Reorient fixel directions


fixelreorient [ options ]  fixel_in warp fixel_out
  • fixel_in: the input fixel directory

  • 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

  • fixel_out: the output fixel directory. If the the input and output directories are the same, the existing directions file will be replaced (providing the -force option is supplied). If a new directory is supplied then the fixel directions and all other fixel data will be copied to the new directory.


Reorientation is performed by transforming the vector representing the fixel direction with the Jacobian (local affine transform) computed at each voxel in the warp, then re-normalising the vector.


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.


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: David Raffelt (

Copyright: Copyright (c) 2008-2024 the MRtrix3 contributors.

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