Tools for MRI diffusion in human and non-human primates
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
- Share your experience with Diffusion MRI
- 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.