Neuroimaging Cookbook 🧠🍳📓

Project info

Title: Neuroimaging Cookbook 🧠🍳📓 image

Project lead: Shawn Rhoads GitHub: @shawnrhoads Twitter: @ShawnRhoads56 Mattermost: shawnrhoads

If you are reading this because of Brainhack MTL 2020ish, feel free to contact @SamGuay if you have any question! Twitter: @SamGuay_ Mattermost: SamGuay_

Project collaborators: TBD! Contributions of any kind are welcome!

Registered Brainhack Global 2020 Event: Brainhack DC

Brainhack MTL 2020ish

Project Description: Anyone ever Google how to accomplish a task for neuroimaging data more than once? For example, I’ve Googled “how to extract a mask from a parcellation scheme” or “how to output the time series from an ROI to a .csv file” hundreds of times because I can’t remember the exact command/function or flags to pass (and every time I am reminded just how many times I’ve visited the same webpages): image

There are countless software packages with widely different commands and options to perform all sorts of different functions when working with neuroimaging data. But remembering them all is nearly impossible!

The Neuroimaging Cookbook will centralize “code snippets” (or “recipes”) for different, specific, and simple tasks in neuroimaging that people can incorporate in their own analysis pipelines. And most importantly, it would be scalable so that anyone can contribute their random, useful code snippet.

The idea is inspired by 30 Seconds of Code (specifically, 30 Seconds of Python), where people can easily reference code (across software) for different neuroimaging tasks like: how to convert across different image formats (e.g., BRIK/HEAD, img/hdr, nii, etc), flatten the lower triangle of a representational similarity matrix, extract a mask from a parcellation, output the time-series from an ROI to a .csv /.txt file, etc. Not exactly tutorials, but “code snippets” that people can adapt for their own scripts, apps, or Jupyter Notebooks.

Data to use: N/A

Link to project repository/sources:

Goals for Brainhack Global 2020: Easy:


Good first issues:

  1. Create first batch of recipes for use in the cookbook (Team 1)
  2. Develop the cookbook webpage (Team 2)

Skills (at least one of these):

Tools/Software/Methods to Use:

Communication channels:

Project labels

Project Submission

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Contributions: All contributions will be recognized in the cookbook and follow the all-contributors specification. Contributions of any kind are welcome!

Jan 1, 0001 12:00 AM