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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()

Inputs:

    [Mandatory]

    [Optional]
    all_param: (a boolean)
            flag: --allparams
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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: -2
    ref_file: (an existing file name)
            reference file to get center of rotation
            flag: %s, position: -1
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    average_scaling: (a float)
            Average Scaling
    backward_half_transform: (a list of items which are a list of items
             which are a float)
            Backwards Half Transform
    determinant: (a float)
            Determinant
    forward_half_transform: (a list of items which are a list of items
             which are a float)
            Forward Half Transform
    left_right_orientation_preserved: (a boolean)
            True if LR orientation preserved
    rot_angles: (a list of items which are a float)
            rotation angles
    rotation_translation_matrix: (a list of items which are a list of
             items which are a float)
            Rotation and Translation Matrix
    scales: (a list of items which are a float)
            Scales (x,y,z)
    skews: (a list of items which are a float)
            Skews
    translations: (a list of items which are a float)
            translations

## 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()

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode 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 (int or long))
            flag: %d, position: -1
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'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 (int or long))
            flag: %d, position: -2
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `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)

References:: None

## ConvertWarp

Link to code

Wraps command convertwarp

Use FSL convertwarp 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
    'convertwarp --ref=T1.nii --rel --warp1=warpfield.nii --out=T1_concatwarp.nii.gz'
    >>> res = warputils.run()

Inputs:

    [Mandatory]
    reference: (an existing file name)
            Name of a file in target space of the full transform.
            flag: --ref=%s, position: 1

    [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 unicode 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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'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: (u'y-' or u'y' or u'x' or u'x-' or u'z' or u'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
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    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.

References:: None

## 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
            flag: %s, position: -1

    [Optional]
    args: (a unicode 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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `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

References:: None

## CopyGeom

Link to code

Wraps command fslcpgeom

Use fslcpgeom to copy the header geometry information to another image. Copy certain parts of the header information (image dimensions, voxel dimensions, voxel dimensions units string, image orientation/origin or qform/sform info) from one image to another. Note that only copies from Analyze to Analyze or Nifti to Nifti will work properly. Copying from different files will result in loss of information or potentially incorrect settings.

Inputs:

    [Mandatory]
    dest_file: (an existing file name)
            destination image
            flag: %s, position: 1
    in_file: (an existing file name)
            source image
            flag: %s, position: 0

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_dims: (a boolean)
            Do not copy image dimensions
            flag: -d, position: -1
    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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `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 geometry header

References:: None

## 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
            flag: %s, position: 0

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    crop_list: (a list of items which are a tuple of the form: (an
             integer (int or long), an integer (int or long)))
            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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    roi_file: (a file name)
            output file
            flag: %s, position: 1
    t_min: (an integer (int or long))
            flag: %d, position: 8
    t_size: (an integer (int or long))
            flag: %d, position: 9
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    x_min: (an integer (int or long))
            flag: %d, position: 2
    x_size: (an integer (int or long))
            flag: %d, position: 3
    y_min: (an integer (int or long))
            flag: %d, position: 4
    y_size: (an integer (int or long))
            flag: %d, position: 5
    z_min: (an integer (int or long))
            flag: %d, position: 6
    z_size: (an integer (int or long))
            flag: %d, position: 7

Outputs:

    roi_file: (an existing file name)

References:: None

## 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)
            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 (int or long))
            (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

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `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
            flag: --vn

Outputs:

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

References:: None

## ImageMaths

Link to code

Wraps command fslmaths

Use FSL fslmaths command to allow mathematical manipulation of images FSL info

### 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

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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 unicode string)
            string defining the operation, i. e. -add
            flag: %s, position: 2
    out_data_type: (u'char' or u'short' or u'int' or u'float' or
             u'double' or u'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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    suffix: (a unicode string)
            out_file suffix
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `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)

References:: None

## 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
            flag: -i %s, position: 0

    [Optional]
    args: (a unicode 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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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 (int or long), 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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'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 (int or long))
            <x y z> requested spatial coordinate (instead of mask)
            flag: -c %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `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)
            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

References:: None

## 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
            flag: %s, position: 2
    op_string: (a unicode 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

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'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
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    out_stat: (any value)
            stats output

References:: None

## InvWarp

Link to code

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()

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
    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 unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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 (int or long))
            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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'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
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

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

References:: None

## 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: (u't' or u'x' or u'y' or u'z' or u'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

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `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
            flag: %.2f, position: -1

Outputs:

    merged_file: (an existing file name)

