dwi2response

Synopsis

Estimate response function(s) for spherical deconvolution

Usage

dwi2response algorithm [ options ] ...
  • algorithm: Select the algorithm to be used to complete the script operation; additional details and options become available once an algorithm is nominated. Options are: dhollander, fa, manual, msmt_5tt, tax, tournier

Description

dwi2response offers different algorithms for performing various types of response function estimation. The name of the algorithm must appear as the first argument on the command-line after ‘dwi2response’. The subsequent arguments and options depend on the particular algorithm being invoked.

Each algorithm available has its own help page, including necessary references; e.g. to see the help page of the ‘fa’ algorithm, type ‘dwi2response fa’.

Options

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

General dwi2response options

  • -mask Provide an initial mask for response voxel selection
  • -voxels Output an image showing the final voxel selection(s)
  • -shells The b-value(s) to use in response function estimation (comma-separated list in case of multiple b-values, b=0 must be included explicitly)
  • -lmax The maximum harmonic degree(s) for response function estimation (comma-separated list in case of multiple b-values)

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.

Author: Robert E. Smith (robert.smith@florey.edu.au) and Thijs Dhollander (thijs.dhollander@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/.

dwi2response dhollander

Synopsis

An improved version of the Dhollander et al. (2016) algorithm for unsupervised estimation of WM, GM and CSF response functions; does not require a T1 image (or segmentation thereof). This implementation includes the Dhollander et al. (2019) improvements for single-fibre WM response function estimation.

Usage

dwi2response dhollander input out_sfwm out_gm out_csf [ options ]
  • input: Input DWI dataset
  • out_sfwm: Output single-fibre WM response function text file
  • out_gm: Output GM response function text file
  • out_csf: Output CSF response function text file

Options

Options for the ‘dhollander’ algorithm

  • -erode Number of erosion passes to apply to initial (whole brain) mask. Set to 0 to not erode the brain mask. (default: 3)
  • -fa FA threshold for crude WM versus GM-CSF separation. (default: 0.2)
  • -sfwm Final number of single-fibre WM voxels to select, as a percentage of refined WM. (default: 0.5 per cent)
  • -gm Final number of GM voxels to select, as a percentage of refined GM. (default: 2 per cent)
  • -csf Final number of CSF voxels to select, as a percentage of refined CSF. (default: 10 per cent)

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

General dwi2response options

  • -mask Provide an initial mask for response voxel selection
  • -voxels Output an image showing the final voxel selection(s)
  • -shells The b-value(s) to use in response function estimation (comma-separated list in case of multiple b-values, b=0 must be included explicitly)
  • -lmax The maximum harmonic degree(s) for response function estimation (comma-separated list in case of multiple b-values)

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

  • Dhollander, T.; Raffelt, D. & Connelly, A. Unsupervised 3-tissue response function estimation from single-shell or multi-shell diffusion MR data without a co-registered T1 image. ISMRM Workshop on Breaking the Barriers of Diffusion MRI, 2016, 5
  • Dhollander, T.; Mito, R.; Raffelt, D. & Connelly, A. Improved white matter response function estimation for 3-tissue constrained spherical deconvolution. Proc Intl Soc Mag Reson Med, 2019, 555

Author: Thijs Dhollander (thijs.dhollander@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/.

dwi2response fa

Synopsis

Use the old FA-threshold heuristic for single-fibre voxel selection and response function estimation

Usage

dwi2response fa input output [ options ]
  • input: The input DWI
  • output: The output response function text file

Options

Options specific to the ‘fa’ algorithm

  • -erode Number of brain mask erosion steps to apply prior to threshold (not used if mask is provided manually)
  • -number The number of highest-FA voxels to use
  • -threshold Apply a hard FA threshold, rather than selecting the top voxels

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

General dwi2response options

  • -mask Provide an initial mask for response voxel selection
  • -voxels Output an image showing the final voxel selection(s)
  • -shells The b-value(s) to use in response function estimation (comma-separated list in case of multiple b-values, b=0 must be included explicitly)
  • -lmax The maximum harmonic degree(s) for response function estimation (comma-separated list in case of multiple b-values)

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

  • Tournier, J.-D.; Calamante, F.; Gadian, D. G. & Connelly, A. Direct estimation of the fiber orientation density function from diffusion-weighted MRI data using spherical deconvolution. NeuroImage, 2004, 23, 1176-1185

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

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/.

dwi2response manual

Synopsis

Derive a response function using an input mask image alone (i.e. pre-selected voxels)

Usage

dwi2response manual input in_voxels output [ options ]
  • input: The input DWI
  • in_voxels: Input voxel selection mask
  • output: Output response function text file

Options

Options specific to the ‘manual’ algorithm

  • -dirs Manually provide the fibre direction in each voxel (a tensor fit will be used otherwise)

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

General dwi2response options

  • -mask Provide an initial mask for response voxel selection
  • -voxels Output an image showing the final voxel selection(s)
  • -shells The b-value(s) to use in response function estimation (comma-separated list in case of multiple b-values, b=0 must be included explicitly)
  • -lmax The maximum harmonic degree(s) for response function estimation (comma-separated list in case of multiple b-values)

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.

