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.

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 on a machine that has MATLAB installed.

Running QC via the turnkey command#

The following example illustrates how to execute the QC calls via the QuNex Turnkey functionality.

Running QC via the turnkey command - example#

First define the relevant variables:

BOLDS="blink"  # --> This variable allows you to select BOLDS by name tag via the batch file

run_turnkey call for QC command:

qunex run_turnkey \
    --batchfile="${INPUT_BATCH_FILE}" \
    --workingdir="${WORK_DIR}" \
    --projectname="${STUDY_NAME}" \
    --path="${WORK_DIR}/${STUDY_NAME}" \
    --sessions="${SESSIONS_LIST}" \
    --turnkeytype="${RUNTURNKEY_TYPE}" \
    --turnkeysteps="${RUNTURNKEY_STEPS}" \
    --overwritestep="yes" \
    --modality="BOLD" \
    --bolddata="${BOLDS}" \
    --boldprefix="BOLD" \