---
name: "mvpa-prep-fmri"
section: "1"
platform: "linux"
package: "python-mvpa"
version: "0.4.8-1"
release: "Debian 7 (Wheezy)"
platforms: ["linux"]
url: "https://new.carta.tech/mvpa-prep-fmri"
---

# mvpa-prep-fmri(1)

preprocess fMRI data for PyMVPA

## 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