xenial (1) pymvpa2-ofmotionqc.1.gz

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

AUTHOR

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

COPYRIGHT

       Copyright © 2006-2015 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.