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