Obtain fixel-fixel correpondence between a subject fixel image and a template fixel mask


fixelcorrespondence [ options ]  subject_data template_directory output_directory output_data
  • subject_data: the input subject fixel data file. This should be a file inside the fixel directory
  • template_directory: the input template fixel directory.
  • output_directory: the output fixel directory.
  • output_data: the name of the output fixel data file. This will be placed in the output fixel directory


It is assumed that the subject image has already been spatially normalised and is aligned with the template. The output fixel image will have the same fixels (and directions) of the template.


  • -angle value the max angle threshold for computing inter-subject fixel correspondence (Default: 45 degrees)

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) 2008-2017 the MRtrix3 contributors

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