Extract diffusion-weighted volumes, b=0 volumes, or certain shells from a DWI dataset
dwiextract [ options ] input output
- input: the input DW image.
- output: the output image (diffusion-weighted volumes by default).
Calculate the mean b=0 image from a 4D DWI series:
$ dwiextract dwi.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3
The dwiextract command extracts all volumes for which the b-value is (approximately) zero; the resulting 4D image can then be provided to the mrmath command to calculate the mean intensity across volumes for each voxel.
- -bzero Output b=0 volumes (instead of the diffusion weighted volumes, if -singleshell is not specified).
- -no_bzero Output only non b=0 volumes (default, if -singleshell is not specified).
- -singleshell Force a single-shell (single non b=0 shell) output. This will include b=0 volumes, if present. Use with -bzero to enforce presence of b=0 volumes (error if not present) or with -no_bzero to exclude them.
DW gradient table import options¶
- -grad file Provide the diffusion-weighted gradient scheme used in the acquisition in a text file. This should be supplied as a 4xN text file with each line is in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the applied gradient, and b gives the b-value in units of s/mm^2. If a diffusion gradient scheme is present in the input image header, the data provided with this option will be instead used.
- -fslgrad bvecs bvals Provide the diffusion-weighted gradient scheme used in the acquisition in FSL bvecs/bvals format files. If a diffusion gradient scheme is present in the input image header, the data provided with this option will be instead used.
DW shell selection options¶
- -shells b-values specify one or more b-values to use during processing, as a comma-separated list of the desired approximate b-values (b-values are clustered to allow for small deviations). Note that some commands are incompatible with multiple b-values, and will report an error if more than one b-value is provided.
WARNING: note that, even though the b=0 volumes are never referred to as shells in the literature, they still have to be explicitly included in the list of b-values as provided to the -shell option! Several algorithms which include the b=0 volumes in their computations may otherwise return an undesired result.
DW gradient table export options¶
- -export_grad_mrtrix path export the diffusion-weighted gradient table to file in MRtrix format
- -export_grad_fsl bvecs_path bvals_path export the diffusion-weighted gradient table to files in FSL (bvecs / bvals) format
Options for importing phase-encode tables¶
- -import_pe_table file import a phase-encoding table from file
- -import_pe_eddy config indices import phase-encoding information from an EDDY-style config / index file pair
Options for selecting volumes based on phase-encoding¶
- -pe desc select volumes with a particular phase encoding; this can be three comma-separated values (for i,j,k components of vector direction) or four (direction & total readout time)
- -strides spec specify the strides of the output data in memory; either as a comma-separated list of (signed) integers, or as a template image from which the strides shall be extracted and used. The actual strides produced will depend on whether the output image format can support it.
- -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 (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).
- -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.
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
Copyright: Copyright (c) 2008-2020 the MRtrix3 contributors.
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For more details, see http://www.mrtrix.org/.