mvpa-prep-fmri(1) preprocess fMRI data for PyMVPA


mvpa-prep-fmri [OPTIONS] <fmri-data>


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).


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