.. _fixelcorrespondence:

fixelcorrespondence
===================

Synopsis
--------

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

Usage
--------

::

    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 fixel directory where the output file will be written.
-  *output_data*: the name of the output fixel data file. This will be placed in the output fixel directory

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

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.

Options
-------

-  **-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; 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:** David Raffelt (david.raffelt@florey.edu.au)

**Copyright:** Copyright (c) 2008-2022 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/.


