“How to?” 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

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

Attention

More videos on track-processing and extract are in the making and will be published soon! Stay tuned for updates!