Skip to main content

This lesson introduces the practical exercises which accompany the previous lessons on animal and human connectomes in the brain and nervous system. 

Difficulty level: Intermediate
Duration: 4:10
Speaker: : Dan Goodman

This tutorial introduces pipelines and methods to compute brain connectomes from fMRI data. With corresponding code and repositories, participants can follow along and learn how to programmatically preprocess, curate, and analyze functional and structural brain data to produce connectivity matrices. 

Difficulty level: Intermediate
Duration: 1:39:04

This video demonstrates each required step for preprocessing T1w anatomical data in brainlife.io.

Difficulty level: Beginner
Duration: 3:28
Speaker: :

The Allen Mouse Brain Atlas is a genome-wide, high-resolution atlas of gene expression throughout the adult mouse brain. This tutorial describes the basic search and navigation features of the Allen Mouse Brain Atlas.

Difficulty level: Beginner
Duration: 6:40

The Allen Developing Mouse Brain Atlas is a detailed atlas of gene expression across mouse brain development. This tutorial describes the basic search and navigation features of the Allen Developing Mouse Brain Atlas.

Difficulty level: Beginner
Duration: 6:35
Speaker: : Unknown

This tutorial demonstrates how to use the differential search feature of the Allen Mouse Brain Atlas to find gene markers for different regions of the brain, as well as to visualize this gene expression in three-dimensional space. Differential search is also available for the Allen Developing Mouse Brain Atlas and the Allen Human Brain Atlas.

Difficulty level: Beginner
Duration: 6:31
Speaker: : Unknown

This module covers some basic anatomy such as the brain’s major divisions (brainstem, cerebellum, cerebrum), the cerebral lobes (frontal, temporal, parietal, and occipital), the central and peripheral nervous systems, theories of cognition, and brain orientation terms.

Difficulty level: Beginner
Duration: 11:54
Speaker: : Harrison Canning

This is a hands-on tutorial on PLINK, the open source whole genome association analysis toolset. The aims of this tutorial are to teach users how to perform basic quality control on genetic datasets, as well as to identify and understand GWAS summary statistics. 

Difficulty level: Intermediate
Duration: 1:27:18
Speaker: : Dan Felsky

In this third and final hands-on tutorial from the Research Workflows for Collaborative Neuroscience workshop, you will learn about workflow orchestration using open source tools like DataJoint and Flyte. 

Difficulty level: Intermediate
Duration: 22:36
Speaker: : Daniel Xenes

In this hands-on session, you will learn how to explore and work with DataLad datasets, containers, and structures using Jupyter notebooks. 

Difficulty level: Beginner
Duration: 58:05

This video will document the process of uploading data into a brainlife project using ezBIDS.

Difficulty level: Beginner
Duration: 6:15
Speaker: :

This short video walks you through the steps of publishing a dataset on brainlife, an open-source, free and secure reproducible neuroscience analysis platform.

Difficulty level: Beginner
Duration: 1:18
Speaker: :

This video will document the process of visualizing the provenance of each step performed to generate a data object on brainlife.

Difficulty level: Beginner
Duration: 0:21
Speaker: :

This video will document the process of downloading and running the "reproduce.sh" script, which will automatically run all of the steps to generate a data object locally on a user's machine.

Difficulty level: Beginner
Duration: 3:44
Speaker: :

This video will document the process of creating a pipeline rule for batch processing on brainlife.

Difficulty level: Intermediate
Duration: 0:57
Speaker: :

This short video shows how a brainlife.io publication can be opened from the Data Deposition page of the journal Nature Scientific Data.

Difficulty level: Beginner
Duration: 2:25
Speaker: :

In this tutorial, you will learn the basic features of uploading and versioning your data within OpenNeuro.org.

Difficulty level: Beginner
Duration: 5:36
Speaker: : OpenNeuro

This tutorial shows how to share your data in OpenNeuro.org.

Difficulty level: Beginner
Duration: 1:22
Speaker: : OpenNeuro

Following the previous two tutorials on uploading and sharing data with OpenNeuro.org, this tutorial briefly covers how to run various analyses on your datasets.

Difficulty level: Beginner
Duration: 2:26
Speaker: : OpenNeuro

This video introduces the key principles for data organization and explains how you could make your data FAIR for data sharing on EBRAINS.

Difficulty level: Beginner
Duration: 10:54