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1 change: 1 addition & 0 deletions .gitignore
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# renv sandbox needed for renv version 0.16.0
renv/sandbox # OPTIONAL
.positai
24 changes: 12 additions & 12 deletions index.md
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| | |
| --- | --- |
| Date | Friday 25th July 2025 |
| Time | 1:00 - 5:00 PM Eastern Daylight Time |
| Location | Westin Harbour Castle, Pier 7&8 - Toronto, Canada |
| Date | Friday 10th July 2026 |
| Time | 8:00AM - 12:00PM British Summer Time |
| Location | Aurora Ballroom 2, 3, 5, 6 — InterContinental-The O2 — London, United Kingdom |
| Format | In-person workshop |

The workshop will provide practical information and an enhanced understanding
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| Webinar Title | Slides |
| --- | --- |
| [Data Structure and Formats](https://training.alz.org/products/4520/neuroimaging-pia-basics-of-neuroimaging-data-structure-and-formats) |[Slides](files/1_BasicsNeuroimaging_StructureFormat-Griffanti.pdf) |

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| [The Basics of Neuroimaging: Structural Magnetic Resonance Imaging (MRI)](https://training.alz.org/products/4524/neuroimaging-pia-the-basics-of-neuroimaging-structural-magnetic-resonance-imaging-mri) | [Slides](files/2_BasicsNeuroimaging_StructuralMRI-Cash.pdf) |

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| [Positron emission tomography (PET)](https://training.alz.org/products/4525/neuroimaging-pia-the-basics-of-neuroimaging-positron-emission-tomography-pet) | [Slides](files/3_BasicsNeuroimaging_PET-Betthauser.pdf) |

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| [Diffusion-Weighted Imaging (DWI)](https://training.alz.org/products/4526/neuroimaging-pia-the-basics-of-neuroimaging-diffusion-weighted-imaging-dwi) | [Slides](files/4_BasicsNeuroimaging_Diffusion_AlexaPB.pdf) |

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| [Functional Magnetic Resonance Imaging (fMRI)](https://training.alz.org/products/4528/neuroimaging-pia-the-basics-of-neuroimaging-functional-magnetic-resonance-imaging-fmri) | [Slides](files/5_BasicsNeuroimaging_Functional_Luigi.pdf) |

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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](./command-line.md)

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::::::::::::::::::::::::::::::::::::::::::

### Agenda
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| Time | Topic | Leader(s) |
| --- | --- | --- |
| 1:00-1:10 PM | Opening Remarks | David Cash and Tobey Betthauser |
| 1:10-1:40 PM | Image data: Basic Structure and Function | Ludovica Griffanti |
| 1:40-2:10 PM | Structural MRI | David Cash |
| 2:10-2:20 PM | Break | |
| 2:20-2:50 PM | Introduction to Advanced Imaging Analysis Sections (PET, dMRI,fMRI) | Tobey Betthauser, Alexa Pichet Binette, Luigi Lorenzini |
| 2:50-3:40 PM | Independent working session 1: Diffsion MRI, functional MRI, PET | Facilitated by all organizers |
| 3:40-3:50 PM | Break | |
| 3:50-4:40 PM | Independent working session 2: Diffsion MRI, functional MRI, PET | Facilitated by all organizers |
| 4:40-5:00 PM | Wrapup, Q&A, feedback | David Cash and Tobey Betthauser |
| 8:00-8:10 AM | Opening Remarks | David Cash and Tobey Betthauser |
| 8:10-8:40 AM | Image data: Basic Structure and Function | Ludovica Griffanti |
| 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 |
| 11:40AM - 12:00 PM | Wrapup, Q&A, feedback | David Cash and Tobey Betthauser |



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| Name | Organization |
| --- | --- |
| David Cash | UCL Queen Square Institute of Neurology, United Kingdom |
| Luigi Lorenzini | Amsterdam UMC, Netherlands |
| Luigi Lorenzini | University of Genoa, Italy |
| Ludovica Griffanti | University of Oxford, United Kingdom |
| Tobey Betthauser | University of Wisconsin, U.S.A. |
| Alexa Pichet Binette | Lund University, Sweden |
| Alexa Pichet Binette | Université de Montréal, Canada |

### Acknowledgements
These lessons are developed as part of the [Health and Biosciences IDEAS](https://healthbioscienceideas.github.io) project, which is a training initiative funded by [UKRI Innovation Scholars](https://www.ukri.org/opportunity/innovation-scholars-data-science-training-in-health-bioscience/) (MR/V03863X/1)

Thanks to the generous support of the Alzheimer's Association, the [International Society to Advance Alzheimer's Research and Treatment (ISTAART)](https://action.alz.org/personifyebusiness/default.aspx?tabid=1516) and the ISTAART Neuroimaging Professional Interest Area in terms of travel funding for the organizers.

Data for this course comes from:

* [Open Access Series of Imaging Studies](https://www.oasis-brains.org/)(OASIS) dataset. Many thanks to Pamela LaMontaigne and the OASIS team as Washington University for their support with the data.
* [Wisconsin Registry for Alzheimer's Prevention](https://wrap.wisc.edu/). Many thanks to the WRAP study teams and participants at the University of Wisconsin-Madison for their contributions.
* Chris Rorden's [dcm_validate data set](https://github.com/neurolabusc/dcm_validate). More information on this validation data set can be found in the [accompanying paper](https://www.nature.com/articles/s41597-025-05503-w).
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Expand Up @@ -8,7 +8,7 @@ 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. Here are the requirements for AWS
AppStream2.0 from the manufacturer’s website: Users can access AppStream 2.0
WorkSpaces from the manufacturer’s website: Users can access WorkSpaces
through an HTML5-capable web browser on a desktop computer such as a Windows,
Mac, Chromebook, or Linux computer. HTML5-capable web browsers that can be
used include the following: Google Chrome, Safari, Microsoft Edge.
Expand Down Expand Up @@ -67,7 +67,7 @@ This is now on the virtual machine's clipboard. You can past this in by
right-clicking in a terminal window and selecting paste.
![](fig/appstream_terminal_righclick.png){alt="Right click mouse in terminal"}

And voila! You shoudl see the paste in the virtual machine.
And voila! You should see the paste in the virtual machine.
![](fig/appstream_terminal_pasted.png){alt="Text pasted into terminal"}

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