nipype.interfaces.ants.utils module

ANTs’ utilities.

class nipype.interfaces.ants.utils.AI(**inputs)

Bases: ANTSCommand

Wrapped executable: antsAI.

Calculate the optimal linear transform parameters for aligning two images.

Examples

>>> AI(
...     fixed_image='structural.nii',
...     moving_image='epi.nii',
...     metric=('Mattes', 32, 'Regular', 1),
... ).cmdline
'antsAI -c [10,1e-06,10] -d 3 -m Mattes[structural.nii,epi.nii,32,Regular,1]
-o initialization.mat -p 0 -s [20,0.12] -t Affine[0.1] -v 0'

>>> AI(fixed_image='structural.nii',
...    moving_image='epi.nii',
...    metric=('Mattes', 32, 'Regular', 1),
...    search_grid=(12, (1, 1, 1)),
... ).cmdline
'antsAI -c [10,1e-06,10] -d 3 -m Mattes[structural.nii,epi.nii,32,Regular,1]
-o initialization.mat -p 0 -s [20,0.12] -g [12.0,1x1x1] -t Affine[0.1] -v 0'
Mandatory Inputs:

  • fixed_image (a pathlike object or string representing an existing file) – Image to which the moving_image should be transformed.

  • metric (a tuple of the form: (‘Mattes’ or ‘GC’ or ‘MI’, an integer, ‘Regular’ or ‘Random’ or ‘None’, 0.0 <= a floating point number <= 1.0)) – The metric(s) to use. Maps to a command-line argument: -m %s.

  • moving_image (a pathlike object or string representing an existing file) – Image that will be transformed to fixed_image.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • convergence (a tuple of the form: (1 <= an integer <= 10000, a float, 1 <= an integer <= 100)) – Convergence. Maps to a command-line argument: -c [%d,%g,%d]. (Nipype default value: (10, 1e-06, 10))

  • dimension (3 or 2) – Dimension of output image. Maps to a command-line argument: -d %d. (Nipype default value: 3)

  • 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’) – Environment variables. (Nipype default value: {})

  • fixed_image_mask (a pathlike object or string representing an existing file) – Fixed mage mask. Maps to a command-line argument: -x %s.

  • moving_image_mask (a pathlike object or string representing an existing file) – Moving mage mask. Requires inputs: fixed_image_mask.

  • num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)

  • output_transform (a pathlike object or string representing a file) – Output file name. Maps to a command-line argument: -o %s. (Nipype default value: initialization.mat)

  • principal_axes (a boolean) – Align using principal axes. Maps to a command-line argument: -p %d. Mutually exclusive with inputs: blobs. (Nipype default value: False)

  • search_factor (a tuple of the form: (a float, 0.0 <= a floating point number <= 1.0)) – Search factor. Maps to a command-line argument: -s [%g,%g]. (Nipype default value: (20, 0.12))

  • search_grid (a tuple of the form: (a float, a tuple of the form: (a float, a float, a float)) or a tuple of the form: (a float, a tuple of the form: (a float, a float))) – Translation search grid in mm. Maps to a command-line argument: -g %s.

  • transform (a tuple of the form: (‘Affine’ or ‘Rigid’ or ‘Similarity’, a floating point number > 0.0)) – Several transform options are available. Maps to a command-line argument: -t %s[%g]. (Nipype default value: ('Affine', 0.1))

  • verbose (a boolean) – Enable verbosity. Maps to a command-line argument: -v %d. (Nipype default value: False)

Outputs:

output_transform (a pathlike object or string representing an existing file) – Output file name.

class nipype.interfaces.ants.utils.AffineInitializer(**inputs)

Bases: ANTSCommand

Wrapped executable: antsAffineInitializer.

