recon_manual: Reconstruction from Motion Correction to Skull Strip

In muschellij2/freesurfer: Wrapper Functions for 'Freesurfer'

Reconstruction from Motion Correction to Skull Strip

Description

Reconstruction from Freesurfer for Step 1-5 (Motion Correction to Skull Strip), which calls -autorecon1 in recon-all

Usage

recon_con1(infile, outdir = NULL, subjid, verbose = TRUE)

autorecon1(infile, outdir = NULL, subjid, verbose = TRUE)

recon_con2(infile, outdir = NULL, subjid, verbose = TRUE)

autorecon2(infile, outdir = NULL, subjid, verbose = TRUE)

recon_con3(infile, outdir = NULL, subjid, verbose = TRUE)

autorecon3(infile, outdir = NULL, subjid, verbose = TRUE)

Arguments

infile	Input filename (dcm or nii)
outdir	Output directory
subjid	subject id
verbose	print diagnostic messages

Value

Result of system

Note

See https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all for the steps of each autorecon1-3. If you set infile = NULL, then you can omit the -i flag in recon-all.

muschellij2/freesurfer documentation built on Nov. 28, 2023, 4:45 a.m.