Running quality control (QC) across modalities#

The QuNex suite provides both qualitative (i.e. visual) and quantitative QC metrics after key processing steps.

The run_qc command provides the following types of quality control:

  • Raw NIFTI visual QC

  • T1w visual QC

  • T2w visual QC

  • Myelin map visual QC

  • BOLD visual QC

  • BOLD temporal Signal-to-noise (SNR)

  • BOLD FC QC for scalar and pconn data

  • Running BOLD QC with tag selection

Refer to the Notes and Examples sections of the command's online documentation to find information describing each QC command and how to execute it.

Summarising quality control across a whole study#

run_qc reports on one session at a time. To see the study as a whole — how much movement is typical, which sessions stand out from the rest of your own sample, and which of them have not been through a processing stage at all — use run_qc_summary. It reads the quality control information the pipelines have already written for every session and compiles it into study level tables and an interactive report.

Motion scrubbing and BOLD 'grayplots' QC#

The general_plot_bold_timeseries command is used to create a plot of BOLD time series for quality control inspection. Specifically, it allows plotting of BOLD statistics as well as a "watershed" type plots, where intensities of voxels over time are plotted as shades of gray. The command can plot a configurable number of elements from multiple BOLD images, which allows visual inspection of preprocessing effects.

For complete documentation and extensive usage description see general_plot_bold_timeseries or run qunex general_plot_bold_timeseries --help.