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# interfaces.fsl.utils

## AvScale

Link to code

Wraps command avscale

Use FSL avscale command to extract info from mat file output of FLIRT

### Examples

avscale = AvScale() avscale.inputs.mat_file = ‘flirt.mat’ res = avscale.run() # doctest: +SKIP

Inputs:

    [Mandatory]
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    mat_file: (an existing file name)
            mat file to read
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    average_scaling
            Average Scaling
    backward_half_transform
            Backwards Half Transform
    determinant
            Determinant
    forward_half_transform
            Forward Half Transform
    left_right_orientation_preserved: (a boolean)
            True if LR orientation preserved
    rotation_translation_matrix
            Rotation and Translation Matrix
    scales
            Scales (x,y,z)
    skews
            Skews

## Complex

Link to code

Wraps command fslcomplex

fslcomplex is a tool for converting complex data Examples ~~~~~~~~ >>> cplx = Complex() >>> cplx.inputs.complex_in_file = “complex.nii” >>> cplx.real_polar = True >>> res = cplx.run() # doctest: +SKIP

Inputs:

    [Mandatory]
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    complex_cartesian: (a boolean)
            mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
             complex_polar, complex_split, complex_merge
    complex_in_file: (an existing file name)
    complex_in_file2: (an existing file name)
    complex_merge: (a boolean)
            mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
             complex_polar, complex_split, complex_merge, start_vol, end_vol
    complex_out_file: (a file name)
            mutually_exclusive: complex_out_file, magnitude_out_file,
             phase_out_file, real_out_file, imaginary_out_file, real_polar,
             real_cartesian
    complex_polar: (a boolean)
            mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
             complex_polar, complex_split, complex_merge
    complex_split: (a boolean)
            mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
             complex_polar, complex_split, complex_merge
    end_vol: (an integer)
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    imaginary_in_file: (an existing file name)
    imaginary_out_file: (a file name)
            mutually_exclusive: complex_out_file, magnitude_out_file,
             phase_out_file, real_polar, complex_cartesian, complex_polar,
             complex_split, complex_merge
    magnitude_in_file: (an existing file name)
    magnitude_out_file: (a file name)
            mutually_exclusive: complex_out_file, real_out_file,
             imaginary_out_file, real_cartesian, complex_cartesian,
             complex_polar, complex_split, complex_merge
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    phase_in_file: (an existing file name)
    phase_out_file: (a file name)
            mutually_exclusive: complex_out_file, real_out_file,
             imaginary_out_file, real_cartesian, complex_cartesian,
             complex_polar, complex_split, complex_merge
    real_cartesian: (a boolean)
            mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
             complex_polar, complex_split, complex_merge
    real_in_file: (an existing file name)
    real_out_file: (a file name)
            mutually_exclusive: complex_out_file, magnitude_out_file,
             phase_out_file, real_polar, complex_cartesian, complex_polar,
             complex_split, complex_merge
    real_polar: (a boolean)
            mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
             complex_polar, complex_split, complex_merge
    start_vol: (an integer)
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    complex_out_file: (a file name)
    imaginary_out_file: (a file name)
    magnitude_out_file: (a file name)
    phase_out_file: (a file name)
    real_out_file: (a file name)

## ConvertXFM

Link to code

Wraps command convert_xfm

Use the FSL utility convert_xfm to modify FLIRT transformation matrices.

