Reconstruction from Motion Correction to Skull Strip

Source: R/recon_manual.R

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

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.