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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).
  • -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) 2008-2018 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/

MRtrix3 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

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

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