### Examples

    >>> import nipype.interfaces.fsl as fsl
    >>> invt = fsl.ConvertXFM()
    >>> invt.inputs.in_file = "flirt.mat"
    >>> invt.inputs.invert_xfm = True
    >>> invt.inputs.out_file = 'flirt_inv.mat'
    >>> invt.cmdline
    'convert_xfm -omat flirt_inv.mat -inverse flirt.mat'

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            input transformation matrix
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    concat_xfm: (a boolean)
            write joint transformation of two input matrices
            mutually_exclusive: invert_xfm, concat_xfm, fix_scale_skew
            requires: in_file2
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    fix_scale_skew: (a boolean)
            use secondary matrix to fix scale and skew
            mutually_exclusive: invert_xfm, concat_xfm, fix_scale_skew
            requires: in_file2
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name)
            input transformation matrix
    in_file2: (an existing file name)
            second input matrix (for use with fix_scale_skew or concat_xfm
    invert_xfm: (a boolean)
            invert input transformation
            mutually_exclusive: invert_xfm, concat_xfm, fix_scale_skew
    out_file: (a file name)
            final transformation matrix
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    out_file: (an existing file name)
            output transformation matrix

## ExtractROI

Link to code

Wraps command fslroi

Uses FSL Fslroi command to extract region of interest (ROI) from an image.

You can a) take a 3D ROI from a 3D data set (or if it is 4D, the same ROI is taken from each time point and a new 4D data set is created), b) extract just some time points from a 4D data set, or c) control time and space limits to the ROI. Note that the arguments are minimum index and size (not maximum index). So to extract voxels 10 to 12 inclusive you would specify 10 and 3 (not 10 and 12).

### Examples

    >>> from nipype.interfaces.fsl import ExtractROI
    >>> from nipype.testing import anatfile
    >>> fslroi = ExtractROI(in_file=anatfile, roi_file='bar.nii', t_min=0,
    ...                     t_size=1)
    >>> fslroi.cmdline == 'fslroi %s bar.nii 0 1' % anatfile
    True

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            input file
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    crop_list: (a list of items which are a tuple of the form: (an
             integer, an integer))
            list of two tuples specifying crop options
            mutually_exclusive: x_min, x_size, y_min, y_size, z_min, z_size,
             t_min, t_size
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name)
            input file
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    roi_file: (a file name)
            output file
    t_min: (an integer)
    t_size: (an integer)
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    x_min: (an integer)
    x_size: (an integer)
    y_min: (an integer)
    y_size: (an integer)
    z_min: (an integer)
    z_size: (an integer)

Outputs:

    roi_file: (an existing file name)

## FilterRegressor

Link to code

Wraps command fsl_regfilt

Data de-noising by regressing out part of a design matrix

Uses simple OLS regression on 4D images

Inputs:

    [Mandatory]
    design_file: (an existing file name)
            name of the matrix with time courses (e.g. GLM design or MELODIC
            mixing matrix)
    filter_all: (a boolean)
            use all columns in the design file in denoising
            mutually_exclusive: filter_columns
    filter_columns: (a list of items which are an integer)
            (1-based) column indices to filter out of the data
            mutually_exclusive: filter_all
    in_file: (an existing file name)
            input file name (4D image)
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    design_file: (an existing file name)
            name of the matrix with time courses (e.g. GLM design or MELODIC
            mixing matrix)
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    filter_all: (a boolean)
            use all columns in the design file in denoising
            mutually_exclusive: filter_columns
    filter_columns: (a list of items which are an integer)
            (1-based) column indices to filter out of the data
            mutually_exclusive: filter_all
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name)
            input file name (4D image)
    mask: (an existing file name)
            mask image file name
    out_file: (a file name)
            output file name for the filtered data
    out_vnscales: (a boolean)
            output scaling factors for variance normalization
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    var_norm: (a boolean)
            perform variance-normalization on data

Outputs:

    out_file: (an existing file name)
            output file name for the filtered data

## ImageMaths

Link to code

Wraps command fslmaths

Use FSL fslmaths command to allow mathematical manipulation of images

FSL info

### Examples

    >>> from nipype import fsl
    >>> from nipype.testing import anatfile
    >>> maths = fsl.ImageMaths(in_file=anatfile, op_string= '-add 5',
    ...                        out_file='foo_maths.nii')
    >>> maths.cmdline == 'fslmaths %s -add 5 foo_maths.nii' % anatfile
    True

