Nipoppy Tutorial Dataset

This dataset was created to serve as an example dataset for the Nipoppy tutorials.

Download data

Besides cloning this repo, you can download the data

via the browser: Click on the green button "Code" on the right upper corner in this repo and select "Download Zip"

or

via the command line:

wget -O tutorial-dataset.zip https://github.com/nipoppy/tutorial-datset/archive/refs/heads/main.zip

Unzip once downloaded.

Using the data

Following the Nipoppy tutorials, the data is used for different steps in the Nipoppy framework. Commands assume the Nipoppy dataset is called my-example-study as instructed in the Nipoppy tutorials. Instructions are given in the order they will appear in the Nipoppy tutorial series.

./manifest.tsv

During the nipoppy init tutorial we will create this manifest.tsv file. Should you not watch this tutorial or run in any errors related to the manifest.tsv, you can use this one.

./reorg

• intented for: nipoppy reorg tutorial

• steps:

  1. move the content of the tutorial-dataset/reorg directory to the sourcedata/imaging/pre_reorg directory of your Nipoppy dataset, i.e.:

  mv tutorial-dataset/reorg/* my-example-study/sourcedata/imaging/pre_reorg
  

  Do this while watching the nipoppy reorg video and you are instructed to do so in the tutorial.

Note: Data of one subject was copied in order to create multiple subjects with different modalities for training purposes. Hence, all data stems from one subject.

./bidsify

• intended for: nipoppy bidsify tutorial

• steps:

  1. move the dcm2bids_config.json to the code directory of your Nipoppy dataset, i.e.:

  mv tutorial-dataset/bidsify/dcm2bids_config.json my-example-study/code
  

  2. move the participants.tsv as well as the dataset_description.json to the bids directory of your Nipoppy dataset, i.e.:

  mv -t my-example-study/bids tutorial-dataset/bidsify/participants.tsv tutorial-dataset/bidsify/dataset_description.json
  

./process

• intended for: nipoppy process tutorial, only necessary for users who didn't follow the previous tutorials and want to start with a BIDS dataset.

• steps:

  1. move the content of tutorial-dataset/process to the bids directory of your Nipoppy dataset, i.e.:

  mv tutorial-dataset/process/* my-example-study/bids
  

  2. (If you haven't done so for the previous tutorial) move the participants.tsv as well as the dataset_description.json to the bids directory of your Nipoppy dataset, i.e.:

  mv -t my-example-study/bids tutorial-dataset/process/participants.tsv tutorial-dataset/process/dataset_description.json
  

Note: participants.tsv contains made-up phenotypic data.

./extract

• intended for: nipoppy extract tutorial

• steps:

  1. move the content of the tutorial-dataset/extract directory to the derivatives directory of your Nipoppy dataset, i.e.:

  mv tutorial-dataset/extract/* my-example-study/derivatives
  

Note: We removed some of the freesurfer output to scale down the size of the repository. Files that are needed for nipoppy track-processing and running the fs_stats pipeline are still present.

Acknowledgements

Data is a phantom dataset generated at the University of Arizona on our Siemens Skyra 3T with Syngo MR VE11c software on 2018_02_08. It was retrieved from https://datasets.datalad.org/repronim/heudiconv-tutorial-example/.

We thank the Heudiconv Team and Dianne Patterson for making this data available.