CONN fcMRI workshop
in-depth training on the use of CONN for functional connectivity analyses
next CONN workshop:
online 2025 Sept 12 - Oct 13
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During the past four years (2021-date), graduate students, postdocs, and researchers from 181 institutions and 29 different countries have participated in the CONN workshop. Join this global community and learn everything CONN has to offer at the next CONN workshop online, starting Sept 12th 2025!
American University, USA
Arizona State University, USA
Auburn University, USA
Beth Israel Deaconess Medical Center, USA
Bielefeld University, Germany
Boston University, USA
Brown University, USA
Brigham and Women's Hospital, USA
Cambridge University, UK
Cardiff University, UK
Carelton University, Canada
Catholic University of Korea, South Korea
Central Institute of Mental Health, Germany
Champalimaud Foundation, Portugal
Chiba University, Japan
Chonnam National University, South Korea
Christ University, India
Christian Albrecht University of Kiel, Germany
Centre Hospitalier Universitaire de Saint Etienne, France
Columbia University, USA
Commonwealth Scientific and Industry Research Organisation, Australia
Concordia University, Canada
Cornell University, USA
Dartmouth College, USA
Dell Medical School, USA
Dr D Y Patil Medical College, India
Emma Pendleton Bradley Hospital
Emory University, USA
Federal University of Rio Grande do Norte, Brazil
Fundación Intecnus, Argentina
George Mason University, USA
Georgetown University, USA
Ghent University, Belgium
Griffith University, Australia
Hannover Medical School, Germany
Harvard University, USA
Hospital Clínico San Carlos, Spain
Hospital Italiano de Buenos Aires, Argentina
Hospital Universitari Joan XXIII, Spain
Icahn School of Medicine at Mount Sinai, USA
Institut National de la Santé Et de la Recherche Médicale, France
Johns Hopkins University, USA
Keio University, Japan
Kessler Foundation, USA
King Saud University, Saudi Arabia
King's College London, UK
Konkuk University, South Korea
KU Leuven University, Belgium
Kyoto University, Japan
Kyung Hee University, South Korea
Leibniz Institute for Neurobiology Magdeburg, Germany
Ludwig-Maximilians-Universität München, Germany
Massachusetts General Hospital (MGH), USA
Max Planck Institute for Human Cognitive and Brain Sciences, Germany
McGill University, Canada
McLean Hospital, USA
McMaster University, Canada
Medical University of South Carolina, USA
Medical University Vienna, Austria
MIT (Massachusetts Institute of Technology), USA
Nanyang Technology University, Singapore
National Cheng Kung University Hospital, Taiwan
National Hospital for Paraplegia, Spain
National Hospital Organization Tokyo Medical Center, Japan
National Institute of Mental Health (NIMH), USA
National Institutes of Information and Communications Technology, Japan
New York University, USA
New York University Abu Dhabi, UAE
Northeastern University, USA
Ohio University, USA
Örebro University, Sweden
Osaka University, Japan
Otto von Guericke University Magdeburg, Germany
Paris Brain Institute, Prance
Penn State University, USA
Polish Academy of Sciences, Poland
Radboud University, Netherlands
Redeemer University, Canada
Reichman University, Israel
Royal Holloway University of London, UK
Royal's Institute of Mental Health Research, Canada
RWTH Aachen University, Germany
Samsung Medical Center, South Korea
San Diego State University, USA
Scintillon Institute, USA
Semmelweis University, Hungary
Soonchunhyang University, South Korea
Spaulding Rehabilitation Hospital Boston, USA
St Jude Children's Research Hospital, USA
St Vincent's Hospital, Australia
Stanford University, USA
Technical University of Munich, Germany
Texas A&M University, USA
Ulsan National Institute of Science and Technology, South Korea
Umeå University, Sweden
Universidade de Santiago de Compostela, Spain
Università degli studi di Genova, Italy
Università degli Studi di Padova, Italy
Università degli Studi di Parma, Italy
Università degli Studi di Torino, Italy
Università degli Studi di Trento, Italy
Universitat Internacional de Catalunya, Spain
Universitat Jaume I, Spain
Universitat Pompeu Fabra, Spain
Universitätsmedizin Greifswald, Germany
Université Catholique de Louvain, Belgium
Université de Bordeaux, France
Université de Montréal, Canada
Université du Québec à Montréal, Canada
