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# nipype.interfaces.fsl.maths module

The maths module provides higher-level interfaces to some of the operations that can be performed with the fslmaths command-line program.

## AR1Image

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

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

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> dimension‘T’ or ‘X’ or ‘Y’ or ‘Z’

>   Dimension to find AR(1) coefficientacross. Maps to a command-line argument: `-%sar1` (position: 4). (Nipype default value: `T`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## ApplyMask

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

> Use fslmaths to apply a binary mask to another image.

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> mask_filea pathlike object or string representing an existing file

>   Binary image defining mask space. Maps to a command-line argument: `-mas %s` (position: 4).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## BinaryMaths

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

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

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> operand_filea pathlike object or string representing an existing file

>   Second image to perform operation with. Maps to a command-line argument: `%s` (position: 5). Mutually exclusive with inputs: `operand_value`.

> operand_valuea float

>   Value to perform operation with. Maps to a command-line argument: `%.8f` (position: 5). Mutually exclusive with inputs: `operand_file`.

> operation‘add’ or ‘sub’ or ‘mul’ or ‘div’ or ‘rem’ or ‘max’ or ‘min’

>   Operation to perform. Maps to a command-line argument: `-%s` (position: 4).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## ChangeDataType

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

> Use fslmaths to change the datatype of an image.

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Output data type. Maps to a command-line argument: `-odt %s` (position: -1).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## DilateImage

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

> Use fslmaths to perform a spatial dilation of an image.

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> operation‘mean’ or ‘modal’ or ‘max’

>   Filtering operation to perfoem in dilation. Maps to a command-line argument: `-dil%s` (position: 6).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> kernel_filea pathlike object or string representing an existing file

>   Use external file for kernel. Maps to a command-line argument: `%s` (position: 5). Mutually exclusive with inputs: `kernel_size`.

> kernel_shape‘3D’ or ‘2D’ or ‘box’ or ‘boxv’ or ‘gauss’ or ‘sphere’ or ‘file’

>   Kernel shape to use. Maps to a command-line argument: `-kernel %s` (position: 4).

> kernel_sizea float

>   Kernel size - voxels for box/boxv, mm for sphere, mm sigma for gauss. Maps to a command-line argument: `%.4f` (position: 5). Mutually exclusive with inputs: `kernel_file`.

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## ErodeImage

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

> Use fslmaths to perform a spatial erosion of an image.

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> kernel_filea pathlike object or string representing an existing file

>   Use external file for kernel. Maps to a command-line argument: `%s` (position: 5). Mutually exclusive with inputs: `kernel_size`.

> kernel_shape‘3D’ or ‘2D’ or ‘box’ or ‘boxv’ or ‘gauss’ or ‘sphere’ or ‘file’

>   Kernel shape to use. Maps to a command-line argument: `-kernel %s` (position: 4).

> kernel_sizea float

>   Kernel size - voxels for box/boxv, mm for sphere, mm sigma for gauss. Maps to a command-line argument: `%.4f` (position: 5). Mutually exclusive with inputs: `kernel_file`.

> minimum_filtera boolean

>   If true, minimum filter rather than erosion by zeroing-out. Maps to a command-line argument: `%s` (position: 6). (Nipype default value: `False`)

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## IsotropicSmooth

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

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

> fwhma float

>   Fwhm of smoothing kernel [mm]. Maps to a command-line argument: `-s %.5f` (position: 4). Mutually exclusive with inputs: `sigma`.

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> sigmaa float

>   Sigma of smoothing kernel [mm]. Maps to a command-line argument: `-s %.5f` (position: 4). Mutually exclusive with inputs: `fwhm`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## MathsCommand

Link to code

> Bases: FSLCommand

> Wrapped executable: `fslmaths`.

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## MaxImage

Link to code

> Bases: MathsCommand

> Wrapped executable: `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'

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> dimension‘T’ or ‘X’ or ‘Y’ or ‘Z’

>   Dimension to max across. Maps to a command-line argument: `-%smax` (position: 4). (Nipype default value: `T`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## MaxnImage

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

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

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> dimension‘T’ or ‘X’ or ‘Y’ or ‘Z’

>   Dimension to index max across. Maps to a command-line argument: `-%smaxn` (position: 4). (Nipype default value: `T`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## MeanImage

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

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

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> dimension‘T’ or ‘X’ or ‘Y’ or ‘Z’

>   Dimension to mean across. Maps to a command-line argument: `-%smean` (position: 4). (Nipype default value: `T`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## MedianImage

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

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

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> dimension‘T’ or ‘X’ or ‘Y’ or ‘Z’

>   Dimension to median across. Maps to a command-line argument: `-%smedian` (position: 4). (Nipype default value: `T`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## MinImage

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

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

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> dimension‘T’ or ‘X’ or ‘Y’ or ‘Z’

>   Dimension to min across. Maps to a command-line argument: `-%smin` (position: 4). (Nipype default value: `T`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## MultiImageMaths

Link to code

> Bases: MathsCommand

> Wrapped executable: `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'

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> op_stringa string

>   Python formatted string of operations to perform. Maps to a command-line argument: `%s` (position: 4).

