1. 目的
2. コマンド
3. 使用例
3.1. FSLアルゴリズムを用いる場合
3.2. FreeSurferアルゴリズムを用いる場合
4. 結果

1. 目的

  • MRtrixを用いた5TT(five-tissue-type)画像の生成

2. コマンド

MRtrixの5ttgenを用いて、次の5つの組織(five-tissue-type: 5TT)画像を生成する。

  1. Cortical grey matter
  2. Sub-cortical grey matter
  3. White matter
  4. CSF
  5. Pathological tissue



     Generate a 5TT image suitable for ACT


     5ttgen [ 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: freesurfer, fsl, gif,


     5ttgen acts as a 'master' script for generating a five-tissue-type (5TT)
     segmented tissue image suitable for use in Anatomically-Constrained
     Tractography (ACT). A range of different algorithms are available for
     completing this task. When using this script, the name of the algorithm to
     be used must appear as the first argument on the command-line after
     '5ttgen'. The subsequent compulsory arguments and options available depend
     on the particular algorithm being invoked.

     Each algorithm available also has its own help page, including necessary
     references; e.g. to see the help page of the 'fsl' algorithm, type '5ttgen

Options common to all 5ttgen algorithms

     Do NOT crop the resulting 5TT image to reduce its size (keep the same
     dimensions as the input image)

     Represent the amygdalae and hippocampi as sub-cortical grey matter in the
     5TT image

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.

基本的な使い方は、以下の通り。5ttgenのアルゴリズムは、freesurfer, fsl, gif, hsvsがあるが、ここではfreesurferとfslのアルゴリズムについて使い方を解説する。

5ttgen [アルゴリズム] <入力画像> <出力画像>

3. 使用例

3.1. FSLアルゴリズムを用いる場合


5ttgen fsl T1w.nii.gz 5tt.nii.gz

3.2. FreeSurferアルゴリズムを用いる場合




5ttgen freesurfer aparc+aseg.mgz 5tt.nii.gz

4. 結果


  1. Cortical grey matter
  2. Sub-cortical grey matter
  3. White matter
  4. CSF
  5. Pathological tissue


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