fixelreorient [ options ]  input warp output
  • input: the input fixel image.
  • warp: a 4D deformation field used to perform reorientation. Reorientation is performed by applying the Jacobian affine transform in each voxel in the warp, then re-normalising the vector representing the fixel direction
  • output: the output fixel image.


Reorient fixel directions using the local affine transformation (Jacobian matrix) of an input warp.


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: David Raffelt (

Copyright: Copyright (c) 2008-2016 the MRtrix3 contributors

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