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bids-standard / bep001

Project management repository (primarily issues) for BIDS Extension Proposal 001
Creative Commons Attribution 4.0 International
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Collect real data for Examples #11

Closed Gilles86 closed 4 years ago

Gilles86 commented 5 years ago

Let's collect some actual data that we can use as examples for the BEP001.

One candidate already is Chris G's 7T dataset: https://openneuro.org/datasets/ds000113

Wietske van der Zwaag's 3D EPI MP2RAGEs: https://www.sciencedirect.com/science/article/pii/S2352340918308825

I am most likely to also share some ME-MP2RAGE data.

Gilles86 commented 5 years ago

Does anyone have some MPM or MT-data to share?

KirstieJane commented 5 years ago

There's this openly available hRMI (MPM) data: https://github.molgen.mpg.de/hMRI-group/Toolbox/wiki/HmriDemoDataset

Gilles86 commented 5 years ago

Bit of a mundane question, but: where should we put these example datasets? Github tends to not work very well with large data files. What is a good alternative?

agahkarakuzu commented 5 years ago

I think Open Science Framework is a good option.

agahkarakuzu commented 5 years ago

@Gilles86 happy to share example datasets for the (remaining) methods I listed here. I also created a project on OSF, I can transfer its ownership to you and invite collaborators if everyone is OK to upload here.

Gilles86 commented 5 years ago

@Gilles86 happy to share example datasets for the (remaining) methods I listed here. I also created a project on OSF, I can transfer its ownership to you and invite collaborators if everyone is OK to upload here.

Would be great!

KirstieJane commented 5 years ago

Here's an osf repository that @emdupre created for the tedana:tada: project: https://osf.io/bpe8h/

Seems like a similar idea for BEP001 examples would be great.

akhanf commented 5 years ago

I can contribute a session with MP2RAGE, Sa2RAGE, multi echo GRE (mag, phase)

KirstieJane commented 5 years ago

Assigned to @Gilles86, @tiborauer & @christophephillips to add their data to an osf project.

@agahkarakuzu to give write access to already existing OSF project: https://osf.io/k4bs5. 😸

satra commented 5 years ago

we currently have a test-retest single subject MPM dataset that can be added as well.

agahkarakuzu commented 4 years ago

I started pushing some example data to OSF. Here is my checklist for the examples I can collect:

My examples wont be "complete datasets", but would make a decent demonstration as a starting point.

@Gilles86 will bring in examples for

Side note, for ME-MP2RAGE please see the qMRI applications that can be derived from an existing grouping suffix subsection. I think ME-MP2RAGE worths being listed there, and other qMRI applications that can use an existing suffix but can create new use cases by alternations to the additional parameters. That table eventually should put things in better context on the relevance between suffixes and various qMRI applications.

agahkarakuzu commented 4 years ago

@lazaral I saw that you created a new project in OSF for MPM data (https://osf.io/zthwr/). I will soon add all the people on zthwr to https://osf.io/k4bs5/. We can keep all the examples in one place, would make our life easier. Would you mind uploading your examples dataset to k4bs5 ?

Edit:

I've just added you and C. Phillips to the OSF page for BEP001, you have read/write access.

lazaral commented 4 years ago

Yes that's a great idea - thank you @agahkarakuzu !

ChristophePhillips commented 4 years ago

Thanks @agahkarakuzu ! I've been playing with the hMRI toolbox example dataset and will try to push them there, as soon as I've got an 'acceptable BIDSified version' of them. :-)