pymvpa2-ofmotionqc - Online in the Cloud

PROGRAM:

NAME

pymvpa2-ofmotionqc - BOLD fMRI motion QC plot for an OpenFMRI dataset

SYNOPSIS

pymvpa2 ofmotionqc [--version] [-h] --path PATH [-t ID] [--estimate-fname NAME]
[--relative REF REF] [--exclude-subjs ID [ID ...]] [--estimate-order LABEL] [--rad2deg]
[--outlier-minthresh OUTLIER_MINTHRESH] [--outlier-stdthresh OUTLIER_STDTHRESH] [--savefig
SAVEFIG]

DESCRIPTION

Generate a QC plot for BOLD fMRI motion estimates from an OpenFMRI dataset.

The generated figure consists of two subplots: one for translation and one for rotation.
The L2-norm for each motion type is plotted. Runs 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 run. In
that case the entire motion time series for that run is plotted as an outlier. IDs for
detected outliers are printed to the console. Note that these IDs do not account for
missing data or excluded subjects. However, in case of no missing data and no excluded
subjects they do correspond to numerical subject IDs.

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.

--path PATH
path to the root directory of the OpenFMRI dataset

-t ID, --task ID
ID of the task with BOLD fMRI data for the QC plot. Default: 1

--estimate-fname NAME
name of the files with the motion estimates in each BOLD task run folder. Default:
bold_moest.txt

--relative REF REF
recode all estimates as the difference to the estimate for volume X in run Y
(--relative Y X). Zero-based indices!

--exclude-subjs ID [ID ...]
list of space-separated suject IDs to exclude from the QC analysis

--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 SAVEFIG
file name to store the QC figure under. Default: None

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