Nobrainer and Nobrainer-Zoo: A 3D Deep Learning based Image Analysis Framework and model repository

Title

Nobrainer and Nobrainer-Zoo: A 3D Deep Learning based Image Analysis Framework and model repository

Leaders

• Satrajit Ghosh,
• Dorota Jarecka,
• Hoda Rajaei,
• Aakanksha Rana,
• Dhritiman Das

Collaborators

Patrick McClure

Brainhack Global 2021 Event

Brainhack MIT

Project Description

Nobrainer is a deep learning toolbox for 3D neuroimaging data analysis. It includes many deep learning tools including data preprocessing pipelines, various model structures, trained models, etc. In this brainhack, we are going to extend various aspects of this toolbox. It spans from data curation to adding new implementations to the toolbox.

Link to project repository/sources

• https://github.com/neuronets/nobrainer
• https://github.com/neuronets/zoo

Goals for Brainhack Global

Accomplish these 5 mini projects

https://github.com/neuronets/Brainhack-MIT-Neuro/issues

Good first issues

1. issue one: Develop ipynb of develop mini functionalities.

2. issue two: Curate the dataset to run with the ipynbs

Communication channels

https://mattermost.brainhack.org/brainhack/channels/brainhack-mit-neuro

Skills

• Python: Intermediate

Not Required but is a plus:

• Datalad
• Tensorflow-basics

Onboarding documentation

na

What will participants learn?

deep learning, MRI data preprocessing, containers

Data to use

openneuro

Number of collaborators

3

Credit to collaborators

Contribution will be highlighted in Nobrainer repo.

Image

https://github.com/neuronets/mit-brainhack2021/blob/main/assets/img/image1.gif

Type

coding_methods, data_management, documentation, tutorial_recording, visualization

Development status

1_basic structure

Topic

data_visualisation, deep_learning, diversity_inclusivity_equality, MR_methodologies

Tools

Datalad, Tensorflow, Nobrainer

Programming language

Python, html_css

Modalities

MRI

Git skills

1_commit_push

Anything else?

na

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.