run_first_all

pecifies the input image (T1-weighted)

specifies the output image basename (extensions will be added to this)

oprefix

specifies that the input image has been brain extracted

brain_extracted

a restricted set of structures to be segmented

structures

specifies the affine registration matrix to standard space (optional)

affine

(character) operations to be passed to <code>run_first_all</code>

opts

(logical) print out command before running

verbose

Wrapper for <code>run_first_all</code> from FSL for FIRST analysis 
segmentation of subcortical structures

Wrapper functions that interface with 'FSL'
<http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>, a powerful and commonly-used 'neuroimaging'
software, using system commands. The goal is to be able to interface with 'FSL'
completely in R, where you pass R objects of class 'nifti', implemented by
package 'oro.nifti', and the function executes an 'FSL' command and returns an R
object of class 'nifti' if desired.

run_first_all: Run FIRST All

Description

Usage

Arguments

Value