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 -fslgrad bvecs bvals tournier dwi.mif wm.txt'
>>> resp.run()                                 

Inputs:

[Mandatory]
algorithm: ('msmt_5tt' or 'dhollander' or 'tournier' or 'tax')
        response estimation algorithm (multi-tissue)
        flag: %s, position: -6
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: ('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
csf_file: (a file name)
        output CSF response text file
        flag: %s, position: -1
environ: (a dictionary with keys which are a bytes or None or a value
         of class 'str' and with values which are a bytes or None or a value
         of class 'str', 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: ('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
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