> operand_filesa list of items which are a pathlike object or string representing an existing file

>   List of file names to plug into op string.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## PercentileImage

Link to code

> Bases: MathsCommand

> Wrapped executable: `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'

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> dimension‘T’ or ‘X’ or ‘Y’ or ‘Z’

>   Dimension to percentile across. Maps to a command-line argument: `-%sperc` (position: 4). (Nipype default value: `T`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> perc0 <= a long integer <= 100

>   Nth percentile (0-100) of FULL RANGE across dimension. Maps to a command-line argument: `%f` (position: 5).

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## SpatialFilter

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

> Use fslmaths to spatially filter an image.

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> operation‘mean’ or ‘median’ or ‘meanu’

>   Operation to filter with. Maps to a command-line argument: `-f%s` (position: 6).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> kernel_filea pathlike object or string representing an existing file

>   Use external file for kernel. Maps to a command-line argument: `%s` (position: 5). Mutually exclusive with inputs: `kernel_size`.

> kernel_shape‘3D’ or ‘2D’ or ‘box’ or ‘boxv’ or ‘gauss’ or ‘sphere’ or ‘file’

>   Kernel shape to use. Maps to a command-line argument: `-kernel %s` (position: 4).

> kernel_sizea float

>   Kernel size - voxels for box/boxv, mm for sphere, mm sigma for gauss. Maps to a command-line argument: `%.4f` (position: 5). Mutually exclusive with inputs: `kernel_file`.

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## StdImage

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

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

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> dimension‘T’ or ‘X’ or ‘Y’ or ‘Z’

>   Dimension to standard deviate across. Maps to a command-line argument: `-%sstd` (position: 4). (Nipype default value: `T`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## TemporalFilter

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

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

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> highpass_sigmaa float

>   Highpass filter sigma (in volumes). Maps to a command-line argument: `-bptf %.6f` (position: 4). (Nipype default value: `-1`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> lowpass_sigmaa float

>   Lowpass filter sigma (in volumes). Maps to a command-line argument: `%.6f` (position: 5). (Nipype default value: `-1`)

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## Threshold

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

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

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> thresha float

>   Threshold value. Maps to a command-line argument: `%s` (position: 4).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> direction‘below’ or ‘above’

>   Zero-out either below or above thresh value. (Nipype default value: `below`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> use_nonzero_voxelsa boolean

>   Use nonzero voxels to calculate robust range. Requires inputs: `use_robust_range`.

> use_robust_rangea boolean

>   Interpret thresh as percentage (0-100) of robust range.

> out_filea pathlike object or string representing a file

>   Image written after calculations.

## UnaryMaths

Link to code

> Bases: MathsCommand

> Wrapped executable: `fslmaths`.

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

> in_filea pathlike object or string representing an existing file

>   Image to operate on. Maps to a command-line argument: `%s` (position: 2).

> operation‘exp’ or ‘log’ or ‘sin’ or ‘cos’ or ‘tan’ or ‘asin’ or ‘acos’ or ‘atan’ or ‘sqr’ or ‘sqrt’ or ‘recip’ or ‘abs’ or ‘bin’ or ‘binv’ or ‘fillh’ or ‘fillh26’ or ‘index’ or ‘edge’ or ‘nan’ or ‘nanm’ or ‘rand’ or ‘randn’ or ‘range’

>   Operation to perform. Maps to a command-line argument: `-%s` (position: 4).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for calculations (default is float). Maps to a command-line argument: `-dt %s` (position: 1).

> nan2zerosa boolean

>   Change NaNs to zeros before doing anything. Maps to a command-line argument: `-nan` (position: 3).

> out_filea pathlike object or string representing a file

>   Image to write. Maps to a command-line argument: `%s` (position: -2).

> output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’

>   Datatype to use for output (default uses input type). Maps to a command-line argument: `-odt %s` (position: -1).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing a file

>   Image written after calculations.