Open jerdra opened 2 years ago
Hi @brainhackorg/project-monitors my project is ready!
For Twitter:
Niviz: Tired of neuroimaging QC being slow, manual, and painful? Want to contribute to, and shape the development of a relatively new project? Niviz and Niviz-Rater are companion apps that were developed to help streamline neuroimaging QC through (1) Automating image generation with a simple config file (2) Providing a simple web interface to facilitate the QC process and handling all the boring stuff behind the scenes!
Hi @jerdra, I recently stumbled across these projects (niviz and niviz-rater) while prepping for another Brainhack. I thought you might find our web-based image viewer project interesting given the interactive QC work you're doing. We have some Vue, React, and vanilla JS examples.
https://github.com/niivue/niivue
If you have any suggestions, feel free to submit an issue on our repo page.
@jedra: @cdrake and I are NiiVue contributors. We will both be virtually attending the BrainHack DC, which will be held concurrently with BrainHack Toronto. I think there is a lot of opportunity for collaboration.
Hi @hanayik and @neurolabusc!
Thanks for posting in this issue, all the work you've listed looks incredibly well thought out! I'd be more than happy to sit in for a brainstorming session and share our works with each other. I'm a bit pressed for time today but happy to drop in over the next two days if you have a session planned :) Should we open up a channel on mattermost for general QC discussion and perhaps planning?
If you're interested in learning more about niviz, the Toronto hack is planning tool demos tomorrow 10:30-12:00pm EST, schedule is posted here: https://brainhackto.github.io/global-toronto-12-2021/. I'd love to hear your thoughts, feedback and perhaps ideas on how we can work together
Finally, I haven't had the chance to look too deeply into niivue
and niimath
but from a high-level view it looks like we're approaching QC from a slightly different standpoint, so I'm very interested to learn more about your approach and vision over the coming days
Title
Niviz: Configurable quality control image generation and rating
Leaders
Jerrold Jeyachandra @jerdra
Collaborators
None
Brainhack Global 2021 Event
BrainHack Toronto
Project Description
The process of QCing is universally boring, terrible and inefficient.
The Problem with QC
Most pipelines people write and use don't generate QC images, especially those that are as user-friendly as widely established pipelines such as fMRIPREP
Even then, the QC images that are generated do not necessarily match how users end up QC'ing and rating images.
Most of the time users must figure out their own way to record and organize their QC results, this is incredibly variable across individuals. Your collaborator might use differing definitions, organizational principles, and file formats for storing their QC results than you.
Comparing rated images is often slow, manual and therefore painful. Often-times users have doubt about their ratings and would want to compare it to other images with the same rating. Doing this is often a very manual process (i.e lookup similar QC ratings on your spreadsheet, find file, open both images and compare)
The Solution - Niviz
Niviz is a simple, configurable Python-based tool that:
niviz-rater
that collects generated QC images (or any set of images organized in a BIDS-style dataset!!!) into an interactive QC interface. In addition, QC can be configured to suit the user's needs using (yet another) simple YAML file.Link to project repository/sources
QC image generation
https://github.com/TIGRab/niviz
QC web application
https://github.com/jerdra/niviz-rater
Goals for Brainhack Global
Both niviz and niviz-rater are relatively new projects and therefore require a bit of maintenance and organizational effort. The primary goals are as follows:
Niviz
Niviz Rater
Good first issues
Issues can be found under:
https://github.com/TIGRLab/niviz/issues
https://github.com/jerdra/niviz-rater/issues
Look for the
good first issue
label for easy topics!Communication channels
https://mattermost.brainhack.org/brainhack/channels/brainhack-toronto
We'll probably create our own channel if this picks up interest :)
Skills
The repositories are primarily written in Python and Javascript, these components are mostly independent from one another so you don't need to know both!
Python
Intermediate
Git
Intermediate
Javascript
Familiarity with Svelte framework is preferred. I'm still learning myself!
Onboarding documentation
Contributing
What will participants learn?
Depending on which repository you contribute to:
Niviz
Niviz-Rater
Bottle
for building python web applicationspeewee
Data to use
As part of contributing to the documentation efforts of this project, we'd like to host some OSF sample data.
Niviz
Some image data from a pipeline like fMRIPrep
Niviz-Rater
Some QC image data so that users can play around with writing a YAML specification file and using the QC interface
Number of collaborators
3
Credit to collaborators
Project contributers will be included using the GitHub allcontributors bot. I'm still setting this up :see_no_evil:
Image
Leave this text if you don't have an image yet.
Type
coding_methods, documentation, visualization
Development status
1_basic structure
Topic
data_visualisation, other
Tools
Nipype, other
Programming language
documentation, Python, html_css, javascript
Modalities
DWI, fMRI, MRI
Git skills
1_commit_push, 2_branches_PRs
Anything else?
No response
Things to do after the project is submitted and ready to review.
Hi @brainhackorg/project-monitors my project is ready!