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MVPA-PREP-FMRI

MVPA-PREP-FMRI

Section: User Commands (1) Updated: February 2011
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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


 

Index

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

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