.. _fixelfilter:

fixelfilter
===================

Synopsis
--------

Perform filtering operations on fixel-based data

Usage
--------

::

    fixelfilter [ options ]  input filter output

-  *input*: the input: either a fixel data file, or a fixel directory (see Description)
-  *filter*: the filtering operation to perform; options are: connect, smooth
-  *output*: the output: either a fixel data file, or a fixel directory (see Description)

Description
-----------

If the first input to the command is a specific fixel data file, then a filtered version of only that file will be generated by the command. Alternatively, if the input is the location of a fixel directory, then the command will create a duplicate of the fixel directory, and apply the specified filter operation to all fixel data files within the directory.

Options
-------

-  **-matrix file** provide a fixel-fixel connectivity matrix for filtering operations that require it

Options specific to the "connect" filter
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

-  **-threshold_value value** specify a threshold for the input fixel data file values (default = 0.5)

-  **-threshold_connectivity value** specify a fixel-fixel connectivity threshold for connected-component analysis (default = 0.10000000000000001)

Options specific to the "smooth" filter
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

-  **-fwhm value** the full-width half-maximum (FWHM) of the spatial component of the smoothing filter (default = 10mm)

-  **-minweight value** apply a minimum threshold to smoothing weights (default = 0.01)

-  **-mask image** only perform smoothing within a specified binary fixel mask

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
^^^^^^^^^^

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:** Robert E. Smith (robert.smith@florey.edu.au)

**Copyright:** Copyright (c) 2008-2025 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/.


