MATLAB demos, Invaild BIDS data sets, first release

[Malin Sandström]

Dear all,

This is a follow up from the BIDS-MATLAB meeting held in September.

MATLAB demos - please share if you have demos with data sets

During the meeting we identified a need to have MATLAB-based demos using BIDS-MATLAB. If you have any demos with data sets, please share them - or just the links to data sets - with us. Remi is happy to help BIDS-convert datasets people use in their demos or tutorials,  if needed.

Invalid BIDS data sets wanted

Several meeting attendees reported finding a lot of "invalid" BIDS datasets and that cleaning those takes ages. The BIDS maintainers are interested in receiving information about such datasets, so they can improve user guidelines, and Remi is interested in invalid BIDS data sets to better understand how bids-matlab could help with data cleaning.   

Planned first release      

Just a reminder that there should be a first official first release of BIDS-MATLAB in December (before the holidays). So it would be good to make suggestions for change on the API or behaviors before then.

Malin & Remi

[Francois Tadel, Mr [Affiliate]]

Hi Malin,

Some BIDS datasets are distributed from the Brainstorm website - they are used in the online tutorials (automated processing scripts at the end of the pages).
The SEEG/ECOG datasets are included in the BIDS-examples, but we had to remove them from OpenNeuro because we could not distribute them as public domain (CC0).

• SEEG+ECOG+MRI:
  https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG
  ftp://neuroimage.usc.edu/pub/tutorials/sample_ecog.zip
• SEEG+MRI:
  https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity
  ftp://neuroimage.usc.edu/pub/tutorials/tutorial_epimap.zip
• MEG+MRI+DWI:
  https://neuroimage.usc.edu/brainstorm/Tutorials/FemMedianNerve
  ftp://neuroimage.usc.edu/pub/tutorials/sample_fem.zip
  
• MEG resting-state:
  https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega
  ftp://neuroimage.usc.edu/pub/tutorials/sample_omega.zip
  

We also have a full tutorial based on the 16 subject Wakeman/Henson multimodal dataset, also from the BIDS-examples repo:

• https://openneuro.org/datasets/ds000117
• https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle
• https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup

I haven't updated these datasets in a while, some might have issues - it would make them even better use cases for you :)
Please let me know if you find anything suspicious that we should consider fixing.

Best wishes,
François



Le 12/10/21 à 08:02, Malin Sandström a écrit :

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[Remi Gau]

Thanks François !

Will try to create some more bids-matlab demos based on those.

[Dr Cyril, Pernet]

@remi, talk to Chris - they have scanned the open neuro datasets for those with massive gitignore ...

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-- 
Dr Cyril Pernet, PhD, OHBM fellow, SSI fellow
Neurobiology Research Unit, 
Building 8057, Blegdamsvej 9
Copenhagen University Hospital, Rigshospitalet
DK-2100 Copenhagen, Denmark

wamc...@gmail.com
https://cpernet.github.io/
https://orcid.org/0000-0003-4010-4632

[Remi Gau]

Will ping him.

Thanks

--

Rémi Gau

[Guiomar Niso]

Thanks François!

We have these two MEG-BIDS datasets in OpenNeuro (brainstorm auditory and omega sample), that I've been updating from time to time, in case a BIDS version is needed:

https://openneuro.org/datasets/ds000246

https://openneuro.org/datasets/ds000247

Cheers,

Guiomar