interfaces.fsl.maths

AR1Image

Link to code

Wraps the executable command fslmaths.

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

Inputs:

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

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

Outputs:

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

References:

None

ApplyMask

Link to code

Wraps the executable command fslmaths.

Use fslmaths to apply a binary mask to another image.

Inputs:

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

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

Outputs:

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

References:

None

BinaryMaths

Link to code

Wraps the executable command fslmaths.

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

Inputs:

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

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

Outputs:

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

References:

None

ChangeDataType

Link to code

Wraps the executable command fslmaths.

Use fslmaths to change the datatype of an image.

Inputs:

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

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

Outputs:

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

References:

None

DilateImage

Link to code

Wraps the executable command fslmaths.

Use fslmaths to perform a spatial dilation of an image.

Inputs:

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

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

Outputs:

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

References:

None

ErodeImage

Link to code

Wraps the executable command fslmaths.

Use fslmaths to perform a spatial erosion of an image.

Inputs:

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

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

Outputs:

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

References:

None

IsotropicSmooth

Link to code

Wraps the executable command fslmaths.

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

Inputs:

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

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

Outputs:

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

References:

None

MathsCommand

Link to code

Wraps the executable command fslmaths.

Inputs:

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

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

Outputs:

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

References:

None

MaxImage

Link to code

Wraps the executable command fslmaths.

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

Examples

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

Inputs:

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

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

Outputs:

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

References:

None

MaxnImage

Link to code

Wraps the executable command fslmaths.

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

Inputs:

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

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

Outputs:

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

References:

None

MeanImage

Link to code

Wraps the executable command fslmaths.

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

Inputs:

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

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

Outputs:

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

References:

None

MedianImage

Link to code

Wraps the executable command fslmaths.

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

Inputs:

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

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

Outputs:

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

References:

None

MinImage

Link to code

Wraps the executable command fslmaths.

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

Inputs:

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

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

Outputs:

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

References:

None

MultiImageMaths

Link to code

Wraps the executable command fslmaths.

Use fslmaths to perform a sequence of mathematical operations.

Examples

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

Inputs:

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

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

Outputs:

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

References:

None

PercentileImage

Link to code

Wraps the executable command fslmaths.

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

Examples

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

Inputs:

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

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

Outputs:

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

References:

None

SpatialFilter

Link to code

Wraps the executable command fslmaths.

Use fslmaths to spatially filter an image.

Inputs:

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

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

Outputs:

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

References:

None

StdImage

Link to code

Wraps the executable command fslmaths.

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

Inputs:

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

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

Outputs:

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

References:

None

TemporalFilter

Link to code

Wraps the executable command fslmaths.

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

Inputs:

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

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

Outputs:

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

References:

None

Threshold

Link to code

Wraps the executable command fslmaths.

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

Inputs:

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

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

Outputs:

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

References:

None

UnaryMaths

Link to code

Wraps the executable command fslmaths.

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

Inputs:

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

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

Outputs:

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

References:

None