Inputs:

    [Mandatory]
    in_file: (an existing file name)
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name)
    in_file2: (an existing file name)
    op_string: (a string)
            string defining the operation, i. e. -add
    out_data_type: ('char' or 'short' or 'int' or 'float' or 'double' or
             'input')
            output datatype, one of (char, short, int, float, double, input)
    out_file: (a file name)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    suffix: (a string)
            out_file suffix
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    out_file: (an existing file name)

## ImageMeants

Link to code

Wraps command fslmeants

Use fslmeants for printing the average timeseries (intensities) to the screen (or saves to a file). The average is taken over all voxels in the mask (or all voxels in the image if no mask is specified)

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            input file for computing the average timeseries
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    eig: (a boolean)
            calculate Eigenvariate(s) instead of mean (output will have 0 mean)
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name)
            input file for computing the average timeseries
    mask: (an existing file name)
            input 3D mask
    nobin: (a boolean)
            do not binarise the mask for calculation of Eigenvariates
    order: (an integer, nipype default value: 1)
            select number of Eigenvariates
    out_file: (a file name)
            name of output text matrix
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    show_all: (a boolean)
            show all voxel time series (within mask) instead of averaging
    spatial_coord: (a list of items which are an integer)
            <x y z> requested spatial coordinate (instead of mask)
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    transpose: (a boolean)
            output results in transpose format (one row per voxel/mean)
    use_mm: (a boolean)
            use mm instead of voxel coordinates (for -c option)

Outputs:

    out_file: (an existing file name)
            path/name of output text matrix

## ImageStats

Link to code

Wraps command fslstats

Use FSL fslstats command to calculate stats from images

FSL info

### Examples

    >>> from nipype.interfaces.fsl import ImageStats
    >>> from nipype.testing import funcfile
    >>> stats = ImageStats(in_file=funcfile, op_string= '-M')
    >>> stats.cmdline == 'fslstats %s -M'%funcfile
    True

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            input file to generate stats of
    op_string: (a string)
            string defining the operation, options are applied in order, e.g. -M
            -l 10 -M will report the non-zero mean, apply a threshold and then
            report the new nonzero mean
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name)
            input file to generate stats of
    mask_file: (an existing file name)
            mask file used for option -k %s
    op_string: (a string)
            string defining the operation, options are applied in order, e.g. -M
            -l 10 -M will report the non-zero mean, apply a threshold and then
            report the new nonzero mean
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    split_4d: (a boolean)
            give a separate output line for each 3D volume of a 4D timeseries
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    out_stat
            stats output

## InvWarp

Link to code

Wraps command invwarp

Use FSL Invwarp to inverse a FNIRT warp

### Examples

    >>> from nipype.interfaces.fsl import InvWarp
    >>> invwarp = InvWarp()
    >>> invwarp.inputs.warp = "struct2mni.nii"
    >>> invwarp.inputs.reference = "anatomical.nii"
    >>> invwarp.cmdline
    'invwarp --out=struct2mni_inverse.nii.gz --ref=anatomical.nii --warp=struct2mni.nii'
    >>> res = invwarp.run()

Inputs:

    [Mandatory]
    reference: (an existing file name)
            Name of a file in target space. Note that the target space is now
            different from the target space that was used to create the --warp
            file. It would typically be the file that was specified with the
            --in argument when running fnirt.
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    warp: (an existing file name)
            Name of file containing warp-coefficients/fields. This would
            typically be the output from the --cout switch of fnirt (but can
            also use fields, like the output from --fout).

