amp2response

Synopsis

Estimate response function coefficients based on the DWI signal in single-fibre voxels

Usage

amp2response [ options ]  amps mask directions response
  • amps: the amplitudes image
  • mask: the mask containing the voxels from which to estimate the response function
  • directions: a 4D image containing the estimated fibre directions
  • response: the output zonal spherical harmonic coefficients

Description

This command uses the image data from all selected single-fibre voxels concurrently, rather than simply averaging their individual spherical harmonic coefficients. It also ensures that the response function is non-negative, and monotonic (i.e. its amplitude must increase from the fibre direction out to the orthogonal plane).

If multi-shell data are provided, and one or more b-value shells are not explicitly requested, the command will generate a response function for every b-value shell (including b=0 if present).

Options

  • -isotropic estimate an isotropic response function (lmax=0 for all shells)
  • -noconstraint disable the non-negativity and monotonicity constraints
  • -directions path provide an external text file containing the directions along which the amplitudes are sampled

DW Shell selection options

  • -shell list specify one or more diffusion-weighted gradient shells to use during processing, as a comma-separated list of the desired approximate b-values. Note that some commands are incompatible with multiple shells, and will throw an error if more than one b-value is provided.
  • -lmax values specify the maximum harmonic degree of the response function to estimate (can be a comma-separated list for multi-shell data)

Standard options

  • -info display information messages.
  • -quiet do not display information messages or progress status.
  • -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)
  • -failonwarn terminate program if a warning is produced
  • -help display this information page and exit.
  • -version display version information and exit.

Author: Robert E. Smith (robert.smith@florey.edu.au)

Copyright: Copyright (c) 2008-2017 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/.

MRtrix 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/.