Working with Neuro Imaging Data and the Brain Imaging Data Structure (BIDS)

Canadian Open Neuroscience Platform (CONP)

Online

October 22nd to November 19th, 2021

11:00 am to 1:30 pm

Instructors: Hannes Almgren, Amin Banihashemi, Kesavi Kanagasabai, Davide Momi, Bradley Karat, Ladan Shahshahani, Shreyas Harita, Yu-Fang Yang

Helpers: Sara Stephenson, James Desjardins

General Information

This is a pilot workshop, testing out a lesson that is still under development. The lesson authors would appreciate any feedback you can give them about the lesson content and suggestions for how it could be further improved.

Registration: https://mcgill.zoom.us/meeting/register/tZcucOitqj0rHtRQFuG0KVxGyNvzs6mpR7bz.

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

When: October 22nd to November 19th, 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 you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email jdesjard@sharcnet.ca for more information.

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

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1, October 22nd

Before starting	Pre-workshop survey
11:00 am to 1:30 pm	Introduction to working with MRI data and BIDS with Python

Day 2, October 29th

11:00 am to 1:30 pm	Structural neuro-imaging analysis in Python

Day 3, November 5th

11:00 am to 1:30 pm	dMRI analysis in Python
11:00 am to 11:20 am	Introduction to Diffusion MRI data
11:20 am to 11:40 am	Preprocessing dMRI data
11:40 am to 11:55 am	Break
11:55 am to 12:00 pm	Local fiber orientation reconstruction
12:00 pm to 12:20 pm	Diffusion Tensor Imaging (DTI)
12:20 pm to 12:35 pm	Constrained Spherical Deconvolution (CSD)
12:35 pm to 12:50 am	Break
12:50 pm to 12:55 pm	Tractography
12:55 pm to 1:00 pm	Local tractography
1:00 pm to 1:15 pm	Deterministic tractography
1:15 pm to 1:30 pm	Probabilistic tractography
End	Post-workshop survey

Day 4, November 12th

11:00 am to 1:30 pm	Resting-state analysis in Python

Day 5, November 19

11:00 am to 11:05 pm	Setup
11:05 am to 11:25 pm	Introduction to EEG-BIDS
11:25 am to 11:50 pm	Matlab: need to knows
11:50 am to 12:15 pm	Initializing data into BIDS
12:15 pm to 12:40 pm	The EEG structure elements
12:40 pm to 1:05 pm	Basic ERP processing
1:05 pm to 1:30 pm	Scripting from the history
End	Post-workshop survey

The lesson taught in this workshop is being piloted and a precise schedule is yet to be established. The workshop will include regular breaks. Please contact the workshop organisers if you would like more information about the planned schedule.

Setup

To participate in a workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

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 Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) 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:

Two monitors: If you have two monitors, plan to have the tool you are learning up on one monitor and the video conferencing software on the other.
Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.

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

Please check the “Setup” page of each lesson:

https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/

https://carpentries-incubator.github.io/SDC-BIDS-sMRI

https://carpentries-incubator.github.io/SDC-BIDS-dMRI

https://carpentries-incubator.github.io/SDC-BIDS-fMRI

https://carpentries-incubator.github.io/SDC-BIDS-EEG-EEGLAB

https://carpentries-incubator.github.io/SDC-EEGLAB

for instructions to follow to obtain the software and data you will need to follow the lesson.