.. AUTO-GENERATED FILE -- DO NOT EDIT!

interfaces.fsl.utils
====================


.. _nipype.interfaces.fsl.utils.AvScale:


.. index:: AvScale

AvScale
-------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L554>`__

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
                flag: %s
        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
                flag: %s, position: 0
        output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
                 'NIFTI')
                FSL output type

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

.. _nipype.interfaces.fsl.utils.Complex:


.. index:: Complex

Complex
-------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L1434>`__

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
                flag: %s
        complex_cartesian: (a boolean)
                flag: -complex, position: 1
                mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
                 complex_polar, complex_split, complex_merge
        complex_in_file: (an existing file name)
                flag: %s, position: 2
        complex_in_file2: (an existing file name)
                flag: %s, position: 3
        complex_merge: (a boolean)
                flag: -complexmerge, position: 1
                mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
                 complex_polar, complex_split, complex_merge, start_vol, end_vol
        complex_out_file: (a file name)
                flag: %s, position: -3
                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)
                flag: -complexpolar, position: 1
                mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
                 complex_polar, complex_split, complex_merge
        complex_split: (a boolean)
                flag: -complexsplit, position: 1
                mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
                 complex_polar, complex_split, complex_merge
        end_vol: (an integer)
                flag: %d, position: -1
        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)
                flag: %s, position: 3
        imaginary_out_file: (a file name)
                flag: %s, position: -3
                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)
                flag: %s, position: 2
        magnitude_out_file: (a file name)
                flag: %s, position: -4
                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)
                flag: %s, position: 3
        phase_out_file: (a file name)
                flag: %s, position: -3
                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)
                flag: -realcartesian, position: 1
                mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
                 complex_polar, complex_split, complex_merge
        real_in_file: (an existing file name)
                flag: %s, position: 2
        real_out_file: (a file name)
                flag: %s, position: -4
                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)
                flag: -realpolar, position: 1
                mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
                 complex_polar, complex_split, complex_merge
        start_vol: (an integer)
                flag: %d, position: -2

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)

.. _nipype.interfaces.fsl.utils.ConvertWarp:


.. index:: ConvertWarp

ConvertWarp
-----------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L1698>`__

Wraps command **convertwarp**

Use FSL `convertwarp <http://fsl.fmrib.ox.ac.uk/fsl/fsl-4.1.9/fnirt/warp_utils.html>`_
for combining multiple transforms into one.