References:: None

## MotionOutliers

Link to code

Wraps command fsl_motion_outliers

Use FSL fsl_motion_outliers`http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLMotionOutliers`_ to find outliers in timeseries (4d) data. Examples ~~~~~~~~ >>> from nipype.interfaces.fsl import MotionOutliers >>> mo = MotionOutliers() >>> mo.inputs.in_file = “epi.nii” >>> mo.cmdline # doctest: +ELLIPSIS ‘fsl_motion_outliers -i epi.nii -o epi_outliers.txt -p epi_metrics.png -s epi_metrics.txt’ >>> res = mo.run() # doctest: +SKIP

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            unfiltered 4D image
            flag: -i %s

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    dummy: (an integer (int or long))
            number of dummy scans to delete (before running anything and
            creating EVs)
            flag: --dummy=%d
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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 for calculating metric
            flag: -m %s
    metric: (u'refrms' or u'dvars' or u'refmse' or u'fd' or u'fdrms')
            metrics: refrms - RMS intensity difference to reference volume as
            metric [default metric], refmse - Mean Square Error version of
            refrms (used in original version of fsl_motion_outliers), dvars -
            DVARS, fd - frame displacement, fdrms - FD with RMS matrix
            calculation
            flag: --%s
    no_motion_correction: (a boolean)
            do not run motion correction (assumed already done)
            flag: --nomoco
    out_file: (a file name)
            output outlier file name
            flag: -o %s
    out_metric_plot: (a file name)
            output metric values plot (DVARS etc.) file name
            flag: -p %s
    out_metric_values: (a file name)
            output metric values (DVARS etc.) file name
            flag: -s %s
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    threshold: (a float)
            specify absolute threshold value (otherwise use box-plot cutoff =
            P75 + 1.5*IQR)
            flag: --thresh=%g

Outputs:

    out_file: (an existing file name)
    out_metric_plot: (an existing file name)
    out_metric_values: (an existing file name)

References:: None

## 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 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

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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: (u'float' or u'int', nipype default value: float)
            write output with float or int
            flag: %s, position: 2
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'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
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `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
            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

References:: None

## 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
            flag: %s, position: 1
    in_source: (u'spm' or u'fsl')
            which program generated the motion parameter file - fsl, spm
    plot_type: (u'rotations' or u'translations' or u'displacement')
            which motion type to plot - rotations, translations, displacement
            flag: %s

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    plot_size: (a tuple of the form: (an integer (int or long), an
             integer (int or long)))
            plot image height and width
            flag: %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `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

References:: None

## 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
            flag: %s, position: 1

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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 unicode string or a list of items which are a unicode
             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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    plot_finish: (an integer (int or long))
            final column from in-file to plot
            flag: --finish=%d
            mutually_exclusive: plot_range
    plot_range: (a tuple of the form: (an integer (int or long), an
             integer (int or long)))
            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 (int or long), an
             integer (int or long)))
            plot image height and width
            flag: %s
    plot_start: (an integer (int or long))
            first column from in-file to plot
            flag: --start=%d
            mutually_exclusive: plot_range
    sci_notation: (a boolean)
            switch on scientific notation
            flag: --sci
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    title: (a unicode string)
            plot title
            flag: %s
    x_precision: (an integer (int or long))
            precision of x-axis labels
            flag: --precision=%d
    x_units: (an integer (int or long), 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

References:: None

## 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
            flag: %s, position: 0

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `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

References:: None

## 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)
            flag: %s

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `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)

References:: None

## RobustFOV

Link to code

Wraps command robustfov

Automatically crops an image removing lower head and neck.

Interface is stable 5.0.0 to 5.0.9, but default brainsize changed from 150mm to 170mm.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            input filename
            flag: -i %s, position: 0

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    brainsize: (an integer (int or long))
            size of brain in z-dimension (default 170mm/150mm)
            flag: -b %d
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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_roi: (a file name)
            ROI volume output name
            flag: -r %s
    out_transform: (a file name)
            Transformation matrix in_file to out_roi output name
            flag: -m %s
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    out_roi: (an existing file name)
            ROI volume output name
    out_transform: (an existing file name)
            Transformation matrix in_file to out_roi output name

References:: None

## 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
            flag: -i %s

    [Optional]
    args: (a unicode 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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    slice_direction: (u'x' or u'y' or u'z')
            slicing direction
            flag: -d %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `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

References:: None

## 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
            flag: %s, position: 1

    [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 unicode 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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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 (int or long))
            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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    sample_axial: (an integer (int or long))
            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: (u'x' or u'y' or u'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 (int or long))
            slice number to save in picture
            flag: -%d, position: 11
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `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
            flag: -e %.3f, position: 6

Outputs:

    out_file: (an existing file name)
            picture to write

References:: None

## Smooth

Link to code

Wraps command fslmaths

Use fslmaths to smooth the image

### Examples

Setting the kernel width using sigma:

