MVPA-PREP-FMRI

Section: User Commands (1) Updated: February 2011 Local index Up

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

This document was created by man2html, using the manual pages.
Time: 21:24:09 GMT, April 16, 2011