Estimate response function coefficients based on the DWI signal in single-fibre voxels


amp2response [ options ]  amps mask directions response
  • amps: the amplitudes image
  • mask: the mask containing the voxels from which to estimate the response function
  • directions: a 4D image containing the estimated fibre directions
  • response: the output zonal spherical harmonic coefficients


This command uses the image data from all selected single-fibre voxels concurrently, rather than simply averaging their individual spherical harmonic coefficients. It also ensures that the response function is non-negative, and monotonic (i.e. its amplitude must increase from the fibre direction out to the orthogonal plane).

If multi-shell data are provided, and one or more b-value shells are not explicitly requested, the command will generate a response function for every b-value shell (including b=0 if present).


  • -isotropic estimate an isotropic response function (lmax=0 for all shells)
  • -noconstraint disable the non-negativity and monotonicity constraints
  • -directions path provide an external text file containing the directions along which the amplitudes are sampled

DW shell selection options

  • -shells b-values specify one or more b-values to use during processing, as a comma-separated list of the desired approximate b-values (b-values are clustered to allow for small deviations). Note that some commands are incompatible with multiple b-values, and will report an error if more than one b-value is provided. WARNING: note that, even though the b=0 volumes are never referred to as shells in the literature, they still have to be explicitly included in the list of b-values as provided to the -shell option! Several algorithms which include the b=0 volumes in their computations may otherwise return an undesired result.
  • -lmax values specify the maximum harmonic degree of the response function to estimate (can be a comma-separated list for multi-shell data)

Standard options

  • -info display information messages.
  • -quiet do not display information messages or progress status. Alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.
  • -debug display debugging messages.
  • -force force overwrite of output files. Caution: Using the same file as input and output might cause unexpected behaviour.
  • -nthreads number use this number of threads in multi-threaded applications (set to 0 to disable multi-threading).
  • -help display this information page and exit.
  • -version display version information and exit.


Smith, R. E.; Dhollander, T. & Connelly, A. Constrained linear least squares estimation of anisotropic response function for spherical deconvolution. ISMRM Workshop on Breaking the Barriers of Diffusion MRI, 23.

Author: Robert E. Smith (

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