Tools for MRI diffusion in human and non-human primates

[julfou81]

Title

Tools for MRI diffusion in human and non-human primates

Leaders

• Julien Sein (@julfou81)
• David Meunier
• Arnaud Le Troter
• Hugo Dary

Collaborators

No response

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)

Skills:

• MRI diffusion (general knowledge) 50%
• MRI processing 50%
• pipelining (30-70%)

Communication channels :

• https://mattermost.brainhack.org/brainhack/channels/mri_diffusion
• https://github.com/Centre-IRM-INT/MRI_Diffusion
• https://univ-amu-fr.zoom.us/j/92141093977?pwd=cEorbHI3bzVFZlVwSE9FRVZiaUNGZz09

Programed schedule

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

Link to project repository/sources

https://github.com/Centre-IRM-INT/MRI_Diffusion

Good first issues

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

Skills

• MRI diffusion (general knowledge) 50%
• MRI processing 50%
• pipelining (30-70%)

Onboarding documentation

No response

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

more

Credit to collaborators

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

Image

Type

coding_methods, documentation, pipeline_development

Development status

0_concept_no_content

Topic

connectome, data_visualisation, diffusion, MR_methodologies, reproducible_scientific_methods, tractography

Tools

DIPY, Freesurfer, FSL, Jupyter, MRtrix, Nipype

Programming language

containerization, documentation, Python, shell_scripting, unix_command_line

Modalities

DWI, MRI

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.

• Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
• Twitter-sized summary of your project pitch.

[julfou81]

Hi @brainhackorg/project-monitors my project is ready!

[julfou81]

Twitter summary:

BrainHack Marseille: Tools for MRI Diffusion in human and non-human primates.
We aim at sharing expertise, identify specific problems encountered by users, and to define quality metrics along different processing steps.

[Remi-Gau]

I assume this has been cross checked by the Organizers in Marseille: will proceed to publishing accordingly.

[julfou81]

Hi @Remi-Gau, thanks! Yes it is an official project from BrainHack Marseille: project number 8:
https://brainhack-marseille.github.io