interfaces.ants.utils

AverageAffineTransform

Link to code

Wraps command 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'

Inputs:

[Mandatory]
dimension: (3 or 2)
        image dimension (2 or 3)
        flag: %d, position: 0
output_affine_transform: (a file name)
        Outputfname.txt: the name of the resulting transform.
        flag: %s, position: 1
transforms: (a list of items which are an existing file name)
        transforms to average
        flag: %s, position: 3

[Optional]
args: (a string)
        Additional parameters to the command
        flag: %s
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 (int or long), nipype default value: 1)
        Number of ITK threads to use
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:

affine_transform: (an existing file name)
        average transform file

AverageImages

Link to code

Wraps command 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'

Inputs:

[Mandatory]
dimension: (3 or 2)
        image dimension (2 or 3)
        flag: %d, position: 0
images: (a list of items which are an existing file name)
        image to apply transformation to (generally a coregistered
        functional)
        flag: %s, position: 3
normalize: (a boolean)
        Normalize: if true, the 2nd imageis divided by its mean. This will
        select the largest image to average into.
        flag: %d, position: 2

[Optional]
args: (a string)
        Additional parameters to the command
        flag: %s
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 (int or long), 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.
        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:

output_average_image: (an existing file name)
        average image file

JacobianDeterminant

Link to code

Wraps command ANTSJacobian

Examples

>>> 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)
        flag: %d, position: 0
warp_file: (an existing file name)
        input warp file
        flag: %s, position: 1

[Optional]
args: (a string)
        Additional parameters to the command
        flag: %s
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
norm_by_total: (0 or 1)
        normalize jacobian by total in mask to adjust for head size
        flag: %d, position: 5
num_threads: (an integer (int or long), 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
        flag: %s, position: 2
projection_vector: (a list of items which are a float)
        vector to project warp against
        flag: %s, position: 6
template_mask: (an existing file name)
        template mask to adjust for head size
        flag: %s, position: 4
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
use_log: (0 or 1)
        log transform the jacobian determinant
        flag: %d, position: 3

Outputs:

jacobian_image: (an existing file name)
        (log transformed) jacobian image

MultiplyImages

Link to code

Wraps command 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'

Inputs:

[Mandatory]
dimension: (3 or 2)
        image dimension (2 or 3)
        flag: %d, position: 0
first_input: (an existing file name)
        image 1
        flag: %s, position: 1
output_product_image: (a file name)
        Outputfname.nii.gz: the name of the resulting image.
        flag: %s, position: 3
second_input: (an existing file name or a float)
        image 2 or multiplication weight
        flag: %s, position: 2

[Optional]
args: (a string)
        Additional parameters to the command
        flag: %s
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 (int or long), nipype default value: 1)
        Number of ITK threads to use
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:

output_product_image: (an existing file name)
        average image file