Initialize an affine transform (as in antsBrainExtraction.sh)

>>> from nipype.interfaces.ants import AffineInitializer
>>> init = AffineInitializer()
>>> init.inputs.fixed_image = 'fixed1.nii'
>>> init.inputs.moving_image = 'moving1.nii'
>>> init.cmdline
'antsAffineInitializer 3 fixed1.nii moving1.nii transform.mat 15.000000 0.100000 0 10'
Mandatory Inputs:

  • fixed_image (a pathlike object or string representing an existing file) – Reference image. Maps to a command-line argument: %s (position: 1).

  • moving_image (a pathlike object or string representing an existing file) – Moving image. Maps to a command-line argument: %s (position: 2).

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • dimension (3 or 2) – Dimension. Maps to a command-line argument: %s (position: 0). (Nipype default value: 3)

  • 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’) – Environment variables. (Nipype default value: {})

  • local_search (an integer) – determines if a local optimization is run at each search point for the set number of iterations. Maps to a command-line argument: %d (position: 7). (Nipype default value: 10)

  • num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)

  • out_file (a pathlike object or string representing a file) – Output transform file. Maps to a command-line argument: %s (position: 3). (Nipype default value: transform.mat)

  • principal_axes (a boolean) – Whether the rotation is searched around an initial principal axis alignment. Maps to a command-line argument: %d (position: 6). (Nipype default value: False)

  • radian_fraction (0.0 <= a floating point number <= 1.0) – Search this arc +/- principal axes. Maps to a command-line argument: %f (position: 5). (Nipype default value: 0.1)

  • search_factor (a float) – Increments (degrees) for affine search. Maps to a command-line argument: %f (position: 4). (Nipype default value: 15.0)

Outputs:

out_file (a pathlike object or string representing a file) – Output transform file.

class nipype.interfaces.ants.utils.AverageAffineTransform(**inputs)

Bases: ANTSCommand

Wrapped executable: AverageAffineTransform.

Examples

>>> from nipype.interfaces.ants import AverageAffineTransform
>>> avg = AverageAffineTransform()
>>> avg.inputs.dimension = 3
>>> avg.inputs.transforms = ['trans.mat', 'func_to_struct.mat']
>>> avg.inputs.output_affine_transform = 'MYtemplatewarp.mat'
>>> avg.cmdline
'AverageAffineTransform 3 MYtemplatewarp.mat trans.mat func_to_struct.mat'
Mandatory Inputs:

  • dimension (3 or 2) – Image dimension (2 or 3). Maps to a command-line argument: %d (position: 0).

  • output_affine_transform (a pathlike object or string representing a file) – Outputfname.txt: the name of the resulting transform. Maps to a command-line argument: %s (position: 1).

  • transforms (a list of items which are a pathlike object or string representing an existing file) – Transforms to average. Maps to a command-line argument: %s (position: 3).

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %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’) – Environment variables. (Nipype default value: {})

  • num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)

Outputs:

affine_transform (a pathlike object or string representing an existing file) – Average transform file.

class nipype.interfaces.ants.utils.AverageImages(**inputs)

Bases: ANTSCommand

Wrapped executable: AverageImages.

Examples

>>> from nipype.interfaces.ants import AverageImages
>>> avg = AverageImages()
>>> avg.inputs.dimension = 3
>>> avg.inputs.output_average_image = "average.nii.gz"
>>> avg.inputs.normalize = True
>>> avg.inputs.images = ['rc1s1.nii', 'rc1s1.nii']
>>> avg.cmdline
'AverageImages 3 average.nii.gz 1 rc1s1.nii rc1s1.nii'
Mandatory Inputs:

  • dimension (3 or 2) – Image dimension (2 or 3). Maps to a command-line argument: %d (position: 0).

  • images (a list of items which are a pathlike object or string representing an existing file) – Image to apply transformation to (generally a coregistered functional). Maps to a command-line argument: %s (position: 3).

  • normalize (a boolean) – Normalize: if true, the 2nd image is divided by its mean. This will select the largest image to average into. Maps to a command-line argument: %d (position: 2).

