pymvpa2-prep-fmri1

Usage

Overview

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 [Default: 0]

-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