Package: freesurfer 1.8.1.902

freesurfer: Wrapper Functions for 'FreeSurfer'

Wrapper functions that interface with 'Freesurfer' <https://surfer.nmr.mgh.harvard.edu/>, 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.

Authors:John Muschelli [aut, cre, cph], Athanasia Mo Mowinckel [ctb]

freesurfer_1.8.1.902.tar.gz
freesurfer_1.8.1.902.zip(r-4.7)freesurfer_1.8.1.902.zip(r-4.6)freesurfer_1.8.1.902.zip(r-4.5)
freesurfer_1.8.1.902.tgz(r-4.6-any)freesurfer_1.8.1.902.tgz(r-4.5-any)
freesurfer_1.8.1.902.tar.gz(r-4.7-any)freesurfer_1.8.1.902.tar.gz(r-4.6-any)
freesurfer_1.8.1.902.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
freesurfer/json (API)
NEWS

# Install 'freesurfer' in R:
install.packages('freesurfer', repos = c('https://muschellij2.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/muschellij2/freesurfer/issues

Datasets:
  • fs_lut - Freesurfer look up table

On CRAN:

Conda:

7.16 score 10 stars 73 scripts 216 downloads 92 exports 13 dependencies

Last updated from:5953d538f0. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK155
source / vignettesOK166
linux-release-x86_64OK156
macos-release-arm64OK104
macos-oldrel-arm64OK138
windows-develOK116
windows-releaseOK140
windows-oldrelOK130
wasm-releaseOK107

Exports:aparcs_to_bgaparcstats2tableaparcstats2table.helpasegstats2tableasegstats2table.helpautorecon1autorecon2autorecon3checkmncconstruct_subj_dirconvert_surfacefreesurfer_dirfreesurfer_read_curvfreesurfer_read_surffreesurferdirfs_cmdfs_dirfs_helpfs_imgextfs_sitrepfs_subj_dirfs_versionget_fsget_fs_homeget_fs_licenseget_fs_outputget_fs_settingget_fs_sourceget_fs_subdirget_fs_verbosityget_mni_binhave_fsmnc2niimnc2nii.helpmri_convertmri_convert.helpmri_defacemri_infomri_info.helpmri_maskmri_mask.helpmri_normalizemri_normalize.helpmri_segment.helpmri_surf2surfmri_surf2surf.helpmri_synthstripmri_synthstrip.helpmri_watershedmri_watershed.helpmris_convertmris_convert_annotmris_convert_curvmris_convert_normalsmris_convert_vertexmris_convert.helpmris_euler_numbermris_euler_number.helpnii2mncnii2mnc.helpnu_correctnu_correct.helpread_annotationread_aseg_statsread_fs_labelread_fs_tableread_mghread_mgzread_mncread_stats_tablereadmghreadmgzreconrecon_allrecon_con1recon_con2recon_con3recon_stepsreconnerset_fs_subj_dirstats2tablesurf_convertsurface_to_objsurface_to_trianglessynthstriptemp_filetrac_alltrac_bedposttrac_pathtrac_preptrackertracker.help

Dependencies:abindbitopsclilifecyclematrixStatsneurobaseoro.niftiR.methodsS3R.ooR.utilsRcpprlangRNifti

Advanced usage & future plans

Rendered fromadvance_future.Rmdusingknitr::rmarkdownon May 09 2026.

Last update: 2026-04-09
Started: 2026-04-09

Analyzing and Visualizing Freesurfer Outputs

Rendered fromanalysing_visualizing.Rmdusingknitr::rmarkdownon May 09 2026.

Last update: 2026-04-09
Started: 2026-04-09

Core Image Processing

Rendered fromimage_processing.Rmdusingknitr::rmarkdownon May 09 2026.

Last update: 2026-04-09
Started: 2026-04-09

Getting Started and Setting Up freesurfer in R

Rendered fromfreesurfer.Rmdusingknitr::rmarkdownon May 09 2026.

