freesurfer: Wrapper Functions for 'Freesurfer'

Wrapper functions that interface with 'Freesurfer' (https://, 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.

Install the latest version of this package by entering the following in R:
AuthorJohn Muschelli <>
Date of publication2016-09-28 19:34:59
MaintainerJohn Muschelli <>

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Man pages

aparcstats2table: Parcellation Stats to Table Parcellation Stats to Table Help

aparcs_to_bg: Convert Freesurfer aparcs Table to brainGraph

asegstats2table: Parcellation Stats to Table Parcellation Stats to Table Help

check_fs_result: Check Freesurfer Result

checkmnc-methods: Force object to filename with .mnc extension

construct_subj_dir: Construct Subject Directory

freesurferdir: Get Freesurfer's Directory

freesurfer_read3: Freesurfer Read 3 records

freesurfer_read3_con: Freesurfer Read 3 records

freesurfer_read_curv: Read Freesufer Curv file

freesurfer_read_surf: Read Freesurfer Surface file

fs_cmd: FS Command Wrapper

fs_help: Wrapper for getting Freesurfer help

fs_imgext: Determine extension of image based on FSLOUTPUTTYPE

fs_subj_dir: Determine Freesurfer Subjects Directory

fs_version: Find Freesurfer Version

get_fs: Create command declaring FREESURFER_HOME

get_fs_output: Determine Freesurfer output type

have_fs: Logical check if Freesurfer is accessible

mnc2nii: Convert MNC to NIfTI MNC to NIfTI Help

mri_convert: Use Freesurfers MRI Converter MRI Normalize Help

mri_info: MRI information MRI information Help

mri_mask: Use Freesurfers MRI Mask MRI Normalize Help

mri_normalize: Use Freesurfers MRI Normalize Algorithm MRI Normalize Help

mris_convert: Use Freesurfers MRIs Converter Help file for Freesurfers MRIs Converter

mri_segment: Use Freesurfers MRI Segmentation Algorithm MRI Segment Help

mris_euler_number: MRI Euler Number MRI Euler Number Help

mri_surf2surf: Use Freesurfers 'mri_surf2surf' function to resamples one... Freesurfers mri_surf2surf Help

mri_watershed: Use Freesurfers MRI Watershed Algorithm MRI Watershed Help

nii2mnc: Convert NIfTI to MNC Convert NIfTI to MNC Help

nu_correct: Use Freesurfers Non-Uniformity Correction Non-Uniformity Correction Help

read_aseg_stats: Read Anatomical Segmentation Statistics

read_fs_table: Read Freesurfer Table Output

recon: Reconstruction from Freesurfer

recon_all: Reconstruction from Freesurfer for All Steps

recon_manual: Reconstruction from Motion Correction to Skull Strip

reconner: Reconstruction Helper for recon from Freesurfer

run_check_fs_cmd: Run and Check a Freesurfer Command

set_fs_subj_dir: Set Freesurfer Subjects Directory

surf_convert: Convert Surface Data to ASCII

trac_all: Tract Reconstruction Helper for trac-all from Freesurfer for...

tracker: Tract Reconstruction Helper for trac-all from Freesurfer

trac_manual: Tract Reconstruction for Each Step


aparcstats2table Man page Man page
aparcs_to_bg Man page
asegstats2table Man page Man page
autorecon1 Man page
autorecon2 Man page
autorecon3 Man page
check_fs_result Man page
checkmnc Man page
checkmnc,character-method Man page
checkmnc,list-method Man page
checkmnc-methods Man page
checkmnc,nifti-method Man page
construct_subj_dir Man page
ensure_mnc Man page
freesurferdir Man page
freesurfer_dir Man page
freesurfer_read3 Man page
freesurfer_read3_con Man page
freesurfer_read_curv Man page
freesurfer_read_surf Man page
fs_cmd Man page
fs_dir Man page
fs_help Man page
fs_imgext Man page
fs_subj_dir Man page
fs_version Man page
get_fs Man page
get_fs_output Man page
have_fs Man page
mnc2nii Man page Man page
mri_convert Man page Man page
mri_info Man page Man page
mri_mask Man page Man page
mri_normalize Man page Man page
mris_convert Man page Man page
mri_segment Man page Man page
mris_euler_number Man page Man page
mri_surf2surf Man page Man page
mri_watershed Man page Man page
nii2mnc Man page Man page
nu_correct Man page Man page
read_aseg_stats Man page
read_fs_table Man page
recon Man page
recon_all Man page
recon_con1 Man page
recon_con1,recon_con2,recon_con3 Man page
recon_con2 Man page
recon_con3 Man page
reconner Man page
run_check_fs_cmd Man page
set_fs_subj_dir Man page
surf_convert Man page
trac_all Man page
trac_bedpost Man page
tracker Man page
trac_path Man page
trac_prep Man page


R/reconner.R R/checkmnc.R R/freesurfer_read3.R R/mri_watershed.R R/mri_normalize.R R/run_check_fs_cmd.R R/mri_mask.R R/nii2mnc.R R/recon.R R/nu_correct.R R/mri_convert.R R/mris_euler_number.R R/check_fs_result.R R/mri_surf2surf.R R/trac_manual.R R/mri_info.R R/mnc2nii.R R/construct_subj_dir.R R/recon_all.R R/mri_segment.R R/recon_manual.R R/surf_convert.R R/read_aseg_stats.R R/read_fs_table.R R/fs_help.R R/aparcs_to_bg.R R/tracker.R R/trac_all.R R/mris_convert.R R/asegstats2table.R R/fs_cmd.R R/fs_version.R R/aparcstats2table.R R/fs_setup.R
man/ man/fs_version.Rd man/freesurfer_read3.Rd man/freesurfer_read_curv.Rd man/mris_euler_number.Rd man/ man/freesurfer_read3_con.Rd man/ man/mri_mask.Rd man/fs_cmd.Rd man/mnc2nii.Rd man/ man/fs_subj_dir.Rd man/mri_surf2surf.Rd man/mri_info.Rd man/aparcstats2table.Rd man/trac_all.Rd man/ man/ man/ man/mris_convert.Rd man/run_check_fs_cmd.Rd man/reconner.Rd man/recon_all.Rd man/freesurferdir.Rd man/freesurfer_read_surf.Rd man/fs_imgext.Rd man/nu_correct.Rd man/tracker.Rd man/trac_manual.Rd man/ man/mri_watershed.Rd man/construct_subj_dir.Rd man/recon_manual.Rd man/asegstats2table.Rd man/read_aseg_stats.Rd man/nii2mnc.Rd man/ man/mri_normalize.Rd man/aparcs_to_bg.Rd man/recon.Rd man/set_fs_subj_dir.Rd man/ man/read_fs_table.Rd man/mri_segment.Rd man/get_fs.Rd man/ man/ man/ man/fs_help.Rd man/get_fs_output.Rd man/check_fs_result.Rd man/have_fs.Rd man/surf_convert.Rd man/mri_convert.Rd man/checkmnc-methods.Rd man/

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