Examples
~~~~~~~~

>>> from nipype.interfaces.fsl import ConvertWarp
>>> warputils = ConvertWarp()
>>> warputils.inputs.warp1 = "warpfield.nii"
>>> warputils.inputs.reference = "T1.nii"
>>> warputils.inputs.relwarp = True
>>> warputils.inputs.output_type = "NIFTI_GZ"
>>> warputils.cmdline # doctest: +ELLIPSIS
'convertwarp --ref=T1.nii --rel --warp1=warpfield.nii --out=T1_concatwarp.nii.gz'
>>> res = invwarp.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        reference: (an existing file name)
                Name of a file in target space of the full transform.
                flag: --ref=%s, position: 1
        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]
        abswarp: (a boolean)
                If set it indicates that the warps in --warp1 and --warp2 should be
                interpreted as absolute. I.e. the values in --warp1/2 are the
                coordinates in the next space, rather than displacements. This flag
                is ignored if --warp1/2 was created by fnirt, which always creates
                relative displacements.
                flag: --abs
                mutually_exclusive: relwarp
        args: (a string)
                Additional parameters to the command
                flag: %s
        cons_jacobian: (a boolean)
                Constrain the Jacobian of the warpfield to lie within specified
                min/max limits.
                flag: --constrainj
        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
        jacobian_max: (a float)
                Maximum acceptable Jacobian value for constraint (default 100.0)
                flag: --jmax=%f
        jacobian_min: (a float)
                Minimum acceptable Jacobian value for constraint (default 0.01)
                flag: --jmin=%f
        midmat: (an existing file name)
                Name of file containing mid-warp-affine transform
                flag: --midmat=%s
        out_abswarp: (a boolean)
                If set it indicates that the warps in --out should be absolute, i.e.
                the values in --out are displacements from the coordinates in --ref.
                flag: --absout
                mutually_exclusive: out_relwarp
        out_file: (a file name)
                Name of output file, containing warps that are the combination of
                all those given as arguments. The format of this will be a field-
                file (rather than spline coefficients) with any affine components
                included.
                flag: --out=%s, position: -1
        out_relwarp: (a boolean)
                If set it indicates that the warps in --out should be relative, i.e.
                the values in --out are displacements from the coordinates in --ref.
                flag: --relout
                mutually_exclusive: out_abswarp
        output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
                 'NIFTI')
                FSL output type
        postmat: (an existing file name)
                Name of file containing an affine transform (applied last). It could
                e.g. be an affine transform that maps the MNI152-space into a better
                approximation to the Talairach-space (if indeed there is one).
                flag: --postmat=%s
        premat: (an existing file name)
                filename for pre-transform (affine matrix)
                flag: --premat=%s
        relwarp: (a boolean)
                If set it indicates that the warps in --warp1/2 should be
                interpreted as relative. I.e. the values in --warp1/2 are
                displacements from the coordinates in the next space.
                flag: --rel
                mutually_exclusive: abswarp
        shift_direction: ('y-' or 'y' or 'x' or 'x-' or 'z' or 'z-')
                Indicates the direction that the distortions from --shiftmap goes.
                It depends on the direction and polarity of the phase-encoding in
                the EPI sequence.
                flag: --shiftdir=%s
                requires: shift_in_file
        shift_in_file: (an existing file name)
                Name of file containing a "shiftmap", a non-linear transform with
                displacements only in one direction (applied first, before premat).
                This would typically be a fieldmap that has been pre-processed using
                fugue that maps a subjects functional (EPI) data onto an undistorted
                space (i.e. a space that corresponds to his/her true anatomy).
                flag: --shiftmap=%s
        warp1: (an existing file name)
                Name of file containing initial warp-fields/coefficients (follows
                premat). This could e.g. be a fnirt-transform from a subjects
                structural scan to an average of a group of subjects.
                flag: --warp1=%s
        warp2: (an existing file name)
                Name of file containing secondary warp-fields/coefficients (after
                warp1/midmat but before postmat). This could e.g. be a fnirt-
                transform from the average of a group of subjects to some standard
                space (e.g. MNI152).
                flag: --warp2=%s

Outputs::

        out_file: (an existing file name)
                Name of output file, containing the warp as field or coefficients.

.. _nipype.interfaces.fsl.utils.ConvertXFM:


.. index:: ConvertXFM

ConvertXFM
----------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L1050>`__

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
                flag: %s, position: -1
        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
                flag: %s
        concat_xfm: (a boolean)
                write joint transformation of two input matrices
                flag: -concat, position: -3
                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
                flag: -fixscaleskew, position: -3
                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_file2: (an existing file name)
                second input matrix (for use with fix_scale_skew or concat_xfm
                flag: %s, position: -2
        invert_xfm: (a boolean)
                invert input transformation
                flag: -inverse, position: -3
                mutually_exclusive: invert_xfm, concat_xfm, fix_scale_skew
        out_file: (a file name)
                final transformation matrix
                flag: -omat %s, position: 1
        output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
                 'NIFTI')
                FSL output type

Outputs::

        out_file: (an existing file name)
                output transformation matrix

.. _nipype.interfaces.fsl.utils.ExtractROI:


.. index:: ExtractROI

ExtractROI
----------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L217>`__

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
                flag: %s, position: 0
        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
                flag: %s
        crop_list: (a list of items which are a tuple of the form: (an
                 integer, an integer))
                list of two tuples specifying crop options
                flag: %s, position: 2
                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
        output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
                 'NIFTI')
                FSL output type
        roi_file: (a file name)
                output file
                flag: %s, position: 1
        t_min: (an integer)
                flag: %d, position: 8
        t_size: (an integer)
                flag: %d, position: 9
        x_min: (an integer)
                flag: %d, position: 2
        x_size: (an integer)
                flag: %d, position: 3
        y_min: (an integer)
                flag: %d, position: 4
        y_size: (an integer)
                flag: %d, position: 5
        z_min: (an integer)
                flag: %d, position: 6
        z_size: (an integer)
                flag: %d, position: 7

Outputs::

        roi_file: (an existing file name)

.. _nipype.interfaces.fsl.utils.FilterRegressor:


.. index:: FilterRegressor

FilterRegressor
---------------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L422>`__

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)
                flag: -d %s, position: 3
        filter_all: (a boolean)
                use all columns in the design file in denoising
                flag: -f '%s', position: 4
                mutually_exclusive: filter_columns
        filter_columns: (a list of items which are an integer)
                (1-based) column indices to filter out of the data
                flag: -f '%s', position: 4
                mutually_exclusive: filter_all
        in_file: (an existing file name)
                input file name (4D image)
                flag: -i %s, position: 1
        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
                flag: %s
        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
        mask: (an existing file name)
                mask image file name
                flag: -m %s
        out_file: (a file name)
                output file name for the filtered data
                flag: -o %s, position: 2
        out_vnscales: (a boolean)
                output scaling factors for variance normalization
                flag: --out_vnscales
        output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
                 'NIFTI')
                FSL output type
        var_norm: (a boolean)
                perform variance-normalization on data
                flag: --vn

Outputs::

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

.. _nipype.interfaces.fsl.utils.ImageMaths:


.. index:: ImageMaths

ImageMaths
----------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L348>`__

Wraps command **fslmaths**

Use FSL fslmaths command to allow mathematical manipulation of images
`FSL info <http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/intro/index.htm#fslutils>`_


Examples
~~~~~~~~

