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Using brainlife.io

This course provides several visual walkthroughs documenting how to execute various processes in brainlife.io, an open-source, free and secure reproducible neuroscience analysis platform. The platform allows to analyze Magnetic Resonance Imaging (MRI), electroencephalography (EEG) and magnetoencephalography (MEG) data. Data can either be uploaded from local computers or imported from public archives such as OpenNeuro.org. Over 400+ data processing apps are available on brainlife.io to build custom data workflows. Thousands of jobs can be submitted using shared clusters or on users' compute resource. Users can perform group-level statistical analysis or apply machine learning methods using Jupyter notebooks. A single record containing the entire data workflow (from raw data to published figures) can be published addressed with a unique digital object identifier (DOI).

Course Features
Tutorials
Visual Walkthroughs
Lessons of this Course
1
1
Duration:
2:41

This brief video provides an introduction to brainlife.io, a free cloud computing platform for neuroimaging data analysis. 

2
2
Duration:
2:00

This quick visual walkthrough presents the steps required in uploading data into a brainlife project using the graphical user interface (GUI). 

3
3
Duration:
6:15

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

4
4
Duration:
0:35

This short walkthrough documents the steps needed to find a dataset in OpenNeuro, a free and open platform for sharing MRI, MEG, EEG, iEEG, ECoG, ASL, and PET data, and import it directly to a brainlife project. 

5
5
Duration:
1:18

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

6
6
Duration:
1:07

This lesson provides a brief visual walkthrough on the necessary steps when copying data from one brainlife project to another. 

7
7
Duration:
1:28

This lesson visually documents the process of uploading data to brainlife via the command line interface (CLI). 

8
8
Duration:
0:34

This video shows how to use the brainlife.io interface to edit the participants' info file. This file is the ParticipantInfo.json file of the Brain Imaging Data Structure (BIDS).

9
9
Duration:
3:43

This video will document the process of running an app on brainlife, from data staging to archiving of the final data outputs.

10
10
Duration:
0:21

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

11
11
Duration:
3:44

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.

12
12
Duration:
0:57

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

13
13
Duration:
0:53

This video will document the process of launching a Jupyter Notebook for group-level analyses directly from brainlife.

14
14
Duration:
1:45

This brief video walks you through the steps necessary when creating a project on brainlife.io. 

15
15
Duration:
6:35

This lesson describes and shows four different ways one may upload their data to brainlife.io.

16
16
Duration:
1:11

This quick video presents some of the various visualizers available on brainlife.io

17
17
Duration:
3:28

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

18
18
Duration:
0:30

This brief video rus through how to make an accout on brainlife.io.

19
19
Duration:
0:25

This video will demonstrate how to create and launch a pipeline using FreeSurfer on brainlife.io.

20
20
Duration:
1:33

This video will document how to run a correlation analysis between the gray matter volume of two different structures using the output from brainlife app-freesurfer-stats.

21
21
Duration:
2:25

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

22
22
Duration:
2:18

This short video shows how data in a brainlife.io publication can be opened from a DOI inside a published article. The video provides an example of how the DOI deposited on the journal can be opened with a web browser to redirect to the associated data publication on brainlife.io.

23
23
Duration:
1:06

This video will document the process of importing a dataset archived on OpenNeuro from the Datasets tab into a brainlife project.