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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

278

Version

1.6.8

License

GPL-3

Maintainer

John Muschelli

Last Published

December 8th, 2020

Functions in freesurfer (1.6.8)

checkmnc-methods

Force object to filename with .mnc extension

freesurfer_read3

Freesurfer Read 3 records

aparcstats2table

Parcellation Stats to Table

asegstats2table

Parcellation Stats to Table

Convert Freesurfer aparcs Table to brainGraph

asegstats2table.help

Parcellation Stats to Table Help

convert_surface

Convert Freesurfer Surface

aparcstats2table.help

Parcellation Stats to Table Help

check_fs_result

Check Freesurfer Result

Determine Freesurfer Subjects Directory

Find Freesurfer Version

Use Freesurfers MRI Mask

MRI information Help

mris_convert.help

Help file for Freesurfers MRIs Converter

MRI information

Use Freesurfers MRIs Converter

MRI Normalize Help

mri_convert.help

MRI Normalize Help

freesurfer_read3_con

Freesurfer Read 3 records

freesurfer_read_curv

Read Freesufer Curv file

Determine extension of image based on FSLOUTPUTTYPE

MNC to NIfTI Help

freesurfer_read_surf

Read Freesurfer Surface file

construct_subj_dir

Construct Subject Directory

Get Freesurfer's Directory

Use Freesurfers MRI Converter

mris_convert_normals

Convert Surface to Surface normals

Use Freesurfers MRI Segmentation Algorithm

mri_segment.help

MRI Segment Help

Freesurfer look up table (LUT)

mris_convert_vertex

Convert Surface to vertex file

Use Freesurfers MRI Watershed Algorithm

Convert NIfTI to MNC

mri_watershed.help

MRI Watershed Help

Reconstruction from Freesurfer

Reconstruction from Freesurfer for All Steps

Convert Freesurfer Surface to Wavefront OBJ

Convert Surface Data to ASCII

Read MGH or MGZ File

FS Command Wrapper

Wrapper for getting Freesurfer help

Create command declaring FREESURFER_HOME

Convert NIfTI to MNC Help

Logical check if Freesurfer is accessible

mris_euler_number

MRI Euler Number

surface_to_triangles

Convert Freesurfer Surface to Triangles

Reconstruction Helper for recon from Freesurfer

mris_euler_number.help

MRI Euler Number Help

Reconstruction from Motion Correction to Skull Strip

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

Use Freesurfers mri_surf2surf function to resamples one cortical surface onto another

read_annotation

Read Freesurfer annotation file

Convert MNC to NIfTI

mri_surf2surf.help

Freesurfers mri_surf2surf Help

read_aseg_stats

Read Anatomical Segmentation Statistics

run_check_fs_cmd

Run and Check a Freesurfer Command

set_fs_subj_dir

Set Freesurfer Subjects Directory

Determine Freesurfer output type

Use Freesurfers MRI Normalize Algorithm

mri_normalize.help

MRI Normalize Help

Use Freesurfers Non-Uniformity Correction

mris_convert_annot

Convert Annotation file

nu_correct.help

Non-Uniformity Correction Help

Read Label File

mris_convert_curv

Convert Curvature file

Tract Reconstruction for Each Step

Read Freesurfer Table Output

Tract Reconstruction Helper for trac-all from Freesurfer