.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.9.
.TH MVPA-PREP-FMRI "1" "April 2012" "mvpa-prep-fmri 0.4.8" "User Commands"
.SH NAME
mvpa-prep-fmri \- preprocess fMRI data for PyMVPA
.SH SYNOPSIS
.B mvpa-prep-fmri
[\fIOPTIONS\fR] \fI<fmri-data>\fR
.SH 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:
.PP
\- extract an example volume
.PP
\- perform motion correction using the example volume as reference
.PP
\- conservative skull\-stripping and brain mask generation
.PP
\- masking of the motion\-corrected timeseries with the brain mask
.PP
All results will be stored either in the current directory, or in a
subdirectory with the subject ID (if specified).
.SH OPTIONS
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-v\fR VERBOSE, \fB\-\-verbose\fR=\fIVERBOSE\fR, \fB\-\-verbosity\fR=\fIVERBOSE\fR
Verbosity level of output
.TP
\fB\-h\fR, \fB\-\-help\fR, \fB\-\-sos\fR
Show this help message and exit
.TP
\fB\-s\fR SUBJ, \fB\-\-subject\-id\fR=\fISUBJ\fR
Subject ID used as output path
.TP
\fB\-e\fR EXFUNC, \fB\-\-example\-func\-vol\fR=\fIEXFUNC\fR
Volume (numeric ID or 'last', 'first', 'middle') to be
used as an example functional image. Default: 10
.TP
\fB\-m\fR MCFLIRT_OPTS, \fB\-\-mcflirt\-options\fR=\fIMCFLIRT_OPTS\fR
Options for MCFLIRT. '\-plots' is auto\-added
.TP
\fB\-p\fR, \fB\-\-mcflirt\-plots\fR
Create a .pdf with plots of motion parameters
.TP
\fB\-b\fR BET_OPTS, \fB\-\-bet\-options\fR=\fIBET_OPTS\fR
Options for BET. '\-m' is auto\-added. Default: '\-f 0.3'
for a safe guess of the brain outline