NAME

       pymvpa2-prep-fmri - preprocess fMRI data for PyMVPA

SYNOPSIS

       pymvpa2-prep-fmri [OPTIONS] <fmri-data>

DESCRIPTION

       Tiny  tool  to  prepare a directory for a typical analysis of fMRI data with PyMVPA. Tools
       from the FSL suite will be used for preprocessing. It takes a 4D fMRI timeseries as  input
       and performs the following steps:

       - extract an example volume

       - perform motion correction using the example volume as reference

       - conservative skull-stripping and brain mask generation

       - masking of the motion-corrected timeseries with the brain mask

       All  results will be stored either in the current directory, or in a subdirectory with the
       subject ID (if specified).

OPTIONS

       --version
              show program's version number and exit

       -v VERBOSE, --verbose=VERBOSE, --verbosity=VERBOSE
              Verbosity level of output [Default: 0]

       -h, --help, --sos
              Show this help message and exit

       -s SUBJ, --subject-id=SUBJ
              Subject ID used as output path

       -e EXFUNC, --example-func-vol=EXFUNC
              Volume (numeric ID  or  'last',  'first',  'middle')  to  be  used  as  an  example
              functional image. Default: 10

       -m MCFLIRT_OPTS, --mcflirt-options=MCFLIRT_OPTS
              Options for MCFLIRT. '-plots' is auto-added

       -p, --mcflirt-plots
              Create a .pdf with plots of motion parameters

       -b BET_OPTS, --bet-options=BET_OPTS
              Options  for  BET.  '-m'  is  auto-added. Default: '-f 0.3' for a safe guess of the
              brain outline