    [Optional]
    absolute: (a boolean)
            If set it indicates that the warps in --warp should be interpreted
            as absolute, provided that it is not created by fnirt (which always
            uses relative warps). If set it also indicates that the output --out
            should be absolute.
            mutually_exclusive: relative
    args: (a string)
            Additional parameters to the command
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inverse_warp: (a file name)
            Name of output file, containing warps that are the "reverse" of
            those in --warp. This will be a field-file (rather than a file of
            spline coefficients), and it will have any affine component included
            as part of the displacements.
    jacobian_max: (a float)
            Maximum acceptable Jacobian value for constraint (default 100.0)
    jacobian_min: (a float)
            Minimum acceptable Jacobian value for constraint (default 0.01)
    niter: (an integer)
            Determines how many iterations of the gradient-descent search that
            should be run.
    noconstraint: (a boolean)
            Do not apply Jacobian constraint
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    reference: (an existing file name)
            Name of a file in target space. Note that the target space is now
            different from the target space that was used to create the --warp
            file. It would typically be the file that was specified with the
            --in argument when running fnirt.
    regularise: (a float)
            Regularisation strength (deafult=1.0).
    relative: (a boolean)
            If set it indicates that the warps in --warp should be interpreted
            as relative. I.e. the values in --warp are displacements from the
            coordinates in the --ref space. If set it also indicates that the
            output --out should be relative.
            mutually_exclusive: absolute
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    warp: (an existing file name)
            Name of file containing warp-coefficients/fields. This would
            typically be the output from the --cout switch of fnirt (but can
            also use fields, like the output from --fout).

Outputs:

    inverse_warp: (an existing file name)
            Name of output file, containing warps that are the "reverse" of
            those in --warp.

## Merge

Link to code

Wraps command fslmerge

Use fslmerge to concatenate images

Images can be concatenated across time, x, y, or z dimensions. Across the time (t) dimension the TR is set by default to 1 sec.

Note: to set the TR to a different value, specify ‘t’ for dimension and specify the TR value in seconds for the tr input. The dimension will be automatically updated to ‘tr’.

### Examples

    >>> from nipype.interfaces.fsl import Merge
    >>> merger = Merge()
    >>> merger.inputs.in_files = ['functional2.nii', 'functional3.nii']
    >>> merger.inputs.dimension = 't'
    >>> merger.inputs.output_type = 'NIFTI_GZ'
    >>> merger.cmdline
    'fslmerge -t functional2_merged.nii.gz functional2.nii functional3.nii'
    >>> merger.inputs.tr = 2.25
    >>> merger.cmdline
    'fslmerge -tr functional2_merged.nii.gz functional2.nii functional3.nii 2.25'

Inputs:

    [Mandatory]
    dimension: ('t' or 'x' or 'y' or 'z' or 'a')
            dimension along which to merge, optionally set tr input when
            dimension is t
    in_files: (a list of items which are an existing file name)
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    dimension: ('t' or 'x' or 'y' or 'z' or 'a')
            dimension along which to merge, optionally set tr input when
            dimension is t
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_files: (a list of items which are an existing file name)
    merged_file: (a file name)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    tr: (a float)
            use to specify TR in seconds (default is 1.00 sec), overrides
            dimension and sets it to tr

Outputs:

    merged_file: (an existing file name)

## Overlay

Link to code

Wraps command overlay

Use FSL’s overlay command to combine background and statistical images
  into one volume

### Examples

    >>> from nipype.interfaces import fsl
    >>> combine = fsl.Overlay()
    >>> combine.inputs.background_image = 'mean_func.nii.gz'
    >>> combine.inputs.auto_thresh_bg = True
    >>> combine.inputs.stat_image = 'zstat1.nii.gz'
    >>> combine.inputs.stat_thresh = (3.5, 10)
    >>> combine.inputs.show_negative_stats = True
    >>> res = combine.run()

Inputs:

