On-Demand Integration of OpenNeuro and CBRAIN for Scalable and Reproducible Neuroimaging
Poster No:
1831
Submission Type:
Late-Breaking Abstract Submission
Authors:
Serge Boroday1,2, Pierre Rioux1,2, Natacha Beck1,2, Darcy Quesnel1,2, Xuan Pham1,2, Najmeh Khalili-Mahani1,2, Reza Adalat1,2, Samir Das1,2, Bryan Caron1,2, Alan Evans1,2
Institutions:
1McGill Centre for Integrative Neuroscience (MCIN), Montreal, Canada, 2Montreal Neurological Institute (MNI), McGill University, Montreal, Canada
First Author:
Serge Boroday
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
Co-Author(s):
Pierre Rioux
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
Natacha Beck
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
Darcy Quesnel
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
Xuan Pham
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
Najmeh Khalili-Mahani, Co-author
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
Reza Adalat
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
Samir Das
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
Bryan Caron
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
Alan Evans
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montreal, Canada|Montreal, Canada
Late Breaking Reviewer(s):
Introduction:
CBRAIN (Sherif et al., 2014) is an open-source web-based collaborative research platform and a portal that lowers technical barriers associated with large-scale neuroimaging research. It facilitates data-sharing and provenance tracking of results obtained from processing large-scale data through computationally intensive scientific pipelines using high-performance computing (HPC) clusters and cloud facilities. Within CBRAIN, users can either upload and register their own data or benefit from a number of connected data repositories. Most of the featured data collections are only available to certain categories of users. Exceptions are the Canadian Open Neuroscience Platform (CONP), which is available to all CBRAIN users, and the most recent addition, OpenNeuro (Markiewicz et al., 2021). To integrate OpenNeuro-one of the largest and fastest-growing community collections of BIDS datasets-we adopted an on-demand automatic dataset configuration and file transfer approach.
Methods:
For scalability we leveraged CBRAIN's own integration of DataLad, a data management and versioning system (Halchenko et al., 2021), which facilitates automatic retrieval of files from OpenNeuro into CBRAIN. Retrieval of a particular OpenNeuro dataset is performed upon user request, either through OpenNeuro or CBRAIN's web interface, but the dataset remains registered with CBRAIN indefinitely. OpenNeuro's Datasets GitHub organisation is used to facilitate DataLad based access to data. While usually GitHub is not well suited to host large data files, DataLad compensates for this by involving additional external storage facilities, such as AWS S3. Once a dataset is retrieved, its metadata remains in CBRAIN storage, while the bulk of data is cached by CBRAIN based on usage.
On the OpenNeuro portal each dataset offers a button (Figure 1) that directs users to CBRAIN, where they can perform analyses of that dataset. If a dataset of interest is not yet available in CBRAIN, the user is presented with a dataset specific page to perform an on-demand configuration of the dataset in CBRAIN with a single-click, without any need for intervention from the CBRAIN administrator (Figure 2a). Once configured the OpenNeuro dataset is available to all CBRAIN users without any additional setup (Figure 2b). This approach avoids mirroring all OpenNeuro datasets, prioritizing only those required by CBRAIN users.
For user convenience, derivatives are registered in CBRAIN as separate file collections from the original data, though they share the same DataLad data provider instance and project. This ensures that the sometimes voluminous derivatives are not consuming storage resources, unless needed.
On the OpenNeuro portal each dataset offers a button (Figure 1) that directs users to CBRAIN, where they can perform analyses of that dataset. If a dataset of interest is not yet available in CBRAIN, the user is presented with a dataset specific page to perform an on-demand configuration of the dataset in CBRAIN with a single-click, without any need for intervention from the CBRAIN administrator (Figure 2a). Once configured the OpenNeuro dataset is available to all CBRAIN users without any additional setup (Figure 2b). This approach avoids mirroring all OpenNeuro datasets, prioritizing only those required by CBRAIN users.
For user convenience, derivatives are registered in CBRAIN as separate file collections from the original data, though they share the same DataLad data provider instance and project. This ensures that the sometimes voluminous derivatives are not consuming storage resources, unless needed.
Results:
This integration enables users to analyze OpenNeuro datasets using over 160 containerized neuroimaging pipelines-such as Civet, fMRIPrep, FreeSurfer, and ANTs-directly within CBRAIN, reducing the need for manual data handling and configuration.
One challenge encountered is that a small number of OpenNeuro dataset versions are not available on GitHub and thus unable to be accessed via DataLad. This can sometimes occur due to a large git commit exceeding GitHub's limits or for reasons related to the way dataset authors maintain and handle the dataset. However, OpenNeuro is aware of this issue and continues to work toward resolution. The CBRAIN and OpenNeuro teams communicate as needed when such error conditions are encountered.
One challenge encountered is that a small number of OpenNeuro dataset versions are not available on GitHub and thus unable to be accessed via DataLad. This can sometimes occur due to a large git commit exceeding GitHub's limits or for reasons related to the way dataset authors maintain and handle the dataset. However, OpenNeuro is aware of this issue and continues to work toward resolution. The CBRAIN and OpenNeuro teams communicate as needed when such error conditions are encountered.
Conclusions:
The integration of OpenNeuro with CBRAIN provides a streamlined experience for both OpenNeuro and CBRAIN users. By bridging OpenNeuro and CBRAIN, we offer the neuroimaging community a robust, scalable, and reproducible computational framework that facilitates efficient data sharing, analysis, and collaboration.
We aim to continue improving the user experience for analyzing OpenNeuro and other popular datasets using this approach.
We aim to continue improving the user experience for analyzing OpenNeuro and other popular datasets using this approach.
Neuroinformatics and Data Sharing:
Databasing and Data Sharing 1
Workflows 2
Informatics Other
Novel Imaging Acquisition Methods:
Anatomical MRI
BOLD fMRI
Keywords:
Computational Neuroscience
Data analysis
Data Organization
Electroencephaolography (EEG)
Informatics
MRI
Neurological
Open Data
Open-Source Code
Open-Source Software
1|2Indicates the priority used for review
Abstract Information
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Provide references using APA citation style.
Markiewicz, C. J. et al.(2021). The OpenNeuro resource for sharing of neuroscience data. eLife, 10 (e71774). https://doi.org/10.7554/eLife.71774
Sherif, T. et al. (2014). CBRAIN: A web-based, distributed computing platform for collaborative neuroimaging research. Frontiers in Neuroinformatics, 8(54), 1-13. https://doi.org/10.3389/fninf.2014.00054