>>> from nipype.interfaces 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)
                flag: %s, position: 1
        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
                flag: %s
        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_file2: (an existing file name)
                flag: %s, position: 3
        op_string: (a string)
                string defining the operation, i. e. -add
                flag: %s, position: 2
        out_data_type: ('char' or 'short' or 'int' or 'float' or 'double' or
                 'input')
                output datatype, one of (char, short, int, float, double, input)
                flag: -odt %s, position: 5
        out_file: (a file name)
                flag: %s, position: 4
        output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
                 'NIFTI')
                FSL output type
        suffix: (a string)
                out_file suffix

Outputs::

        out_file: (an existing file name)

.. _nipype.interfaces.fsl.utils.ImageMeants:


.. index:: ImageMeants

ImageMeants
-----------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L64>`__

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
                flag: -i %s, position: 0
        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
                flag: %s
        eig: (a boolean)
                calculate Eigenvariate(s) instead of mean (output will have 0 mean)
                flag: --eig
        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
        mask: (an existing file name)
                input 3D mask
                flag: -m %s
        nobin: (a boolean)
                do not binarise the mask for calculation of Eigenvariates
                flag: --no_bin
        order: (an integer, nipype default value: 1)
                select number of Eigenvariates
                flag: --order=%d
        out_file: (a file name)
                name of output text matrix
                flag: -o %s
        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
                flag: --showall
        spatial_coord: (a list of items which are an integer)
                <x y z> requested spatial coordinate (instead of mask)
                flag: -c %s
        transpose: (a boolean)
                output results in transpose format (one row per voxel/mean)
                flag: --transpose
        use_mm: (a boolean)
                use mm instead of voxel coordinates (for -c option)
                flag: --usemm

Outputs::

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

.. _nipype.interfaces.fsl.utils.ImageStats:


.. index:: ImageStats

ImageStats
----------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L477>`__

Wraps command **fslstats**

Use FSL fslstats command to calculate stats from images
`FSL info
<http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/intro/index.htm#fslutils>`_


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
                flag: %s, position: 2
        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
                flag: %s, position: 3
        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
                flag: %s
        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
        mask_file: (an existing file name)
                mask file used for option -k %s
        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
                flag: -t, position: 1

Outputs::

        out_stat
                stats output

.. _nipype.interfaces.fsl.utils.InvWarp:


.. index:: InvWarp

InvWarp
-------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L1350>`__

Wraps command **invwarp**

Use FSL Invwarp to invert a FNIRT warp


Examples
~~~~~~~~

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

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.
                flag: --ref=%s
        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).
                flag: --warp=%s

        [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.
                flag: --abs
                mutually_exclusive: relative
        args: (a string)
                Additional parameters to the command
                flag: %s
        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.
                flag: --out=%s
        jacobian_max: (a float)
                Maximum acceptable Jacobian value for constraint (default 100.0)
                flag: --jmax=%f
        jacobian_min: (a float)
                Minimum acceptable Jacobian value for constraint (default 0.01)
                flag: --jmin=%f
        niter: (an integer)
                Determines how many iterations of the gradient-descent search that
                should be run.
                flag: --niter=%d
        noconstraint: (a boolean)
                Do not apply Jacobian constraint
                flag: --noconstraint
        output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
                 'NIFTI')
                FSL output type
        regularise: (a float)
                Regularization strength (deafult=1.0).
                flag: --regularise=%f
        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.
                flag: --rel
                mutually_exclusive: absolute

Outputs::

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

.. _nipype.interfaces.fsl.utils.Merge:


.. index:: Merge

Merge
-----

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L150>`__

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
                flag: -%s, position: 0
        in_files: (a list of items which are an existing file name)
                flag: %s, position: 2
        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
                flag: %s
        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
        merged_file: (a file name)
                flag: %s, position: 1
        output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
                 'NIFTI')
                FSL output type
        tr: (a float)
                use to specify TR in seconds (default is 1.00 sec), overrides
                dimension and sets it to tr
                flag: %.2f, position: -1

Outputs::

        merged_file: (an existing file name)

.. _nipype.interfaces.fsl.utils.Overlay:


.. index:: Overlay

Overlay
-------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L648>`__

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() #doctest: +SKIP

Inputs::

        [Mandatory]
        auto_thresh_bg: (a boolean)
                automatically threshold the background image
                flag: -a, position: 5
                mutually_exclusive: auto_thresh_bg, full_bg_range, bg_thresh
        background_image: (an existing file name)
                image to use as background
                flag: %s, position: 4
        bg_thresh: (a tuple of the form: (a float, a float))
                min and max values for background intensity
                flag: %.3f %.3f, position: 5
                mutually_exclusive: auto_thresh_bg, full_bg_range, bg_thresh
        full_bg_range: (a boolean)
                use full range of background image
                flag: -A, position: 5
                mutually_exclusive: auto_thresh_bg, full_bg_range, bg_thresh
        stat_image: (an existing file name)
                statistical image to overlay in color
                flag: %s, position: 6
        stat_thresh: (a tuple of the form: (a float, a float))
                min and max values for the statistical overlay
                flag: %.2f %.2f, position: 7
        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
                flag: %s
        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
        out_file: (a file name)
                combined image volume
                flag: %s, position: -1
        out_type: ('float' or 'int', nipype default value: float)
                write output with float or int
                flag: %s, position: 2
        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
                flag: %s, position: 8
                mutually_exclusive: stat_image2
        stat_image2: (an existing file name)
                second statistical image to overlay in color
                flag: %s, position: 9
                mutually_exclusive: show_negative_stats
        stat_thresh2: (a tuple of the form: (a float, a float))
                min and max values for second statistical overlay
                flag: %.2f %.2f, position: 10
        transparency: (a boolean, nipype default value: True)
                make overlay colors semi-transparent
                flag: %s, position: 1
        use_checkerboard: (a boolean)
                use checkerboard mask for overlay
                flag: -c, position: 3

Outputs::

        out_file: (an existing file name)
                combined image volume

.. _nipype.interfaces.fsl.utils.PlotMotionParams:


.. index:: PlotMotionParams

PlotMotionParams
----------------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L937>`__

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() #doctest: +SKIP


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 :class:`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
                flag: %s, position: 1
        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
                flag: %s
        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
                flag: %s
        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
        out_file: (a file name)
                image to write
                flag: -o %s
        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
                flag: %s

Outputs::

        out_file: (an existing file name)
                image to write

.. _nipype.interfaces.fsl.utils.PlotTimeSeries:


.. index:: PlotTimeSeries

PlotTimeSeries
--------------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L854>`__

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() #doctest: +SKIP

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
                flag: %s, position: 1
        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
                flag: %s
        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
        labels: (a string or a list of items which are a string)
                label or list of labels
                flag: %s
        legend_file: (an existing file name)
                legend file
                flag: --legend=%s
        out_file: (a file name)
                image to write
                flag: -o %s
        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
                flag: --finish=%d
                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
                flag: %s
                mutually_exclusive: plot_start, plot_finish
        plot_size: (a tuple of the form: (an integer, an integer))
                plot image height and width
                flag: %s
        plot_start: (an integer)
                first column from in-file to plot
                flag: --start=%d
                mutually_exclusive: plot_range
        sci_notation: (a boolean)
                switch on scientific notation
                flag: --sci
        title: (a string)
                plot title
                flag: %s
        x_precision: (an integer)
                precision of x-axis labels
                flag: --precision=%d
        x_units: (an integer, nipype default value: 1)
                scaling units for x-axis (between 1 and length of in file)
                flag: -u %d
        y_max: (a float)
                maximum y value
                flag: --ymax=%.2f
                mutually_exclusive: y_range
        y_min: (a float)
                minumum y value
                flag: --ymin=%.2f
                mutually_exclusive: y_range
        y_range: (a tuple of the form: (a float, a float))
                min and max y axis values
                flag: %s