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %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’) – Environment variables. (Nipype default value: {})

  • num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)

  • output_average_image (a pathlike object or string representing a file) – The name of the resulting image. Maps to a command-line argument: %s (position: 1). (Nipype default value: average.nii)

Outputs:

output_average_image (a pathlike object or string representing an existing file) – Average image file.

class nipype.interfaces.ants.utils.ComposeMultiTransform(**inputs)

Bases: ANTSCommand

Wrapped executable: ComposeMultiTransform.

Take a set of transformations and convert them to a single transformation matrix/warpfield.

Examples

>>> from nipype.interfaces.ants import ComposeMultiTransform
>>> compose_transform = ComposeMultiTransform()
>>> compose_transform.inputs.dimension = 3
>>> compose_transform.inputs.transforms = ['struct_to_template.mat', 'func_to_struct.mat']
>>> compose_transform.cmdline
'ComposeMultiTransform 3 struct_to_template_composed.mat
struct_to_template.mat func_to_struct.mat'
Mandatory Inputs:

transforms (a list of items which are a pathlike object or string representing an existing file) – Transforms to average. Maps to a command-line argument: %s (position: 3).

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • dimension (3 or 2) – Image dimension (2 or 3). Maps to a command-line argument: %d (position: 0). (Nipype default value: 3)

  • 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’) – Environment variables. (Nipype default value: {})

  • num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)

  • output_transform (a pathlike object or string representing a file) – The name of the resulting transform. Maps to a command-line argument: %s (position: 1).

  • reference_image (a pathlike object or string representing a file) – Reference image (only necessary when output is warpfield). Maps to a command-line argument: %s (position: 2).

Outputs:

output_transform (a pathlike object or string representing an existing file) – Composed transform file.

class nipype.interfaces.ants.utils.CreateJacobianDeterminantImage(**inputs)

Bases: ANTSCommand

Wrapped executable: CreateJacobianDeterminantImage.

Examples

>>> from nipype.interfaces.ants import CreateJacobianDeterminantImage
>>> jacobian = CreateJacobianDeterminantImage()
>>> jacobian.inputs.imageDimension = 3
>>> jacobian.inputs.deformationField = 'ants_Warp.nii.gz'
>>> jacobian.inputs.outputImage = 'out_name.nii.gz'
>>> jacobian.cmdline
'CreateJacobianDeterminantImage 3 ants_Warp.nii.gz out_name.nii.gz'
Mandatory Inputs:

  • deformationField (a pathlike object or string representing an existing file) – Deformation transformation file. Maps to a command-line argument: %s (position: 1).

  • imageDimension (3 or 2) – Image dimension (2 or 3). Maps to a command-line argument: %d (position: 0).

  • outputImage (a pathlike object or string representing a file) – Output filename. Maps to a command-line argument: %s (position: 2).

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • doLogJacobian (0 or 1) – Return the log jacobian. Maps to a command-line argument: %d (position: 3).

  • 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’) – Environment variables. (Nipype default value: {})

  • num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)

  • useGeometric (0 or 1) – Return the geometric jacobian. Maps to a command-line argument: %d (position: 4).

Outputs:

jacobian_image (a pathlike object or string representing an existing file) – Jacobian image.

class nipype.interfaces.ants.utils.ImageMath(**inputs)

Bases: ANTSCommand, CopyHeaderInterface

Wrapped executable: ImageMath.

Operations over images.

Examples

>>> ImageMath(
...     op1='structural.nii',
...     operation='+',
...     op2='2').cmdline
'ImageMath 3 structural_maths.nii + structural.nii 2'

>>> ImageMath(
...     op1='structural.nii',
...     operation='Project',
...     op2='1 2').cmdline
'ImageMath 3 structural_maths.nii Project structural.nii 1 2'

>>> ImageMath(
...     op1='structural.nii',
...     operation='G',
...     op2='4').cmdline
'ImageMath 3 structural_maths.nii G structural.nii 4'

>>> ImageMath(
...     op1='structural.nii',
...     operation='TruncateImageIntensity',
...     op2='0.005 0.999 256').cmdline
'ImageMath 3 structural_maths.nii TruncateImageIntensity structural.nii 0.005 0.999 256'

By default, Nipype copies headers from the first input image (op1) to the output image. For some operations, as the PadImage operation, the header cannot be copied from inputs to outputs, and so copy_header option is automatically set to False.

