Processing steps

MouseFlow pipeline consist of 9 different steps for the diffusion weighted image (DWI) processing.

../_images/mouseflow_graph.png

Input

  • Diffusion weighted image (DWI)

  • b-values

  • b-vectors

DWI processes

  • Brain extraction (FSL)

  • Denoising (Mrtrix3)

  • Eddy (FSL)

  • N4 bias correction (ANTs)

  • Resample (Dipy)

  • DTI metrics (Dipy)

  • QBALL metrics (Dipy)

Tractography

  • Local tracking