Summary and Schedule
| Date | Friday 26th July 2024 |
| Time | 8AM - 12PM Eastern Daylight Time |
| Location | Marriott Philadelphia Downtown |
| Format | In-person workshop |
The workshop will provide practical information and an enhanced understanding on how to work with and analyze medical imaging data from magnetic resonance imaging (MRI) and positron imaging tomography (PET).
The initial portion of the workshop will focus on understanding the basic structure of an image, how to traverse images, data extraction, and how voxels relate to world coordinates.
Subsequent lectures will be followed by interactive sessions to demonstrate simple workflows including tissue segmentation, registration, and pre-processing steps for fMRI, DTI, and PET. The objective of the workshop is to ensure participants gain an in-depth appreciation of commonly used interpretive clinical and or research applications for each methodology.
Target Audience
This hands-on workshop can serve as a beginner or refresher course for established investigators, clinicians, and trainees involved in using imaging techniques to study Alzheimer’s disease, related disorders and normal ageing. Participants from any career stage are encouraged to join, including undergraduate students, graduate students, post-doctoral researchers and assistant professors engaged in clinical practice, research or teaching.
Requirements
Registrants must bring their own laptops to do the exercises (tablets or smartphones will not be sufficient). You will be provided with this repository and links to the “Basics of Neuroimaging” series of AAIC webinars. To get the most out of this workshop, we strongly recommend that you watch these webinars ahead of time. The links to the webinars and the slides are below.
At the workshop, we will all be using a standard environment, using a virtual machine (VM) hosted on the cloud. This ensures that everyone will be seeing the exact same screen for these lessons, regardless of if you are using a Mac or Windows operating system. You can find out more how to access this virtual machine below.
We will be using a Linux terminal to enter commands on the Unix shell. Before attending the session, you may want to familiarize yourself with the shell by running through the Command line lesson
Agenda
The workshop will consist of hands-on interactive sessions. The first session will focus on understanding the basic structure of imaging data, how to traverse images, data extraction, and how voxels relate to world coordinates. We will then go through the basic processing steps involving structural MRI data, demonstrating simple workflows including tissue segmentation, and registration.
The second half will consist of two independent working sessions, where facilitators will present interactive tutorials around different forms of neuroimaging analysis (structural MRI, fMRI, DTI or PET data), and the participants will then work on the tutorials of their choice, with assistance from the facilitators. The objective of the workshop is to ensure participants gain an understanding of how to start processing and analyzing various imaging modalities used in dementia research.
| Time | Topic | Leader(s) |
|---|---|---|
| 8:00-8:10 AM | Opening Remarks | David Cash and Tobey Betthauser |
| 8:10-8:40 AM | Image data: Basic Structure and Function | David Cash and Tobey Betthauser |
| 8:40-9:10 AM | Structural MRI | David Cash |
| 9:10-9:20 AM | Break | |
| 9:20-9:50 AM | Introduction to Advanced Imaging Analysis Sections (PET, dMRI,fMRI) | Tobey Betthauser, Alexa Pichet Binette, Luigi Lorenzini |
| 9:50-10:40 AM | Independent working session 1: Diffsion MRI, functional MRI, PET | Facilitated by all organizers |
| 10:40-10:50 AM | Break | |
| 10:50-11:40 AM | Independent working session 2: Diffsion MRI, functional MRI, PET | Facilitated by all organizers |
| 11:40 AM - 12:00 PM | Wrapup, Q&A, feedback | David Cash and Tobey Betthauser |
| Setup Instructions | Download files required for the lesson | |
| Duration: 00h 00m | 1. Imaging Data: Structure And Formats |
How is imaging data represented in a computer? What are some of the popular imaging formats used? How do I view and navigate around an image/ |
| Duration: 00h 32m | 2. Structural MRI: Bias Correction, Segmentation and Image Registration |
How do I process and quantify structural MRI scans? How do I register MRI with other modalities? How do I get key metrics out? |
| Duration: 01h 37m | 3. Processing and analysing PET brain images |
What does positron emission tomography measure? What are some common processing steps used for PET quantification? How can I extract key measurements of tracer binding from dynamic PET data? |
| Duration: 02h 22m | 4. Diffusion-weighted imaging (DWI) |
What does diffusion weighted imaging measure? What processing steps are needed when working with diffusion weigthed imaging data? What types of analyses are used with diffusion imaging in dementia resaerch? |
| Duration: 02h 34m | 5. Functional Magnetic Resonance Imaging (fMRI) |
What generates the signal that fMRI is measuring? What preprocessing steps are needed before analysing fMRI data? What type of analysis can I perform on pre-processed fMRI data? |
| Duration: 02h 46m | 6. Extra: Using the Command Line |
What is the command line interface? Why is it helpful in neuroimaging analysis? What are some common commands that I need to know? |
| Duration: 02h 58m | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
Connecting to your virtual machine
This page will tell you how to access your personal virtual (VM) to run these lessons. The virtual machine is essentially a “computer within a computer”. For this workshop, we have created virtual machines that have all the necessary software to perform the lessons.
Cloud based instructions
If you have completed the pre-survey questionnaire, then you should have received two emails. These may be located in your spam email:
- One should be from the email address no-reply@accounts.eu-west-2.amazonappstream.com with the title Start accessing your apps using Amazon AppStream 2.0. This will have the link to set your password and log in for the first time.
- A second email should come from the same email with the title
Amazon AppStream 2.0: New apps available.
- Click on the login link, and you should see the following page.
- Click on the Desktop item. It will then launch a
computer and you will be able to see the Desktop on the screen
- You will see a status message that it is starting your machine.
After that you should see a desktop of the computer you will be doing
the lesson with.
- If you get an error message saying “Resources not available, please wait a few minutes, as there will be more virtual machines spinning up to match the demand.
If you did not supply an email yet, please approach an instructor and we will setup your account
Organizing Committee
The following committee members have been developing and testing the content and will be on-hand to lead the sessions and assist individuals.
| Name | Organization |
|---|---|
| David Cash | UCL Queen Square Institute of Neurology, United Kingdom |
| Luigi Lorenzini | Amsterdam UMC, Netherlands |
| Ludovica Griffanti | University of Oxford, United Kingdom |
| Tobey Betthauser | University of Wisconsin, U.S.A. |
| Alexa Pichet Binette | Lund University, Sweden |
| Tavia Evans | Erasmus Medical Center, Netherlands |
Acknowledgements
These lessons are developed as part of the Health and Biosciences IDEAS project, which is a training initiative funded by UKRI Innovation Scholars (MR/V03863X/1)
Thanks to the generous support of the Alzheimer’s Association, the International Society to Advance Alzheimer’s Research and Treatment (ISTAART) and the ISTAART Neuroimaging Professional Interest Area in terms of travel funding for the organizers.
The data for this course comes from the Open Access Series of Imaging Studies(OASIS) dataset and the Wisconsin Registry for Alzheimer’s Prevention. Many thanks to Pamela LaMontaigne and the OASIS team as Washington University for their support with the data. Thanks to the WRAP study teams and participants at the University of Wisconsin-Madison for their contributions.
Special thanks to Christian Haselgrove (NITRC-CE), Courtney Waugh (Amazon), and Mark Watts (UCL) for their support in creating the infrastructure for this project.