Tools for MRI diffusion in human and non-human primates


Tools for MRI diffusion in human and non-human primates



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Brainhack Global 2021 Event

Brainhack Marseille

Project Description

There are many pipelines for processing diffusion MRI data (diffuse, qsiprep, mrtrix pipelines, FSL pipelines, dipy, Designer, etc.). For newcomers in the field of Diffusion MRI, it may be overwhelming to pick the tools that best fits the needs, as well as to define the needs themselves.

(NHP specific) : NHP image processing has specific challenges such as image reorientation, which can be more tricky when the Diffusion Vectors as to follow the transformation applied to the diffusion images.

We aim at sharing expertise, identify specific problems encountered by users, and define quality metrics (quality of orientation vectors, qualitative and quantitative quality check of processing stages)

(NHP specific) : We also aim at integrating segmentations computed externally to mrtrix and FSL pipelines, that are non-specific pipelines (i.e. also available for human images)


Communication channels :

Programed schedule

Tuesday 7th December, 2pm CET : discussion on tools and pipelines for MRI diffusion processing

Good first issues

  1. Share your experience with Diffusion MRI
  2. Share the difficulties you encountered with Diffusion MRI processing


Onboarding documentation

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What will participants learn?

Participant will learn about all the wonderful tools are already present out there and hopefully they will find the ones that best fit their needs. They may also find new solutions to process diffusion in NHP (non-human primate) images.

Data to use

No response

Number of collaborators


Credit to collaborators

Project contributor are listed on the README file of the project GitHub page




coding_methods, documentation, pipeline_development

Development status



connectome, data_visualisation, diffusion, MR_methodologies, reproducible_scientific_methods, tractography


DIPY, Freesurfer, FSL, Jupyter, MRtrix, Nipype

Programming language

containerization, documentation, Python, shell_scripting, unix_command_line



Git skills

0_no_git_skills, 1_commit_push

Anything else?

No response

Things to do after the project is submitted and ready to review.

Jan 1, 0001 12:00 AM