1. 目的
2. コマンド
3. 使用例
3.1. 前準備
3.2. 拡散MRIのバイアス(信号ムラ)補正

1. 目的

  • MRtrixを用いた拡散MRIのバイアス(信号ムラ)補正

2. コマンド





     Perform B1 field inhomogeneity correction for a DWI volume series


     dwibiascorrect [ options ] algorithm ...

        algorithm    Select the algorithm to be used to complete the script operation;
                     additional details and options become available once an
                     algorithm is nominated. Options are: ants, fsl

Options for importing the diffusion gradient table

  -grad GRAD
     Provide the diffusion gradient table in MRtrix format

  -fslgrad bvecs bvals
     Provide the diffusion gradient table in FSL bvecs/bvals format

Options common to all dwibiascorrect algorithms

  -mask image
     Manually provide a mask image for bias field estimation

  -bias image
     Output the estimated bias field

Additional standard options for Python scripts

     do not delete intermediate files during script execution, and do not delete
     scratch directory at script completion.

  -scratch /path/to/scratch/
     manually specify the path 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

     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.

  -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.


dwibiascorrect ants <入力画像> <出力画像>



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



dwibiascorrect ants DWI.mif DWI_unbiased.mif -bias bias.mif


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