Home · Quickstart · Documentation · About · Nipy

# interfaces.mrtrix3.preprocess

## ResponseSD

Link to code

Wraps command dwi2response

Estimate response function(s) for spherical deconvolution using the specified algorithm.

### Example

    >>> import nipype.interfaces.mrtrix3 as mrt
    >>> resp = mrt.ResponseSD()
    >>> resp.inputs.in_file = 'dwi.mif'
    >>> resp.inputs.algorithm = 'tournier'
    >>> resp.inputs.grad_fsl = ('bvecs', 'bvals')
    >>> resp.cmdline
    'dwi2response tournier -fslgrad bvecs bvals dwi.mif wm.txt'
    >>> resp.run()

Inputs:

    [Mandatory]
    algorithm: (u'msmt_5tt' or u'dhollander' or u'tournier' or u'tax')
            response estimation algorithm (multi-tissue)
            flag: %s, position: 1
    in_file: (an existing file name)
            input DWI image
            flag: %s, position: -5

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    bval_scale: (u'yes' or u'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
    csf_file: (a file name)
            output CSF response text file
            flag: %s, position: -1
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    gm_file: (a file name)
            output GM response text file
            flag: %s, position: -2
    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
    max_sh: (an integer (int or long))
            maximum harmonic degree of response function
            flag: -lmax %d
    mtt_file: (a file name)
            input 5tt image
            flag: %s, position: -4
    nthreads: (an integer (int or long))
            number of threads. if zero, the number of available cpus will be
            used
            flag: -nthreads %d
    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
    wm_file: (a file name, nipype default value: wm.txt)
            output WM response text file
            flag: %s, position: -3

Outputs:

    csf_file: (a file name)
            output CSF response text file
            flag: %s
    gm_file: (a file name)
            output GM response text file
            flag: %s
    wm_file: (a file name)
            output WM response text file
            flag: %s