>>> pad = ImageMath(
...     op1='structural.nii',
...     operation='PadImage')
>>> pad.inputs.copy_header
False

While the operation is set to PadImage, setting copy_header = True will have no effect.

>>> pad.inputs.copy_header = True
>>> pad.inputs.copy_header
False

For any other operation, copy_header can be enabled/disabled normally:

>>> pad.inputs.operation = "ME"
>>> pad.inputs.copy_header = True
>>> pad.inputs.copy_header
True
Mandatory Inputs:

  • op1 (a pathlike object or string representing an existing file) – First operator. Maps to a command-line argument: %s (position: -3).

  • operation (‘m’ or ‘vm’ or ‘+’ or ‘v+’ or ‘-’ or ‘v-’ or ‘/’ or ‘^’ or ‘max’ or ‘exp’ or ‘addtozero’ or ‘overadd’ or ‘abs’ or ‘total’ or ‘mean’ or ‘vtotal’ or ‘Decision’ or ‘Neg’ or ‘Project’ or ‘G’ or ‘MD’ or ‘ME’ or ‘MO’ or ‘MC’ or ‘GD’ or ‘GE’ or ‘GO’ or ‘GC’ or ‘ExtractContours’ or ‘Translate’ or ‘4DTensorTo3DTensor’ or ‘ExtractVectorComponent’ or ‘TensorColor’ or ‘TensorFA’ or ‘TensorFADenominator’ or ‘TensorFANumerator’ or ‘TensorMeanDiffusion’ or ‘TensorRadialDiffusion’ or ‘TensorAxialDiffusion’ or ‘TensorEigenvalue’ or ‘TensorToVector’ or ‘TensorToVectorComponent’ or ‘TensorMask’ or ‘Byte’ or ‘CorruptImage’ or ‘D’ or ‘MaurerDistance’ or ‘ExtractSlice’ or ‘FillHoles’ or ‘Convolve’ or ‘Finite’ or ‘FlattenImage’ or ‘GetLargestComponent’ or ‘Grad’ or ‘RescaleImage’ or ‘WindowImage’ or ‘NeighborhoodStats’ or ‘ReplicateDisplacement’ or ‘ReplicateImage’ or ‘LabelStats’ or ‘Laplacian’ or ‘Canny’ or ‘Lipschitz’ or ‘MTR’ or ‘Normalize’ or ‘PadImage’ or ‘SigmoidImage’ or ‘Sharpen’ or ‘UnsharpMask’ or ‘PValueImage’ or ‘ReplaceVoxelValue’ or ‘SetTimeSpacing’ or ‘SetTimeSpacingWarp’ or ‘stack’ or ‘ThresholdAtMean’ or ‘TriPlanarView’ or ‘TruncateImageIntensity’) – Mathematical operations. Maps to a command-line argument: %s (position: 3).

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s (position: -1).

  • copy_header (a boolean) – Copy headers of the original image into the output (corrected) file. (Nipype default value: True)

  • dimension (an integer) – Dimension of output image. Maps to a command-line argument: %d (position: 1). (Nipype default value: 3)

  • 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’) – Environment variables. (Nipype default value: {})

  • num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)

  • op2 (a pathlike object or string representing an existing file or a string) – Second operator. Maps to a command-line argument: %s (position: -2).

  • output_image (a pathlike object or string representing a file) – Output image file. Maps to a command-line argument: %s (position: 2).

Outputs:

output_image (a pathlike object or string representing an existing file) – Output image file.

class nipype.interfaces.ants.utils.LabelGeometry(**inputs)

Bases: ANTSCommand

Wrapped executable: LabelGeometryMeasures.