    [Mandatory]
    auto_thresh_bg: (a boolean)
            automatically threhsold the background image
            mutually_exclusive: auto_thresh_bg, full_bg_range, bg_thresh
    background_image: (an existing file name)
            image to use as background
    bg_thresh: (a tuple of the form: (a float, a float))
            min and max values for background intensity
            mutually_exclusive: auto_thresh_bg, full_bg_range, bg_thresh
    full_bg_range: (a boolean)
            use full range of background image
            mutually_exclusive: auto_thresh_bg, full_bg_range, bg_thresh
    stat_image: (an existing file name)
            statistical image to overlay in color
    stat_thresh: (a tuple of the form: (a float, a float))
            min and max values for the statistical overlay
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    auto_thresh_bg: (a boolean)
            automatically threhsold the background image
            mutually_exclusive: auto_thresh_bg, full_bg_range, bg_thresh
    background_image: (an existing file name)
            image to use as background
    bg_thresh: (a tuple of the form: (a float, a float))
            min and max values for background intensity
            mutually_exclusive: auto_thresh_bg, full_bg_range, bg_thresh
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    full_bg_range: (a boolean)
            use full range of background image
            mutually_exclusive: auto_thresh_bg, full_bg_range, bg_thresh
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    out_file: (a file name)
            combined image volume
    out_type: ('float' or 'int', nipype default value: float)
            write output with float or int
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    show_negative_stats: (a boolean)
            display negative statistics in overlay
            mutually_exclusive: stat_image2
    stat_image: (an existing file name)
            statistical image to overlay in color
    stat_image2: (an existing file name)
            second statistical image to overlay in color
            mutually_exclusive: show_negative_stats
    stat_thresh: (a tuple of the form: (a float, a float))
            min and max values for the statistical overlay
    stat_thresh2: (a tuple of the form: (a float, a float))
            min and max values for second statistical overlay
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    transparency: (a boolean, nipype default value: True)
            make overlay colors semi-transparent
    use_checkerboard: (a boolean)
            use checkerboard mask for overlay

Outputs:

    out_file: (an existing file name)
            combined image volume

## PlotMotionParams

Link to code

Wraps command fsl_tsplot

Use fsl_tsplot to plot the estimated motion parameters from a realignment program.

### Examples

    >>> import nipype.interfaces.fsl as fsl
    >>> plotter = fsl.PlotMotionParams()
    >>> plotter.inputs.in_file = 'functional.par'
    >>> plotter.inputs.in_source = 'fsl'
    >>> plotter.inputs.plot_type = 'rotations'
    >>> res = plotter.run()

### Notes

The ‘in_source’ attribute determines the order of columns that are expected in the source file. FSL prints motion parameters in the order rotations, translations, while SPM prints them in the opposite order. This interface should be able to plot timecourses of motion parameters generated from other sources as long as they fall under one of these two patterns. For more flexibilty, see the `fsl.PlotTimeSeries` interface.

Inputs:

    [Mandatory]
    in_file: (an existing file name or a list of items which are an
             existing file name)
            file with motion parameters
    in_source: ('spm' or 'fsl')
            which program generated the motion parameter file - fsl, spm
    plot_type: ('rotations' or 'translations' or 'displacement')
            which motion type to plot - rotations, translations, displacement
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name or a list of items which are an
             existing file name)
            file with motion parameters
    in_source: ('spm' or 'fsl')
            which program generated the motion parameter file - fsl, spm
    out_file: (a file name)
            image to write
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    plot_size: (a tuple of the form: (an integer, an integer))
            plot image height and width
    plot_type: ('rotations' or 'translations' or 'displacement')
            which motion type to plot - rotations, translations, displacement
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    out_file: (an existing file name)
            image to write

## PlotTimeSeries

Link to code

Wraps command fsl_tsplot

Use fsl_tsplot to create images of time course plots.

