Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Jul 1;154:150-158.
doi: 10.1016/j.neuroimage.2016.08.009. Epub 2016 Aug 7.

A Simple but Useful Way to Assess fMRI Scan Qualities

Affiliations
Free PMC article

A Simple but Useful Way to Assess fMRI Scan Qualities

Jonathan D Power. Neuroimage. .
Free PMC article

Abstract

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.

Trial registration: ClinicalTrials.gov NCT01031407.

Conflict of interest statement

Conflict of interest

The author declares no conflicts of interest with regard to this work.

Figures

Figure 1
Figure 1. Thermal noise can obscure structured signals
Two scans of the MyConnectome database are shown with motion traces at top, undenoised signals at middle, and blurred but otherwise undenoised signals at the bottom. These data are 2.4 × 2.4 × 2.4 mm voxels acquired every 1.16 seconds. The blurring occurs within brain compartment masks defined by FreeSurfer so that signals are not combined across brain compartments. Blurring averages away thermal noise, revealing structured signals. Note that periodic head motion is present and that similarly periodic signals become visible in the gray matter upon reduction of thermal noise (yellow arrows). See Online Movie 1 for such plots of all MyConnectome scans.
Figure 2
Figure 2. Motion is sometimes paired with prolonged signal decreases
Scans from six subjects of the University of California at Los Angeles (UCLA) site of the ABIDE database are shown following the conventions of Figure 1. These data are 3 × 3 × 4 mm voxels acquired every 3 seconds. See Figure S1 and S2 for similar examples in the Utah School of Medicine (USM) and New York University (NYU) ABIDE scans, or Online Movie 2 for plots of all subjects from these ABIDE sites. Purple arrows denote motion with prominent signal decreases afterwards, light blue arrows denote motion without such prominent signal decreases.
Figure 3
Figure 3. Deep breaths iscriminate motions with subsequent signal decreases from motions without subsequent signal decreases
Scans from 4 subjects of the NIH cohort are shown following the conventions of Figure 2. Respiratory belt traces are in arbitrary units. These data are 1.7 × 1.7 × 3 mm voxels acquired every 3.5 seconds. As in Figure 2, purple arrows denote motion with prominent signal decreases afterwards, light blue arrows denote motion without such prominent signal decreases.
Figure 4
Figure 4. Abnormalities without obvious causes may be hardware-related artifacts
Scans from 2 subjects of the NIH cohort are shown following the conventions of Figure 3, illustrating sudden, dramatic, and pervasive signal changes with no obvious cause (yellow arrows).
Figure 5
Figure 5. Interrelationships among motion, respiration, and heart rate
For 3 NIH subjects, 5 minutes of heart rate, respiratory, and head motion traces are shown. Note the slightly lagged modulation of heart rate by respiratory cycle; this finding is called “sinus arrhythmia”, a normal finding in most children and adults. Also note that transient elevations in heart rate accompany deep inspiration, which in turn is often marked by head motion. See additional examples of these plots in Figure S4 and Online Movie 3 for plots of all NIH subjects.
Figure 6
Figure 6. Examining single scans before and after a denoising step
A scan from the HCP dataset is shown before and after FIX-ICA. Purple arrows denote breaths (see blue respiratory traces). These data are 2 × 2 × 2 mm voxels acquired every 0.72 seconds. Only 8 minutes of the 15-minute scan are shown because the data are highly sampled in time and the image becomes “cramped” if more time is included. See Figure S5 and S6 for additional examples, or Online Movie 4 for plots of all HCP subjects.

Similar articles

See all similar articles

Cited by 19 articles

See all "Cited by" articles

Publication types

MeSH terms

Associated data

Feedback