                mutually_exclusive: y_min, y_max

Outputs::

        out_file: (an existing file name)
                image to write

.. _nipype.interfaces.fsl.utils.PowerSpectrum:


.. index:: PowerSpectrum

PowerSpectrum
-------------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L1163>`__

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() # doctest: +SKIP

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                input 4D file to estimate the power spectrum
                flag: %s, position: 0
        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
                flag: %s
        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
        out_file: (a file name)
                name of output 4D file for power spectrum
                flag: %s, position: 1
        output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
                 'NIFTI')
                FSL output type

Outputs::

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

.. _nipype.interfaces.fsl.utils.Reorient2Std:


.. index:: Reorient2Std

Reorient2Std
------------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L1261>`__

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() # doctest: +SKIP

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                flag: %s
        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
                flag: %s
        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
        out_file: (a file name)
                flag: %s
        output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
                 'NIFTI')
                FSL output type

Outputs::

        out_file: (an existing file name)

.. _nipype.interfaces.fsl.utils.SigLoss:


.. index:: SigLoss

SigLoss
-------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L1220>`__

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() # doctest: +SKIP

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                b0 fieldmap file
                flag: -i %s
        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
                flag: %s
        echo_time: (a float)
                echo time in seconds
                flag: --te=%f
        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
        mask_file: (an existing file name)
                brain mask file
                flag: -m %s
        out_file: (a file name)
                output signal loss estimate file
                flag: -s %s
        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
                flag: -d %s

Outputs::

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

.. _nipype.interfaces.fsl.utils.Slicer:


.. index:: Slicer

Slicer
------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L763>`__

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() #doctest: +SKIP

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                input volume
                flag: %s, position: 1
        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
                flag: -A, position: 10
                mutually_exclusive: single_slice, middle_slices, all_axial,
                 sample_axial
                requires: image_width
        args: (a string)
                Additional parameters to the command
                flag: %s
        colour_map: (an existing file name)
                use different colour map from that stored in nifti header
                flag: -l %s, position: 4
        dither_edges: (a boolean)
                produce semi-transparent (dithered) edges
                flag: -t, position: 7
        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
                flag: %s, position: 2
        image_width: (an integer)
                max picture width
                flag: %d, position: -2
        intensity_range: (a tuple of the form: (a float, a float))
                min and max intensities to display
                flag: -i %.3f %.3f, position: 5
        label_slices: (a boolean, nipype default value: True)
                display slice number
                flag: -L, position: 3
        middle_slices: (a boolean)
                output picture of mid-sagittal, axial, and coronal slices
                flag: -a, position: 10
                mutually_exclusive: single_slice, middle_slices, all_axial,
                 sample_axial
        nearest_neighbour: (a boolean)
                use nearest neighbor interpolation for output
                flag: -n, position: 8
        out_file: (a file name)
                picture to write
                flag: %s, position: -1
        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
                flag: -S %d, position: 10
                mutually_exclusive: single_slice, middle_slices, all_axial,
                 sample_axial
                requires: image_width
        scaling: (a float)
                image scale
                flag: -s %f, position: 0
        show_orientation: (a boolean, nipype default value: True)
                label left-right orientation
                flag: %s, position: 9
        single_slice: ('x' or 'y' or 'z')
                output picture of single slice in the x, y, or z plane
                flag: -%s, position: 10
                mutually_exclusive: single_slice, middle_slices, all_axial,
                 sample_axial
                requires: slice_number
        slice_number: (an integer)
                slice number to save in picture
                flag: -%d, position: 11
        threshold_edges: (a float)
                use threshold for edges
                flag: -e %.3f, position: 6

Outputs::

        out_file: (an existing file name)
                picture to write

.. _nipype.interfaces.fsl.utils.Smooth:


.. index:: Smooth

Smooth
------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L103>`__

Wraps command **fslmaths**

Use fslmaths to smooth the image

Inputs::

        [Mandatory]
        fwhm: (a float)
                flag: -kernel gauss %f -fmean, position: 1
        in_file: (an existing file name)
                flag: %s, position: 0
        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
                flag: %s
        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
        output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
                 'NIFTI')
                FSL output type
        smoothed_file: (a file name)
                flag: %s, position: 2

Outputs::

        smoothed_file: (an existing file name)

.. _nipype.interfaces.fsl.utils.Split:


.. index:: Split

Split
-----

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L297>`__

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
                flag: -%s, position: 2
        in_file: (an existing file name)
                input filename
                flag: %s, position: 0
        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
                flag: %s
        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
        out_base_name: (a string)
                outputs prefix
                flag: %s, position: 1
        output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
                 'NIFTI')
                FSL output type

Outputs::

        out_files: (an existing file name)

.. _nipype.interfaces.fsl.utils.SwapDimensions:


.. index:: SwapDimensions

SwapDimensions
--------------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L1121>`__

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
                flag: %s, position: 1
        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
                flag: %s %s %s
        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
                flag: %s
        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
        out_file: (a file name)
                image to write
                flag: %s
        output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
                 'NIFTI')
                FSL output type

Outputs::

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

.. _nipype.interfaces.fsl.utils.WarpPoints:


.. index:: WarpPoints

WarpPoints
----------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L1752>`__

Wraps command **img2imgcoord**

Use FSL `img2imgcoord <http://fsl.fmrib.ox.ac.uk/fsl/fsl-4.1.9/flirt/overview.html>`_
to transform point sets. Accepts plain text files and vtk files.

.. Note:: transformation of TrackVis trk files is not yet implemented


Examples
~~~~~~~~

