.. _5tt2vis:

5tt2vis
===================

Synopsis
--------

Generate an image for visualisation purposes from an ACT 5TT segmented anatomical image

Usage
--------

::

    5tt2vis [ options ]  input output

-  *input*: the input 4D tissue-segmented image
-  *output*: the output 3D image for visualisation

Options
-------

-  **-bg value** image intensity of background (default: 0)

-  **-cgm value** image intensity of cortical grey matter (default: 0.5)

-  **-sgm value** image intensity of sub-cortical grey matter (default: 0.75)

-  **-wm value** image intensity of white matter (default: 1)

-  **-csf value** image intensity of CSF (default: 0.15)

-  **-path value** image intensity of pathological tissue (default: 2)

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:** 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/.


