“How to” tutorial video series¶

Learn all about the Nipoppy toolbox and its protocol and experience a full usage of all Nipoppy functionalities by following our tutorial series!

This tutorial series is meant to give you a hands-on experience of the Nipoppy toolbox. Please have Nipoppy installed on your device (see Installation) and have our example dataset ready:

$ git clone https://github.com/nipoppy/tutorial-dataset.git

or visit the GitHub repo and download the data without using git. We show in the videos how to!

1. nipoppy init¶

In this tutorial we will cover how to create a new Nipoppy dataset. More concretely, we will

run the nipoppy init command
discover the directories that follow the Nipoppy specification
explore the nipoppy status command
modify the content of the manifest.tsv file according to our dataset
and run the nipoppy track-curation --regenerate command

Duration: 7:43m

2. nipoppy pipeline¶

In this tutorial we will cover how to install a pipeline in a Nipoppy dataset. More concretely, we will

explore the nipoppy pipeline subcommands
learn how to share containers
set pipeline configurations

Duration: 6:31m

Go here to find more info about docker support

3. nipoppy reorg¶

In this tutorial we will cover how to reorganize imaging sourcedata. More concretely, we will

explore the sourcedata directory
run the nipoppy reorg command
and look at the curation_status.tsv file

Duration: 6:06m

4. nipoppy bidsify¶

In this tutorial we will cover how to bidsify imaging sourcedata. More concretely, we will

install the dcm2bids pipeline
explore the nipoppy bidsify command
run nipoppy bidsify on our imaging sourcedata

Duration: 8:31m

5. nipoppy process¶

In this tutorial we will cover how to run processing pipelines on imaging data. More concretely, we will

check the prerequisites to run mriqc on our dataset
execute the nipoppy process command
explore the created output

Duration: 5:26m

6. nipoppy track-processing¶

In this tutorial we will cover how to track the processing status of our imaging data with Nipoppy. More concretely, we will

run the nipoppy track-processing command
get to know the processing_status.tsv file
and explore the Neurobagel digest dashboard

Duration: 4:21m

7. nipoppy extract¶

In this tutorial we will cover how to extract imaging-derived phenotypes (IDPs) from our imaging data by running the nipoppy extract command.

Duration: 3:55m