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 (int or long))
        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 (int or long))
        maximum harmonic degree of response function
        flag: -lmax %d
nthreads: (an integer (int or long))
        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