>>> from nipype.interfaces.fsl import WarpPoints
>>> warppoints = WarpPoints()
>>> warppoints.inputs.in_coords = 'surf.txt'
>>> warppoints.inputs.src_file = 'epi.nii'
>>> warppoints.inputs.dest_file = 'T1.nii'
>>> warppoints.inputs.warp_file = 'warpfield.nii'
>>> warppoints.inputs.coord_mm = True
>>> warppoints.cmdline # doctest: +ELLIPSIS
'img2imgcoord -mm -dest T1.nii -src epi.nii -warp warpfield.nii surf.txt'
>>> res = invwarp.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        dest_file: (an existing file name)
                filename of destination image
                flag: -dest %s
        in_coords: (an existing file name)
                filename of file containing coordinates
                flag: %s, position: -1
        src_file: (an existing file name)
                filename of source image
                flag: -src %s
        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
                flag: %s
        coord_mm: (a boolean)
                all coordinates in mm
                flag: -mm
                mutually_exclusive: coord_vox
        coord_vox: (a boolean)
                all coordinates in voxels - default
                flag: -vox
                mutually_exclusive: coord_mm
        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
        out_file: (a file name)
                output file name
        warp_file: (an existing file name)
                filename of warpfield (e.g. intermediate2dest_warp.nii.gz)
                flag: -warp %s
                mutually_exclusive: xfm_file
        xfm_file: (an existing file name)
                filename of affine transform (e.g. source2dest.mat)
                flag: -xfm %s
                mutually_exclusive: warp_file

Outputs::

        out_file: (an existing file name)
                Name of output file, containing the warp as field or coefficients.

.. _nipype.interfaces.fsl.utils.WarpPointsToStd:


.. index:: WarpPointsToStd

WarpPointsToStd
---------------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L1911>`__

Wraps command **img2stdcoord**

Use FSL `img2stdcoord <http://fsl.fmrib.ox.ac.uk/fsl/fsl-4.1.9/flirt/overview.html>`_
to transform point sets to standard space coordinates. Accepts plain text files and
vtk files.

