Extract the peaks of a spherical harmonic function in each voxel
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.
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:
- -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).
- -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.
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 (firstname.lastname@example.org)
Copyright: Copyright (c) 2008-2019 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/.