %s, position: 0
in_xfm: (a unicode string)
transform to apply
flag: -trans %s, position: 1
out_file: (a unicode string)
flag: -out %s, position: 3
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (a file name)
cheese
diffeoScalarVolTask¶
Wraps command deformationScalarVolume
Applies diffeomorphic transform to a scalar volume
>>> import nipype.interfaces.dtitk as dtitk >>> node = dtitk.diffeoScalarVolTask() >>> node.inputs.in_volume = 'fa.nii.gz' >>> node.inputs.in_xfm = 'ants_Warp.nii.gz' >>> node.run()
Inputs:
[Mandatory]
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a value
of class 'str', nipype default value: {})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
in_flip: (a unicode string)
flag: -flip %s, position: 5
in_interp: (a unicode string)
0 trilin, 1 NN
flag: -interp %s, position: 7
in_target: (a unicode string)
flag: -target %s, position: 3
in_type: (a unicode string)
flag: -type %s, position: 6
in_volume: (a unicode string)
moving volume
flag: -in %s, position: 0
in_vsize: (a unicode string)
flag: -vsize %s, position: 4
in_xfm: (a unicode string)
transform to apply
flag: -trans %s, position: 2
out_file: (a unicode string)
flag: -out %s, position: 1
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (a file name)
moved volume
diffeoSymTensor3DVolTask¶
Wraps command deformationSymTensor3DVolume
Applies diffeomorphic transform to a tensor volume
>>> import nipype.interfaces.dtitk as dtitk >>> node = dtitk.diffeoSymTensor3DVolTask() >>> node.inputs.in_tensor = 'diffusion.nii' >>> node.inputs.in_xfm = 'ants_Warp.nii.gz' >>> node.run()
Inputs:
[Mandatory]
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a value
of class 'str', nipype default value: {})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
in_target: (a unicode string)
flag: -target %s, position: 2
in_tensor: (a unicode string)
moving tensor
flag: -in %s, position: 0
in_xfm: (a unicode string)
transform to apply
flag: -trans %s, position: 1
out_file: (a unicode string)
flag: -out %s, position: 3
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (a file name)
cheese