QA

Quality Assurance (QA) reports are generated for all functional MR data acquired at the CNI. These reports should appear in the "datasets" column in the NIMS browser page within an hour after the scan finishes.

Finding the QA report

QA reports appear in the datasets column of NIMS.

The QA reports take anywhere from a few minutes to an hour to compute, depending on the scan resolution and duration. To view the report, double-click the QA dataset and a pop-over will open showing the motion and spike plots, as well as some global QA values.

What's in the QA report

The QA code is still under active development, so we will likely be adding more metrics to the report in the near future. Right now, the report will give you an overall temporal SNR value (median tSNR of all brain voxels), the number of "spikes" detected, a plot of the mean displacement (both absolute and relative displacements), and a plot of the mean signal (in z-score units) from each slice of the brain. This last plot is useful for detecting spikes in your data, and for determining if the spikes are caused by your subject (e.g., motion) or by a possible problem with the scanner (e.g., white-pixel noise). When a subject moves, even a little, you will often see spikes that span several or all slices. But a white-pixel noise problem typically only affects one slice at a time. Note that the first few time points are ignored for the spike plot. Also, the motion estimation uses the middle time point as the reference volume.

Note that you can get the exact value of any datapoint by hovering your mouse over one of the curves. Also note that the frame numbers start at zero rather than one. Some examples of QA reports are shown below.

Examples of QA reports

A good subject and well-behaved scanner:

A bad subject and well-behaved scanner:

A good subject and spikey scanner:

Technical Details

The QA report generation code is part of the NIMS codebase and is available on Github.