Fast Tractography Streamline Search

[StongeEtienne]

Title

Fast Tractography Streamline Search.

• Hierarchical search using a space partitioning tree (binary search tree / KD-tree ).
• Using an adapted distance measure (Entry-wise matrix distance).

Leaders

Etienne St-Onge ( estonge in mattermost)

Collaborators

No response

Brainhack Global 2021 Event

Brainhack Montreal

Project Description

Create a repository for a Fast tractography / streamline search method.
And develop useful scripts / methods.

Link to project repository/sources

https://github.com/StongeEtienne/tractography-search

Goals for Brainhack Global

• Find an optimized space partitionning tree that can be adapted (Nanoflann).
• Adapt distances adapted for tractography streamlines (L21 entry-wise).
• Create, adapt and optimize the search function, (C++, with python "binder").
• Discuss & choose a Library architecture / structure.
• Create usefull scripts to search streamlines within a tractogram.
• Clustering algorithms using a sparse distance matrix.

Good first issues

1. issue one: Discuss about the project (how can you help with this project or learn about tractography).
2. issue two: Code or improve functions to search for similar streamlines.
3. issue three: Create scripts and utlity functions.

Communication channels

https://mattermost.brainhack.org/brainhack/channels/tractography-search

Skills

• Python : Any level (want to learn python for diffusion / tractography ?)
• Python : Intermediate (want to do streamline clustering ?)
• C++ : Intermediate (want to improve / optimize "core" functions)

Onboarding documentation

No response

What will participants learn?

How to interact with streamlines / tractography in python. (Dipy / ScilPy / Tractoflow)

Data to use

No response

Number of collaborators

3

Credit to collaborators

To define !

Image

Type

method_development

Development status

0_concept_no_content

Topic

connectome, diffusion, tractography

Tools

DIPY

Programming language

C++, Python

Modalities

DWI

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.

[Remi-Gau]

@StongeEtienne let me know if I should put this on the website by pinging @brainhackorg/project-monitors

[StongeEtienne]

@Remi-Gau
Feel free to do it, if you want or think it will be useful to others, (or to give more visibility)

[Remi-Gau]

OK will do.

One small suggestion: would be good to create actual issues on your repo to provide a "forum" to guide new comers and answer their questions.