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

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. E.g. when estimating a voxel-based measure of mean axon diameter, a fixel’s mean axon diameter should be weigthed by its relative volume within the voxel. Note that AFD can be used as a psuedomeasure of fixel 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).
  • -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) 2008-2018 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/

MRtrix3 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 http://www.mrtrix.org/