### Examples

    >>> import nipype.interfaces.fsl as fsl
    >>> plotter = fsl.PlotTimeSeries()
    >>> plotter.inputs.in_file = 'functional.par'
    >>> plotter.inputs.title = 'Functional timeseries'
    >>> plotter.inputs.labels = ['run1', 'run2']
    >>> plotter.run()

Inputs:

    [Mandatory]
    in_file: (an existing file name or a list of items which are an
             existing file name)
            file or list of files with columns of timecourse information
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name or a list of items which are an
             existing file name)
            file or list of files with columns of timecourse information
    labels: (a string or a list of items which are a string)
            label or list of labels
    legend_file: (an existing file name)
            legend file
    out_file: (a file name)
            image to write
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    plot_finish: (an integer)
            final column from in-file to plot
            mutually_exclusive: plot_range
    plot_range: (a tuple of the form: (an integer, an integer))
            first and last columns from the in-file to plot
            mutually_exclusive: plot_start, plot_finish
    plot_size: (a tuple of the form: (an integer, an integer))
            plot image height and width
    plot_start: (an integer)
            first column from in-file to plot
            mutually_exclusive: plot_range
    sci_notation: (a boolean)
            switch on scientific notation
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    title: (a string)
            plot title
    x_precision: (an integer)
            precision of x-axis labels
    x_units: (an integer, nipype default value: 1)
            scaling units for x-axis (between 1 and length of in file)
    y_max: (a float)
            maximum y value
            mutually_exclusive: y_range
    y_min: (a float)
            minumum y value
            mutually_exclusive: y_range
    y_range: (a tuple of the form: (a float, a float))
            min and max y axis values
            mutually_exclusive: y_min, y_max

Outputs:

    out_file: (an existing file name)
            image to write

## PowerSpectrum

Link to code

Wraps command fslpspec

Use FSL PowerSpectrum command for power spectrum estimation.

### Examples

    >>> from nipype.interfaces import fsl
    >>> pspec = fsl.PowerSpectrum()
    >>> pspec.inputs.in_file = 'functional.nii'
    >>> res = pspec.run()

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            input 4D file to estimate the power spectrum
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name)
            input 4D file to estimate the power spectrum
    out_file: (a file name)
            name of output 4D file for power spectrum
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    out_file: (an existing file name)
            path/name of the output 4D power spectrum file

## Reorient2Std

Link to code

Wraps command fslreorient2std

fslreorient2std is a tool for reorienting the image to match the approximate orientation of the standard template images (MNI152).

### Examples

    >>> reorient = Reorient2Std()
    >>> reorient.inputs.in_file = "functional.nii"
    >>> res = reorient.run()

Inputs:

    [Mandatory]
    in_file: (an existing file name)
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name)
    out_file: (a file name)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    out_file: (an existing file name)

## SigLoss

Link to code

Wraps command sigloss

Estimates signal loss from a field map (in rad/s)

### Examples

    >>> sigloss = SigLoss()
    >>> sigloss.inputs.in_file = "phase.nii"
    >>> sigloss.inputs.echo_time = 0.03
    >>> res = sigloss.run()

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            b0 fieldmap file
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    echo_time: (a float)
            echo time in seconds
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name)
            b0 fieldmap file
    mask_file: (an existing file name)
            brain mask file
    out_file: (a file name)
            output signal loss estimate file
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    slice_direction: ('x' or 'y' or 'z')
            slicing direction
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    out_file: (an existing file name)
            signal loss estimate file

## Slicer

Link to code

Wraps command slicer

Use FSL’s slicer command to output a png image from a volume.

### Examples

    >>> from nipype.interfaces import fsl
    >>> from nipype.testing import example_data
    >>> slice = fsl.Slicer()
    >>> slice.inputs.in_file = example_data('functional.nii')
    >>> slice.inputs.all_axial = True
    >>> slice.inputs.image_width = 750
    >>> res = slice.run()

