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cfitz
@cfitz
hi! Looks like you guys got this setup!
Kirstie Whitaker
@KirstieJane
:wave:
Isla
@Islast
Hi! Does anyone know of any BIDS converters that handle multi-echo acquisitions?
Park-Patrick
@Park-Patrick
Hi @Islast! I don't know of a converter that handles them, but here's a script that I wrote to match the json files with the correct echo file
Isla
@Islast
Thank @Park-Patrick this is a really big help!
Park-Patrick
@Park-Patrick
No problem!
Remi Gau
@Remi-Gau
I had in mind to write up a couple of matlab functions to create reports of acquisition details contained in a BIDS data set. A bit like pybids does: https://github.com/INCF/pybids/tree/master/bids/reports.
I was tempted to add them to the BIDS start kit but I am not sure they would fit in there. So I was wondering if anyone knew of another repo where they could be more at home.
Kirstie Whitaker
@KirstieJane
I think they really would work for the starter kit please!!
(Tagging @Remi-Gau!)
Remi Gau
@Remi-Gau
Oh. Ok then. That project has found a home.
Kirstie Whitaker
@KirstieJane
Amazing! I’m on holiday this weekend but go ahead and open an issue if you’d like to, or submit a pull request if you’re already ready!
We didn’t get around to documenting the useful functions in the wiki very well, so a new page in there might be helpful. But I’ll let you have a think about what you feel would be the best medium!
(I mean - the scripts are in the repo but the wiki might tell first visitors that they exist and what they do at a high level)
matrixbot
@matrixbot
remi_gau Will most likely open an issue so it doesn't appear out of nowhere for other contributors who might have missed this. I was actually about to do this when I realized that BIDS-SK was maybe not the right place for it.
remi_gau Well I will write the gist of the code first and then add a brief descrition in the wiki I guess.
Kirstie Whitaker
@KirstieJane
Perfect!! Yep - definitely a great place for the contribution!!
dorahermes
@dorahermes
@Remi-Gau Sounds great for the bids starters kit! This is a different issue from the issue wrt cleaning up the current Matlab code to create the templates, correct?
matrixbot
@matrixbot
remi_gau Correct. The latter is just me being OCD and for users who code with the matlab IDE that has not automatic word wrap.
dorahermes
@dorahermes
ok, great, thanks so much for both!
Isla
@Islast
Hi everyone, does anyone know where I can find heudiconv documentation for BIDS use beyond the slide show at http://nipy.org/heudiconv
Kirstie Whitaker
@KirstieJane
Hi @Islast! @chrisfilo sent these two links to the nipype channel but I think they might have been meant for you :smile_cat:
matrixbot
@matrixbot
Chris Gorgolewski Thanks Kirstie!
Kirstie Whitaker
@KirstieJane
(Although I think that second link is to the slide show you've been using)
matrixbot
@matrixbot
Chris Gorgolewski There is also a link to James Kent video tutorial there.
Kirstie Whitaker
@KirstieJane
:+1: unfortunately the video doesn't describe the functionality we need. @Islast opened an issue so we'll see if the developers can help nipy/heudiconv#256
Isla
@Islast
Thank you for the help though Chris
Ankit Gupta
@ankiitgupta7
Hello there!
Can I get any information about GSOC'19 idealist at this place?
And any idea about the public chat platform specifically for GSoC(Google Summer of Code)?
Ankit Gupta
@ankiitgupta7
I went through the article(https://www.nature.com/articles/sdata201644#introduction) on BIDS and understood the idea behind it and other things associated with it...
Would be happy to get guided on things I could do next!
Thanks in advance.
matrixbot
@matrixbot
Chris Gorgolewski Kirstie Whitaker (Gitter): is BIDS Starter Kit going to be a project at GSOC 2019?
Kirstie Whitaker
@KirstieJane
Hi @ankiitgupta7! Thank you for pinging us!
I'm not sure if this project will be part of GSOC next year.... @Park-Patrick - what do you think - would you recommend us running it again with a new student?
@dorahermes @emdupre @chrisfilo - what do you think too?
Park-Patrick
@Park-Patrick
Hi @ankiitgupta7 @KirstieJane @dorahermes @emdupre @chrisfilo . Great to see there's interest for continuing this! A couple directions I can think of are improvements to the BIDS Apps section or institutional level conversion (i.e. direct scanner to PC). Happy to chat more with anyone interested about the project/program itself
Ankit Gupta
@ankiitgupta7
Hello there again! I was asking about availability all the projects ideas in general for GSOC'19 at INCF. But due to no further information about it I went through the past projects at INCF randomly and got to know about BIDS. In the meantime, I fixed a basic issue(#72) just to get started(or get noticed!). Still open to continue with BIDS if assisted further and also if it's anyhow involved with any project in GSOC'19.
Kirstie Whitaker
@KirstieJane
Thanks @ankiitgupta7! I got an email from Malin at INCF this week and she's hoping to post a list of projects that INCF will coordinate for GSOC 19 by the end of this week. I think twitter will be the best place to keep an eye on those updates :smile_cat:
Ankit Gupta
@ankiitgupta7
@KirstieJane Thanks for reply. Please go through the issue #72 again, and see if I have done it properly. Just wanted a feedback on that and also things I can touch upon next!
Kirstie Whitaker
@KirstieJane
Looks great @ankiitgupta7! Thank you :sparkles:
Adam Li
@adam2392

Hi, iEEG epilepsy researcher here. I wanted to ask about how to best annotate white matter and other channels that might not be part of your interest. Other examples include: out, csf, ventricle. Ideally there is a place to annotate this within the BIDS layout for iEEG data. This specifically comes up for SEEG (depth electrodes).

Currently iEEG-BIDS has "status", which is constrained to "good/bad", and status_description. Would this be the right data points to modify to account fo rhtat.

Park-Patrick
@Park-Patrick
Hi @adam2392 I'm not an expert in iEEG, but you may find some useful info on the forum: https://neurostars.org/tags/bids. Otherwise some authors on the paper are active on the BIDS github as well
Kirstie Whitaker
@KirstieJane
Thanks for asking @adam2392 and ditto @Park-Patrick's answer - I think neurostars is the best place to ask here - but once you know the answer it might be great to add to the starter kit??