tensor2metric

Synopsis

Generate maps of tensor-derived parameters

Usage

tensor2metric [ options ]  tensor
  • tensor: the input tensor image.

Options

  • -adc image compute the mean apparent diffusion coefficient (ADC) of the diffusion tensor. (sometimes also referred to as the mean diffusivity (MD))
  • -fa image compute the fractional anisotropy (FA) of the diffusion tensor.
  • -ad image compute the axial diffusivity (AD) of the diffusion tensor. (equivalent to the principal eigenvalue)
  • -rd image compute the radial diffusivity (RD) of the diffusion tensor. (equivalent to the mean of the two non-principal eigenvalues)
  • -cl image compute the linearity metric of the diffusion tensor. (one of the three Westin shape metrics)
  • -cp image compute the planarity metric of the diffusion tensor. (one of the three Westin shape metrics)
  • -cs image compute the sphericity metric of the diffusion tensor. (one of the three Westin shape metrics)
  • -value image compute the selected eigenvalue(s) of the diffusion tensor.
  • -vector image compute the selected eigenvector(s) of the diffusion tensor.
  • -num sequence specify the desired eigenvalue/eigenvector(s). Note that several eigenvalues can be specified as a number sequence. For example, ‘1,3’ specifies the principal (1) and minor (3) eigenvalues/eigenvectors (default = 1).
  • -modulate choice specify how to modulate the magnitude of the eigenvectors. Valid choices are: none, FA, eigval (default = FA).
  • -mask image only perform computation within the specified binary brain mask 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.
  • -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

Basser, P. J.; Mattiello, J. & Lebihan, D. MR diffusion tensor spectroscopy and imaging. Biophysical Journal, 1994, 66, 259-267

Westin, C. F.; Peled, S.; Gudbjartsson, H.; Kikinis, R. & Jolesz, F. A. Geometrical diffusion measures for MRI from tensor basis analysis. Proc Intl Soc Mag Reson Med, 1997, 5, 1742


Author: Thijs Dhollander (thijs.dhollander@gmail.com) & Ben Jeurissen (ben.jeurissen@uantwerpen.be) & J-Donald Tournier (jdtournier@gmail.com)

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/.