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            input volume
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    all_axial: (a boolean)
            output all axial slices into one picture
            mutually_exclusive: single_slice, middle_slices, all_axial,
             sample_axial
            requires: image_width
    args: (a string)
            Additional parameters to the command
    colour_map: (an existing file name)
            use different colour map from that stored in nifti header
    dither_edges: (a boolean)
            produce semi-transparaent (dithered) edges
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    image_edges: (an existing file name)
            volume to display edge overlay for (useful for checking registration
    image_width: (an integer)
            max picture width
    in_file: (an existing file name)
            input volume
    intensity_range: (a tuple of the form: (a float, a float))
            min and max intensities to display
    label_slices: (a boolean, nipype default value: True)
            display slice number
    middle_slices: (a boolean)
            output picture of mid-sagital, axial, and coronal slices
            mutually_exclusive: single_slice, middle_slices, all_axial,
             sample_axial
    nearest_neighbour: (a boolean)
            use nearest neighbour interpolation for output
    out_file: (a file name)
            picture to write
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    sample_axial: (an integer)
            output every n axial slices into one picture
            mutually_exclusive: single_slice, middle_slices, all_axial,
             sample_axial
            requires: image_width
    scaling: (a float)
            image scale
    show_orientation: (a boolean, nipype default value: True)
            label left-right orientation
    single_slice: ('x' or 'y' or 'z')
            output picture of single slice in the x, y, or z plane
            mutually_exclusive: single_slice, middle_slices, all_axial,
             sample_axial
            requires: slice_number
    slice_number: (an integer)
            slice number to save in picture
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    threshold_edges: (a float)
            use threshold for edges

Outputs:

    out_file: (an existing file name)
            picture to write

## Smooth

Link to code

Wraps command fslmaths

Use fslmaths to smooth the image

Inputs:

    [Mandatory]
    fwhm: (a float)
    in_file: (an existing file name)
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    fwhm: (a float)
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name)
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    smoothed_file: (a file name)
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    smoothed_file: (an existing file name)

## Split

Link to code

Wraps command fslsplit

Uses FSL Fslsplit command to separate a volume into images in time, x, y or z dimension.

Inputs:

    [Mandatory]
    dimension: ('t' or 'x' or 'y' or 'z')
            dimension along which the file will be split
    in_file: (an existing file name)
            input filename
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    dimension: ('t' or 'x' or 'y' or 'z')
            dimension along which the file will be split
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name)
            input filename
    out_base_name: (a string)
            outputs prefix
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    out_files: (an existing file name)

## SwapDimensions

Link to code

Wraps command fslswapdim

Use fslswapdim to alter the orientation of an image.

This interface accepts a three-tuple corresponding to the new orientation. You may either provide dimension ids in the form of (-)x, (-)y, or (-z), or nifti-syle dimension codes (RL, LR, AP, PA, IS, SI).

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            input image
    new_dims: (a tuple of the form: ('x' or '-x' or 'y' or '-y' or 'z' or
             '-z' or 'RL' or 'LR' or 'AP' or 'PA' or 'IS' or 'SI', 'x' or '-x'
             or 'y' or '-y' or 'z' or '-z' or 'RL' or 'LR' or 'AP' or 'PA' or
             'IS' or 'SI', 'x' or '-x' or 'y' or '-y' or 'z' or '-z' or 'RL' or
             'LR' or 'AP' or 'PA' or 'IS' or 'SI'))
            3-tuple of new dimension order
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name)
            input image
    new_dims: (a tuple of the form: ('x' or '-x' or 'y' or '-y' or 'z' or
             '-z' or 'RL' or 'LR' or 'AP' or 'PA' or 'IS' or 'SI', 'x' or '-x'
             or 'y' or '-y' or 'z' or '-z' or 'RL' or 'LR' or 'AP' or 'PA' or
             'IS' or 'SI', 'x' or '-x' or 'y' or '-y' or 'z' or '-z' or 'RL' or
             'LR' or 'AP' or 'PA' or 'IS' or 'SI'))
            3-tuple of new dimension order
    out_file: (a file name)
            image to write
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    out_file: (an existing file name)
            image with new dimensions