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# interfaces.fsl.maths

## AR1Image

Link to code

Wraps command fslmaths

Use fslmaths to generate an AR1 coefficient image across a given dimension. (Should use -odt float and probably demean first)

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    dimension: (u'T' or u'X' or u'Y' or u'Z', nipype default value: T)
            dimension to find AR(1) coefficientacross
            flag: -%sar1, position: 4
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## ApplyMask

Link to code

Wraps command fslmaths

Use fslmaths to apply a binary mask to another image.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2
    mask_file: (an existing file name)
            binary image defining mask space
            flag: -mas %s, position: 4

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## BinaryMaths

Link to code

Wraps command fslmaths

Use fslmaths to perform mathematical operations using a second image or a numeric value.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2
    operand_file: (an existing file name)
            second image to perform operation with
            flag: %s, position: 5
            mutually_exclusive: operand_value
    operand_value: (a float)
            value to perform operation with
            flag: %.8f, position: 5
            mutually_exclusive: operand_file
    operation: (u'add' or u'sub' or u'mul' or u'div' or u'rem' or u'max'
             or u'min')
            operation to perform
            flag: -%s, position: 4

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## ChangeDataType

Link to code

Wraps command fslmaths

Use fslmaths to change the datatype of an image.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            output data type
            flag: -odt %s, position: -1

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## DilateImage

Link to code

Wraps command fslmaths

Use fslmaths to perform a spatial dilation of an image.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2
    operation: (u'mean' or u'modal' or u'max')
            filtering operation to perfoem in dilation
            flag: -dil%s, position: 6

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    kernel_file: (an existing file name)
            use external file for kernel
            flag: %s, position: 5
            mutually_exclusive: kernel_size
    kernel_shape: (u'3D' or u'2D' or u'box' or u'boxv' or u'gauss' or
             u'sphere' or u'file')
            kernel shape to use
            flag: -kernel %s, position: 4
    kernel_size: (a float)
            kernel size - voxels for box/boxv, mm for sphere, mm sigma for gauss
            flag: %.4f, position: 5
            mutually_exclusive: kernel_file
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## ErodeImage

Link to code

Wraps command fslmaths

Use fslmaths to perform a spatial erosion of an image.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    kernel_file: (an existing file name)
            use external file for kernel
            flag: %s, position: 5
            mutually_exclusive: kernel_size
    kernel_shape: (u'3D' or u'2D' or u'box' or u'boxv' or u'gauss' or
             u'sphere' or u'file')
            kernel shape to use
            flag: -kernel %s, position: 4
    kernel_size: (a float)
            kernel size - voxels for box/boxv, mm for sphere, mm sigma for gauss
            flag: %.4f, position: 5
            mutually_exclusive: kernel_file
    minimum_filter: (a boolean, nipype default value: False)
            if true, minimum filter rather than erosion by zeroing-out
            flag: %s, position: 6
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## IsotropicSmooth

Link to code

Wraps command fslmaths

Use fslmaths to spatially smooth an image with a gaussian kernel.

Inputs:

    [Mandatory]
    fwhm: (a float)
            fwhm of smoothing kernel [mm]
            flag: -s %.5f, position: 4
            mutually_exclusive: sigma
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2
    sigma: (a float)
            sigma of smoothing kernel [mm]
            flag: -s %.5f, position: 4
            mutually_exclusive: fwhm

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## MathsCommand

Link to code

Wraps command fslmaths

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## MaxImage

Link to code

Wraps command fslmaths

Use fslmaths to generate a max image across a given dimension.

### Examples

    >>> from nipype.interfaces.fsl.maths import MaxImage
    >>> maxer = MaxImage()
    >>> maxer.inputs.in_file = "functional.nii"
    >>> maxer.dimension = "T"
    >>> maxer.cmdline
    'fslmaths functional.nii -Tmax functional_max.nii'

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    dimension: (u'T' or u'X' or u'Y' or u'Z', nipype default value: T)
            dimension to max across
            flag: -%smax, position: 4
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## MaxnImage

Link to code

Wraps command fslmaths

Use fslmaths to generate an image of index of max across a given dimension.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    dimension: (u'T' or u'X' or u'Y' or u'Z', nipype default value: T)
            dimension to index max across
            flag: -%smaxn, position: 4
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## MeanImage

Link to code

Wraps command fslmaths

Use fslmaths to generate a mean image across a given dimension.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    dimension: (u'T' or u'X' or u'Y' or u'Z', nipype default value: T)
            dimension to mean across
            flag: -%smean, position: 4
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## MedianImage

Link to code

Wraps command fslmaths

Use fslmaths to generate a median image across a given dimension.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    dimension: (u'T' or u'X' or u'Y' or u'Z', nipype default value: T)
            dimension to median across
            flag: -%smedian, position: 4
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## MinImage

Link to code

Wraps command fslmaths

Use fslmaths to generate a minimum image across a given dimension.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    dimension: (u'T' or u'X' or u'Y' or u'Z', nipype default value: T)
            dimension to min across
            flag: -%smin, position: 4
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## MultiImageMaths

Link to code

Wraps command fslmaths

Use fslmaths to perform a sequence of mathematical operations.

