jcohenadad commented 4 years ago

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:

Julien Cohen-Adad @jcohenadad,
Ryan Topfer @rtopfer
Alexandre D'Astous @po09i
Gaspard Cereza @gaspardcereza
Eva Alonso-Ortiz @evaalonsoortiz
Jason Stockmann @jaystock

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):

[x] Link to your project: could be a code repository, a shared document, etc. See here
[x] Include your Mattermost handle. 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] 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
[x] Twitter-size summary of your project pitch, cf. here
[x] Provide an image of your project for the OHBM brainhack website
[x] 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):

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

llevitis commented 4 years ago

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?

jcohenadad commented 4 years ago

@llevitis thank you so much for the quick review-- yes, definitely! we will add an image within the next 1-2 days.

gaspardcereza commented 4 years ago

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 commented 4 years ago

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

jcohenadad commented 4 years ago

@Remi-Gau Twitter project pitch added 😊

Remi-Gau commented 4 years ago

Wow. Thanks. Will tweet right away.

cmaumet commented 4 years ago

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 commented 4 years ago

Camille, do you mind sharing the registration link with me? Thank you! Do I have to register for OHBM to participate?

Jason

Sent from my iPhone

On Jun 13, 2020, at 10:35 AM, Camille Maumet notifications@github.com wrote:

    External Email - Use Caution

Hi @jcohenadadhttps://github.com/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!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/ohbm/hackathon2020/issues/128#issuecomment-643631818, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGCOLG4VGPRZ7GAGJHX2GMTRWOFAPANCNFSM4NS4TPFQ.

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cmaumet commented 4 years ago

@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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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!

cmaumet commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

I registered for the Hackathon ($25 fee) but I do not know how to join the Shimming Toolbox project specifically. Sorry for the confusion.

--- Jason

From: Julien Cohen-Adad notifications@github.com Reply-To: ohbm/hackathon2020 reply@reply.github.com Date: Monday, June 15, 2020 at 10:42 AM To: ohbm/hackathon2020 hackathon2020@noreply.github.com Cc: jaystock jaystock@nmr.mgh.harvard.edu, Mention mention@noreply.github.com Subject: Re: [ohbm/hackathon2020] shimming-toolbox: Ecosystem for real-time shimming with MRI (#128) {Disarmed}

    External Email - Use Caution

Hi @jcohenadadhttps://github.com/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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/ohbm/hackathon2020/issues/128#issuecomment-644177100, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGCOLG3YIW6ZVSJ6AJCHH6TRWYXJ5ANCNFSM4NS4TPFQ. [ { "@context": "http://schema.org", "@type": "EmailMessage", "potentialAction": { "@type": "ViewAction", "target": "https://github.com/ohbm/hackathon2020/issues/128#issuecomment-644177100", "url": "https://github.com/ohbm/hackathon2020/issues/128#issuecomment-644177100", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { "@type": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

cmaumet commented 4 years ago

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 commented 4 years ago

Camille, sorry, that link you shared doesn’t seem to work for me…

From: Camille Maumet notifications@github.com Reply-To: ohbm/hackathon2020 reply@reply.github.com Date: Monday, June 15, 2020 at 11:35 AM To: ohbm/hackathon2020 hackathon2020@noreply.github.com Cc: jaystock jaystock@nmr.mgh.harvard.edu, Mention mention@noreply.github.com Subject: Re: [ohbm/hackathon2020] shimming-toolbox: Ecosystem for real-time shimming with MRI (#128) {Disarmed}

    External Email - Use Caution

Oh @jaystockhttps://github.com/jaystock, thanks for that! All you need to do now to complete your registration now is to fill in the form here<framaforms.org/registration-for-ohbm-brainhack-step-12-1589173979> to provide us with important additional info. Thank you!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/ohbm/hackathon2020/issues/128#issuecomment-644208365, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGCOLG2CCITHE2N2PZEXIGLRWY5SHANCNFSM4NS4TPFQ. [ { "@context": "http://schema.org", "@type": "EmailMessage", "potentialAction": { "@type": "ViewAction", "target": "https://github.com/ohbm/hackathon2020/issues/128#issuecomment-644208365", "url": "https://github.com/ohbm/hackathon2020/issues/128#issuecomment-644208365", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { "@type": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

tashrifbillah commented 4 years ago

Interested to work on it!

po09i commented 4 years ago

@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 commented 4 years ago

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

po09i commented 4 years ago

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

ohbm / hackathon2020

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

Project info

Additional project info

OHBMHackathon #Brainhack #OHBM2020

Project submission

Submission checklist