Examine the values in spherical harmonic images to estimate (and optionally change) the SH basis used


shbasis [ options ]  SH [ SH ... ]
  • SH: the input image(s) of SH coefficients.


In previous versions of MRtrix, the convention used for storing spherical harmonic coefficients was a non-orthonormal basis (the m!=0 coefficients were a factor of sqrt(2) too large). This error has been rectified in the new MRtrix (assuming that compilation was performed without the USE_NON_ORTHONORMAL_SH_BASIS symbol defined), but will cause issues if processing SH data that was generated using an older version of MRtrix (or vice-versa).

This command provides a mechanism for testing the basis used in storage of image data representing a spherical harmonic series per voxel, and allows the user to forcibly modify the raw image data to conform to the desired basis.


  • -convert mode convert the image data in-place to the desired basis (if necessary). Options are: old, new, native (whichever basis MRtrix is compiled for; most likely the new orthonormal basis), force_oldtonew, force_newtoold. Note that for the “force_*” choices should ideally only be used in cases where the command is unable to automatically determine the SH basis using the existing image data.

Standard options

  • -info display information messages.
  • -quiet do not display information messages or progress status.
  • -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)
  • -failonwarn terminate program if a warning is produced
  • -help display this information page and exit.
  • -version display version information and exit.

Author: Robert E. Smith (

Copyright: Copyright (c) 2008-2017 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

MRtrix 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.

For more details, see