Université Grenoble Alpes, France
University College London (UCL), UK
University Health Network, Canada
University Hospital Bonn, Germany
University Hospital Jena, Germany
University Medical Center Groningen, Netherlands
University Medical Center Goettingen, Germany
University of Alabama, USA
University of Alabama at Birmingham, USA
University of Alberta, Canada
University of Amsterdam, Netherlands
University of Arizona, USA
University of Bern, Switzerland
University of British Columbia, Canada
University of California San Diego, USA
University of California San Francisco, USA
University of California Irvine, USA
University of California Los Angeles, USA
University of Cincinnati, USA
University of Colorado Boulder, USA
University of Colorado Anschutz, USA
University of Connecticut, USA
University of Delaware, USA
University of Deusto, Spain
University of Florida, USA
University of Freiburg, Germany
University of Geneva, Switzerland
University of Glasgow, UK
University of Haifa, Israel
University of Hong Kong, China
University of Illinois, USA
University of Innsbruck, Austria
University of Kentucky, USA
University of Liverpool, UK
University of Ljubljana, Slovenia
University of Luzern, Switzerland
University of Maryland Baltimore, USA
University of Maryland College Park, USA
University of Massachussets, USA
University of Michigan, USA
University of Minnesota, USA
University of Missouri, USA
University of Montreal, Canada
University of Muenster, Germany
University of Nebraska, USA
University of North Carolina at Chapel Hill, USA
University of Nottingham, UK
University of Oldenburg, Germany
University of Oregon, USA
University of Ottowa, Canada
University of Pittsburgh, USA
University of Queensland, Australia
University of Rochester, USA
University of Southern California, USA
University of Texas, USA
University of Tokyo, Japan
University of Toronto, Canada
University of Toronto Scarborough, Canada
University of Utah, USA
University of Vienna, Austria
University of Waterloo, Canada
University of Wisconsin Milwaukee, USA
University of Zürich, Switzerland
Uppsala University, Sweden
Upstate Medical University, USA
Uskudar University, Turkey
Vanderbilt University, USA
Virginia Tech University, USA
Wake Forest University, USA
Washington University in St. Louis, USA
West Virginia University, USA
Yale University, USA
Resting-state functional connectivity has taken the brain imaging community by storm. Five to ten minutes of MRI data collection from almost any subject or patient can reveal organized systems of activity in the brain that can be used in a wide variety of ways for basic and clinical research, and even to guide non-invasive brain stimulation.
CONN is one of the most popular software packages for functional connectivity Magnetic Resonance Imaging (fcMRI) analyses of resting state and task fMRI data, with over 6,000 published studies to date using CONN. It is ranked in the top 1% most frequently viewed and downloaded neuroimaging tools in NITRC, and it enjoys a large and active user community, with over 2,000,000 page-views and 14,000 user-support posts.
In this workshop the neuroimaging researcher and lead developer of CONN, Alfonso Nieto-Castanon, brings his exceptional expertise to offer a course covering all aspects of functional connectivity Magnetic Resonance Imaging (fcMRI) analyses in CONN. The course welcomes both new and existing users. It covers basic and advanced features of CONN presented alongside a comprehensive review of key topics and state-of-the-art methods in functional connectivity analyses. Classroom presentations are followed by substantial time for questions and exercises using CONN with expert guidance available. Course attendees receive a CONN certificate of completion at the end of the workshop.
This workshop is offered in two different modalities (offered at different times):
The first is online/virtual through Zoom, where the full course contents are presented over a period of 5 weeks, with 3½-hour live classes twice a week. All live Zoom meetings are also recorded and made available to participants to review at any time during the course and up to one month after the course ends. There are also optional practice homework assignments every week and faculty is available during office-hour segments for additional questions or support.
