bionic (1) pymvpa2-plotmotionqc.1.gz

NAME

       scatter -  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

       scatter not available: No module named _tkinter, please install the python-tk package

       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.

       pymvpa2-plotmotionqc 2.6.4

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.

scatter not available: No module named _tkinter, pJanuaryn2018l the python-tk package                 SCATTER(1)