Hands on brain dynamics on the connectome sinergia online summer school 2021

Oct 11-12, 2021

Instructors: Sebastien Tourbier, Isotta Rigoni, Nicolas Roehri, Maria Rubega, Jolan Heyse, Joan Rué-Queralt, Katharina Glomb, Ane Lopez-Gonzalez, Manel Vila-Vida

General Information

Brain Dynamics on the Connectome Sinergia Online Summer School 2021 aims to introduce advanced topics in multimodal brain connectomics. The lectures and tutorials follow the structure of a pipeline to estimate structural connectivity from diffusion MRI data, dynamic functional connectivity from M/EEG recordings and integrate them together with computational modeling.

Who can attend?: This summer school is open to anyone from engineers to doctors. You don't need to have any previous knowledge of the tools that will be presented at the workshop before. However, it is highly recommended to be familiar with neuroimaging, the UNIX shell environment, and be confortable with scripting/programming in python and matlab. Note that his summer school is subject to online registration via this form. However, a maximal number of 70 participants has been reached and anyone applying now will be put on a waiting list.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: Oct 11-12, 2021. Add to your Google Calendar.

Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if there is anything we can do to make this workshop more accessible to you.

Contact: Please email joan.rue-quelralt@chuv.ch or sebastien.tourbier@alumni.epfl.ch for more information.

Roles: To learn more about the roles at the Summer School (who will be doing what), refer to the Carpentries Workshop FAQ.

Schedule

Day 1

08:30 Introductory words by Patric Hagmann
09:00 Get to know each other
09:30 Building the Connectome
10:00 Morning break
10:30 Diffusion and Tractography
11:00 EEG Basics
11:30 Electrical Source Imaging
12:00 Lunch break
13:00 Tutorial 1 - Brain Imaging Data Structure BIDS
14:00 Tutorial 2 - Anatomical and Diffusion pipelines
15:00 Afternoon break
15:30 Tutorial 3 - EEG pipeline
16:30 Social event

Day 2

   
09:00 Analysis of Brain Networks
09:30 Functional Connectivity (FC) and Dynamic FC
10:00 Morning break
10:30 Combining Structure and Function
11:00 Connectome Spectral Analysis
11:30 Computational Modelling
12:00 Lunch break
13:00 Tutorial 4 - Dynamic Functional Connectivity
14:00 Tutorial 5 - Connectome Spectral Analysis
15:00 Afternoon break
15:30 Tutorial 6 - Computational Modelling
16:30 Wrap up by Serge Vulliemoz

Setup

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Software Carpentry or ReproNim workshops, you could learn by "coding along" with the Instructors at the time of the tutorials. To do this, you will need to have both the window for the running Virtual Machine and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

This blog post from The Carpentries includes detailed information on how to set up your screen to follow along during the workshop.

Getting ready with the virtual machine provided for the tutorials

Install Virtual Box

Download and import the VM image file

Note: You will needs at least 50GB of space available

Configure a shared folder

Once the VM is imported, you can configure one or multiple local folder(s) to be mounted inside your VM to easily share files back and forth.

Start the VM

A few tools included in the VM require the use of a license and so you will need to provide your own at first use. More details are provided in the two next sections.

FreeSurfer license

A license key must be obtained to make the FreeSurfer tools operational. Obtaining a license is free and comes in the form of a license.txt file.

  1. Get one: if you do not have a Freesurfer license.txt key file yet, you can get one at the following link
  2. Install: once you obtain the license.txt file, download it inside the VM (for instance you can use the shared folder previously configured) and copy it to the FreeSurfer installation directory (i.e. "$HOME/Softwares/freesurfer" defined by the $FREESURFER_HOME environment variable).

Trackvis license

A license key must be obtained to be able to use Trackvis, a tool for viewing fibers reconstructed with tractography.

  1. Get one: if you do not have a Trackvis license key yet, you can get one by creating a new account at the download request page of Trackvis website.
  2. Validate: once your account is created and you have received the email with a summary of your Name / Institution / License Key, you can start Trackvis. To do so, open a terminal and type trackvis. Fill the fields with the information in the email and type "OK".

Congrats, you are all set!

Issues

Frequently Asked Questions (FAQ)

  1. When installing the VM I get the error code E_INVALIDARG (0x80070057) (Windows) / VBOX_E_IPRT_ERROR (0x80BB0005) (MacOSX):

    This error is related to a lack of space in the disk. You should free some space (>70GB) before importing the Virtual Machine Image (.ova file).

  2. I don’t have space in my laptop / PC. Can I install the VM in an SSD / Hard drive?

    Yes, it won’t be the optimal solution in terms of speed, but it is possible. You will need to go to:

    Virtual Machine > Preferences > Genera > Default Machine Folder

    and change the location to be in the external drive. Make sure to delete the folder created by a failed import in the old “Default Machine Folder”. Otherwise you might get the same error as in 1).

  3. One of the software crashes during execution.

    This is probably related to a lack of computational resources dedicated to the VM. You can try increasing them. We recommend setting them to at least 12 GB of RAM and the maximum amount of cores available to the VM.

  4. How can I copy the Freesurfer license to the appropriate folder in the VM?

    You need to first configure a shared folder before starting the VM. Then you will be able to transfer files back and forth from your computer to the VM. You can find the instructions on how to do this in this section of the tutorial materials.

  5. How should I access the presentations and tutorials? Via Zoom or GatherTown?

    The best way is by using the Auditorium link in GatherTown. In this way, others would know that you are around in the virtual space of the summerschool and will be able to interact with you. This would also make the task of going back and forth from GatherTown to Zoom easier. But anyone is free to access directly from Zoom. Be aware that interactions with the speakers during the breaks will only be possible in GatherTown.

  6. Where should I ask my questions to be considered during the lecture and tutorial sessions?

    You should ask your questions in the two following Slack channels dedicated to the lectures and tutorials separately on the summerschool Slack workspace:

    If you haven’t joined the Slack workspace yet, you can join it here!