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# interfaces.mrtrix3.preprocess

## ResponseSD

Link to code

Wraps command dwi2response

Generate an appropriate response function from the image data for spherical deconvolution.

[1] | Tax, C. M.; Jeurissen, B.; Vos, S. B.; Viergever, M. A. and Leemans, A., Recursive calibration of the fiber response function for spherical deconvolution of diffusion MRI data. NeuroImage, 2014, 86, 67-80

### Example

    >>> import nipype.interfaces.mrtrix3 as mrt
    >>> resp = mrt.ResponseSD()
    >>> resp.inputs.in_file = 'dwi.mif'
    >>> resp.inputs.in_mask = 'mask.nii.gz'
    >>> resp.inputs.grad_fsl = ('bvecs', 'bvals')
    >>> resp.cmdline
    'dwi2response -fslgrad bvecs bvals -mask mask.nii.gz dwi.mif response.txt'
    >>> resp.run()

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            input diffusion weighted images
            flag: %s, position: -2
    out_file: (a file name, nipype default value: response.txt)
            output file containing SH coefficients
            flag: %s, position: -1

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    bval_scale: ('yes' or 'no')
            specifies whether the b - values should be scaled by the square of
            the corresponding DW gradient norm, as often required for multishell
            or DSI DW acquisition schemes. The default action can also be set in
            the MRtrix config file, under the BValueScaling entry. Valid choices
            are yes / no, true / false, 0 / 1 (default: true).
            flag: -bvalue_scaling %s
    disp_mult: (a float)
            dispersion of FOD lobe must not exceed some threshold as determined
            by this multiplier and the FOD dispersion in other single-fibre
            voxels. The threshold is: (mean + (multiplier * (mean - min)));
            default = 1.0. Criterion is only applied in second pass of RF
            estimation.
            flag: -dispersion_multiplier %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
    grad_file: (an existing file name)
            dw gradient scheme (MRTrix format
            flag: -grad %s
    grad_fsl: (a tuple of the form: (an existing file name, an existing
             file name))
            (bvecs, bvals) dw gradient scheme (FSL format
            flag: -fslgrad %s %s
    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_bval: (an existing file name)
            bvals file in FSL format
    in_bvec: (an existing file name)
            bvecs file in FSL format
            flag: -fslgrad %s %s
    in_mask: (an existing file name)
            provide initial mask image
            flag: -mask %s
    int_mult: (a float)
            integral of FOD lobe must not be outside some range as determined by
            this multiplier and FOD lobe integral in other single-fibre voxels.
            The range is: (mean +- (multiplier * stdev)); default = 2.0.
            Criterion is only applied in second pass of RF estimation.
            flag: -integral_multiplier %f
    iterations: (an integer)
            maximum number of iterations per pass
            flag: -max_iters %d
    max_change: (a float)
            maximum percentile change in any response function coefficient; if
            no individual coefficient changes by more than this fraction, the
            algorithm is terminated.
            flag: -max_change %f
    max_sh: (an integer)
            maximum harmonic degree of response function
            flag: -lmax %d
    nthreads: (an integer)
            number of threads. if zero, the number of available cpus will be
            used
            flag: -nthreads %d
    out_sf: (a file name)
            write a mask containing single-fibre voxels
            flag: -sf %s
    shell: (a list of items which are a float)
            specify one or more dw gradient shells
            flag: -shell %s
    terminal_output: ('stream' or 'allatonce' or 'file' or '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
    test_all: (a boolean)
            re-test all voxels at every iteration
            flag: -test_all
    vol_ratio: (a float)
            maximal volume ratio between the sum of all other positive lobes in
            the voxel and the largest FOD lobe
            flag: -volume_ratio %f

Outputs:

    out_file: (an existing file name)
            the output response file
    out_sf: (a file name)
            mask containing single-fibre voxels