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  "Type": "Package",
  "Package": "freesurfer",
  "Title": "Wrapper Functions for 'FreeSurfer'",
  "Version": "1.8.1.902",
  "Authors@R": "c(\nperson(\"John\", \"Muschelli\", , \"muschellij2@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-6469-1750\")),\nperson(\"Athanasia Mo\", \"Mowinckel\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-5756-0223\"))\n)",
  "Description": "Wrapper functions that interface with 'Freesurfer'\n<https://surfer.nmr.mgh.harvard.edu/>, a powerful and\ncommonly-used 'neuroimaging' software, using system commands.\nThe goal is to be able to interface with 'Freesurfer'\ncompletely in R, where you pass R objects of class 'nifti',\nimplemented by package 'oro.nifti', and the function executes\nan 'Freesurfer' command and returns an R object of class\n'nifti' or necessary output.",
  "License": "GPL-3",
  "URL": "https://muschellij2.github.io/freesurfer/,\nhttps://github.com/muschellij2/freesurfer",
  "BugReports": "https://github.com/muschellij2/freesurfer/issues",
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  "SystemRequirements": "FreeSurfer (https://freesurfer.net/)",
  "Repository": "https://ggsegverse.r-universe.dev",
  "Date/Publication": "2026-04-08 19:04:47 UTC",
  "RemoteUrl": "https://github.com/drmowinckels/freesurfer",
  "RemoteRef": "refactor",
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  "Author": "John Muschelli [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0001-6469-1750>),\nAthanasia Mo Mowinckel [ctb] (ORCID:\n<https://orcid.org/0000-0002-5756-0223>)",
  "Maintainer": "John Muschelli <muschellij2@gmail.com>",
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  "_created": "2026-05-08T09:02:59.000Z",
  "_published": "2026-05-22T13:51:18.846Z",
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  "_homeurl": "https://github.com/muschellij2/freesurfer",
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    "aparcs_to_bg",
    "aparcstats2table",
    "aparcstats2table.help",
    "asegstats2table",
    "asegstats2table.help",
    "autorecon1",
    "autorecon2",
    "autorecon3",
    "checkmnc",
    "construct_subj_dir",
    "convert_surface",
    "freesurfer_dir",
    "freesurfer_read_curv",
    "freesurfer_read_surf",
    "freesurferdir",
    "fs_cmd",
    "fs_dir",
    "fs_help",
    "fs_imgext",
    "fs_sitrep",
    "fs_subj_dir",
    "fs_version",
    "get_fs",
    "get_fs_home",
    "get_fs_license",
    "get_fs_output",
    "get_fs_setting",
    "get_fs_source",
    "get_fs_subdir",
    "get_fs_verbosity",
    "get_mni_bin",
    "have_fs",
    "mnc2nii",
    "mnc2nii.help",
    "mri_convert",
    "mri_convert.help",
    "mri_deface",
    "mri_info",
    "mri_info.help",
    "mri_mask",
    "mri_mask.help",
    "mri_normalize",
    "mri_normalize.help",
    "mri_segment.help",
    "mri_surf2surf",
    "mri_surf2surf.help",
    "mri_synthstrip",
    "mri_synthstrip.help",
    "mri_watershed",
    "mri_watershed.help",
    "mris_convert",
    "mris_convert_annot",
    "mris_convert_curv",
    "mris_convert_normals",
    "mris_convert_vertex",
    "mris_convert.help",
    "mris_euler_number",
    "mris_euler_number.help",
    "nii2mnc",
    "nii2mnc.help",
    "nu_correct",
    "nu_correct.help",
    "read_annotation",
    "read_aseg_stats",
    "read_fs_label",
    "read_fs_table",
    "read_mgh",
    "read_mgz",
    "read_mnc",
    "read_stats_table",
    "readmgh",
    "readmgz",
    "recon",
    "recon_all",
    "recon_con1",
    "recon_con2",
    "recon_con3",
    "recon_steps",
    "reconner",
    "set_fs_subj_dir",
    "stats2table",
    "surf_convert",
    "surface_to_obj",
    "surface_to_triangles",
    "synthstrip",
    "temp_file",
    "trac_all",
    "trac_bedpost",
    "trac_path",
    "trac_prep",
    "tracker",
    "tracker.help"
  ],
  "_datasets": [
    {
      "name": "fs_lut",
      "title": "Freesurfer look up table (LUT)",
      "object": "fs_lut",
