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_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
args : a 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)
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing 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_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
mask_file : a pathlike object or string representing an existing file
Binary image defining mask space. Maps to a command-line argument: -mas %s (position: 4).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing 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_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
operand_file : a 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_value : a 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).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing file
Image written after calculations.

ChangeDataType

Link to code

Bases: MathsCommand

Wrapped executable: fslmaths.

Use fslmaths to change the datatype of an image.

in_file : a 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).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing 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_file : a 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).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a 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_file : a 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_size : a 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.
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing 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_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a 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_file : a 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_size : a 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_filter : a boolean
If true, minimum filter rather than erosion by zeroing-out. Maps to a command-line argument: %s (position: 6). (Nipype default value: False)
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing 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.

fwhm : a float
Fwhm of smoothing kernel [mm]. Maps to a command-line argument: -s %.5f (position: 4). Mutually exclusive with inputs: sigma.
in_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
sigma : a float
Sigma of smoothing kernel [mm]. Maps to a command-line argument: -s %.5f (position: 4). Mutually exclusive with inputs: fwhm.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing file
Image written after calculations.

MathsCommand

Link to code

Bases: FSLCommand

Wrapped executable: fslmaths.

in_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing 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"  # doctest: +SKIP
>>> maxer.dimension = "T"
>>> maxer.cmdline  # doctest: +SKIP
'fslmaths functional.nii -Tmax functional_max.nii'
in_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
args : a 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)
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing 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_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
args : a 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)
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing 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_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
args : a 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)
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing 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_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
args : a 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)
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing 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_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
args : a 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)
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing 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_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
op_string : a string
Python formatted string of operations to perform. Maps to a command-line argument: %s (position: 4).
operand_files : a list of items which are a pathlike object or string representing an existing file
List of file names to plug into op string.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing 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"  # doctest: +SKIP
>>> percer.dimension = "T"
>>> percer.perc = 90
>>> percer.cmdline  # doctest: +SKIP
'fslmaths functional.nii -Tperc 90 functional_perc.nii'
in_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
args : a 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)
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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.
perc : 0 <= a long integer <= 100
Nth percentile (0-100) of FULL RANGE across dimension. Maps to a command-line argument: %f (position: 5).
out_file : a pathlike object or string representing an existing file
Image written after calculations.

SpatialFilter

Link to code

Bases: MathsCommand

Wrapped executable: fslmaths.

Use fslmaths to spatially filter an image.

in_file : a 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).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a 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_file : a 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_size : a 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.
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing 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_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
args : a 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)
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing 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_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a 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_sigma : a 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_sigma : a float
Lowpass filter sigma (in volumes). Maps to a command-line argument: %.6f (position: 5). (Nipype default value: -1)
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing 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_file : a pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).
thresh : a float
Threshold value. Maps to a command-line argument: %s (position: 4).
args : a 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)
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_voxels : a boolean
Use nonzero voxels to calculate robust range. Requires inputs: use_robust_range.
use_robust_range : a boolean
Interpret thresh as percentage (0-100) of robust range.
out_file : a pathlike object or string representing an existing 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_file : a 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).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a 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).
nan2zeros : a boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).
out_file : a 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_file : a pathlike object or string representing an existing file
Image written after calculations.