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¶
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 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) coefficient across. 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
ApplyMask¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
BinaryMaths¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
ChangeDataType¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
DilateImage¶
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 perform in dilation. Maps to a command-line argument:
-dil%s
(position: 6).
- argsa 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
ErodeImage¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
IsotropicSmooth¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
MathsCommand¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
MaxImage¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
MaxnImage¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
MeanImage¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
MedianImage¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
MinImage¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
MultiImageMaths¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
PercentileImage¶
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 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’ or ‘GIFTI’
FSL output type.
- perc0 <= an 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¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
StdImage¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
TemporalFilter¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.
Threshold¶
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 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’ or ‘GIFTI’
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¶
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 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’ or ‘GIFTI’
FSL output type.
- out_filea pathlike object or string representing a file
Image written after calculations.