Extract the peaks of a spherical harmonic function in each voxel


sh2peaks [ options ]  SH output
  • SH: the input image of SH coefficients.
  • output: the output image. Each volume corresponds to the x, y & z component of each peak direction vector in turn.


Peaks of the spherical harmonic function in each voxel are located by commencing a Newton search along each of a set of pre-specified directions

The spherical harmonic coefficients are stored according the conventions described the main documentation, which can be found at the following link:


  • -num peaks the number of peaks to extract (default: 3).
  • -direction phi theta (multiple uses permitted) the direction of a peak to estimate. The algorithm will attempt to find the same number of peaks as have been specified using this option.
  • -peaks image the program will try to find the peaks that most closely match those in the image provided.
  • -threshold value only peak amplitudes greater than the threshold will be considered.
  • -seeds file specify a set of directions from which to start the multiple restarts of the optimisation (by default, the built-in 60 direction set is used)
  • -mask image only perform computation within the specified binary brain mask image.
  • -fast use lookup table to compute associated Legendre polynomials (faster, but approximate).

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).
  • -config key value (multiple uses permitted) temporarily set the value of an MRtrix config file entry.
  • -help display this information page and exit.
  • -version display version information and exit.


Jeurissen, B.; Leemans, A.; Tournier, J.-D.; Jones, D.K.; Sijbers, J. Investigating the prevalence of complex fiber configurations in white matter tissue with diffusion magnetic resonance imaging. Human Brain Mapping, 2013, 34(11), 2747-2766

Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137

Author: J-Donald Tournier (

Copyright: Copyright (c) 2008-2020 the MRtrix3 contributors.

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