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TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity
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jchoude Merge pull request #2 from GuillaumeTh/ENH_mask_normalization
ENH compute a WM mask for normalization
Latest commit 1ad0b78 May 8, 2019

TractoFlow pipeline

The TractoFlow pipeline is a fully automated and reproducible dMRI processing pipeline. TractoFlow takes raw DWI, b-values, b-vectors, T1 weighted image (and a reversed phase encoded b=0 if available) to process DTI, fODF metrics and a whole brain tractogram.


TractoFlow documentation is available here:

This documentation presents how to install and launch TractoFlow on a local computer and a High Performance Computer.

If you are a user and NOT A DEVELOPER, we HIGHLY RECOMMEND following the instructions on the documentation website.


If you are on Linux, we recommend using the Singularity container to run TractoFlow

Prebuild Singularity images are available here:

FOR DEVELOPERS: The Singularity repository is available here: singularity-TractoFlow


If you are on MacOS or Windows, we recommend using the Docker container to run TractoFlow

Prebuilt Docker images are available here:


Diffusion processes

  • preliminary DWI brain extraction (FSL)
  • denoise DWI (Mrtrix3)
  • topup (FSL)
  • eddy (FSL)
  • extract B0 (Scilpy)
  • dwi brain extraction (FSL)
  • N4 DWI (ANTs)
  • crop DWI (Scilpy)
  • upsample DWI (Scilpy)
  • upsample B0 (Scilpy)

T1 processes

  • denoise T1 (Scilpy)
  • N4 T1 (ANTs)
  • resample T1 (Scilpy)
  • T1 brain extraction (ANTs)
  • crop T1 (Scilpy)
  • registration on diffusion (ANTs)
  • tissue segmentation (FSL)

Metrics processes

  • extract DTI shells (configurable in nextflow.config) (Scilpy)
  • dti metrics (Scilpy)
  • extract fODF shells (configurable in nextflow.config) (Scilpy)
  • compute fiber response function (Scilpy)
  • mean fiber response function (Scilpy)
  • fODF and fODF-derived metrics (Scilpy)
  • particle filter tractography maps (Scilpy)
  • seeding mask (Scilpy)
  • particle filter tracking (Scilpy)


See USAGE or run nextflow run --help


To refer to TractoFlow, please see References section on TractoFlow documentation

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