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freesurfer

The goal of freesurfer is a port/wrapper of Freesurfer to R.

Much of the operations of Freesurfer are incorporated. This package is very useful for structural imaging, such as MRI. Some of the fMRI functionality has not been ported or has limited capability.

Installation

You can install the released version of freesurfer from CRAN with:

install.packages("freesurfer")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("muschellij2/freesurfer")

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Version

Install

install.packages('freesurfer')

Monthly Downloads

296

Version

1.8.1

License

GPL-3

Maintainer

John Muschelli

Last Published

May 12th, 2025

Functions in freesurfer (1.8.1)

Use Freesurfers MRI Mask

MRI Normalize Help

mris_convert_curv

Convert Curvature file

Determine extension of image based on FSLOUTPUTTYPE

Freesurfer look up table (LUT)

mris_convert_annot

Convert Annotation file

FS Command Wrapper

Logical check if Freesurfer is accessible

Convert MNC to NIfTI

Read Label File

Create command declaring FREESURFER_HOME

Determine Freesurfer output type

Use Freesurfers MRI Segmentation Algorithm

mris_euler_number

MRI Euler Number

Wrapper for getting Freesurfer help

Use Freesurfers mri_surf2surf function to resamples one cortical surface onto another

mri_convert.help

MRI Normalize Help

mri_surf2surf.help

Freesurfers mri_surf2surf Help

mri_segment.help

MRI Segment Help

Use Freesurfers Non-Uniformity Correction

Get Freesurfer's Directory

freesurfer_read_surf

Read Freesurfer Surface file

MRI information

MRI information Help

Use Freesurfers MRI Normalize Algorithm

mris_euler_number.help

MRI Euler Number Help

Convert NIfTI to MNC Help

Convert NIfTI to MNC

Convert Surface Data to ASCII

Convert Freesurfer Surface to Wavefront OBJ

Read Freesurfer Table Output

MNC to NIfTI Help

Reconstruction from Motion Correction to Skull Strip

Reconstruction Helper for recon from Freesurfer

Tract Reconstruction for Each Step

Tract Reconstruction Helper for trac-all from Freesurfer

Use Freesurfers MRI Watershed Algorithm

mri_watershed.help

MRI Watershed Help

Use Freesurfers MRI SynthStrip

Use Freesurfers MRI Converter

mri_synthstrip.help

MRI Normalize Help

mri_normalize.help

MRI Normalize Help

nu_correct.help

Non-Uniformity Correction Help

run_check_fs_cmd

Run and Check a Freesurfer Command

set_fs_subj_dir

Set Freesurfer Subjects Directory

Use Freesurfers MRIs Converter

mris_convert.help

Help file for Freesurfers MRIs Converter

mris_convert_normals

Convert Surface to Surface normals

mris_convert_vertex

Convert Surface to vertex file

Read MGH or MGZ File

surface_to_triangles

Convert Freesurfer Surface to Triangles

Tract Reconstruction Helper for trac-all from Freesurfer for All Steps

read_annotation

Read Freesurfer annotation file

Reconstruction from Freesurfer for All Steps

Reconstruction from Freesurfer

read_aseg_stats

Read Anatomical Segmentation Statistics

asegstats2table.help

Parcellation Stats to Table Help

check_fs_result

Check Freesurfer Result

freesurfer_read3

Freesurfer Read 3 records

aparcstats2table.help

Parcellation Stats to Table Help

convert_surface

Convert Freesurfer Surface

construct_subj_dir

Construct Subject Directory

Convert Freesurfer aparcs Table to brainGraph

aparcstats2table

Parcellation Stats to Table

asegstats2table

Parcellation Stats to Table

checkmnc-methods

Force object to filename with .mnc extension

freesurfer_read_curv

Read Freesufer Curv file

freesurfer_read3_con

Freesurfer Read 3 records

Determine Freesurfer Subjects Directory

Find Freesurfer Version