Example Dataset for the BrainSuite BIDS App

This repository contains a subset of data from four subjects from the Amsterdam Open MRI Collection's Population Imaging of Psychology 2 (AOMIC-PIOP2) open-access dataset available from OpenNeuro, along with the files required to perform a demonstration of BrainSuite BIDS App's participant-level processing and BrainSuite Dashboard's quality control functionality. These examples are described in our bioRxiv manuscript and OHBM2023 abstract.

The files and directories in this repository include:

• AOMIC-PIOP2 : a BIDS-compliant study directory containing data from 4 participants; modalities include T1-weighted (T1-w), diffusion MRI (dMRI), resting-state functional MRI (rs-fMRI).
• aomic-piop2_preprocspec.json : a JSON file containing parameters for T1-weighted, dMRI, and rs-fMRI processing.
• eddyPrep: Two text files required for running FSL's eddy during participant-level processing. These files contain information regarding acquisition parameters for diffusion MRI data.
• README.md : brief information regarding this repository.

This demo will guide you through the steps necessary to process the T1w, dMRI, and rsfMRI data from the 4 participants as well as visualize intermediate outputs using the BrainSuite Dashboard. An example of the output produced from this dataset is available at https://brainsuite.github.io/DashboardDemo/.

Instructions for running participant-level workflows and BrainSuite Dashboard

Complete instructions for running this demo are available at https://brainsuite.org/BIDS/walkthrough/.

Support

Additional details regarding the BrainSuite BIDS App and its usage can be found on the BrainSuite website BIDS page. Please submit any questions or comments as issues on our BrainSuite BIDS App GitHub repository.

AOMIC-PIOP2 Dataset License

These data are freely available under a CC0 license.

References

Citation for the complete AOMIC-PIOP2 dataset:

• Snoek, L., van der Miesen, M. M., Van Der Leij, A., Beemsterboer, T., Eigenhuis, A., & Steven Scholte, H. (2020). AOMIC-PIOP2. OpenNeuro. [Dataset] doi: 10.18112/openneuro.ds002790.v2.0.0

Citation for the dataset paper:

• Snoek, L., van der Miesen, M. M., Beemsterboer, T., Van Der Leij, A., Eigenhuis, A., & Steven Scholte, H. (2021). The Amsterdam Open MRI Collection, a set of multimodal MRI datasets for individual difference analyses. Scientific data, 8(1), 85.

BrainSuite BIDS App citations:

• Kim Y, Joshi AA, Choi S, Joshi SH, Bhushan C, Varadarajan D, Haldar JP, Leahy RM, Shattuck DW (2023) BrainSuite BIDS App: Containerized Workflows for MRI Analysis. bioRxiv 2023.03.14.532686; doi: 10.1101/2023.03.14.532686

• Kim Y, Joshi AA, Choi S, Joshi SH, Bhushan C, Varadarajan D, Haldar JP, Leahy RM, Shattuck DW (2023) The BrainSuite BIDS App. To be presented at the 2023 Annual Meeting of the Organization for Human Brain Mapping (OHBM2023), Montreal, Canada July 2023.