dwigradcheck

Synopsis

Check the orientation of the diffusion gradient table

Usage

dwigradcheck input [ options ]
  • input: The input DWI series to be checked

Description

Note that the corrected gradient table can be output using the -export_grad_{mrtrix,fsl} option.

Note that if the -mask command-line option is not specified, the MRtrix3 command dwi2mask will automatically be called to derive a binary mask image to be used for streamline seeding and to constrain streamline propagation. More information on mask derivation from DWI data can be found at the following link: https://mrtrix.readthedocs.io/en/3.0.3/dwi_preprocessing/masking.html

Options

  • -mask image Provide a mask image within which to seed & constrain tracking
  • -number Set the number of tracks to generate for each test

Options for importing the diffusion gradient table

  • -grad Provide the diffusion gradient table in MRtrix format
  • -fslgrad bvecs bvals Provide the diffusion gradient table in FSL bvecs/bvals format

Options for exporting the diffusion gradient table

  • -export_grad_mrtrix grad Export the final gradient table in MRtrix format
  • -export_grad_fsl bvecs bvals Export the final gradient table in FSL bvecs/bvals format

Additional standard options for Python scripts

  • -nocleanup do not delete intermediate files during script execution, and do not delete scratch directory at script completion.
  • -scratch /path/to/scratch/ manually specify the path in which to generate the scratch directory.
  • -continue <ScratchDir> <LastFile> continue the script from a previous execution; must provide the scratch directory path, and the name of the last successfully-generated file.

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.
  • -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

  • Jeurissen, B.; Leemans, A.; Sijbers, J. Automated correction of improperly rotated diffusion gradient orientations in diffusion weighted MRI. Medical Image Analysis, 2014, 18(7), 953-962

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

Copyright: Copyright (c) 2008-2022 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/.