fixel2voxel

Synopsis

Convert a fixel-based sparse-data image into some form of scalar image

Usage

fixel2voxel [ options ]  fixel_in operation image_out
  • fixel_in: the input fixel data file
  • operation: the operation to apply, one of: mean, sum, product, min, max, absmax, magmax, count, complexity, sf, dec_unit, dec_scaled, split_data, split_dir.
  • image_out: the output scalar image.

Description

Fixel data can be reduced to voxel data in a number of ways:

  • Some statistic computed across all fixel values within a voxel: mean, sum, product, min, max, absmax, magmax
  • The number of fixels in each voxel: count
  • Some measure of crossing-fibre organisation: complexity, sf (‘single-fibre’)
  • A 4D directionally-encoded colour image: dec_unit, dec_scaled
  • A 4D scalar image of fixel values with one 3D volume per fixel: split_data
  • A 4D image of fixel directions, stored as three 3D volumes per fixel direction: split_dir

The -weighted option deals with the case where there is some per-fixel metric of interest that you wish to collapse into a single scalar measure per voxel, but each fixel possesses a different volume, and you wish for those fixels with greater volume to have a greater influence on the calculation than fixels with lesser volume. For instance, when estimating a voxel-based measure of mean axon diameter from per-fixel mean axon diameters, a fixel’s mean axon diameter should be weigthed by its relative volume within the voxel in the calculation of that voxel mean.

Options

  • -number N use only the largest N fixels in calculation of the voxel-wise statistic; in the case of “split_data” and “split_dir”, output only the largest N fixels, padding where necessary.
  • -weighted fixel_in weight the contribution of each fixel to the per-voxel result according to its volume.

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.

References

  • Reference for ‘complexity’ operation:Riffert, T. W.; Schreiber, J.; Anwander, A. & Knosche, T. R. Beyond Fractional Anisotropy: Extraction of bundle-specific structural metrics from crossing fibre models. NeuroImage, 2014, 100, 176-191

Author: Robert E. Smith (robert.smith@florey.edu.au) & David Raffelt (david.raffelt@florey.edu.au)

Copyright: Copyright (c) 2008-2019 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 http://mozilla.org/MPL/2.0/.

Covered Software is provided under this License on an “as is” basis, without warranty of any kind, either expressed, implied, or statutory, including, without limitation, warranties that the Covered Software is free of defects, merchantable, fit for a particular purpose or non-infringing. See the Mozilla Public License v. 2.0 for more details.

For more details, see http://www.mrtrix.org/.