.. _mrdegibbs:

mrdegibbs
===================

Synopsis
--------

Remove Gibbs Ringing Artifacts

Usage
--------

::

    mrdegibbs [ options ]  in out

-  *in*: the input image.
-  *out*: the output image.

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

This application attempts to remove Gibbs ringing artefacts from MRI images using the method of local subvoxel-shifts proposed by Kellner et al. (see reference below for details).

This command is designed to run on data directly after it has been reconstructed by the scanner, before any interpolation of any kind has taken place. You should not run this command after any form of motion correction (e.g. not after dwifslpreproc). Similarly, if you intend running dwidenoise, you should run denoising before this command to not alter the noise structure, which would impact on dwidenoise's performance.

Note that this method is designed to work on images acquired with full k-space coverage. Running this method on partial Fourier ('half-scan') data may lead to suboptimal and/or biased results, as noted in the original reference below. There is currently no means of dealing with this; users should exercise caution when using this method on partial Fourier data, and inspect its output for any obvious artefacts. 

Options
-------

-  **-axes list** select the slice axes (default: 0,1 - i.e. x-y).

-  **-nshifts value** discretization of subpixel spacing (default: 20).

-  **-minW value** left border of window used for TV computation (default: 1).

-  **-maxW value** right border of window used for TV computation (default: 3).

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
^^^^^^^^^^

Kellner, E; Dhital, B; Kiselev, V.G & Reisert, M. Gibbs-ringing artifact removal based on local subvoxel-shifts. Magnetic Resonance in Medicine, 2016, 76, 1574–1581.

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:** Ben Jeurissen (ben.jeurissen@uantwerpen.be) & J-Donald Tournier (jdtournier@gmail.com)

**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/.


