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# interfaces.fsl.maths

## 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
    mask_file: (an existing file name)
            binary image defining mask space

    [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
    internal_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for calculations (default is float)
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
    out_file: (a file name)
            image to write
    output_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for output (default uses input type)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
            FSL output type

Outputs:

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

## 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
    operand_file: (an existing file name)
            second image to perform operation with
            mutually_exclusive: operand_value
    operand_value: (a float)
            value to perform operation with
            mutually_exclusive: operand_file
    operation: ('add' or 'sub' or 'mul' or 'div' or 'rem' or 'max' or 'min')
            operation to perform

    [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
    internal_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for calculations (default is float)
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
    out_file: (a file name)
            image to write
    output_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for output (default uses input type)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
            FSL output type

Outputs:

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

## 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
    output_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            output data type

    [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
    internal_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for calculations (default is float)
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
    out_file: (a file name)
            image to write
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
            FSL output type

Outputs:

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

## 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
    operation: ('mean' or 'modal' or 'max')
            filtering operation to perfoem in dilation

    [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
    internal_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for calculations (default is float)
    kernel_file: (an existing file name)
            use external file for kernel
            mutually_exclusive: kernel_size
    kernel_shape: ('3D' or '2D' or 'box' or 'boxv' or 'gauss' or 'sphere' or 'file')
            kernel shape to use
    kernel_size: (a float)
            kernel size - voxels for box/boxv, mm for sphere, mm sigma for gauss
            mutually_exclusive: kernel_file
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
    out_file: (a file name)
            image to write
    output_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for output (default uses input type)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
            FSL output type

Outputs:

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

## 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

    [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
    internal_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for calculations (default is float)
    kernel_file: (an existing file name)
            use external file for kernel
            mutually_exclusive: kernel_size
    kernel_shape: ('3D' or '2D' or 'box' or 'boxv' or 'gauss' or 'sphere' or 'file')
            kernel shape to use
    kernel_size: (a float)
            kernel size - voxels for box/boxv, mm for sphere, mm sigma for gauss
            mutually_exclusive: kernel_file
    minimum_filter: (a boolean, nipype default value: False)
            if true, minimum filter rather than erosion by zeroing-out
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
    out_file: (a file name)
            image to write
    output_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for output (default uses input type)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
            FSL output type

Outputs:

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

## 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
            mutually_exclusive: sigma
    in_file: (an existing file name)
            image to operate on
    sigma: (a float)
            sigma of smoothing kernel
            mutually_exclusive: fwhm

    [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
    internal_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for calculations (default is float)
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
    out_file: (a file name)
            image to write
    output_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for output (default uses input type)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
            FSL output type

Outputs:

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

## MathsCommand

Link to code

Wraps command fslmaths

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on

    [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
    internal_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for calculations (default is float)
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
    out_file: (a file name)
            image to write
    output_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for output (default uses input type)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
            FSL output type

Outputs:

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

## 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

    [Optional]
    args: (a string)
            Additional parameters to the command
    dimension: ('T' or 'X' or 'Y' or 'Z', nipype default value: T)
            dimension to mean across
    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
    internal_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for calculations (default is float)
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
    out_file: (a file name)
            image to write
    output_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for output (default uses input type)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
            FSL output type

Outputs:

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

## 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 functional1.nii -add functional2.nii -mul -1 -div functional3.nii functional4.nii

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            image to operate on
    op_string: (a string)
            python formatted string of operations to perform
    operand_files: (an existing file name)
            list of file names to plug into op string

    [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
    internal_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for calculations (default is float)
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
    out_file: (a file name)
            image to write
    output_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for output (default uses input type)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
            FSL output type

Outputs:

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

## 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
    operation: ('mean' or 'median' or 'meanu')
            operation to filter with

    [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
    internal_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for calculations (default is float)
    kernel_file: (an existing file name)
            use external file for kernel
            mutually_exclusive: kernel_size
    kernel_shape: ('3D' or '2D' or 'box' or 'boxv' or 'gauss' or 'sphere' or 'file')
            kernel shape to use
    kernel_size: (a float)
            kernel size - voxels for box/boxv, mm for sphere, mm sigma for gauss
            mutually_exclusive: kernel_file
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
    out_file: (a file name)
            image to write
    output_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for output (default uses input type)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
            FSL output type

Outputs:

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

## 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

    [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
    highpass_sigma: (a float, nipype default value: -1)
            highpass filter sigma (in volumes)
    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: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for calculations (default is float)
    lowpass_sigma: (a float, nipype default value: -1)
            lowpass filter sigma (in volumes)
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
    out_file: (a file name)
            image to write
    output_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for output (default uses input type)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
            FSL output type

Outputs:

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

## 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
    thresh: (a float)
            threshold value

    [Optional]
    args: (a string)
            Additional parameters to the command
    direction: ('below' or 'above', nipype default value: below)
            zero-out either below or above thresh value
    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
    internal_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for calculations (default is float)
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
    out_file: (a file name)
            image to write
    output_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for output (default uses input type)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
            FSL output type
    use_nonzero_voxels: (a boolean)
            use nonzero voxels to caluclate robust range
            requires: use_robust_range
    use_robust_range: (a boolean)
            inteperet thresh as percentage (0-100) of robust range

Outputs:

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

## 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
    operation: ('exp' or 'log' or 'sin' or 'cos' or 'sqr' or 'sqrt' or 'recip' or 'abs' or
             'bin' or 'index')
            operation to perform

    [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
    internal_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for calculations (default is float)
    nan2zeros: (a boolean)
            change NaNs to zeros before doing anything
    out_file: (a file name)
            image to write
    output_datatype: ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
            datatype to use for output (default uses input type)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
            FSL output type

Outputs:

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