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

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/.

dwi2response msmt_5tt

Synopsis

Derive MSMT-CSD tissue response functions based on a co-registered five-tissue-type (5TT) image

Usage

dwi2response msmt_5tt input in_5tt out_wm out_gm out_csf [ options ]
  • input: The input DWI
  • in_5tt: Input co-registered 5TT image
  • out_wm: Output WM response text file
  • out_gm: Output GM response text file
  • out_csf: Output CSF response text file

Options

Options specific to the ‘msmt_5tt’ algorithm

  • -dirs Manually provide the fibre direction in each voxel (a tensor fit will be used otherwise)
  • -fa Upper fractional anisotropy threshold for GM and CSF voxel selection (default: 0.2)
  • -pvf Partial volume fraction threshold for tissue voxel selection (default: 0.95)
  • -wm_algo algorithm dwi2response algorithm to use for WM single-fibre voxel selection (default: tournier)
  • -sfwm_fa_threshold Sets -wm_algo to fa and allows to specify a hard FA threshold for single-fibre WM voxels, which is passed to the -threshold option of the fa algorithm (warning: overrides -wm_algo option)

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

General dwi2response options

  • -mask Provide an initial mask for response voxel selection
  • -voxels Output an image showing the final voxel selection(s)
  • -shells The b-value(s) to use in response function estimation (comma-separated list in case of multiple b-values, b=0 must be included explicitly)
  • -lmax The maximum harmonic degree(s) for response function estimation (comma-separated list in case of multiple b-values)

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.; Tournier, J.-D.; Dhollander, T.; Connelly, A. & Sijbers, J. Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data. NeuroImage, 2014, 103, 411-426

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

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/.

dwi2response tax

Synopsis

Use the Tax et al. (2014) recursive calibration algorithm for single-fibre voxel selection and response function estimation

Usage

dwi2response tax input output [ options ]
  • input: The input DWI
  • output: The output response function text file

Options

Options specific to the ‘tax’ algorithm

  • -peak_ratio Second-to-first-peak amplitude ratio threshold
  • -max_iters Maximum number of iterations
  • -convergence Percentile change in any RF coefficient required to continue iterating

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

General dwi2response options

  • -mask Provide an initial mask for response voxel selection
  • -voxels Output an image showing the final voxel selection(s)
  • -shells The b-value(s) to use in response function estimation (comma-separated list in case of multiple b-values, b=0 must be included explicitly)
  • -lmax The maximum harmonic degree(s) for response function estimation (comma-separated list in case of multiple b-values)

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

  • Tax, C. M.; Jeurissen, B.; Vos, S. B.; Viergever, M. A. & Leemans, A. Recursive calibration of the fiber response function for spherical deconvolution of diffusion MRI data. NeuroImage, 2014, 86, 67-80

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

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/.

dwi2response tournier

Synopsis

Use the Tournier et al. (2013) iterative algorithm for single-fibre voxel selection and response function estimation

Usage

dwi2response tournier input output [ options ]
  • input: The input DWI
  • output: The output response function text file

Options

Options specific to the ‘tournier’ algorithm

  • -iter_voxels Number of single-fibre voxels to select when preparing for the next iteration
  • -sf_voxels Number of single-fibre voxels to use when calculating response function
  • -dilate Number of mask dilation steps to apply when deriving voxel mask to test in the next iteration
  • -max_iters Maximum number of iterations

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

General dwi2response options

  • -mask Provide an initial mask for response voxel selection
  • -voxels Output an image showing the final voxel selection(s)
  • -shells The b-value(s) to use in response function estimation (comma-separated list in case of multiple b-values, b=0 must be included explicitly)
  • -lmax The maximum harmonic degree(s) for response function estimation (comma-separated list in case of multiple b-values)

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

  • Tournier, J.-D.; Calamante, F. & Connelly, A. Determination of the appropriate b-value and number of gradient directions for high-angular-resolution diffusion-weighted imaging. NMR Biomedicine, 2013, 26, 1775-1786

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

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/.