Wraps command AverageAffineTransform
>>> 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'
Inputs:
[Mandatory]
dimension: (3 or 2)
image dimension (2 or 3)
output_affine_transform: (a file name)
Outputfname.txt: the name of the resulting transform.
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output
transforms: (an existing file name)
transforms to average
[Optional]
args: (a string)
Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
are a value of type '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
num_threads: (an integer, nipype default value: -1)
Number of ITK threads to use
Outputs:
affine_transform: (an existing file name)
average transform file
Wraps command AverageImages
>>> 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'
Inputs:
[Mandatory]
dimension: (3 or 2)
image dimension (2 or 3)
images: (an existing file name)
image to apply transformation to (generally a coregistered functional)
normalize: (a boolean)
Normalize: if true, the 2nd imageis divided by its mean. This will select the largest
image to average into.
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output
[Optional]
args: (a string)
Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
are a value of type '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
num_threads: (an integer, nipype default value: -1)
Number of ITK threads to use
output_average_image: (a file name, nipype default value: average.nii)
the name of the resulting image.
Outputs:
output_average_image: (an existing file name)
average image file
Wraps command ANTSJacobian
>>> from nipype.interfaces.ants import JacobianDeterminant
>>> jacobian = JacobianDeterminant()
>>> jacobian.inputs.dimension = 3
>>> jacobian.inputs.warp_file = 'ants_Warp.nii.gz'
>>> jacobian.inputs.output_prefix = 'Sub001_'
>>> jacobian.inputs.use_log = 1
>>> jacobian.cmdline
'ANTSJacobian 3 ants_Warp.nii.gz Sub001_ 1'
Inputs:
[Mandatory]
dimension: (3 or 2)
image dimension (2 or 3)
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output
warp_file: (an existing file name)
input warp file
[Optional]
args: (a string)
Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
are a value of type '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
num_threads: (an integer, nipype default value: -1)
Number of ITK threads to use
output_prefix: (a file name)
prefix of the output image filename: PREFIX(log)jacobian.nii.gz
Outputs:
jacobian_image: (an existing file name)
(log transformed) jacobian image
Wraps command MultiplyImages
>>> 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'
Inputs:
[Mandatory]
dimension: (3 or 2)
image dimension (2 or 3)
first_input: (an existing file name)
image 1
output_product_image: (a file name)
Outputfname.nii.gz: the name of the resulting image.
second_input: (an existing file name or a float)
image 2 or multiplication weight
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output
[Optional]
args: (a string)
Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
are a value of type '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
num_threads: (an integer, nipype default value: -1)
Number of ITK threads to use
Outputs:
output_product_image: (an existing file name)
average image file