├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── .travis.yml ├── CRAN-SUBMISSION ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── aparcs_to_bg.R ├── aparcstats2table.R ├── asegstats2table.R ├── check_fs_result.R ├── checkmnc.R ├── construct_subj_dir.R ├── convert_surface.R ├── freesurfer_read3.R ├── fs_cmd.R ├── fs_help.R ├── fs_lut.R ├── fs_setup.R ├── fs_version.R ├── mnc2nii.R ├── mri_convert.R ├── mri_deface.R ├── mri_info.R ├── mri_mask.R ├── mri_normalize.R ├── mri_segment.R ├── mri_surf2surf.R ├── mri_synthstrip.R ├── mri_watershed.R ├── mris_convert.R ├── mris_convert_annot.R ├── mris_convert_curv.R ├── mris_convert_normals.R ├── mris_convert_vertex.R ├── mris_euler_number.R ├── nii2mnc.R ├── nu_correct.R ├── read_annotation.R ├── read_aseg_stats.R ├── read_fs_table.R ├── read_label.R ├── readmgz.R ├── readmnc.R ├── recon.R ├── recon_all.R ├── recon_manual.R ├── reconner.R ├── run_check_fs_cmd.R ├── surf_convert.R ├── trac_all.R ├── trac_manual.R └── tracker.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── cran-comments.md ├── data └── fs_lut.rda ├── docs ├── 404.html ├── articles │ ├── exploring_included_data.html │ ├── exploring_included_data_files │ │ ├── anchor-sections-1.0 │ │ │ ├── anchor-sections.css │ │ │ └── anchor-sections.js │ │ ├── figure-html │ │ │ ├── mri_plot-1.png │ │ │ ├── mri_plot2-1.png │ │ │ ├── nu_correct_plot-1.png │ │ │ ├── seg_file-1.png │ │ │ └── watershed_plot-1.png │ │ ├── header-attrs-2.1 │ │ │ └── header-attrs.js │ │ └── header-attrs-2.5 │ │ │ └── header-attrs.js │ └── index.html ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml └── reference │ ├── Rplot001.png │ ├── aparcs_to_bg.html │ ├── aparcstats2table.help.html │ ├── aparcstats2table.html │ ├── asegstats2table.help.html │ ├── asegstats2table.html │ ├── check_fs_result.html │ ├── checkmnc-methods.html │ ├── construct_subj_dir.html │ ├── convert_surface.html │ ├── file14af07b387fdf.nii.log │ ├── file78e642cbe0.nii.log │ ├── freesurfer_read3.html │ ├── freesurfer_read3_con.html │ ├── freesurfer_read_curv.html │ ├── freesurfer_read_surf.html │ ├── freesurferdir.html │ ├── fs_cmd.html │ ├── fs_help.html │ ├── fs_imgext.html │ ├── fs_lut.html │ ├── fs_subj_dir.html │ ├── fs_version.html │ ├── get_fs.html │ ├── get_fs_output.html │ ├── have_fs.html │ ├── index.html │ ├── mnc2nii.help.html │ ├── mnc2nii.html │ ├── mri_convert.help.html │ ├── mri_convert.html │ ├── mri_deface.html │ ├── mri_info.help.html │ ├── mri_info.html │ ├── mri_mask.help.html │ ├── mri_mask.html │ ├── mri_normalize.help.html │ ├── mri_normalize.html │ ├── mri_segment.help.html │ ├── mri_segment.html │ ├── mri_surf2surf.help.html │ ├── mri_surf2surf.html │ ├── mri_watershed.help.html │ ├── mri_watershed.html │ ├── mris_convert.help.html │ ├── mris_convert.html │ ├── mris_convert_annot.html │ ├── mris_convert_curv.html │ ├── mris_convert_normals.html │ ├── mris_convert_vertex.html │ ├── mris_euler_number.help.html │ ├── mris_euler_number.html │ ├── nii2mnc.help.html │ ├── nii2mnc.html │ ├── nu_correct.help.html │ ├── nu_correct.html │ ├── read_annotation.html │ ├── read_aseg_stats.html │ ├── read_fs_label.html │ ├── read_fs_table.html │ ├── readmgz.html │ ├── readmnc.html │ ├── recon.html │ ├── recon_all.html │ ├── recon_manual.html │ ├── reconner.html │ ├── run_check_fs_cmd.html │ ├── set_fs_subj_dir.html │ ├── surf_convert.html │ ├── surface_to_obj.html │ ├── surface_to_triangles.html │ ├── trac_all.html │ ├── trac_manual.html │ └── tracker.html ├── freesurfer.Rproj ├── freesurfer_lut.R ├── inst └── CITATION ├── man ├── aparcs_to_bg.Rd ├── aparcstats2table.Rd ├── aparcstats2table.help.Rd ├── asegstats2table.Rd ├── asegstats2table.help.Rd ├── check_fs_result.Rd ├── checkmnc-methods.Rd ├── construct_subj_dir.Rd ├── convert_surface.Rd ├── 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