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.. _ahelp_3dTqual:
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3dTqual
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Usage: 3dTqual [options] dataset
Computes a `quality index' for each subbrick in a 3D+time dataset.
The output is a 1D time series with the index for each subbrick.
The results are written to stdout.
Note that small values of the index are 'good', indicating that
the subbrick is not very different from the norm. The purpose
of this program is to provide a crude way of screening FMRI
time series for sporadic abnormal images, such as might be
caused by large subject head motion or scanner glitches.
Do not take the results of this program too literally. It
is intended as a GUIDE to help you find data problems, and no
more. It is not an assurance that the dataset is good, and
it may indicate problems where nothing is wrong.
Subbricks with index values much higher than others should be
examined for problems. How you determine what 'much higher' means
is mostly up to you. I suggest graphical inspection of the indexes
(cf. EXAMPLE, infra). As a guide, the program will print (stderr)
the median quality index and the range median3.5*MAD .. median+3.5*MAD
(MAD=Median Absolute Deviation). Values well outside this range might
be considered suspect; if the quality index were normally distributed,
then values outside this range would occur only about 1% of the time.
OPTIONS:
spearman = Quality index is 1 minus the Spearman (rank)
correlation coefficient of each subbrick
with the median subbrick.
[This is the default method.]
quadrant = Similar to spearman, but using 1 minus the
quadrant correlation coefficient as the
quality index.
autoclip = Clip off lowintensity regions in the median subbrick,
automask = so that the correlation is only computed between
highintensity (presumably brain) voxels. The
intensity level is determined the same way that
3dClipLevel works. This prevents the vast number
of nearly 0 voxels outside the brain from biasing
the correlation coefficient calculations.
clip val = Clip off values below 'val' in the median subbrick.
mask MSET = Compute correlation only across masked voxels.
range = Print the median3.5*MAD and median+3.5*MAD values
out with EACH quality index, so that they
can be plotted (cf. Example, infra).
Notes: * These values are printed to stderr in any case.
* This is only useful for plotting with 1dplot.
* The lower value median3.5*MAD is never allowed
to go below 0.
EXAMPLE:
3dTqual range automask fred+orig  1dplot one stdin
will calculate the time series of quality indexes and plot them
to an X11 window, along with the median+/3.5*MAD bands.
NOTE: cf. program 3dToutcount for a somewhat different quality check.
 RWCox  Aug 2001
++ Compile date = Jun 14 2021 {AFNI_21.1.12:linux_ubuntu_16_64}