.. _fixelcrop:

fixelcrop
===================

Synopsis
--------

Crop/remove fixels from sparse fixel image using a binary fixel mask

Usage
--------

::

    fixelcrop [ options ]  input_fixel_directory input_fixel_mask output_fixel_directory

-  *input_fixel_directory*: input fixel directory, all data files and directions file will be cropped and saved in the output fixel directory
-  *input_fixel_mask*: the input fixel data file defining which fixels to crop. Fixels with zero values will be removed
-  *output_fixel_directory*: the output directory to store the cropped directions and data files

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

The mask must be input as a fixel data file the same dimensions as the fixel data file(s) to be cropped.

Options
-------

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) & Rami Tabarra (rami.tabarra@florey.edu.au)

**Copyright:** Copyright (c) 2008-2021 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/.


