MVPA-PREP-FMRI(1)						   User Commands						 MVPA-PREP-FMRI(1)

NAME

       mvpa-prep-fmri - preprocess fMRI data for PyMVPA

SYNOPSIS

       mvpa-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

       -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

mvpa-prep-fmri 0.4.8						    April 2012							 MVPA-PREP-FMRI(1)