1. 目的
2. コマンド

1. 目的

  • 拡散MRIからb値ごとに画像を抽出

2. コマンド




     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


     Output b=0 volumes (instead of the diffusion weighted volumes, if
     -singleshell is not specified).

     Output only non b=0 volumes (default, if -singleshell is not specified).

     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

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

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

     display information messages.

     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.

     display debugging messages.

     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.

     display this information page and exit.

     display version information and exit.


dwiextract -bzero <入力画像> <出力画像>  # b=0のみを抽出
dwiextract -no_bzero <入力画像> <出力画像>  # b=0以外の拡散強調像を抽出
dwiextract -singleshell <入力画像> <出力画像>  # b=0以外の拡散強調像を抽出

3. 使用例

3.1. 前準備

まず、こちらの記事を参考に、拡散MRI(DWI.nii.gz)とそのMPG軸情報(bvecs, bvals)とヘッダー情報(headers.json)をまとめて、MIF形式(DWI.mif)に変換する。

mrconvert -fslgrad bvecs bvals -json_import headers.json DWI.nii.gz DWI.mif

ここで使用する拡散MRI(DWI.mif)は、b=0が1枚、b=1000が64枚、b=2000が64枚で構成されている(全部で129 volumes)。

mrinfo DWI.mif  |grep Dimensions
Dimensions:        130 x 130 x 82 x 129

3.2. b=0のみを抽出


dwiextract -bzero DWI.mif DWI_b0.mif


mrinfo DWI_b0.mif  |grep Dimensions
Dimensions:        130 x 130 x 82 x 1

3.3. b≠0を抽出


dwiextract -no_bzero DWI.mif DWI_nonb0.mif


mrinfo DWI_nonb0.mif  |grep Dimensions
Dimensions:        130 x 130 x 82 x 128

3.4. b値ごとに抽出



dwiextract -shells 1000 DWI.mif DWI_b1000.mif


mrinfo DWI_b1000.mif  |grep Dimensions
Dimensions:        130 x 130 x 82 x 64

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