Running quality control (QC) across modalities
Contents
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:
STUDY_NAME="OP2"
WORK_DIR="/gpfs/loomis/pi/n3/Studies/MBLab/HCPDev"
SESSIONS_LIST="OP268_07032014,OP269_07032014"
INPUT_BATCH_FILE="${WORK_DIR}/${STUDY_NAME}/processing/batch.txt"
RUNTURNKEY_TYPE="local"
RUNTURNKEY_STEPS="run_qc_bold"
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" \
--boldsuffix="Atlas"