Use FSL fsl_motion_outliershttp://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLMotionOutliers_ to find outliers in timeseries (4d) data.
Usage
ni_fsl_motion_outliers(
in_file,
args = NULL,
dummy = NULL,
mask = NULL,
metric = NULL,
no_motion_correction = NULL,
out_file = NULL,
out_metric_plot = NULL,
out_metric_values = NULL,
threshold = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- in_file
Character; file path. unfiltered 4D image Required.
- args
Character. Additional parameters to the command
- dummy
Integer. number of dummy scans to delete (before running anything and creating EVs)
- mask
Character; file path. mask image for calculating metric
- metric
Character; one of: "refrms", "dvars", "refmse", "fd", "fdrms". metrics: refrms - RMS intensity difference to reference volume as metric [default metric], refmse - Mean Square Error version of refrms (used in original version of fsl_motion_outliers), dvars - DVARS, fd - frame displacement, fdrms - FD with RMS matrix calculation
- no_motion_correction
Logical. do not run motion correction (assumed already done)
- out_file
Character; file path. output outlier file name
- out_metric_plot
Character; file path. output metric values plot (DVARS etc.) file name
- out_metric_values
Character; file path. output metric values (DVARS etc.) file name
- threshold
Numeric. specify absolute threshold value (otherwise use box-plot cutoff = P75 + 1.5*IQR)
- .cwd
Working directory override.
- .env
Named character vector of environment variables.
- .engine
Execution engine override.
- .profile
Runtime profile override.
- dry_run
Logical; preview command without executing.
- echo
Logical; echo stdout/stderr in real time.