dwi2response
Synopsis
Estimate response function(s) for spherical deconvolution
Usage
dwi2response algorithm [ options ] ...
algorithm: Select the algorithm to be used; 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”.
More information on response function estimation for spherical deconvolution can be found at the following link: https://mrtrix.readthedocs.io/en/3.0.4/constrained_spherical_deconvolution/response_function_estimation.html
Note that if the -mask command-line option is not specified, the MRtrix3 command dwi2mask will automatically be called to derive an initial voxel exclusion mask. More information on mask derivation from DWI data can be found at: https://mrtrix.readthedocs.io/en/3.0.4/dwi_preprocessing/masking.html
Options
Options for importing the diffusion gradient table
-grad file 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 image Provide an initial mask for response voxel selection
-voxels image Output an image showing the final voxel selection(s)
-shells bvalues 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 if desired)
-lmax values 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 an existing directory 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.; 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) and Thijs Dhollander (thijs.dhollander@gmail.com)
Copyright: Copyright (c) 2008-2024 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
Unsupervised estimation of WM, GM and CSF response functions that does not require a T1 image (or segmentation thereof)
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
Description
This is an improved version of the Dhollander et al. (2016) algorithm for unsupervised estimation of WM, GM and CSF response functions, which includes the Dhollander et al. (2019) improvements for single-fibre WM response function estimation (prior to this update, the “dwi2response tournier” algorithm had been utilised specifically for the single-fibre WM response function estimation step).
Options
Options for the “dhollander” algorithm
-erode iterations Number of erosion passes to apply to initial (whole brain) mask. Set to 0 to not erode the brain mask. (default: 3)
-fa threshold FA threshold for crude WM versus GM-CSF separation. (default: 0.2)
-sfwm percentage Final number of single-fibre WM voxels to select, as a percentage of refined WM. (default: 0.5 per cent)
-gm percentage Final number of GM voxels to select, as a percentage of refined GM. (default: 2 per cent)
-csf percentage Final number of CSF voxels to select, as a percentage of refined CSF. (default: 10 per cent)
-wm_algo algorithm Use external dwi2response algorithm for WM single-fibre voxel selection (options: fa, tax, tournier) (default: built-in Dhollander 2019)
Options for importing the diffusion gradient table
-grad file 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 image Provide an initial mask for response voxel selection
-voxels image Output an image showing the final voxel selection(s)
-shells bvalues 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 if desired)
-lmax values 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 an existing directory 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
If -wm_algo option is not used: 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
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: Thijs Dhollander (thijs.dhollander@gmail.com)
Copyright: Copyright (c) 2008-2024 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 iterations Number of brain mask erosion steps to apply prior to threshold (not used if mask is provided manually)
-number voxels The number of highest-FA voxels to use
-threshold value Apply a hard FA threshold, rather than selecting the top voxels
Options for importing the diffusion gradient table
-grad file 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 image Provide an initial mask for response voxel selection
-voxels image Output an image showing the final voxel selection(s)
-shells bvalues 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 if desired)
-lmax values 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 an existing directory 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
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) 2008-2024 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 image Provide an input image that contains a pre-estimated fibre direction in each voxel (a tensor fit will be used otherwise)
Options for importing the diffusion gradient table
-grad file 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 image Provide an initial mask for response voxel selection
-voxels image Output an image showing the final voxel selection(s)
-shells bvalues 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 if desired)
-lmax values 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 an existing directory 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.; 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) 2008-2024 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 image Provide an input image that contains a pre-estimated fibre direction in each voxel (a tensor fit will be used otherwise)
-fa value Upper fractional anisotropy threshold for GM and CSF voxel selection (default: 0.2)
-pvf fraction Partial volume fraction threshold for tissue voxel selection (default: 0.95)
-wm_algo algorithm dwi2response algorithm to use for WM single-fibre voxel selection (options: fa, tax, tournier; default: tournier)
-sfwm_fa_threshold value 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 file 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 image Provide an initial mask for response voxel selection
-voxels image Output an image showing the final voxel selection(s)
-shells bvalues 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 if desired)
-lmax values 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 an existing directory 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
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) 2008-2024 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 value Second-to-first-peak amplitude ratio threshold
-max_iters iterations Maximum number of iterations (set to 0 to force convergence)
-convergence percentage Percentile change in any RF coefficient required to continue iterating
Options for importing the diffusion gradient table
-grad file 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 image Provide an initial mask for response voxel selection
-voxels image Output an image showing the final voxel selection(s)
-shells bvalues 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 if desired)
-lmax values 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 an existing directory 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
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) 2008-2024 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
-number voxels Number of single-fibre voxels to use when calculating response function
-iter_voxels voxels Number of single-fibre voxels to select when preparing for the next iteration (default = 10 x value given in -number)
-dilate iterations Number of mask dilation steps to apply when deriving voxel mask to test in the next iteration
-max_iters iterations Maximum number of iterations (set to 0 to force convergence)
Options for importing the diffusion gradient table
-grad file 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 image Provide an initial mask for response voxel selection
-voxels image Output an image showing the final voxel selection(s)
-shells bvalues 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 if desired)
-lmax values 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 an existing directory 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
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) 2008-2024 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/.