Remi-Gau
commented
2 years ago hey @Paris-Lyons
this is looking very good to me. will ask @likeajumprope to do a cross check.
Open Paris-Lyons opened 3 years ago
Remi-Gau
commented
2 years ago hey @Paris-Lyons
this is looking very good to me. will ask @likeajumprope to do a cross check.
Remi-Gau
commented
2 years ago Hi @brainhackorg/project-monitors : my project is ready!
likeajumprope
commented
2 years ago looks good from my side too! @Remi-Gau
Title
AEDAPT - A multi-platform virtual desktop environment with fully-preinstalled software for reproducible EEG/MEG/MRI data analysis
Leaders
Collaborators
Brainhack Global 2021 Event
Brainhack Australasia
Project Description
What are you doing, for whom, and why? AEDAPT provides a containerised data analysis graphical environment (based on Neurodesk; https://neurodesk.github.io/) to facilitate reproducible analysis of neuroimaging data by technical and less-technical users alike. It also provides interoperability with other data acquisition/storage/analysis/sharing platforms and utilities. One such utility developed by the AEDAPT team is SOVABIDS -- a graphical converter from raw EEG data to the BIDS standard. AEDAPT and SOVABIDS are funded by the Australian Research Data Commons (ARDC), Swinburne University, University of Queensland and Sydney University. SOVABIDS was also funded by Google Summer of Code.
What makes your project special and exciting? Analysis pipelines for EEG/MEG/MRI data typically rely on specific versions of packages and software, and are dependent on their native operating system. These dependencies mean that a working analysis pipeline may fail or produce different results on a new computer, or even on the same computer after a software update. The frequent release of versions also means that researchers need to spend a lot of time on installing and upgrading software. AEDAPT provides a platform in which anyone, anywhere, using any computer can reproduce the original research findings given the original data and analysis code. Moreover, SOVABIDS allows the conversion of the original data to BIDS, thus making it easier for others to re-analyse the data using other tools.
AEDAPT and SOVABIDS are intended to serve researchers and developers in Australia and worldwide, and would be maintained by the community as open-source projects. It is a great opportunity to familiarise yourself with the neuroscience open-source community, as we are working closely with prominent developers and scientists all around the world.
How to get started? Head over to the resource links below and try Neurodesk (the technological platform on which AEDAPT runs) and SOVABIDS. Both are already tested and usable.
Where to find key resources?
Link to project repository/sources
https://neurodesk.github.io/ https://sovabids.readthedocs.io/
Goals for Brainhack Global
Good first issues
Issue one: Download Neurodesk from https://neurodesk.github.io/ and test it for your EEG/MEG work. This is the technological platform of AEDAPT. Report any problems in: https://github.com/NeuroDesk/neurodesk.github.io/discussions
Issue two: If you have EEG data in the Neuroscan’s (.cnt) format, download SOVABIDS from https://sovabids.readthedocs.io/en/latest/README.html#installation and test it. Alternatively, you can use publicly available EEG .cnt raw data (see below under “data to use”) Report any problems in: https://github.com/yjmantilla/sovabids/issues
Issue three: Adding EEG/MEG workflow examples to our documentation page (workflows that use the tools preinstalled in AEDAPT). There is also the possibility to record video tutorials. https://neurodesk.github.io/tutorials/electrophysiology/ Possible idea: a workflow to convert raw EEG data in the .cnt format to BIDS standard using SOVABIDS, and then preprocess it using EEGLAB (available in AEDAPT).
Communication channels
https://mattermost.brainhack.org/brainhack/channels/virtual-neuro-machine-vnm
Skills
For good first issues:
For main goals:
Onboarding documentation
No response
What will participants learn?
BIDS (https://bids.neuroimaging.io/) Docker containers Github workflows Compiling MATLAB code JSON-RPC API
Data to use
Publicly available Neuroscan’s raw EEG data in .cnt format
Driving simulator experiment Paper: https://www.nature.com/articles/s41597-019-0027-4 Data: https://figshare.com/articles/dataset/The_original_EEG_data_for_driver_fatigue_detection/5202739
Motor imagery experiment Paper: https://www.nature.com/articles/s41597-020-0535-2 Data: https://doi.org/10.7910/DVN/RBN3XG
Number of collaborators
1
Credit to collaborators
Project contributors will be listed on the website, on Github, and potentially be part of publications originating from the project.
Image
Type
coding_methods, documentation, pipeline_development, tutorial_recording
Development status
2_releases_existing
Topic
connectome, data_visualisation, diffusion, EEG_EventRelatedResponseModelling, EEG_source_modelling, hypothesis_testing, ICA, neural_decoding, neural_encoding, neural_networks, PCA, physiology, reproducible_scientific_methods, statistical_modelling, systems_neuroscience
Tools
BIDS, Brainstorm, Datalad, FieldTrip, Freesurfer, Jupyter, MNE, Nipype, SPM
Programming language
containerization, documentation, Matlab, Python, shell_scripting, unix_command_line, html_css
Modalities
behavioral, ECG, ECOG, EEG, eye_tracking, MEG, MRI, TDCS, TMS
Git skills
2_branches_PRs
Anything else?
More information about AEDAPT can be found on our website: aedapt.net
Things to do after the project is submitted.
Hi @Brainhack-Global/project-monitors: my project is ready!