    >>> sm = Smooth()
    >>> sm.inputs.output_type = 'NIFTI_GZ'
    >>> sm.inputs.in_file = 'functional2.nii'
    >>> sm.inputs.sigma = 8.0
    >>> sm.cmdline
    'fslmaths functional2.nii -kernel gauss 8.000 -fmean functional2_smooth.nii.gz'

Setting the kernel width using fwhm:

    >>> sm = Smooth()
    >>> sm.inputs.output_type = 'NIFTI_GZ'
    >>> sm.inputs.in_file = 'functional2.nii'
    >>> sm.inputs.fwhm = 8.0
    >>> sm.cmdline
    'fslmaths functional2.nii -kernel gauss 3.397 -fmean functional2_smooth.nii.gz'

One of sigma or fwhm must be set:

    >>> from nipype.interfaces.fsl import Smooth
    >>> sm = Smooth()
    >>> sm.inputs.output_type = 'NIFTI_GZ'
    >>> sm.inputs.in_file = 'functional2.nii'
    >>> sm.cmdline
    Traceback (most recent call last):
     ~~~
    ValueError: Smooth requires a value for one of the inputs ...

Inputs:

    [Mandatory]
    fwhm: (a float)
            gaussian kernel fwhm, will be converted to sigma in mm (not voxels)
            flag: -kernel gauss %.03f -fmean, position: 1
            mutually_exclusive: sigma
    in_file: (an existing file name)
            flag: %s, position: 0
    sigma: (a float)
            gaussian kernel sigma in mm (not voxels)
            flag: -kernel gauss %.03f -fmean, position: 1
            mutually_exclusive: fwhm

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    smoothed_file: (a file name)
            flag: %s, position: 2
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `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)

References:: None

## 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: (u't' or u'x' or u'y' or u'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

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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 unicode string)
            outputs prefix
            flag: %s, position: 1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    out_files: (a list of items which are an existing file name)

References:: None

## 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
            flag: %s, position: 1
    new_dims: (a tuple of the form: (u'x' or u'-x' or u'y' or u'-y' or
             u'z' or u'-z' or u'RL' or u'LR' or u'AP' or u'PA' or u'IS' or
             u'SI', u'x' or u'-x' or u'y' or u'-y' or u'z' or u'-z' or u'RL' or
             u'LR' or u'AP' or u'PA' or u'IS' or u'SI', u'x' or u'-x' or u'y' or
             u'-y' or u'z' or u'-z' or u'RL' or u'LR' or u'AP' or u'PA' or u'IS'
             or u'SI'))
            3-tuple of new dimension order
            flag: %s %s %s

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `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

References:: None

## WarpPoints

Link to code

Wraps command img2imgcoord

Use FSL img2imgcoord 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
    'img2imgcoord -mm -dest T1.nii -src epi.nii -warp warpfield.nii surf.txt'
    >>> res = warppoints.run()

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

    [Optional]
    args: (a unicode 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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    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.

## WarpPointsFromStd

Link to code

Wraps command std2imgcoord

Use FSL std2imgcoord to transform point sets to standard space coordinates. Accepts plain text coordinates files.

### Examples

    >>> from nipype.interfaces.fsl import WarpPointsFromStd
    >>> warppoints = WarpPointsFromStd()
    >>> 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
    'std2imgcoord -mm -img T1.nii -std mni.nii -warp warpfield.nii surf.txt'
    >>> res = warppoints.run()

Inputs:

    [Mandatory]
    img_file: (an existing file name)
            filename of a destination image
            flag: -img %s
    in_coords: (an existing file name)
            filename of file containing coordinates
            flag: %s, position: -2
    std_file: (an existing file name)
            filename of the image in standard space
            flag: -std %s

    [Optional]
    args: (a unicode 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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    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.

## WarpPointsToStd

Link to code

Wraps command img2stdcoord

Use FSL img2stdcoord 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
    'img2stdcoord -mm -img T1.nii -std mni.nii -warp warpfield.nii surf.txt'
    >>> res = warppoints.run()

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

    [Optional]
    args: (a unicode 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 newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    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.

## WarpUtils

Link to code

Wraps command fnirtfileutils

Use FSL fnirtfileutils 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
    'fnirtfileutils --in=warpfield.nii --outformat=spline --ref=T1.nii --warpres=10.0000,10.0000,10.0000 --out=warpfield_coeffs.nii.gz'
    >>> res = invwarp.run()

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
    write_jacobian: (a boolean, nipype default value: False)
            Switch on --jac flag with automatically generated filename

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    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 (int or long), an
             integer (int or long), an integer (int or long)))
            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: (u'spline' or u'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: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    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

References:: None