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OHBM 2021 Preparations #722
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I'll add, partially in response to @smoia's comment on gitter: That said, every year we've had a different focus for the meeting and I think that variation is important. One brainstorming thought for this year would be to focus on multi-echo data collection & analysis in practice. It seems the user based has crossed enough of a threshold to make this an interesting focus. We could spend have the meeting having a few pre-selected people give mini talks on their experiences and then have space for more open discussion & questions during the second half. That focus would benefit from having a non-core tedana developer as an organizer and/or speaker. I’d encourage @62442katieb (based on: https://doi.org/10.1101/2021.04.01.437293 ) to be a speaker & possibly a co-organizer, but I’m not sure how many other things she’s already volunteered for with the OSR. |
HI @/all! This said, honestly I'm not sure it makes much sense that: Let me explain my point starting from (b): I'm not an active developer nor following development that much any more (in fact, if I'm doing something is to slow you down with the get_coeff development). So if one of the active developers wants to do it, I'd say it would be more appropriate! It's a fun experience, and if you want some suggestions I can help with that. But, if nobody wants to put their face, I have absolutely no problem in doing it again. However. Last year having a panel made sense, because we also had the Symposium and it was a nice combo. I'm not sure what the plan would be this year to justify the panel. Sure, it's a good moment to see the faces and names of people working with ME or around it, but unless there is an active goal we want to reach, it might feel a bit like a lost opportunity. Unless the goal is "updates on what's happening in the ME BOLD world, which can be fun and a good platform for researchers to share their latest works. This said, if there is willingness to do something I can help as a moderator. |
@smoia and I decided to talk about the OSR presentation this Monday, 5/10, at 12:30EST, 6:30CEST. If others, want to join, let me know & I'll send you the meeting link. |
@smoia and I spoke on Monday to discuss an OSR event. We decided that we should propose an emergent session rather than an educational talk or panel. That is similar to what we've done in past years and probably still best fits our goals. That means there isn't a Friday submission deadline, but sooner is better. The submission format is fairly simple and we don't actually need a list of presenters yet so there's a lot of flexibility. Our thought for this year is to focus on multi-echo in practice The guide: https://ohbm.github.io/osr2021/submit/ Preferred time zone (opinions on ETD vs UTC?) Abstract (there’s one line, but it seems like they’re just asking for a few sentences. Note that I’m consciously not mentioning tedana in the abstract, but the related URL likely will be tedana-related): Related URLS: Either tedana.readthedocs.io/ or open an issue that’s specific for this emergent session. I’m leaning towards opening an issue so that we have a place where we can list the presenters and maintain some discussion. Please comment or give a 👍, if you're fine with this. @emdupre @dowdlelt @tsalo @jbteves @eurunuela @javiergcas @notZaki |
@handwerkerd I would prefer we make a new issue specifically and link it, which is something we've typically done for the OHBM posters anyway, and this feels similar. |
I think the format you are proposing as an OSR event is perfect, and happy to collaborate in being a presenter or attendee. I could also provide some points regarding questions (1), (2) and (3) from my perspective. |
Random thought. We have some OHBM-specific repos: |
Also, it's clear they want just one name on the application. It seems more like a point-of-contact rather than a sole presenter. Given what I'm doing now, I'm assuming I'll use my name unless someone else volunteers. We'll be able to list anyone involved with setting this up on the page for the emergent session. OK? |
I just tried to create |
Just created https://github.com/ME-ICA/ohbm-2021-multiecho 😉 |
@eurunuela, The way it's currently set up, I can't directly push edits and (possibly because there's nothing there) I can't fork or create a pull request. At least for now, can you give me authority to push into that repo without reviews? Maybe make me an owner for that repo? Thank you for setting this up! |
Sorry about that. I thought it would let you. Try now. |
@eurunuela Thank you! It works now and https://github.com/ME-ICA/ohbm-2021-multiecho is live with content. Feedback on the text is welcome. I'll plan to submit the proposal later today and we'll be able to add to that site as appropriate. |
I just submitted the proposal for an emergent session using the text above (with some slight grammar corrections) |
Hi @handwerkerd and @smoia ! I'm a bit late to the party (sorry to have missed the discussion). I'm happy to contribute to an emergent session in the OSR, but I'm a tad over-extended during OHBM and my defense is June 24 (🥳 / 😅) so my contribution might be limited. |
@62442katieb The way we proposed the emergent session will allow for some flexibility depending on availabilty. I'll check in as it gets closer. While the run-up to a defense is unlikely to be fun, I hope you enjoy the actual defense. Congratulations! |
I have a very rough draft of the poster in this shared folder The poster is titled "tedana_poster_OHBM2021.pdf" and I'll keep updating that file as I improve it. Things I know still need to be done or places where feedback would be helpful:
|
Quick comment from my phone (I still haven't checked the poster) Re dynamic reports: I'd either use the same page we created last year, or now that @notZaki has run tedana on the 88 Cambridge datasets, it would be really cool to share the reports and results of all those subjects (or at least some of them). I think it is a very good "real-life" scenario to showcase tedana's capabilities. We could even think of automating this process, along with the process of generating figures for the posters for the future too. I'll get back to this issue later today and give feedback on the rest. |
As I said before, it would be great to share the results on the 88 Cambridge datasets.
