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.