Nobrainer: a python framework for neuroimaging data

[Hoda1394]

Project info

Title: Nobrainer: a python framework for neuroimaging data

Project lead: Hoda Rajaei: @Hoda1394 Aakankhsa Rana: @Aakanksha-Rana Dhritiman Das: @dhritimandas Satragit Ghosh:@satra

Timezone: -5UTC (Atlantis)

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 hackathon project, we are going to extend various aspects of this toolbox. This project has different parts depending on your skills. It spans from data curation to adding new implementations to the toolbox.

Link to project: (https://github.com/neuronets/nobrainer)

Mattermost handle: hoda, aakanksha-rana

Goals for the OHBM Brainhack

• Creating benchmark dataset: Organizing a diverse structural imaging data using Openneuro data or any other data platforms for segmentation problem
• Curation and preprocessing: Curation and preprocessing the imaging data
• Visualizatio: Visualizations of input and outputs with nobrainer framework
• Tutorials: Create Nobrainer tutorials

Good first issues: The plan is to first organize a dataset which will consist of structural imaging corresponding to different sequences, sites/scanners, age-groups, and Neurological Disorders. The steps would include planning, organizing, downloading, preprocessing and packaging (in tfrecords type of format) of available the opensource images. The goal of this project is to build algorithms that are robust to different variations observed in images.

Skills: Based on the project goals

• Creating benchmark dataset: bginner pthon, pandas
• Curation and preprocessing: pandas, numpy, nibabel
• Visualization: beginner python, nilearn, nibabel
• Toturials: jupyter notebook or google collab, familiarity with deep learning is preferable

Chat channel:

Image for the OHBM brainhack website

Project submission

Submission checklist

Once the issue is submitted, please check items in this list as you add under 'Additional project info'

Please include the following above (all required):

• [x] Link to your project: could be a code repository, a shared document, etc. See here
• [x] Include your Mattermost handle (i.e. your username). If you do not have an account, please sign up here.
• [x] Goals for the OHBM Brainhack: describe what you want to achieve during this brainhack. See here.
• [x] Flesh out at least 2 "good first issues": those are tasks that do not require any prior knowledge about your project, could be defined as issues in a GitHub repository, or in a shared document, cf here.
• [x] Skills: list skills that would be particularly suitable for your project. We ask you to include at least one non-coding skill, cf. here.
• [x] Chat channel: A link to a chat channel that will be used during the OHBM Brainhack. This can be an existing channel or a new one. We recommend using the Brainhack space on mattermost, cf. here.
• [x] Provide an image of your project for the OHBM brainhack website

You can also include information about (all optional):

• [ ] Someone co-leading the project in the timeslot you have not selected to provide additional visibility.
• [ ] Number of participants, cf. here
• [ ] Twitter-size summary of your project pitch, cf. here
• [ ] Set up a kanban board on your repository to better divide the work and keep track of things, cf here
• [ ] Project snippet for the OHBM Brainhack website, cf. here

We would like to think about how you will credit and onboard new members to your project. We recommend reading references from this section. If you'd like to share your thoughts with future project participants, you can include information about (recommended):

• [ ] Specify how will you acknowledge contributions (e.g. listing members on a contributing page).
• [ ] Provide links to onboarding documents if you have some.

QMENTA has agreed to sponsor the event and provide computational resources through their platform.

• [ ] Get in touch with QMENTA through their Brain Innovation Hub Slack space, if you think your project would benefit from their support.

[Hoda1394]

hi @ohbm/project-monitors: My project is ready!

[tiborauer]

Could you also provide an image, please?

[Hoda1394]

@tiborauer- added an image.