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Functional magnetic resonance imaging (fMRI) offers a rich source of data for studying the neural basis of cognition. Here, we describe the Brain Imaging Analysis Kit (BrainIAK), an open-source, free Python package that provides computationally optimized solutions to key problems in advanced fMRI analysis. A variety of techniques are presently included in BrainIAK: intersubject correlation (ISC) and intersubject functional connectivity (ISFC), functional alignment via the shared response model (SRM), full correlation matrix analysis (FCMA), a Bayesian version of representational similarity analysis (BRSA), event segmentation using hidden Markov models, topographic factor analysis (TFA), inverted encoding models (IEMs), an fMRI data simulator that uses noise characteristics from real data (fmrisim), and some emerging methods. These techniques have been optimized to leverage the efficiencies of high-performance compute (HPC) clusters, and the same code can be seamlessly transferred from a laptop to a cluster. For each of the aforementioned techniques, we describe the data analysis problem that the technique is meant to solve and how it solves that problem; we also include an example Jupyter notebook for each technique and an annotated bibliography of papers that have used and/or described that technique. In addition to the sections describing various analysis techniques in BrainIAK, we have included sections describing the future applications of BrainIAK to real-time fMRI, tutorials that we have developed and shared online to facilitate learning the techniques in BrainIAK, computational innovations in BrainIAK, and how to contribute to BrainIAK. We hope that this manuscript helps readers to understand how BrainIAK might be useful in their research.
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Deep Markov Factor Analysis: Towards Concurrent Temporal and Spatial Analysis of fMRI Data
Factor analysis methods have been widely used in neuroimaging to transfer high dimensional imaging data into low dimensional, ideally interpretable representations. However, most of these methods overlook the highly nonlinear and complex temporal dynamics of neural processes when factorizing their imaging data. In this paper, we present deep Markov factor analysis (DMFA), a generative model that employs Markov property in a chain of low dimensional temporal embeddings together with spatial inductive assumptions, all related through neural networks, to capture temporal dynamics in functional magnetic resonance imaging (fMRI) data, and tackle their high spatial dimensionality, respectively. Augmented with a discrete latent, DMFA is able to cluster fMRI data in its low dimensional temporal embedding with regard to subject and cognitive state variability, therefore, enables validation of a variety of fMRI-driven neuroscientific hypotheses. Experimental results on both synthetic and real fMRI data demonstrate the capacity of DMFA in revealing interpretable clusters and capturing nonlinear temporal dependencies in these high dimensional imaging data.
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- Award ID(s):
- 1835309
- PAR ID:
- 10345366
- Date Published:
- Journal Name:
- Neural Information Processing Systems (NeurIPS)
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract The study presented in this paper applies hidden Markov modeling (HMM) to uncover the recurring patterns within a neural activation dataset collected while designers engaged in a design concept generation task. HMM uses a probabilistic approach that describes data (here, fMRI neuroimaging data) as a dynamic sequence of discrete states. Without prior assumptions on the fMRI data's temporal and spatial properties, HMM enables an automatic inference on states in neurocognitive activation data that are highly likely to occur in concept generation. The states with a higher likelihood of occupancy show more activation in the brain regions from the executive control network, the default mode network, and the middle temporal cortex. Different activation patterns and transfers are associated with these states, linking to varying cognitive functions, for example, semantic processing, memory retrieval, executive control, and visual processing, that characterize possible transitions in cognition related to concept generation. HMM offers new insights into cognitive dynamics in design by uncovering the temporal and spatial patterns in neurocognition related to concept generation. Future research can explore new avenues of data analysis methods to investigate design neurocognition and provide a more detailed description of cognitive dynamics in design.more » « less
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Accepted Manuscript1.0
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