Extracts geometry measures using a label file and an optional image file

Examples

>>> from nipype.interfaces.ants import LabelGeometry
>>> label_extract = LabelGeometry()
>>> label_extract.inputs.dimension = 3
>>> label_extract.inputs.label_image = 'atlas.nii.gz'
>>> label_extract.cmdline
"LabelGeometryMeasures 3 atlas.nii.gz '[]' atlas.csv"

>>> label_extract.inputs.intensity_image = 'ants_Warp.nii.gz'
>>> label_extract.cmdline
'LabelGeometryMeasures 3 atlas.nii.gz ants_Warp.nii.gz atlas.csv'
Mandatory Inputs:

  • intensity_image (a pathlike object or string representing an existing file) – Intensity image to extract values from. This is an optional input. Maps to a command-line argument: %s (position: 2). (Nipype default value: [])

  • label_image (a pathlike object or string representing a file) – Label image to use for extracting geometry measures. Maps to a command-line argument: %s (position: 1).

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • dimension (3 or 2) – Image dimension (2 or 3). Maps to a command-line argument: %d (position: 0). (Nipype default value: 3)

  • 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’) – Environment variables. (Nipype default value: {})

  • num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)

  • output_file (a string) – Name of output file. Maps to a command-line argument: %s (position: 3).

Outputs:

output_file (a pathlike object or string representing an existing file) – CSV file of geometry measures.

class nipype.interfaces.ants.utils.MultiplyImages(**inputs)

Bases: ANTSCommand

Wrapped executable: MultiplyImages.

Examples

>>> from nipype.interfaces.ants import MultiplyImages
>>> test = MultiplyImages()
>>> test.inputs.dimension = 3
>>> test.inputs.first_input = 'moving2.nii'
>>> test.inputs.second_input = 0.25
>>> test.inputs.output_product_image = "out.nii"
>>> test.cmdline
'MultiplyImages 3 moving2.nii 0.25 out.nii'
Mandatory Inputs:

  • dimension (3 or 2) – Image dimension (2 or 3). Maps to a command-line argument: %d (position: 0).

  • first_input (a pathlike object or string representing an existing file) – Image 1. Maps to a command-line argument: %s (position: 1).

  • output_product_image (a pathlike object or string representing a file) – Outputfname.nii.gz: the name of the resulting image. Maps to a command-line argument: %s (position: 3).

  • second_input (a pathlike object or string representing an existing file or a float) – Image 2 or multiplication weight. Maps to a command-line argument: %s (position: 2).

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %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’) – Environment variables. (Nipype default value: {})

  • num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)

Outputs:

output_product_image (a pathlike object or string representing an existing file) – Average image file.

class nipype.interfaces.ants.utils.ResampleImageBySpacing(**inputs)

Bases: ANTSCommand

Wrapped executable: ResampleImageBySpacing.

Resample an image with a given spacing.

Examples

>>> res = ResampleImageBySpacing(dimension=3)
>>> res.inputs.input_image = 'structural.nii'
>>> res.inputs.output_image = 'output.nii.gz'
>>> res.inputs.out_spacing = (4, 4, 4)
>>> res.cmdline
'ResampleImageBySpacing 3 structural.nii output.nii.gz 4 4 4'

>>> res = ResampleImageBySpacing(dimension=3)
>>> res.inputs.input_image = 'structural.nii'
>>> res.inputs.output_image = 'output.nii.gz'
>>> res.inputs.out_spacing = (4, 4, 4)
>>> res.inputs.apply_smoothing = True
>>> res.cmdline
'ResampleImageBySpacing 3 structural.nii output.nii.gz 4 4 4 1'

>>> res = ResampleImageBySpacing(dimension=3)
>>> res.inputs.input_image = 'structural.nii'
>>> res.inputs.output_image = 'output.nii.gz'
>>> res.inputs.out_spacing = (0.4, 0.4, 0.4)
>>> res.inputs.apply_smoothing = True
>>> res.inputs.addvox = 2
>>> res.inputs.nn_interp = False
>>> res.cmdline
'ResampleImageBySpacing 3 structural.nii output.nii.gz 0.4 0.4 0.4 1 2 0'
Mandatory Inputs:

  • input_image (a pathlike object or string representing an existing file) – Input image file. Maps to a command-line argument: %s (position: 2).

