.. _mrmetric:

mrmetric
===================

Synopsis
--------

Computes a dissimilarity metric between two images

Usage
--------

::

    mrmetric [ options ]  image1 image2

-  *image1*: the first input image.
-  *image2*: the second input image.

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

Currently only the mean squared difference is implemented.

Options
-------

-  **-space iteration method** voxel (default): per voxel image1: scanner space of image 1 image2: scanner space of image 2 average: scanner space of the average affine transformation of image 1 and 2 

-  **-interp method** set the interpolation method to use when reslicing (choices: nearest, linear, cubic, sinc. Default: linear).

-  **-metric method** define the dissimilarity metric used to calculate the cost. Choices: diff (squared differences), cc (negative cross correlation). Default: diff). cc is only implemented for -space average and -interp linear.

-  **-mask1 image** mask for image 1

-  **-mask2 image** mask for image 2

-  **-nonormalisation** do not normalise the dissimilarity metric to the number of voxels.

-  **-overlap** output number of voxels that were used.

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:** David Raffelt (david.raffelt@florey.edu.au) and Max Pietsch (maximilian.pietsch@kcl.ac.uk)

**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/


