Add all known and publicly available multi-echo datasets as datalad subdatasets

[jsheunis]

I'm picking this effort up again after receiving a jolt of motivation during the multi-echo community meeting at OHBM 2022. The idea is to curate a datalad "super"dataset that has subdatasets for all known and publicly available multi-echo datasets out there (in any format: BIDS / non-BIDS / raw / derivative). This can then be used as the basis for metadata extraction and catalog generation using datalad-catalog, which means we can easily host a user friendly browser-based catalog of multi-echo fMRI data! Since everything is structured into a datalad dataset, it also means that data access will be streamlined.

I've started making a list here (results from a search on OpenNeuro and from the list of datasets on tedana):

• [x] Multi-echo fMRI replication sample of autobiographical memory, prospection and theory of mind reasoning tasks
  • OpenNeuroDatasets url: https://github.com/OpenNeuroDatasets/ds000210
  • Path in superdataset: raw/autobiographical_memory
• [x] Multi-echo Cambridge
  • OpenNeuroDatasets url: https://github.com/OpenNeuroDatasets/ds000258
  • Path of raw data in superdataset: raw/multi_echo_cambridge
  • Derivative dataset (fmriprep): https://github.com/jsheunis/multi-echo-cambridge-fmriprep
  • Path of dervative data in superdataset: derivatives/multi_echo_cambridge_fmriprep
• [x] Multiband multi-echo imaging of simultaneous oxygenation and flow timeseries for resting state connectivity
  • OpenNeuroDatasets url: https://github.com/OpenNeuroDatasets/ds000216
  • Includes mriqc derivatives
  • Path in superdataset: raw/simultaneous_asl_bold_resting
• [x] Multiband Multi-Echo Simultaneous ASL/BOLD for task-induced functional MRI
  • OpenNeuroDatasets url: https://github.com/OpenNeuroDatasets/ds000254
  • Path in superdataset: raw/simultaneous_asl_bold_task
• [x] Valence processing differs across stimulus modalities
  • OpenNeuroDatasets url: https://github.com/OpenNeuroDatasets/ds001491
  • Path in superdataset: raw/valence_processing
• [x] Multi-echo masking test dataset
  • OpenNeuroDatasets url: https://github.com/OpenNeuroDatasets/ds002156
  • Path in superdataset: raw/masking_test
  • Derivative dataset (fmriprep): https://github.com/jsheunis/masking-test-fmriprep
  • Path of dervative data in superdataset: derivatives/masking_test_fmriprep
• [x] Le Petit Prince: A multilingual fMRI corpus using ecological stimuli
  • OpenNeuroDatasets url: https://github.com/OpenNeuroDatasets/ds003643
  • Path in superdataset: raw/le_petit_prince
  • Derivative dataset (fmriprep): progress being tracked in this issue
  • [ ] TODO: create subdataset of derivatives once available, add to superdataset
• [ ] Cambridge Centre for Ageing Neuroscience (Cam-CAN)
  • URL: https://camcan-archive.mrc-cbu.cam.ac.uk/dataaccess/
  • Data access request required
  • TODO: create minimalistic datalad dataset with dataset-level metadata that links user to access request process.
• [ ] rt-me-fMRI - A task and resting state dataset for real-time, multi-echo fMRI methods development and validation
  • URL: https://doi.org/10.34894/R1TNL8
  • Data access request required
  • TODO: create minimalistic datalad dataset with dataset-level metadata that links user to access request process.
  • TODO: check if datalad-dataverse extension can be used to mirror the dataset as a datalad dataset
• [x] EuskalIBUR
  • OpenNeuroDatasets url: https://github.com/OpenNeuroDatasets/ds003192
  • TODO: add as subdataset to superdataset
• [ ] Neurocognitive aging data release with behavioral, structural, and multi-echo functional MRI measures
  • OpenNeuroDatasets url: https://github.com/OpenNeuroDatasets/ds003592
  • TODO: figure out why the github repo is empty, and try to (help) resolve this so that the datalad dataset can be used (comment left on OpenNeuro dataset: https://openneuro.org/datasets/ds003592/versions/1.0.11)
  • TODO: add as subdataset to superdataset
• [ ] Heart rate variability biofeedback training and emotion regulation
  • OpenNeuroDatasets url: https://github.com/OpenNeuroDatasets/ds003823
  • [x] TODO: add as subdataset to superdataset
  • [ ] TODO: github repo is not a correct datalad dataset (although already installed as subdataset to multi-echo-super) ==> fix this (either on OpenNeuro side, ideally, or with an interim step)

Please add whatever is missing. Tagging @emdupre @smoia @dowdlelt @jbteves @tsalo @eurunuela @handwerkerd

[smoia]

This just made my day.

[tsalo]

Thanks @jsheunis! JSYK, I have converted the Le Petit Prince fMRIPrep derivatives to a Datalad dataset. Unfortunately, my attempts to push the dataset to G-Node GIN have been unsuccessful so far (lots of timeouts on my school's HPC). I am planning to try again soon.

[jsheunis]

Cool, thanks for the note! Good luck :)

[tsalo]

I think I have finally successfully uploaded the Le Petit Prince's fMRIPrep derivatives! https://gin.g-node.org/ME-ICA/ds003643-fmriprep-derivatives

[jsheunis]

Great!