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.

../_images/tractoflow_graph.png

Input

  • 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)

Tractography

  • 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.