NAME¶

pymvpa2-plotmotionqc - BOLD fMRI motion QC plot

SYNOPSIS¶

pymvpa2 plotmotionqc [--version] [-h] [-s FILE [FILE ...]] [--estimate-order LABEL] [--rad2deg] [--outlier-minthresh OUTLIER_MINTHRESH] [--outlier-stdthresh OUTLIER_STDTHRESH] [--savefig FILENAME]

DESCRIPTION¶

Generate 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.

Example

pymvpa2 plotmotionqc -s sub*/func/*run-1_bold_mc.txt -s sub*/func/*run-2_bold_mc.txt --savefig motion.png

OPTIONS¶

--version

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']

--rad2deg

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.

AUTHOR¶

Written by Michael Hanke & Yaroslav Halchenko, and numerous other contributors.

COPYRIGHT¶

Copyright © 2006-2016 PyMVPA developers

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.