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chaselgrove authored Jan 2, 2025
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Expand Up @@ -23,11 +23,17 @@ Managing neuroimaging pipelines often involves handling complex datasets and mul

## Exercise

In this tutorial, you will learn how to use [`nipoppy`](https://nipoppy.readthedocs.io/en/latest/) to address these challenges by:
In this tutorial, you will learn how to use [`nipoppy`](https://nipoppy.readthedocs.io/en/latest/) to manage a simple workflow. In this example, we
start with data that has already been converted into the BIDS representation. If your data is not in BIDS, the instructions at
[Nipoppy](https://nipoppy.readthedocs.io/en/stable/index.html) addresses this more complex task. The workflow in this example is simply a
preexisting *MRIQC* container available at DockerHub. Containerization of more complex workflows are addressed in the *Containerization Tutorial*.
The example facilitates the deployment of the indicated container across all the content of the indicated dataset (subjects, sessions, etc.)
and makes the derived content available to the local metadata store (aka ReproPond) for query with *NeuroBagel*. The key points of this exercise are:

1. **Initializing a project:** Setting up a project directory and configuring necessary files for managing data and pipelines execution on the BIDS dataset [ds004101](https://openneuro.org/datasets/ds004101/versions/1.0.1/download) from OpenNeuro.
2. **Running the pipeline:** Executing the MRIQC 23.1.0 pipeline our example dataset.
3. **Tracking progress:** Monitoring the pipeline's status and ensuring all steps are completed successfully.
4. **Make results available:** Provide the status and results to a *NeuroBagel* node.

## Step-by-step guide

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