### Examples

    >>> from nipype.interfaces.fsl import MultiImageMaths
    >>> maths = MultiImageMaths()
    >>> maths.inputs.in_file = "functional.nii"
    >>> maths.inputs.op_string = "-add %s -mul -1 -div %s"
    >>> maths.inputs.operand_files = ["functional2.nii", "functional3.nii"]
    >>> maths.inputs.out_file = "functional4.nii"
    >>> maths.cmdline
    'fslmaths functional.nii -add functional2.nii -mul -1 -div functional3.nii functional4.nii'

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2
    op_string: (a string)
            python formatted string of operations to perform
            flag: %s, position: 4
    operand_files: (a list of items which are an existing file name)
            list of file names to plug into op string

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## PercentileImage

Link to code

Wraps command fslmaths

Use fslmaths to generate a percentile image across a given dimension.

### Examples

    >>> from nipype.interfaces.fsl.maths import MaxImage
    >>> percer = PercentileImage()
    >>> percer.inputs.in_file = "functional.nii"
    >>> percer.dimension = "T"
    >>> percer.perc = 90
    >>> percer.cmdline
    'fslmaths functional.nii -Tperc 90 functional_perc.nii'

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    dimension: (u'T' or u'X' or u'Y' or u'Z', nipype default value: T)
            dimension to percentile across
            flag: -%sperc, position: 4
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    perc: (0 <= an integer <= 100)
            nth percentile (0-100) of FULL RANGE across dimension
            flag: %f, position: 5
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## SpatialFilter

Link to code

Wraps command fslmaths

Use fslmaths to spatially filter an image.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2
    operation: (u'mean' or u'median' or u'meanu')
            operation to filter with
            flag: -f%s, position: 6

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    kernel_file: (an existing file name)
            use external file for kernel
            flag: %s, position: 5
            mutually_exclusive: kernel_size
    kernel_shape: (u'3D' or u'2D' or u'box' or u'boxv' or u'gauss' or
             u'sphere' or u'file')
            kernel shape to use
            flag: -kernel %s, position: 4
    kernel_size: (a float)
            kernel size - voxels for box/boxv, mm for sphere, mm sigma for gauss
            flag: %.4f, position: 5
            mutually_exclusive: kernel_file
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## StdImage

Link to code

Wraps command fslmaths

Use fslmaths to generate a standard deviation in an image across a given dimension.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    dimension: (u'T' or u'X' or u'Y' or u'Z', nipype default value: T)
            dimension to standard deviate across
            flag: -%sstd, position: 4
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## TemporalFilter

Link to code

Wraps command fslmaths

Use fslmaths to apply a low, high, or bandpass temporal filter to a timeseries.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    highpass_sigma: (a float, nipype default value: -1)
            highpass filter sigma (in volumes)
            flag: -bptf %.6f, position: 4
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    lowpass_sigma: (a float, nipype default value: -1)
            lowpass filter sigma (in volumes)
            flag: %.6f, position: 5
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None

## Threshold

Link to code

Wraps command fslmaths

Use fslmaths to apply a threshold to an image in a variety of ways.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2
    thresh: (a float)
            threshold value
            flag: %s, position: 4

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    direction: (u'below' or u'above', nipype default value: below)
            zero-out either below or above thresh value
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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_nonzero_voxels: (a boolean)
            use nonzero voxels to calculate robust range
            requires: use_robust_range
    use_robust_range: (a boolean)
            interpret thresh as percentage (0-100) of robust range

Outputs:

    out_file: (an existing file name)
            image written after calculations

References:: None

## UnaryMaths

Link to code

Wraps command fslmaths

Use fslmaths to perorm a variety of mathematical operations on an image.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
            flag: %s, position: 2
    operation: (u'exp' or u'log' or u'sin' or u'cos' or u'tan' or u'asin'
             or u'acos' or u'atan' or u'sqr' or u'sqrt' or u'recip' or u'abs' or
             u'bin' or u'binv' or u'fillh' or u'fillh26' or u'index' or u'edge'
             or u'nan' or u'nanm' or u'rand' or u'randn' or u'range')
            operation to perform
            flag: -%s, position: 4

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    internal_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for calculations (default is float)
            flag: -dt %s, position: 1
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
            flag: -nan, position: 3
    out_file: (a file name)
            image to write
            flag: %s, position: -2
    output_datatype: (u'float' or u'char' or u'int' or u'short' or
             u'double' or u'input')
            datatype to use for output (default uses input type)
            flag: -odt %s, position: -1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'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: (an existing file name)
            image written after calculations

References:: None