Extract the peaks of a spherical harmonic function at each voxel, by commencing a Newton search along a set of specified directions


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.


  • -num peaks the number of peaks to extract (default: 3).
  • -direction phi theta 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).
  • -help display this information page and exit.
  • -version display version information and exit.

Author: J-Donald Tournier (

Copyright: Copyright (c) 2008-2018 the MRtrix3 contributors.

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, you can obtain one at

MRtrix3 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

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