.. _mrcat:

mrcat
===================

Synopsis
--------

Concatenate several images into one

Usage
--------

::

    mrcat [ options ]  image1 image2 [ image2 ... ] output

-  *image1*: the first input image.
-  *image2*: additional input image(s).
-  *output*: the output image.

Example usages
--------------

-   *Concatenate individual 3D volumes into a single 4D image series*::

        $ mrcat volume*.mif series.mif

    The wildcard characters will find all images in the current working directory with names that begin with "volume" and end with ".mif"; the mrcat command will receive these as a list of input file names, from which it will produce a 4D image where the input volumes have been concatenated along axis 3 (the fourth axis; the spatial axes are 0, 1 & 2).

Options
-------

-  **-axis axis** specify axis along which concatenation should be performed. By default, the program will use the last non-singleton, non-spatial axis of any of the input images - in other words axis 3 or whichever axis (greater than 3) of the input images has size greater than one.

Data type options
^^^^^^^^^^^^^^^^^

-  **-datatype spec** specify output image data type. Valid choices are: float32, float32le, float32be, float64, float64le, float64be, int64, uint64, int64le, uint64le, int64be, uint64be, int32, uint32, int32le, uint32le, int32be, uint32be, int16, uint16, int16le, uint16le, int16be, uint16be, cfloat32, cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be, int8, uint8, bit.

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:** J-Donald Tournier (jdtournier@gmail.com) and Robert E. Smith (robert.smith@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/.


