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


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

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) 2008-2016 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