The second modality is in-person at the Martinos Center for Biomedical Imaging (MGH / Harvard / MIT) in Boston, where an accelerated one-week version of this course is offered. Classes are held Monday to Friday from 9AM to 5PM during a single week. Course contents are identical to the virtual/online course except for homework assignments, video recordings, or office-hours, which are not offered in the in-person modality due to time constraints.
Course contents include:
Essential topics in CONN such as data import, fMRI preprocessing pipelines, data denoising and quality control procedures, seed-based and ROI-to-ROI functional connectivity measures, or group-level General Linear Model (GLM) analyses and inferences
The theory and practice of all specialized functional connectivity methods available in CONN, including generalized Psycho-Physiological Interaction models, temporal modulation analyses, Independent Component Analyses, voxel-to-voxel connectivity measures, network- and cluster- level statistics, graph theory, functional connectivity MultiVariate Pattern Analyses, or dynamic connectivity analyses
Discussions about many practical aspects of fcMRI analyses, covering topics such as clinical applications of functional connectivity, how to design GLM analyses addressing specific research questions, or how to create batch scripts and use parallelization options in High Performance Computing environments
FAQ
1. How many individuals are accepted into the course?
Due to the interactive nature of this course only 40 people are accepted into each workshop. We apologize in advance if we cannot accommodate all who wish to attend
2. Are there any differences between the online/virtual and in the in-person course?
Faculty, course contents, and live-class hours are identical in the two courses. Other than the venue, the only difference is that office-hours or video-recordings are not offered during the in-person course due to time and logistic constraints
3. How much does the course cost?
Registration fees vary between €1,000 and €2,000 depending on course and applicable discounts. See course registration for details
4. Do postdocs qualify for the student rate?
No, sorry, only full-time graduate students qualify for the student rate (postdocs qualify for the academic rate)
5. I cannot pay by credit card. Do I have any other options?
Yes, you may request an invoice and pay by bank transfer. Initiate your registration normally and send an email to the course administrator requesting a bank transfer option. Please provide your institution details to be included in your invoice, and allow additional time (up to 5 days) for the transfer to be processed
6. When does registration close?
Registration automatically closes when a course is fully booked. Courses have always reached full occupancy, and many registrations take place during the last few weeks before the start of the course. Consider registering earlier to avoid stress and guarantee your place in the workshop
7. How do I prepare for the course?
Before the start of the course you will be asked to prepare your computer and download a sample dataset using the instructions described in the computer setup section. You will also be asked to provide an informal biosketch (no more than two paragraphs in length), to be distributed to the faculty and to other course participants, briefly describing your background, experience, and what you most hope to get out of the program. A few days before the start of the course you will receive a welcome email with instructions to obtain your login credentials and access the course materials
8. I have a conflict and cannot attend some of the classes. Can I view the class recordings later?
Of course, in the online/virtual course all live Zoom meetings are recorded and uploaded to the course website after each class so participants may review them later (these recordings can be viewed at any time during the course and up to one month after the course ends)
9. I already have a dataset that I am working on. Can I use this during the course instead of the sample dataset?
Yes, of course! Using your own data during the course is highly encouraged (please note that due to time constraints particularly in the in-person course we may have limited ability to address or fix issues specific to your own dataset if we are not made aware of these well in advance)
10. I have some questions about my own analyses or data. Is it possible to get your comments on these?
Yes, of course! In addition to in-class Q&A, there is an Open Questions shared document where you can post any questions that you would like us to address during the course. We will try to address some of those questions directly during the live class hours when the topics most relevant to each question are discussed, or during office-hour segments (in the virtual course only) if the questions are too specific or if they require us to take a closer look at your data
11. What are office-hours?
There are typically four office-hour segments during the CONN workshop (in the virtual course only). Each segment consists of an additional unstructured Zoom meeting dedicated to addressing any questions that may have not been already fully addressed either during the course live classes or in the Open Questions document. Attendance is optional, time for questions is divided among all those present, and questions may include problems with the homework or issues specific to your own datasets or analyses
See also:
Documentation: read CONN's manual and find installation and configuration instructions
Support: ask questions about CONN, report bugs or request features
Tutorials: find self-guided tutorials to learn about CONN and start using it right away