get_fs

Finds the Freesurfer from system environment or <code>getOption("freesurfer.path")</code>
for location of Freesurfer functions

Wrapper functions that interface with 'Freesurfer'
<https://surfer.nmr.mgh.harvard.edu/>, a powerful and
commonly-used 'neuroimaging'
software, using system commands. The goal is to be able to interface with
'Freesurfer' completely in R, where you pass R objects of class 'nifti',
implemented by package 'oro.nifti', and the function executes an 'Freesurfer'
command and returns an R object of class 'nifti' or necessary output.

John Muschelli

freesurfer

Wrapper Functions for 'Freesurfer'

Athanasia Mo Mowinckel

get_fs function

<dl><dt>bin_app</dt>
<dd>Should <code>bin</code> be added to the freesurfer path? 
All executables are assumed to be in <code>FREESURFER_HOME/bin/</code>. If not, and 
<code>bin_app = ""</code>, they will be assumed to be in <code>FREESURFER_HOME/</code>.</dd></dl>

Arguments

Create command declaring FREESURFER_HOME — get_fs

<dl>

<dt>bin_app</dt>
<dd>Should <code>bin</code> be added to the freesurfer path? 
All executables are assumed to be in <code>FREESURFER_HOME/bin/</code>. If not, and 
<code>bin_app = ""</code>, they will be assumed to be in <code>FREESURFER_HOME/</code>.</dd>

</dl>

get_fs: Create command declaring FREESURFER_HOME

Description

Usage

Value

Arguments

Examples