recon_all

Reconstruction from Freesurfer for All Steps

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

recon_all function

<dl><dt>infile</dt>
<dd>Input filename (dcm or nii)</dd>
<dt>outdir</dt>
<dd>Output directory</dd>
<dt>subjid</dt>
<dd>subject id</dd>
<dt>verbose</dt>
<dd>print diagnostic messages</dd>
<dt>opts</dt>
<dd>Additional options</dd>
<dt>...</dt>
<dd>arguments passed to <code>reconner</code></dd></dl>

Arguments

Reconstruction from Freesurfer for All Steps — recon_all

<dl>

<dt>infile</dt>
<dd>Input filename (dcm or nii)</dd>


<dt>outdir</dt>
<dd>Output directory</dd>


<dt>subjid</dt>
<dd>subject id</dd>


<dt>verbose</dt>
<dd>print diagnostic messages</dd>


<dt>opts</dt>
<dd>Additional options</dd>


<dt>...</dt>
<dd>arguments passed to <code>reconner</code></dd>

</dl>

recon_all: Reconstruction from Freesurfer for All Steps

Description

Usage

Value

Arguments