I agree but I think that making the flowchart a bit more like a figure would change my opinion.
I find it a bit weird haha but I'd say it's @emdupre who should say whether she's comfortable with it or not.
I think it's well summarized.
AFAIK PowerPoint already captions as you speak and lets you record too. |
@notZaki & @eurunuela I know about https://osf.io/9wcb8/ but are the tedana reports for this preprocessing somewhere online? Sorry if I got out-of-the-loop on this dataset. |
@handwerkerd thanks for putting this together!
could be
and then change
and then link here. |
I didn't upload the tedana output of the cambridge datasets, but that could be done. Not sure if osf will allow the reports to be viewable in the browser though, so might have to consider a different hosting option. |
You're right. I believe osf will just show the html code instead of rendering it. Maybe the reports themselves could go into the OHBM 2021 repo. We could have a folder per dataset with the report and a README with the link to OSF? Only if it can be automatized, of course. |
If OSF can host the HTML files, I think that's the most logical location. Anyone who wants to interact with them can download the relevant files. I can then copy one to the OHBM 2021 repo so that people can interact without downloading. @notZaki, Any chance you can get some or all up today or tomorrow? I'm now working on integrating many of the other comments. |
@jbteves I'm working on cleaning up the wording and formatting, but, as long as we have the space, I think there's a benefit to keeping a decent amount of our governance goals and structures on the poster. We looked at other governance models, realized there wasn't a cut-and-paste model we could use for a project of our size, and adapted other models for our project. We now have something that's slightly unique that might be relevant to other projects, and might attract broader interest and discussion than people solely curious about multi-echo. I want enough info on the poster to potentially prompt discussions. |
New poster version uploaded. Still work to do, particularly cleaning up formatting more and improving the interactive visualization example (I may change to a Cambridge 88 dataset to highlight the fact that those data are now easily available). With help from @jbteves I also added the following factoid: "In the past year we have changed 116 files with 5958 inserted and 3260 deleted lines of code out of ~ 15000 total lines of code!" (this includes metric modularization) |
@handwerkerd I uploaded the reports to a this github repo, and the reports can be accessed from this page. I haven't gone through all the reports. It's possible that some subjects have nicer results than others. |
Thanks for sharing the poster, @handwerkerd , and for all of your work on it !! A few thoughts :
Related to the last point, I don't know if the author list is finalized, but I'd add a few more folks like @jsheunis if we can ! |
@emdupre You should still be able to right click on the poster to see version 2 with the Monty Python pictures. I was still thinking of adding a crown onto your picture. 😄 I won't be able to add much more during the next 24h, but keep giving feedback and I'll try to integrate everything and clean things up over the weekend. |
@emdupre I vaguely remember talking to @jsheunis at submission time, but I can't find any correspondence, so perhaps this was an embarrassing oversight. If he doesn't respond here, I'll include him in the email to all co-authors and ask if he wants to be added. Anyone else who we should consider adding? |
My current main affiliation is: Institute of Neuroscience and Medicine,
Brain & Behaviour (INM-7), Research Center Jülich, Germany.
Here's a link to an SVG of the logo:
https://raw.githubusercontent.com/datalad-handbook/course/master/pics/fzj_logo.svg
I'm not at my laptop now unfortunately, so won't be able to give effective
feedback. But i can do so around 9hours from now. Please let me know if
that will still be in your acceptible time frame. If not, I think trusting
all existing input is something that I'm totally okay with.
…On Sun, 13 Jun 2021, 22:58 Dan Handwerker, ***@***.***> wrote:
@jsheunis <https://github.com/jsheunis> I'm happy to add you. Could you
point me to a logo for your affiliation that I can add to the poster? I'm
hoping to get an almost final version of the poster out in the next few
hours. Feedback is appreciated. The submission deadline is around 30 hours
from when I write this comment.
