.. _mrcrop:

mrcrop
===================

Synopsis
--------

Crop an image to a reduced field of view

Usage
--------

::

    mrcrop [ options ]  image_in image_out

-  *image_in*: the image to be cropped
-  *image_out*: the output path for the resulting cropped image

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

Extent of cropping can be determined using either manual setting of axis dimensions, or a computed mask image corresponding to the brain.

If using a mask, a gap of 1 voxel will be left at all 6 edges of the image such that trilinear interpolation upon the resulting images is still valid.

This is useful for axially-acquired brain images, where the image size can be reduced by a factor of 2 by removing the empty space on either side of the brain.

Options
-------

-  **-mask image** crop the input image according to the spatial extent of a mask image

-  **-axis index start end** crop the input image in the provided axis

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.

--------------



**Author:** Robert E. Smith (robert.smith@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/


