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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

277

Version

1.6.10

License

GPL-3

Maintainer

Last Published

May 14th, 2024

Functions in freesurfer (1.6.10)

freesurferdir

Get Freesurfer's Directory
fs_cmd

FS Command Wrapper
get_fs

Create command declaring FREESURFER_HOME
freesurfer_read_surf

Read Freesurfer Surface file
fs_help

Wrapper for getting Freesurfer help
get_fs_output

Determine Freesurfer output type
mri_surf2surf

Use Freesurfers mri_surf2surf function to resamples one cortical surface onto another
mri_surf2surf.help

Freesurfers mri_surf2surf Help
mri_deface

MRI Deface
mri_convert.help

MRI Normalize Help
mris_convert_annot

Convert Annotation file
mris_convert_curv

Convert Curvature file
mri_normalize

Use Freesurfers MRI Normalize Algorithm
mri_normalize.help

MRI Normalize Help
mris_convert_vertex

Convert Surface to vertex file
mris_convert_normals

Convert Surface to Surface normals
mri_mask.help

MRI Normalize Help
mnc2nii

Convert MNC to NIfTI
mri_mask

Use Freesurfers MRI Mask
have_fs

Logical check if Freesurfer is accessible
mris_euler_number

MRI Euler Number
mri_convert

Use Freesurfers MRI Converter
mris_euler_number.help

MRI Euler Number Help
fs_imgext

Determine extension of image based on FSLOUTPUTTYPE
fs_lut

Freesurfer look up table (LUT)
mnc2nii.help

MNC to NIfTI Help
mri_watershed

Use Freesurfers MRI Watershed Algorithm
readmgz

Read MGH or MGZ File
readmnc

Read MNC File
mri_watershed.help

MRI Watershed Help
nii2mnc

Convert NIfTI to MNC
nu_correct

Use Freesurfers Non-Uniformity Correction
surf_convert

Convert Surface Data to ASCII
surface_to_triangles

Convert Freesurfer Surface to Triangles
nu_correct.help

Non-Uniformity Correction Help
trac_all

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

Reconstruction from Freesurfer
recon_all

Reconstruction from Freesurfer for All Steps
recon_con1

Reconstruction from Motion Correction to Skull Strip
set_fs_subj_dir

Set Freesurfer Subjects Directory
read_annotation

Read Freesurfer annotation file
nii2mnc.help

Convert NIfTI to MNC Help
run_check_fs_cmd

Run and Check a Freesurfer Command
mri_segment.help

MRI Segment Help
mri_info

MRI information
read_fs_label

Read Label File
read_aseg_stats

Read Anatomical Segmentation Statistics
reconner

Reconstruction Helper for recon from Freesurfer
tracker

Tract Reconstruction Helper for trac-all from Freesurfer
trac_prep

Tract Reconstruction for Each Step
mri_info.help

MRI information Help
read_fs_table

Read Freesurfer Table Output
mris_convert

Use Freesurfers MRIs Converter
surface_to_obj

Convert Freesurfer Surface to Wavefront OBJ
mris_convert.help

Help file for Freesurfers MRIs Converter
mri_segment

Use Freesurfers MRI Segmentation Algorithm
freesurfer_read3

Freesurfer Read 3 records
convert_surface

Convert Freesurfer Surface
check_fs_result

Check Freesurfer Result
construct_subj_dir

Construct Subject Directory
asegstats2table.help

Parcellation Stats to Table Help
checkmnc-methods

Force object to filename with .mnc extension
aparcs_to_bg

Convert Freesurfer aparcs Table to brainGraph
asegstats2table

Parcellation Stats to Table
aparcstats2table

Parcellation Stats to Table
aparcstats2table.help

Parcellation Stats to Table Help
freesurfer_read3_con

Freesurfer Read 3 records
fs_subj_dir

Determine Freesurfer Subjects Directory
fs_version

Find Freesurfer Version
freesurfer_read_curv

Read Freesufer Curv file