@article{116,
  author = {Manoj Kumar and Michael Anderson and James Antony and Christopher Baldassano and Paula Brooks and Ming Cai and Po-Hsuan Chen and Cameron Ellis and Gregory Henselman-Petrusek and David Huberdeau and Benjamin Hutchinson and Peeta Li and Qihong Lu and Jeremy Manning and Anne Mennen and Samuel Nastase and Hugo Richard and Anna Schapiro and Nicolas Schuck and Michael Shavrtsman and Narayanan Sundaram and Daniel Suo and Javier Turek and David Turner and Vy Vo and Grant Wallace and Yida Wang and Jamal Williams and Hejia Jang and Xia Zhu and Mihai Capota and Jonathan Cohen and Uri Hasson and Kai Li and Peter Ramadge and Nicholas Turk-Browne and Theodore Willke and Kenneth Norman},
  title = {BrainIAK: The Brain Imaging Analysis Kit.},
  abstract = {<p>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.</p>
},
  year = {2021},
  journal = {Aperture Neuro},
}