SYNOPSISpymvpa2 ,plotmotionqc /[,--version/] [,-h/] [,-s FILE /[,FILE /...]] [,--estimate-order LABEL/] [,--rad2deg/] [,--outlier-minthresh OUTLIER_MINTHRESH/] [,--outlier-stdthresh OUTLIER_STDTHRESH/] [,--savefig FILENAME/]
DESCRIPTIONGenerate a QC plot for (BOLD fMRI) motion estimates of multiple segments.
The generated figure consists of two subplots: one for translation and one for rotation. The L2-norm for each motion type is plotted. Segment boundaries are indicated with dashed vertical lines. The following statistics are visualized
1. Range across subjects (min, max) with a light gray shaded area
2. 50% percentile around the mean with a medium gray shaded area
3. Standard error of the mean (SEM; +/-) with a dark gray shaded area
4. Median across subjects with a black line
5. Outlier subjects are represented as individual red lines
Outliers are defined as subjects that exceed the threshold anywhere within a given segment. In that case the entire motion time series for that segment is plotted as an outlier.
pymvpa2 plotmotionqc -s sub*/func/*run-1_bold_mc.txt -s sub*/func/*run-2_bold_mc.txt --savefig motion.png
- show program's version and license information and exit
- -h, --help, --help-np
- show this help message and exit. --help-np forcefully disables the use of a pager for displaying the help.
- -s FILE [FILE ...], --segment FILE [FILE ...]
- two or more text files with motion estimate time series. This option can be given multiple times (with multiple time series each to generate a multi-segment plot (e.g. for multiple run).
- --estimate-order LABEL
- column order of estimates in the files. `transrot` indicates translation first, followed by rotation. `rottrans` refers to the oposite order. [Default: 'transrot']
- If specified, rotation estimates are assumed to be in radian and will be converted to degrees.
- --outlier-minthresh OUTLIER_MINTHRESH
- absolute minimum threshold of outlier detection. Only value larger than this this threshold will ever be considered as an outlier. [Default: None]
- --outlier-stdthresh OUTLIER_STDTHRESH
- minimum threshold in units of standard deviation for outlier detection. [Default: None]
- --savefig FILENAME
- file name to store the QC figure under. Without this option the figure is shown in an interactive viewer.
AUTHORWritten by Michael Hanke & Yaroslav Halchenko, and numerous other contributors.
COPYRIGHTCopyright © 2006-2016 PyMVPA developers
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