.. _sh2peaks:

sh2peaks
===================

Synopsis
--------

Extract the peaks of a spherical harmonic function in each voxel

Usage
--------

::

    sh2peaks [ options ]  SH output

-  *SH*: the input image of SH coefficients.
-  *output*: the output image. Each volume corresponds to the x, y & z component of each peak direction vector in turn.

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

Peaks of the spherical harmonic function in each voxel are located by commencing a Newton search along each of a set of pre-specified directions

The spherical harmonic coefficients are stored according the conventions described the main documentation, which can be found at the following link:  |br|
https://mrtrix.readthedocs.io/en/3.0.3/concepts/spherical_harmonics.html

Options
-------

-  **-num peaks** the number of peaks to extract (default: 3).

-  **-direction phi theta** *(multiple uses permitted)* the direction of a peak to estimate. The algorithm will attempt to find the same number of peaks as have been specified using this option.

-  **-peaks image** the program will try to find the peaks that most closely match those in the image provided.

-  **-threshold value** only peak amplitudes greater than the threshold will be considered.

-  **-seeds file** specify a set of directions from which to start the multiple restarts of the optimisation (by default, the built-in 60 direction set is used)

-  **-mask image** only perform computation within the specified binary brain mask image.

-  **-fast** use lookup table to compute associated Legendre polynomials (faster, but approximate).

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
^^^^^^^^^^

Jeurissen, B.; Leemans, A.; Tournier, J.-D.; Jones, D.K.; Sijbers, J. Investigating the prevalence of complex fiber configurations in white matter tissue with diffusion magnetic resonance imaging. Human Brain Mapping, 2013, 34(11), 2747-2766

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)

**Copyright:** Copyright (c) 2008-2022 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
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Covered Software is provided under this License on an "as is"
basis, without warranty of any kind, either expressed, implied, or
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Covered Software is free of defects, merchantable, fit for a
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See the Mozilla Public License v. 2.0 for more details.

For more details, see http://www.mrtrix.org/.


