# Task-Based fMRI Analysis Using AFNI

Here, we provide a processing pipeline for functional MRI data using the [AFNI software package](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/index.html).

The tutorial is split into two sections:

1. A single subject walkthrough of how to download data from xnat and preprocess using afni.
2. A group analysis pipeline, including first level preprocessing of all subjects/sessions of demodat2, and continuing on to second level analysis.

To enable both block and event related analyses, we designed a single functional sequence that includes two different concurrent tasks. These are 1) the visual hemifield localizer task (also called the checkerboard, or checks, task) and 2) a button pressing task for motor cortex activation.

## Block Design: The Visual Hemifield Localizer Task

This is a very simple visual task, with alternating 12s blocks of flashing checkerboard stimuli in the left and right visual hemifields. Because of the contralateral organization of visual cortex, we can identify the right visual cortex by selecting voxels that prefer stimulation on the left side of visual space, and vice versa.

## Event-Related Design: Button Pressing Task

To activate areas of the motor cortex, we included a button press task which occurs throughout the alternating flashing checkerboards. At random and variable inter-trial intervals (4, 6, or 8 seconds), the white fixation cross in the center of the screen flashes to either red or blue for 300ms (0.3 seconds). Once the participant sees the color change, they press the corresponding button (right index finger for red, left index finger for blue).

Below is a figure depicting these two concurrent tasks.

<figure><img src="/files/PAkEyTKmHZPjnlUvMmFC" alt="The experiment begins with 12 seconds of a fixation cross on the screen, followed by two concurrent tasks. The &#x22;visual hemifield localizer task&#x22; requires subjects to look at the screen as it shows a flashing checkerboard alternating on the right and left halves of the screen for 12 seconds each. There is a fixation cross that remains on the center of the screen throughout the tasks. At various ITIs, the fixation cross flashes red or blue, prompting the participant to press a button in their right or left hand, respectively. At the end of the tasks, there is another 12 seconds of fixation cross only."><figcaption></figcaption></figure>

The psychopy script and all necessary files can be downloaded here:

{% file src="/files/keRZAkTAp6qGg7GbWv1W" %}


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://docs.ccv.brown.edu/bnc-user-manual/analysis-pipelines/task-based-fmri-analysis-using-afni.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.