flirt

infile

(character) reference image to be registered to

reffile

omat

(numeric) degrees of freedom (default 6 - rigid body)

outfile

retimg

(logical) If retimg, should file be reoriented when read in?
Passed to <code><a rd-options="" href="/link/readnii?package=fslr&version=1.9.2.1" data-mini-rdoc="fslr::readnii">readnii</a></code>.

reorient

(logical) pass to <code><a rd-options="" href="/link/system?package=fslr&version=1.9.2.1" data-mini-rdoc="fslr::system">system</a></code>

intern

opts

(logical) print out command before running

verbose

additional arguments passed to <code><a rd-options="" href="/link/readnii?package=fslr&version=1.9.2.1" data-mini-rdoc="fslr::readnii">readnii</a></code>.


This function calls <code>flirt</code> to register infile to reffile
and either saves the image or returns an object of class nifti, along with the
transformation matrix omat


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.

John Muschelli

fslr

Wrapper Functions for FSL ('FMRIB' Software Library) from
Functional MRI of the Brain ('FMRIB')

flirt function

(logical) If retimg, should file be reoriented when read in?
Passed to <code><a rd-options='' href='readnii'>readnii</a></code>.

(logical) pass to <code><a rd-options='' href='system'>system</a></code>

additional arguments passed to <code><a rd-options='' href='readnii'>readnii</a></code>.

flirt: Register using FLIRT

Description

Usage

Arguments

Value