dwishellmath
Synopsis
Apply an mrmath operation to each b-value shell in a DWI series
Usage
dwishellmath input operation output [ options ]
input: The input diffusion MRI series
operation: The operation to be applied to each shell; this must be one of the following: mean, median, sum, product, rms, norm, var, std, min, max, absmax, magmax
output: The output image series
Description
The output of this command is a 4D image, where each volume corresponds to a b-value shell (in order of increasing b-value), and the intensities within each volume correspond to the chosen statistic having been computed from across the DWI volumes belonging to that b-value shell.
Example usages
To compute the mean diffusion-weighted signal in each b-value shell:
$ dwishellmath dwi.mif mean shellmeans.mif
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
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: Daan Christiaens (daan.christiaens@kcl.ac.uk)
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/.