pymvpa2-plotmotionqc1

Bold fmri motion qc plot

Usage

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

Overview

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.