COINSTAC: A futuristic framework for collaborative big-data research
16:45-17:45 GMT+1 on June 20, 2022
COINSTAC is software to foster collaborative research, removing large barriers to traditional data-centric collaboration approaches. It enables groups of users to run common analyses on their own machines over their own datasets with ease. The results of these analyses are synchronized to the cloud, and undergo aggregate analyses processes using all contributor data. Federated (decentralized) pipelines allow for distributed, iterative, and feature rich analyses to be run, opening new and exciting capabilities for collaborative computation. It also offers data anonymity through differentially private algorithms, so members do not need to fear PHI traceback.
Our goal is to introduce COINSTAC to researchers in developing countries with limited hardware, networking capabilities and technical expertise to make collaborative big-data research possible on a global scale. We would like to hear feedback on our tool in general including potential roadblocks and improvements to make our tool more researcher friendly. We welcome anyone who wants to contribute to the project with their algorithm development skills and coding skills. We would also like to work with organizations together on grants, that could help us answer interesting neuroscience related questions using COINSTAC, that could not have been possible otherwise.
Harmonized analysis of fMRI data using HALFpipe
18:00-19:00 GMT+1 on June 20, 2022
In the ENIGMA consortium, when we set out to do fMRI meta analyses, we encountered a number of issues with how to standardize and harmonize processing across diverse data sets. To attempt to solve these problems, we developed HALFpipe, an easy-to-use pipeline built on top of fMRIPrep and other existing tools.
In this session, it would be great to discuss the advantages and disadvantages of standardized pipelines such as HALFpipe, and more generally, how to integrate the diverse set of pipelines that are being developed within the community.
Brainstorming features and ideas for AFNI
8:00-9:00 GMT+1 on June 21, 2022
The AFNI software developers’ main goal is to helpkeep users close to their data. We receive new insights from researchers all the time, about FMRI, structural MRI, DWI and more analysis tools in AFNI. What would be more features to add/grow/develop? Let’s chat.
Snakebids: Reproducible neuroimaging workflows as BIDS
10:15-11:15 GMT+1 on June 21, 2022
Distributing a reproducible neuroimaging workflow that relies on multiple constituent tools is challenging, but made easier by the use of workflow management tools. One such tool, Snakemake, has become increasingly popular but is challenging to use with BIDS datasets. In this session, we introduce Snakebids, an extension to Snakemake that makes it easier to write clear workflows for processing BIDS-formatted data, and exposes those workflows with the standard BIDS App interface. Our goals are to introduce Snakebids to a wider audience and solicit feedback, feature requests, and/or contributions.
How the Neuroimaging Tools & Resources Collaboratory (NITRC) can help your research
11:15-12:15 GMT+1 on June 21, 2022
Here you will learn what NITRC is doing to enable open science and research. You’ll learn how to find NIH funded software and data resources, how to share your NIH funded resources, how the NITRC Computational Environment can save you time and money, and about the NITRC Community forums, calendar, and news. If OSR members use NITRC already, we invite you to join to share what Collaboratory resources you’ve found helpful to enable your research.
NITRC Image Repository Computational Environment
Physiopy open meeting: Best practices in using physiological data to denoise functional timeseries
17:45-18:45 GMT+1 on June 21, 2022
Physiopy is a community that develops solutions to improve the use of physiological signals (e.g. respiratory and cardiac related signals) in functional neuroimaging. Part of this effort is dedicated to compile best practices on how to record, clean, and use physiological data.
In this emergent session, organizers invite physiological data experts and newbies alike to discuss the best practices in using physiological signals to denoise neuroimaging data (with a focus on functional MRI). In particular, following their Educational Course, organizers will discuss how respiratory and cardiac signals, as well as respiratory and cardiac information captured in the neuroimaging data, should (or should not) be used and modeled in an fMRI experiment.
If you are a physiological data user or expert, or if you are simply curious about how you can use physiological data in your functional MRI setting, this is an emergent session for you!
Discussion of priorities for multi-echo fMRI methods development
10:30-11:30 GMT+1 on June 22, 2022
Multi-echo fMRI is an acquisition method that can be used to empirically identify and remove non-neural noise. There is active research into ways we can use multi-echo information to improve our data. Over the past 5 years, much of this work has been done in open and collaborative framework. tedana.readthedocs.io is both multi-echo denoising software and a hub for educational and support resources for people interested in multi-echo fMRI. The developers of tedana created a roadmap for the main goals of our work and we’re getting near (definitely not there) to accomplishing those goals. We want to use this session to both provide a status report regarding tedana and to open discussion for priorities for multi-echo fMRI development either within or outside of tedana.
NeuroLibre reproducible preprint server
14:45-15:45 GMT+1 on June 22, 2022
NeuroLibre is a curated repository of interactive neuroscience notebooks that seamlessly integrates data, text, code and figures. As we are getting closer to the beta release of NeuroLibre, we would like to solicit community contributions to publish more reproducible preprints! In this session, we would like to introduce the aim & scope of the NeuroLibre. Next, our plan is to showcase how to prepare, submit and publish a collection of notebooks as a full-blown reproducible preprint that belongs to the 21st Century!
Towards an Open Developer Community for Neuroimaging MATLAB Community Toolboxes
17:00-18:00 GMT+1 on June 22, 2022
To support greater coordination and convergence among the varied established and emerging open access software tools which build upon the MATLAB software platform for the neuroimaging field, the MathWorks neuroscience team is planning towards founding an INCF/MathWorks Neuroimaging Working Group. This emergent session is hopefully the start of a regular and active dialogue with current and prospective developers (of varying skills, levels, and interests) in the neuroimaging community.
For the 2022 OSR, the emergent session goals are:
- Provide a forum for MATLAB Community Toolbox project representatives to quickly convey their top goals & challenges (20 mins)
- Hold an interactive survey regarding key MATLAB Community Toolbox topics, including select questions submitted by community at OSR (20 mins)
- Hold an open Q&A discussion, with an “emergent panel” consisting of the project representatives and survey question designers above (20 mins)