A protocol for working with open-source neuroimaging datasets

Abstract

Large, publicly available neuroimaging datasets are becoming increasingly common, but their use presents challenges because of insufficient knowledge of the tool options for data processing and proper data organization. Here, we describe a protocol to lessen these barriers. We describe the steps for the search and download of the open-source dataset. We detail the steps for proper data management and practical guidelines for data analysis. Finally, we give instructions for data and result sharing on public repositories and preprint services. For complete details on the use and execution of this profile, please refer to Horien et al. (2021).

Keywords: Behavior; Bioinformatics; Cognitive Neuroscience; Neuroscience.

Graphical abstract

Figure 1

An overview of open-source datasets and open repositories (A) For each dataset listed in the leftmost column, sample size is indicated, along with the type of data included (‘Data modalities’). ‘Data level’ refers to the level of preprocessing: white circle, raw data; gray circle, some level of preprocessed data; black, processed data (for example, statistical maps, connectivity matrices, etc.). (B) For each open repository (i.e., a collection of open datasets) listed in the leftmost column, an estimate of the number of open datasets is listed. Datasets of interest are highlighted (‘Featured large datasets’). Sample sizes and the number of open datasets are current as of September 2021. Users are encouraged to visit the website associated with each dataset before use, as sample sizes, access conditions, etc. may change. Figure adapted with permission from (Horien et al., 2021).

Figure 2

Steps to download data from OpenNeuro

Figure 3

BIDS format (A) Each participant has folders containing raw anatomical and functional data. (B) Data generated during the course of the study are stored in a derivatives folder.