A simple but useful way to assess fMRI scan qualities

- Presents a plot that summarizes some important features of single fMRI scans.
- Illustrates multiple kinds of noise and unwanted signals using the plot.
- Illustrates signal denoising effects with the plot.
- Includes software tools to make the plot.
- Illustrates the plot in hundreds of subjects from several different sites.

This short “how to” article describes a plot I find useful for assessing fMRI data quality. I discuss the reasoning behind the plot and how it is constructed. I create the plot in scans from several publicly available datasets to illustrate different kinds of fMRI signal variance, ranging from thermal noise to motion artifacts to respiratory-related signals. I also show how the plot can be used to understand the variance removed during denoising. Code to make the plot is provided with the article, and supplemental movies show plots for hundreds of additional subjects.