Functional MRI (fMRI) is one of the most used tools for learning about how the human brain works. It is a noninvasive way to see how different parts of the brain respond to stimuli and support cognitive processes, such as language, remembering, or using tools. I have been using fMRI for over a decade to understand how different kinds of knowledge are organized in the brain. I’m especially interested in two domains of knowledge: how diverse concepts (e.g., “dog”, “hammer”, “hope”) are stored in the brain, which is often referred to as semantic memory, and how spatial information about the environment is stored in memory so that we can navigate around in the world. I established my lab at Jefferson-Moss Rehabilitation Research Institute last year because I want to apply my research to help people who have lost critical functions related to semantic and spatial memory due to stroke or neurodegeneration. Through my role at the Institute, I had the opportunity to organize the recent AFNI (Analysis of Functional NeuroImages) Bootcamp in Philadelphia, which was held April 21-23, 2026.
Highlights from the Recent AFNI Neuroimaging Workshop Hosted at Our Institute
Current Neuroimaging Challenges & How AFNI Helps Solve Them
A major challenge faced by me and other researchers that use fMRI is figuring out how to process and analyze the huge amounts of complex brain data produced in an fMRI experiment. Luckily for us, there are many software packages out there designed to solve these problems and make it easier to be a neuroscientist. However, the large number of fMRI analysis programs makes it difficult for the field of cognitive neuroscience to standardize methods across labs, and for individual researchers to decide which program to use and why. Furthermore, it is not easy to learn how to use these programs—they are sophisticated tools that were built to solve sophisticated problems. Therefore, a lot of training is required to be proficient in using these analysis packages and to perform a successful fMRI experiment. I happily accept the fact that I will always be a student of fMRI research, always learning new ways to study the human brain, and always being impressed by how the field advances to solve new problems.
Throughout my career, I have been using a software package called AFNI in my fMRI experiments. AFNI is a freely available resource for processing and analyzing fMRI data provided by the Scientific and Statistical Computing Core (SSCC) of the National Institute of Mental Health Intramural Research Program. The AFNI team is a wonderful group of brilliant people who are constantly developing new tools for fMRI analysis—and they are very nice, too. They are always available to answer questions (I’ve certainly bugged them many times), and they even offer a course to teach people how to use AFNI to analyze their data. They call it the AFNI Bootcamp. It is an intensive three-day course that covers fMRI data analysis, from the basics to advanced methods. I attended the bootcamp years ago, and I knew that I wanted to bring the AFNI Bootcamp to Philly when I got here.
Bringing the AFNI Bootcamp to Philadelphia
There were a few reasons why I wanted to host the AFNI Bootcamp in Philly. The main reason was that I wanted to provide a resource for brain researchers in the area to learn about fMRI analysis directly from the developers of one of the most used software packages. Second, I wanted to provide an opportunity for researchers from different institutes, who might not know each other or about the research happening in the area, to meet each other, talk about their work, and discuss the issues they face in their fMRI experiments.
To this end, the MindCORE Neuroimaging Center sponsored a pre-Bootcamp event for attendees to tour their facility and see a demo of how fMRI data are collected, (Shout out to the Institute’s own Senior Clinical Research Coordinator, Tejaswini Sudhakar, for being our volunteer subject in the MRI scanner.) Afterward, MindCORE hosted a happy hour on the University of Pennsylvania campus, where attendees got to relax and get to know each other before the intensive AFNI Bootcamp started the next day.
I would like to thank Heather Calvert, the Executive Director of MindCORE, and Brock Kirwan, PhD, the Director of the MindCORE Neuroimaging Center, for their support and invaluable help executing a successful day of educational and social events. A little more selfishly, I just wanted to meet other fMRI researchers in the Philly area so I could learn about what they are doing and potentially start collaborations of my own.
Workshop Attendees, Instructors & Content
I consider the AFNI Bootcamp to be a huge success. Over forty researchers from around the Philly area came together to learn how to use AFNI for fMRI analysis. The attendees represented many institutes and Universities in Philadelphia and the surrounding area—including, Thomas Jefferson University, Jefferson Moss Rehabilitation Research Institute, University of Pennsylvania, Drexel University, Temple University, the Monell Chemical Senses Center, Princeton University, the University of Delaware, and the University of Maryland. Furthermore, the attendees, instructors, and I got to know each other and learn about each other’s work. It was a lot of fun.
The Bootcamp was taught by AFNI developers, Paul Taylor, PhD (Director of the SSCC), Gang Chen, PhD (statistician extraordinaire), and Justin Rajendra (seasoned data wrangler). The trio explained how to process and analyze fMRI data from start to finish with AFNI, and why a researcher might make certain decisions at each step.
For example, they explained what to do if a participant moved too much in the MRI scanner. This is a big problem in fMRI research. They also taught us different analysis strategies and how to implement them using AFNI. Of equal importance, they were available during the breaks to talk to each attendee one-on-one about specific questions they might have about their experiments.
Workshop Impacts & How these Training Opportunities Advance the Field
I certainly learned a lot during the week. I learned new things about how to use AFNI. I also learned about many exciting and important brain research projects happening in the Philly area, and I made new friends in the process. In addition, I learned a lot about planning and executing an event that educates and connects people. First and foremost, I learned that it takes a large amount of work. This event would not have been possible without the support and contributions of many people at our Institute.
Events like the AFNI Bootcamp are a critical part of science. Scientists not only need to learn how to perform experiments and use the newest methods in their field, but they also need opportunities to meet each other and talk about their work. By getting to know about each other’s work, scientists can think about their own work differently, forge collaborations, and support one another.
Another benefit of these types of events, especially for early-stage trainees and non-scientist members of the community, is that they help to demystify neuroscience research. The sheer complexity of the human brain and the mysteries of our own minds can be daunting for someone just learning about the subject. Reaching out to people and explaining concepts in a way that is easy to understand helps early-career scientists gain confidence as they learn. It also helps the community understand what us neuroscientists are up to and why they should care about (and support) brain research. The AFNI instructors made this kind of outreach look easy by giving clear and practical descriptions of complex problems and the sophisticated tools they developed to solve them. I look forward to hosting more events like this that help to build and foster a community of brain researchers in Philly, and to drive new innovations and advances in neuroscience and neurorehabilitation.