.. _sh2metric: sh2metric =================== Synopsis -------- Compute voxel-wise metrics from one or more spherical harmonics images Usage -------- :: sh2metric [ options ] SH [ SH ... ] metric output - *SH*: the input spherical harmonics coefficients image(s) - *metric*: the metrc to compute; one of: entropy, power - *output*: the output metric image Description ----------- Depending on the particular metric being computed, the command may only accept a single input SH image; wheras other metrics may accept multiple SH images as input (eg. ODFs) and compute a single scalar output image. The various metrics available are detailed individually below. "entropy": this metric computes the entropy (in nats, ie. logarithm base e) of one or more spherical harmonics functions. This can be thought of as being inversely proportional to the overall "complexity" of the (set of) spherical harmonics function(s). Used in conjunction with the -invnorm option, the result behaves somewhat akin to an anisotropy measure. "power": this metric computes the sum of squared SH coefficients, which equals the mean-squared amplitude of the spherical function it represents. The spherical harmonic coefficients are stored according to the conventions described in the main documentation, which can be found at the following link: |br| https://mrtrix.readthedocs.io/en/3.0.8/concepts/spherical_harmonics.html Options ------- Options specific to the "entropy" metric ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - **-normalised** normalise the voxel-wise entropy measure to the range [0.0, 1.0] - **-invnorm** compute the complement of the normalised voxel-wise entropy measure (ie. 1.0 - normalised), such that values closer to 1.0 reflect greater concentration of the function - **-directions spec** specify the direction set to be used for SH amplitude sampling; either an input file containing a set of directions, or an integer corresponding to a built-in direction set Options specific to the "power" metric ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - **-spectrum** output the power spectrum, i.e., the power contained within each harmonic degree (l=0, 2, 4, ...) as a 4D image. 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 & debug input data. - **-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 **Copyright:** Copyright (c) 2008-2026 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/.