  • out_spacing (a list of from 2 to 3 items which are a float or a tuple of the form: (a float, a float, a float) or a tuple of the form: (a float, a float)) – Output spacing. Maps to a command-line argument: %s (position: 4).

Optional Inputs:

  • addvox (an integer) – Addvox pads each dimension by addvox. Maps to a command-line argument: %d (position: 6). Requires inputs: apply_smoothing.

  • apply_smoothing (a boolean) – Smooth before resampling. Maps to a command-line argument: %d (position: 5).

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • dimension (an integer) – Dimension of output image. Maps to a command-line argument: %d (position: 1). (Nipype default value: 3)

  • 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’) – Environment variables. (Nipype default value: {})

  • nn_interp (a boolean) – Nn interpolation. Maps to a command-line argument: %d (position: -1). Requires inputs: addvox.

  • num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)

  • output_image (a pathlike object or string representing a file) – Output image file. Maps to a command-line argument: %s (position: 3).

Outputs:

output_image (a pathlike object or string representing an existing file) – Resampled file.

class nipype.interfaces.ants.utils.ThresholdImage(**inputs)

Bases: ANTSCommand, CopyHeaderInterface

Wrapped executable: ThresholdImage.

Apply thresholds on images.

Examples

>>> thres = ThresholdImage(dimension=3)
>>> thres.inputs.input_image = 'structural.nii'
>>> thres.inputs.output_image = 'output.nii.gz'
>>> thres.inputs.th_low = 0.5
>>> thres.inputs.th_high = 1.0
>>> thres.inputs.inside_value = 1.0
>>> thres.inputs.outside_value = 0.0
>>> thres.cmdline
'ThresholdImage 3 structural.nii output.nii.gz 0.500000 1.000000 1.000000 0.000000'

>>> thres = ThresholdImage(dimension=3)
>>> thres.inputs.input_image = 'structural.nii'
>>> thres.inputs.output_image = 'output.nii.gz'
>>> thres.inputs.mode = 'Kmeans'
>>> thres.inputs.num_thresholds = 4
>>> thres.cmdline
'ThresholdImage 3 structural.nii output.nii.gz Kmeans 4'
Mandatory Inputs:

  • copy_header (a boolean) – Copy headers of the original image into the output (corrected) file. (Nipype default value: True)

  • input_image (a pathlike object or string representing an existing file) – Input image file. Maps to a command-line argument: %s (position: 2).

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • dimension (an integer) – Dimension of output image. Maps to a command-line argument: %d (position: 1). (Nipype default value: 3)

  • 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’) – Environment variables. (Nipype default value: {})

  • input_mask (a pathlike object or string representing an existing file) – Input mask for Otsu, Kmeans. Maps to a command-line argument: %s. Requires inputs: num_thresholds.

  • inside_value (a float) – Inside value. Maps to a command-line argument: %f (position: 6). Requires inputs: th_low.

  • mode (‘Otsu’ or ‘Kmeans’) – Whether to run Otsu / Kmeans thresholding. Maps to a command-line argument: %s (position: 4). Mutually exclusive with inputs: th_low, th_high. Requires inputs: num_thresholds.

  • num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)

  • num_thresholds (an integer) – Number of thresholds. Maps to a command-line argument: %d (position: 5).

  • output_image (a pathlike object or string representing a file) – Output image file. Maps to a command-line argument: %s (position: 3).

  • outside_value (a float) – Outside value. Maps to a command-line argument: %f (position: 7). Requires inputs: th_low.

  • th_high (a float) – Upper threshold. Maps to a command-line argument: %f (position: 5). Mutually exclusive with inputs: mode.

  • th_low (a float) – Lower threshold. Maps to a command-line argument: %f (position: 4). Mutually exclusive with inputs: mode.

Outputs:

output_image (a pathlike object or string representing an existing file) – Resampled file.