# 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`](../../api/gmri/run_qc.rst) 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](../../api/gmri/run_qc.rst) to find information describing each QC command and how to execute it.

## Motion scrubbing and BOLD 'grayplots' QC

The [`general_plot_bold_timeseries`](../../api/gmri/general_plot_bold_timeseries.rst) 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`](../../api/gmri/general_plot_bold_timeseries.rst) 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](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`](../../api/gmri/run_turnkey.rst) call for QC command:

````bash
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"
````