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shimming-toolbox: Ecosystem for real-time shimming with MRI #128

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11 of 14 tasks
jcohenadad opened this issue Jun 4, 2020 · 22 comments
Open
11 of 14 tasks

shimming-toolbox: Ecosystem for real-time shimming with MRI #128

jcohenadad opened this issue Jun 4, 2020 · 22 comments
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Americas hub Hackathon project use this tag for submitted projects matlab some knowledge of matlab required Missing reg MR Methodologies some knowledge of MR technologies required
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@jcohenadad
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jcohenadad commented Jun 4, 2020 •
edited by DorienHuijser

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

Project info

The shimming-toolbox is open-source Matlab software enabling a variety of MRI shimming (magnetic field homogenization) techniques for use with custom "multi-coil" arrays or standard manufacturer-supplied hardware.
This project was initiated by the NeuroPoly Lab (Polytechnique Montréal) in collaboration with the Martinos Center for Biomedical Imaging (MGH / Harvard Medical School).

Title:
shimming-toolbox: Ecosystem for real-time shimming with MRI

Project lead:

Timezone:
UTC-5

Hub:
The Americas

Description:
A prerequisite to correcting/shimming the MR "b0" field is of course to measure it (commonly done using a dual-echo gradient-echo sequence). A recent paper by Fatnassi and Zaidi suggests that multi-echo (n>2) sequences may yield better accuracy and higher SNR. This brainhack project aims to implement multi-echo field mapping algorithms and assess their efficiency.

Link to project:
shimming-toolbox repository
shimming-toolbox website

Mattermost handle:
shimming-toolbox channel

Goals for the OHBM Brainhack
Implement B0 field mapping algorithms for more than 2 echoes

  • Selective weighted field-mapping (SWFM)
  • Linear least square fit (LLSf)

Good first issues:

Skills:

  • Matlab coding
  • MR physics (field mapping, phase unwrapping)

Chat channel:
shimming-toolbox Mattermost channel

Video Channel:

Please have a look at the Mattermost channel (pinned posts) for the URL of the video channel, or alternatively, please contact to @jcohenadad on Github.

Additional project info

Acknowledgments
Members contributing will be listed here

Links
Link to Fatnassi and Zaidi

Twitter project pitch
Neuropoly’s shimming-toolbox team participates in OHBM Brainhack Hackathon. This year’s project aims to implement multi-echo field mapping algorithms and assess their efficiency.
https://github.com/shimming-toolbox
@PolyNeuro
#OHBMHackathon #Brainhack #OHBM2020

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. 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.

You can also include information about (all optional):

  • Number of participants, cf. here
  • Twitter-size summary of your project pitch, cf. here
  • Provide an image of your project for the OHBM brainhack website
  • 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.
@jcohenadad jcohenadad added the Hackathon project use this tag for submitted projects label Jun 4, 2020
@gaspardcereza gaspardcereza mentioned this issue Jun 4, 2020
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14 tasks
@Remi-Gau Remi-Gau added this to Needs revision in Project revision Jun 6, 2020
@Remi-Gau Remi-Gau moved this from Needs revision to Submitted in Project revision Jun 6, 2020
@Remi-Gau Remi-Gau added this to To do in Twitter Kanban Jun 6, 2020
@llevitis
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llevitis commented Jun 7, 2020

Hi @jcohenadad - thanks so much for adding this project :)
We're advertising the projects on the hackathon website (https://ohbm.github.io/hackathon2020/hackathon/) - is there an image that you would like us to use for your project?

@llevitis llevitis moved this from Submitted to Needs revision in Project revision Jun 7, 2020
@jcohenadad
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@llevitis thank you so much for the quick review-- yes, definitely! we will add an image within the next 1-2 days.

@jcohenadad jcohenadad mentioned this issue Jun 7, 2020
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@complexbrains complexbrains added matlab some knowledge of matlab required MR Methodologies some knowledge of MR technologies required labels Jun 7, 2020
@Remi-Gau Remi-Gau removed this from To do in Twitter Kanban Jun 7, 2020
@gaspardcereza
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We're advertising the projects on the hackathon website (https://ohbm.github.io/hackathon2020/hackathon/) - is there an image that you would like us to use for your project?