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I know we had conversations at the time of abstract submission and again at the JOSS paper drafting, so I'm a bit fuzzy on what was discussed when ! Sorry about that. I know it's late to get substantive feedback at this point, but I'd include the JOSS co-authors on the email ! Since a lot of the content will link out to interactive content, we can keep incorporating feedback there, too. Thanks for the confirmation, @jsheunis ! Will be great to have you onboard, and any comments you can add are always appreciated :) |
Thank you @emdupre ! I knew I was forgetting to put something on the poster: The link to the submitted JOSS manuscript! As for additional authors, the people on the JOSS manuscript, but not the poster are @effigies @Islast and @prantikk. If any of you want to be authors on this poster, please let me know ASAP. The poster upload deadline is around 24h from when I'm posting this comment. |
I have no additions/changes to add to the poster, which looks great. I particularly like the summary of the governance structure :) Well done! |
IIRC my only contributions have been related to dependency resolution, which feels pretty unrelated to the content of this poster. If you would like me to be on the poster, I'm willing (affiliation: Stanford), but I don't feel a need for credit here. Poster looks good, and I also like the focus on governance. |
@effigies In that case, I won't add you to the poster, but you're, obviously on the JOSS manuscript. |
Sorry that I am a bit late to this party but I am a fan of the poster. It highlights a lot of neat things - and I think the call outs to specific parts of the code are quite nice. Hyperlinks are also great. No complaints here, thanks for putting in all the hard work @handwerkerd and folks. |
I also just updated https://github.com/ME-ICA/ohbm-2021-multiecho with other OHBM multi-echo posters and the interactive reports are now live at: https://me-ica.github.io/ohbm-2021-multiecho/ Of note, @emdupre identified posters by looking for 'multi-echo' or 'multiecho' in titles. We haven't yet done a search for posters with 'multi-echo' in the tags or abstract bodies. if someone feels like compiling them before I get a chance, post the info here: ME-ICA/ohbm-2021-multiecho#2 |
Having the reports is great - the 5-echo one looks to be working fine, but with the 3-echo report I'm getting no component maps (little broken image icon shows, no beautiful maps). |
Good catch @dowdlelt! It works better when I include the figures in the repo. It should be fixed now. |
Just a heads up, those reports don't match the CI which is likely due to differences in hardware/software (unless I'm missing something): |
I think the CI also runs on a fraction of the time series to save time. That said, I just realized I ran without the metric modularization code. Now that it's officially merged, I'll run again so that my reports will match what is now Main. |
What should be the final version of the poster is still at https://drive.google.com/drive/folders/14N7v_AMPcMyzwKHn6J8CUJV2PMpQR4S5?usp=sharing 'tedana_poser_OHBM2021_WithLinks.pdf' has added links to website & is the version I'll upload. |
Poster and presentation are uploaded. Thank you all for your feedback and help! |
I went through the abstract texts and I'm fairly sure I got all the posters that mention multi-echo fMRI in the title or text. I've updated https://github.com/ME-ICA/ohbm-2021-multiecho/ with all those posters and the links. I haven't figured out a good way to see if any talks mention multi-echo in their titles or abstracts. I'll plan to tweet out that link Sunday night or Monday morning. Also, for the people who might be slightly more connected to the OSR than I am (@emdupre @62442katieb @jsheunis @tsalo ) any clue when they're announcing a schedule for emergent talks? If I'm leading a session, it would be nice to have more than 24h to gather the speakers and to make sure I can be available! |
@ME-ICA/tedana-devs I've tentatively scheduled the multi-echo emergent session for Thursday, June 24, at 9:00AM EDT. I'm hoping that is a good time for many of you in multiple time zone. The emergent session schedule still looks fairly open so we may be able to shift. Also, there are 3 presentation times for the tedana poster: |
I'm afraid I won't be able to. I've got an appointment to get vaccinated Thursday morning. I might get to the end of the session at best. |
I can be there on Thursday morning! |
My appointment got cancelled, so I can be there too! |
Thank you both! |
It got cancelled. I was trying to get vaccinated in France (I live 5 minutes away by walking) and apparently they won't vaccinate Spaniards anymore. |
The emergent session is confirmed for Thursday, June 24, at 9:00AM EDT. We're supposed to have 4 presenters total... though given some of the other sessions, I suspect we can stretch that a bit. |
I'll be in the audience. Don't have anything prepared to present, but I'm happy to take part in the informal aspects of the discussion, and if another presenter is direly needed I could put something together. |
@handwerkerd if we have limited amount of presenters (and I guess you'd be already one of them?) I see doing what we thought a bit more difficult - maybe you can take the full lead on this and ask for four other people? I can suggest one or two maybe (and we could all help in the selection, I imagine). |
@smoia, I can take the lead on this, but I also checked and we can have more than 4, but we'd have people bounce on & off the screen. I have plans to invite a few people, but other recommendations are very welcome. |
I just invited a bunch of people to potentially present in the OSR multi-echo session. If you did not receive the email and want to be in-the-loop or help coordinate, let me know. |
Hello, I'll be attending the event. |
Ah, ok, I thought only four people were allowed on stage for the whole event! |
Summary
This is a place to keep track of general OHBM + tedana/multi-echo related preparations
Additional Detail
OHBM posters and videos need to be uploaded by May 25th. That means we should have a good sense of what will be included by mid May. A poster draft that allows time for feedback should be done at least a few days before our May 21 developers' call. The poster can include a 2-3 minute video. If we are ambitious, perhaps we can include multiple speakers on the video. @handwerkerd has already volunteered to take the lead on preparing the poster, but welcomes help.
Open Science Room Education Sessions or Panels need to be submitted by May 15th ( https://ohbm.github.io/osr2021/submit/ ). That means this would need to be completed before our next dev call. Anyone want to take the lead on this. Perhaps @smoia wants to lead this effort again? Otherwise, I suspect he'd be willing to advise someone else who takes the lead.
For the past several years, we haven't had anything tedana specific at the OHBM hackathon. That may again be the case this year, but I wanted to make space for that discussion.
Next Steps
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