Last update: 2026-04-09
Started: 2026-04-09

Running recon-all

Rendered fromrecon-all.Rmdusingknitr::rmarkdownon May 09 2026.

Last update: 2026-04-09
Started: 2026-04-09

Readme and manuals

Help Manual

Help pageTopics
Convert Freesurfer aparcs Table to brainGraphaparcs_to_bg
Force object to filename with .mnc extensioncheckmnc checkmnc,character-method checkmnc,list-method checkmnc,nifti-method checkmnc-methods ensure_mnc
Construct Subject Directoryconstruct_subj_dir
Convert Freesurfer Surfaceconvert_surface
Read Freesufer Curv filefreesurfer_read_curv
Read Freesurfer Surface filefreesurfer_read_surf
Execute FreeSurfer Commands from Rfs_cmd
Get FreeSurfer Directory Pathsfreesurferdir freesurfer_dir fs_dir fs_subj_dir
Wrapper for getting FreeSurfer helpfs_help
Determine extension of image based on Freesurfer output typefs_imgext
Freesurfer look up table (LUT)fs_lut
FreeSurfer Situation Reportfs_sitrep
Find Freesurfer Versionfs_version
Generate FreeSurfer Command Line Environment Setupget_fs
Retrieve FreeSurfer Configuration Settingsget_fs_home get_fs_license get_fs_output get_fs_setting get_fs_source get_fs_subdir get_fs_verbosity get_mni_bin
Logical check if Freesurfer is accessiblehave_fs
Convert MNC to NIfTImnc2nii mnc2nii.help
Convert Medical Image Formats with FreeSurfermri_convert mri_convert.help
MRI Defacemri_deface
MRI informationmri_info
MRI information Helpmri_info.help
Use Freesurfers MRI Maskmri_mask
MRI Normalize Helpmri_mask.help
Use Freesurfers MRI Normalize Algorithmmri_normalize
MRI Normalize Helpmri_normalize.help
Use Freesurfers MRI Segmentation Algorithmmri_segment mri_segment.help
Resample Cortical Surface Data with FreeSurfermri_surf2surf mri_surf2surf.help
Use Freesurfers MRI SynthStripmri_synthstrip synthstrip
MRI Normalize Helpmri_synthstrip.help
Use Freesurfers MRI Watershed Algorithmmri_watershed mri_watershed.help
Convert Cortical Surface File Formats with FreeSurfermris_convert mris_convert.help mris_convert_annot mris_convert_curv mris_convert_normals mris_convert_vertex
MRIs Euler Numbermris_euler_number
MRI Euler Number Helpmris_euler_number.help
Convert NIfTI to MNCnii2mnc nii2mnc.help
Use FreeSurfer's Non-Uniformity Correctionnu_correct nu_correct.help
Read Freesurfer annotation fileread_annotation
Read FreeSurfer Anatomical Segmentation Statisticsread_aseg_stats
Read Label Fileread_fs_label
Read FreeSurfer Table Outputread_fs_table read_stats_table
Read MGH or MGZ Filereadmgh readmgz read_mgh read_mgz
Read MNC Fileread_mnc
FreeSurfer Reconstruction Pipeline Functionsrecon recon_all recon_steps
Manual Freesurfer Reconstruction Workflowautorecon1 autorecon2 autorecon3 recon_con1 recon_con2 recon_con3 recon_manual
Reconstruction Helper for FreeSurfer's recon-allreconner
Generalized Stats to Tableaparcstats2table aparcstats2table.help asegstats2table asegstats2table.help stats2table
Convert Surface Data to ASCIIsurf_convert
Convert Freesurfer Surface to Wavefront OBJsurface_to_obj
Convert Freesurfer Surface to Trianglessurface_to_triangles
Create a Temporary File with a Newly Created Directorytemp_file
FreeSurfer Diffusion Tractography Pipelinetrac tracker tracker.help trac_all trac_bedpost trac_path trac_prep