How to stop worrying and love computational neuroimaging of the visual cortex

Monday, May 20, 2024, 2:00 – 5:00 pm, Banyan/Citrus

Organizers: Noah Benson, University of Washington & Mark Schira, University of Wollongong

Speakers: Noah C. Benson; Fernanda L. Ribeiro; Mark M. Schira

To register or for more information about this workshop, please visit

Contemporary vision science requires substantial computational resources and expertise, yet traditional vision science training does not typically focus on learning, maintaining, or keeping up-to-date with modern computational tools. Simultaneously, the space of open source software tools, such as fMRIprep, and open standards, such as BIDS, available for vision and neuroimaging research has exploded in recent years. This environment greatly facilitates robust and reproducible research but is simultaneously difficult to navigate for investigators of all experience levels.

This workshop will demonstrate how laboratory management, reproducible scientific practices, and contemporary neuroimaging analysis methods can all be greatly simplified using existing tools that abstract away the technical complexities of managing software and hardware resources. We will begin this workshop by introducing the Neurodesk platform (, a free, open-source system for managing laboratory data, installations of research software, and computational jobs for lab members. Neurodesk is modular, includes most common neuroscience software tools, and can run as easily on a researcher’s PC, in the cloud, or on a lab server. All participants in the workshop will be given access to a Neurodesk cloud instance that can be used to follow along with tutorials and examples in the session (no installation required by participants). We will discuss how Neurodesk can be used as a teaching, management, and high performance computing tool before demonstrating the use of several well-established open-source software tools in Neurodesk by creating a simple, reproducible workflow together that is focused in particular on connecting models of the cortical surface to voxel-based analyses, including the drawing of visual area boundaries and features on the cortical surface. Finally, we will discuss cutting-edge tools for brain annotation: convolutional neural networks.

This workshop is intended for all audiences: students and junior researchers can expect to learn about powerful tools and techniques that facilitate high-quality research, while senior investigators can expect to learn about valuable tools for lab management and teaching. All researchers stand to benefit from the adoption of community-supported open-source tools such as Neurodesk and the many independent tools supported by Neurodesk that we will demonstrate.