.. Note:: transformation of TrackVis trk files is not yet implemented


Examples
~~~~~~~~

>>> from nipype.interfaces.fsl import WarpPointsToStd
>>> warppoints = WarpPointsToStd()
>>> warppoints.inputs.in_coords = 'surf.txt'
>>> warppoints.inputs.img_file = 'T1.nii'
>>> warppoints.inputs.std_file = 'mni.nii'
>>> warppoints.inputs.warp_file = 'warpfield.nii'
>>> warppoints.inputs.coord_mm = True
>>> warppoints.cmdline # doctest: +ELLIPSIS
'img2stdcoord -mm -img T1.nii -std mni.nii -warp warpfield.nii surf.txt'
>>> res = invwarp.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        img_file: (an existing file name)
                filename of input image
                flag: -img %s
        in_coords: (an existing file name)
                filename of file containing coordinates
                flag: %s, position: -1
        std_file: (an existing file name)
                filename of destination image
                flag: -std %s
        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
                flag: %s
        coord_mm: (a boolean)
                all coordinates in mm
                flag: -mm
                mutually_exclusive: coord_vox
        coord_vox: (a boolean)
                all coordinates in voxels - default
                flag: -vox
                mutually_exclusive: coord_mm
        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
        out_file: (a file name)
                output file name
        premat_file: (an existing file name)
                filename of pre-warp affine transform (e.g.
                example_func2highres.mat)
                flag: -premat %s
        warp_file: (an existing file name)
                filename of warpfield (e.g. intermediate2dest_warp.nii.gz)
                flag: -warp %s
                mutually_exclusive: xfm_file
        xfm_file: (an existing file name)
                filename of affine transform (e.g. source2dest.mat)
                flag: -xfm %s
                mutually_exclusive: warp_file

Outputs::

        out_file: (an existing file name)
                Name of output file, containing the warp as field or coefficients.

.. _nipype.interfaces.fsl.utils.WarpUtils:


.. index:: WarpUtils

WarpUtils
---------

`Link to code <http://github.com/nipy/nipype/tree/e63e055194d62d2bdc4665688261c03a42fd0025/nipype/interfaces/fsl/utils.py#L1566>`__

Wraps command **fnirtfileutils**

Use FSL `fnirtfileutils <http://fsl.fmrib.ox.ac.uk/fsl/fsl-4.1.9/fnirt/warp_utils.html>`_
to convert field->coefficients, coefficients->field, coefficients->other_coefficients etc


Examples
~~~~~~~~

>>> from nipype.interfaces.fsl import WarpUtils
>>> warputils = WarpUtils()
>>> warputils.inputs.in_file = "warpfield.nii"
>>> warputils.inputs.reference = "T1.nii"
>>> warputils.inputs.out_format = 'spline'
>>> warputils.inputs.warp_resolution = (10,10,10)
>>> warputils.inputs.output_type = "NIFTI_GZ"
>>> warputils.cmdline # doctest: +ELLIPSIS
'fnirtfileutils --in=warpfield.nii --outformat=spline --ref=T1.nii --warpres=10.0000,10.0000,10.0000 --out=warpfield_coeffs.nii.gz'
>>> res = invwarp.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        in_file: (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).
                flag: --in=%s
        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.
                flag: --ref=%s
        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
        write_jacobian: (a boolean, nipype default value: False)
                Switch on --jac flag with automatically generated filename

        [Optional]
        args: (a string)
                Additional parameters to the command
                flag: %s
        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
        knot_space: (a tuple of the form: (an integer, an integer, an
                 integer))
                Alternative (to --warpres) specification of the resolution of the
                output spline-field.
                flag: --knotspace=%d,%d,%d
        out_file: (a file name)
                Name of output file. The format of the output depends on what other
                parameters are set. The default format is a (4D) field-file. If the
                --outformat is set to spline the format will be a (4D) file of
                spline coefficients.
                flag: --out=%s, position: -1
        out_format: ('spline' or 'field')
                Specifies the output format. If set to field (default) the output
                will be a (4D) field-file. If set to spline the format will be a
                (4D) file of spline coefficients.
                flag: --outformat=%s
        out_jacobian: (a file name)
                Specifies that a (3D) file of Jacobian determinants corresponding to
                --in should be produced and written to filename.
                flag: --jac=%s
        output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
                 'NIFTI')
                FSL output type
        warp_resolution: (a tuple of the form: (a float, a float, a float))
                Specifies the resolution/knot-spacing of the splines pertaining to
                the coefficients in the --out file. This parameter is only relevant
                if --outformat is set to spline. It should be noted that if the --in
                file has a higher resolution, the resulting coefficients will
                pertain to the closest (in a least-squares sense) file in the space
                of fields with the --warpres resolution. It should also be noted
                that the resolution will always be an integer multiple of the voxel
                size.
                flag: --warpres=%0.4f,%0.4f,%0.4f
        with_affine: (a boolean)
                Specifies that the affine transform (i.e. that which was specified
                for the --aff parameter in fnirt) should be included as
                displacements in the --out file. That can be useful for interfacing
                with software that cannot decode FSL/fnirt coefficient-files (where
                the affine transform is stored separately from the displacements).
                flag: --withaff

Outputs::

        out_file: (a file name)
                Name of output file, containing the warp as field or coefficients.
        out_jacobian: (a file name)
                Name of output file, containing the map of the determinant of the
                Jacobian
