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BIDS Curation GUI #188

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9 of 14 tasks
AndysWorth opened this issue Jun 13, 2020 · 13 comments
Open
9 of 14 tasks

BIDS Curation GUI #188

AndysWorth opened this issue Jun 13, 2020 · 13 comments
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Americas hub BIDS some knowledge of BIDS required docker / singularity some knowledge of docker / singularity required documentation Improvements or additions to documentation git-1 can commit and push to a repository GUI Work on the Graphic User Interface Hackathon project use this tag for submitted projects javascript some knowledge of javascript required Missing reg MR Methodologies some knowledge of MR technologies required neuroimaging neuroimaging data python some knowledge of python required visualization web frameworks web development frameworks or stacks
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@AndysWorth
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AndysWorth commented Jun 13, 2020 •
edited by DorienHuijser

Project info

Title:
BIDS Curation GUI - A Graphical User Interface to help with BIDS Curation

Project lead:
Maggie Mahan @margaretmahan, Andy Worth @AndysWorth

Timezone:
UTC-5

Hub:
The Americas

Description:
Getting data into the Brain Imaging Data Structure (BIDS) format is non-trivial. Ideally, you set scan acquisition parameters in preparation for BIDS, but mistakes will be made. Non-ideally, you have an old set of scans you want to BIDSify. Wouldn't it be great if you could "see" the entire situation so you can easily locate and understand the problems? Wouldn't you like this picture to come alive to help you curate your data?

DICOM folders to BIDS hierarchy

Link to project:
https://github.com/AndysWorth/BIDS-Curation-GUI

Mattermost handle:
https://mattermost.brainhack.org/brainhack/channels/hbmhack-bids-gui

Goals for the OHBM Brainhack

  • Find out how a GUI can help understand and detect errors in BIDS curation.
  • Learn new skills
  • Contribute to reproducible research

Good first issues:

  • Refine project goals and technology to use
  • Establish basic GUI using React
  • Establish basic workflow based on ReproIn, HeuDiConv, and the BIDS-Validator
  • Create project logo
  • Initial artwork for the GUI

Skills:

  • BIDS, Python, Docker, git
  • React, JavaScript
  • Familiarity with MRI data acquisition and how it can go wrong.
  • Graphic design

Chat channel:
https://mattermost.brainhack.org/brainhack/channels/hbmhack-bids-gui

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):

  • Link to your project: could be a code repository, a shared document, etc. See here
  • Include your Mattermost handle (i.e. your username). If you do not have an account, please sign up here.
  • Goals for the OHBM Brainhack: describe what you want to achieve during this brainhack. See here.
  • 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.
  • Skills: list skills that would be particularly suitable for your project. We ask you to include at least one non-coding skill, cf. here.
  • 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.
  • Video channel: Please create a video channel that will be used during the OHBM Brainhack and share it in your chat channel above. This can be an existing channel or a new one. For instance a jitsi meet room, cf. here.
  • Provide an image of your project for the OHBM brainhack website

You can also include information about (all optional):

  • 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.
@AndysWorth AndysWorth added the Hackathon project use this tag for submitted projects label Jun 13, 2020
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welcome bot commented Jun 13, 2020

Welcome Banner (Image: CC-BY license, The Turing Way Community, & Scriberia. Zenodo. http://doi.org/10.5281/zenodo.3332808)
🎉 Welcome to the 2020 OHBM Hackathon! 🎉 We're really excited to have your input on this repository and welcome your idea! 💖 If you haven't done so already, please make sure you check out our Code of Conduct. Did you issue a new hackathon project? Please check if you have provided all relevant information and an image for the website.

@Remi-Gau Remi-Gau added this to Submitted in Project revision Jun 13, 2020
@Remi-Gau Remi-Gau moved this from Submitted to Add to website in Project revision Jun 13, 2020
@Remi-Gau Remi-Gau added Americas hub documentation Improvements or additions to documentation git-0 no prior git knowledge required GUI Work on the Graphic User Interface javascript some knowledge of javascript required labels Jun 13, 2020
@Remi-Gau
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Hey
Added some labels. Make sure they are OK with you.
Technically your project does not require any git knowledge, correct?

@AndysWorth
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Hey, thanks for the labels! I guess I should add git to the skilz.

@Remi-Gau Remi-Gau added git-1 can commit and push to a repository and removed git-0 no prior git knowledge required labels Jun 13, 2020
@jhlegarreta jhlegarreta added the web frameworks web development frameworks or stacks label Jun 13, 2020
@AndysWorth
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hi @ohbm/project-monitors: My project is ready, thanks!

@complexbrains complexbrains added BIDS some knowledge of BIDS required docker / singularity some knowledge of docker / singularity required MR Methodologies some knowledge of MR technologies required neuroimaging neuroimaging data python some knowledge of python required visualization labels Jun 13, 2020
@complexbrains complexbrains moved this from Add to website to Needs revision in Project revision Jun 13, 2020
@complexbrains
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complexbrains commented Jun 13, 2020 •
edited

Dear @AndysWorth Thank you very much for your project submission. Would you mind sharing a snippet regarding your project if you want it to be listed on the https://ohbm.github.io/hackathon2020/ webpage, please?

I also added several more labels to your project so please do have a look at them and if you are not happy with them please let us know.

As soon as we got them from you the review procedure will be completed and your project will be ready for the Brainhack!

We look forward to hearing from you.

@complexbrains complexbrains moved this from Needs revision to Add to website in Project revision Jun 13, 2020
@jhlegarreta
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@complexbrains Maggie and Andy are already doing it in PR #191 ! 🎉

@Remi-Gau Remi-Gau moved this from Add to website to Needs revision in Project revision Jun 14, 2020
@jhlegarreta
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@AndysWorth do you have a video channel for your project? Would you add that information to the mattermost channel, please? Thanks.

@complexbrains
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Dear @AndysWorth would you mind creating and sharing your video chat link in your Mattermost channel please? Once you are done that, please let us know then we will close the revision process for you and you will be ready to go! Thank you 🤗

@complexbrains complexbrains moved this from Needs revision to Revision in progress in Project revision Jun 15, 2020
@AndysWorth
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AndysWorth commented Jun 15, 2020 •
edited by complexbrains

Removed

@complexbrains
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@AndysWorth I removed the link for any unwanted interference! I saw you already shared it in your Mattermost channel. Then I will complete the revision. Thank you so much! Welcome aboard!

@complexbrains complexbrains moved this from Revision in progress to Done in Project revision Jun 15, 2020
@AndysWorth
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I put a password on the video chat. So, do people just leave the chat up all of the time?

@cmaumet
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cmaumet commented Jun 15, 2020

Hi @margaretmahan! Thanks a lot for your project. Unless I am mistaken, In think that your are not registered yet to the event. Can you please register as soon as possible? Thank you!

@margaretmahan
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margaretmahan commented Jun 16, 2020 via email

@tsalo tsalo mentioned this issue Jun 16, 2020
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Americas hub BIDS some knowledge of BIDS required docker / singularity some knowledge of docker / singularity required documentation Improvements or additions to documentation git-1 can commit and push to a repository GUI Work on the Graphic User Interface Hackathon project use this tag for submitted projects javascript some knowledge of javascript required Missing reg MR Methodologies some knowledge of MR technologies required neuroimaging neuroimaging data python some knowledge of python required visualization web frameworks web development frameworks or stacks
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@cmaumet @jhlegarreta @Remi-Gau @margaretmahan @AndysWorth @complexbrains