Processing steps

TractoFlow pipeline consist of 23 different steps : 14 steps for the diffusion weighted image (DWI) processing and 8 steps for the T1 weighted image processing.



  • Diffusion weighted image (DWI)

  • b-values

  • b-vectors

  • T1 weighted image

  • Reverse phase encoding B0 (Optional)

DWI processes

  • Brain extraction (FSL)

  • Denoising (Mrtrix3)

  • Topup (FSL)

  • Eddy (FSL)

  • N4 bias correction (ANTs)

  • Resample (Dipy)

  • DTI metrics (Dipy)

  • fODF metrics (Dipy)

T1 processes

  • Brain extraction (ANTs)

  • Denoising (Dipy)

  • N4 bias correction (ANTs)

  • Resample (Dipy)

  • Registration (ANTs)

  • Tissue segmentation (FSL)


  • Particule Filter Tractography

  • Local tracking (Optional)

The particle filter tractography is performed by default. Three types of seeding are available: WM-GM interface, WM mask or FA.