.. _fixel2voxel:

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/


