Developing and Validating Open Source Tools for Advanced Neuroimaging Research

Almost all scientific research relies on software. This is particularly true for research that uses neuroimaging technologies, such as functional magnetic resonance imaging (fMRI). These technologies generate massive amounts of data per participant, which must be processed and analyzed using specialized software. A large portion of these tools are developed by teams of researchers, rather than trained software developers. In this kind of ecosystem, where the majority of software creators are scientists, rather than trained programmers, it becomes more important than ever to rely on community- based development, which may explain why most of this software is open source. It is in the development of this kind of research-oriented, open source software that I have focused much of my graduate training, as is reflected in this dissertation.

First, I will describe my work to help develop and maintain tedana, a Python library for denoising multi-echo fMRI data. Second, I will review another library I maintain as the primary developer, NiMARE. NiMARE is a Python library for performing neuroimaging meta-analyses and derivative analyses, such as automated annotation and functional decoding. I will present NiMARE as a hybrid software paper with embedded tutorial code exhibiting the functionality of the library. This paper is currently hosted as a Jupyter book that combines narrative content and code snippets that can be executed online. Finally, in addition to research software development, I have focused my graduate work on performing reproducible, open fMRI research. To that end, I will describe a replication and extension of a recent paper on multi-echo fMRI denoising methods. This replication was organized as a registered report, in which the introduction and methods were submitted for peer review before the analyses were performed. I will conclude with a reflection on how research software development and reproducible research can advance cognitive neuroscience.

Major Professor: Dr. Angela Laird