Hi @llevitis here's the image we would like to use for the hackathon website:
shimming_toolbox_logo

Thank you :)

@Remi-Gau
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@DorienHuijser Can I let you take care of that one? 😄 🙏

This was referenced Jun 12, 2020
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@jcohenadad
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@Remi-Gau Twitter project pitch added 😊

@Remi-Gau
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Wow. Thanks. Will tweet right away.

@Remi-Gau Remi-Gau self-assigned this Jun 12, 2020
@cmaumet
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cmaumet commented Jun 13, 2020

Hi @jcohenadad ! Thanks a lot for your project. Unless I am mistaken, In think that part your project co-leads (Ryan Topfer, Gaspard Cereza, Jason Stockmann) are not registered yet to the event. Can you please ask them to register or list them as project collaborators if they are not joining the event? Thank you!

@jaystock
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jaystock commented Jun 13, 2020 via email

@cmaumet
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cmaumet commented Jun 13, 2020

@jaystock: Sure, here is the link: http://www.humanbrainmapping.org/HackathonReg/. There is no need to be registered to OHBM to attend the hackathon. Thanks!

@gaspardcereza
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Hi @jcohenadad ! Thanks a lot for your project. Unless I am mistaken, In think that part your project co-leads (Ryan Topfer, Gaspard Cereza, Jason Stockmann) are not registered yet to the event. Can you please ask them to register or list them as project collaborators if they are not joining the event? Thank you!

Hi Camille, I should already be registered. My OHBM ID is 42482. Can you check again for my registration ? Tell me if you need any additional info. Thanks !

@cmaumet
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cmaumet commented Jun 13, 2020

Thanks @gaspardcereza! I've just found your record. To finish your registration, I would need you to fill in the form over here. Is that okay for you? Thanks!

@gaspardcereza
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Thanks @gaspardcereza! I've just found your record. To finish your registration, I would need you to fill in the form over here. Is that okay for you? Thanks!

Done. Thank you !

@complexbrains
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Dear @jcohenadad and @aspardcereza I added the link of your video chat room to your Mattermost channel. So your project is ready to go! Welcome aboard!

@complexbrains complexbrains moved this from Needs revision to Done in Project revision Jun 15, 2020
@cmaumet
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cmaumet commented Jun 15, 2020

Hi @jcohenadad ! Unless I am mistaken, I think that your co-lead Jason Stockmann is still not registered to the event. Can you please ask them to register or list them as project collaborators if they are not joining the event? Thank you!

@jcohenadad
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Hi @jcohenadad ! Unless I am mistaken, I think that your co-lead Jason Stockmann is still not registered to the event. Can you please ask them to register or list them as project collaborators if they are not joining the event? Thank you!

hi, he has been informed

@jaystock
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jaystock commented Jun 15, 2020 via email

@cmaumet
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cmaumet commented Jun 15, 2020

Oh @jaystock, thanks for that! All you need to do now to complete your registration now is to fill in the form here to provide us with important additional info. Thank you!

@jaystock
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jaystock commented Jun 15, 2020 via email

@tashrifbillah
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Interested to work on it!

@po09i
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po09i commented Jun 16, 2020

@tashrifbillah Awesome, here is the mattermost channel. Check the kanban board for the todo list! If you have any question, feel free to ask on mattermost!

@tashrifbillah
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mattermost channel isn't working for many of us right now. We reported it to the ongoing Crowdcast session.

@po09i
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po09i commented Jun 16, 2020

Okay then this issue should be good enough until it is fixed. Which issue interests you the most?

@Remi-Gau Remi-Gau removed their assignment Jul 31, 2023
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@jcohenadad @cmaumet @Remi-Gau @llevitis @jaystock @tashrifbillah @complexbrains @po09i @gaspardcereza