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# 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, 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, 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, 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, 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