【MRtrix】拡散MRIからb値ごとに画像を抽出

SYNOPSIS

     Extract diffusion-weighted volumes, b=0 volumes, or certain shells from a
     DWI dataset

USAGE

     dwiextract [ options ] input output

        input        the input DW image.

        output       the output image (diffusion-weighted volumes by default).


EXAMPLE USAGES

     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.

OPTIONS

  -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)

Stride options

  -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.

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 (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.