      "class": [
        "data.frame"
      ],
      "fields": [
        "index",
        "label",
        "R",
        "G",
        "B",
        "A"
      ],
      "rows": 1266,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "aparcs_to_bg",
      "title": "Convert Freesurfer aparcs Table to brainGraph",
      "topics": [
        "aparcs_to_bg"
      ]
    },
    {
      "page": "checkmnc-methods",
      "title": "Force object to filename with .mnc extension",
      "topics": [
        "checkmnc",
        "checkmnc,character-method",
        "checkmnc,list-method",
        "checkmnc,nifti-method",
        "checkmnc-methods",
        "ensure_mnc"
      ]
    },
    {
      "page": "construct_subj_dir",
      "title": "Construct Subject Directory",
      "topics": [
        "construct_subj_dir"
      ]
    },
    {
      "page": "convert_surface",
      "title": "Convert Freesurfer Surface",
      "topics": [
        "convert_surface"
      ]
    },
    {
      "page": "freesurfer_read_curv",
      "title": "Read Freesufer Curv file",
      "topics": [
        "freesurfer_read_curv"
      ]
    },
    {
      "page": "freesurfer_read_surf",
      "title": "Read Freesurfer Surface file",
      "topics": [
        "freesurfer_read_surf"
      ]
    },
    {
      "page": "fs_cmd",
      "title": "Execute FreeSurfer Commands from R",
      "topics": [
        "fs_cmd"
      ]
    },
    {
      "page": "fs_dir",
      "title": "Get FreeSurfer Directory Paths",
      "topics": [
        "freesurferdir",
        "freesurfer_dir",
        "fs_dir",
        "fs_subj_dir"
      ]
    },
    {
      "page": "fs_help",
      "title": "Wrapper for getting FreeSurfer help",
      "topics": [
        "fs_help"
      ]
    },
    {
      "page": "fs_imgext",
      "title": "Determine extension of image based on Freesurfer output type",
      "topics": [
        "fs_imgext"
      ]
    },
    {
      "page": "fs_lut",
      "title": "Freesurfer look up table (LUT)",
      "topics": [
        "fs_lut"
      ]
    },
    {
      "page": "fs_sitrep",
      "title": "FreeSurfer Situation Report",
      "topics": [
        "fs_sitrep"
      ]
    },
    {
      "page": "fs_version",
      "title": "Find Freesurfer Version",
      "topics": [
        "fs_version"
      ]
    },
    {
      "page": "get_fs",
      "title": "Generate FreeSurfer Command Line Environment Setup",
      "topics": [
        "get_fs"
      ]
    },
    {
      "page": "get_fs_setting",
      "title": "Retrieve FreeSurfer Configuration Settings",
      "topics": [
        "get_fs_home",
        "get_fs_license",
        "get_fs_output",
        "get_fs_setting",
        "get_fs_source",
        "get_fs_subdir",
        "get_fs_verbosity",
        "get_mni_bin"
      ]
    },
    {
      "page": "have_fs",
      "title": "Logical check if Freesurfer is accessible",
      "topics": [
        "have_fs"
      ]
    },
    {
      "page": "mnc2nii",
      "title": "Convert MNC to NIfTI",
      "topics": [
        "mnc2nii",
        "mnc2nii.help"
      ]
    },
    {
      "page": "mri_convert",
      "title": "Convert Medical Image Formats with FreeSurfer",
      "topics": [
        "mri_convert",
        "mri_convert.help"
      ]
    },
    {
      "page": "mri_deface",
      "title": "MRI Deface",
      "topics": [
        "mri_deface"
      ]
    },
    {
      "page": "mri_info",
      "title": "MRI information",
      "topics": [
        "mri_info"
      ]
    },
    {
      "page": "mri_info.help",
      "title": "MRI information Help",
      "topics": [
        "mri_info.help"
      ]
    },
    {
      "page": "mri_mask",
      "title": "Use Freesurfers MRI Mask",
      "topics": [
        "mri_mask"
      ]
    },
    {
      "page": "mri_mask.help",
      "title": "MRI Normalize Help",
      "topics": [
        "mri_mask.help"
      ]
    },
    {
      "page": "mri_normalize",
      "title": "Use Freesurfers MRI Normalize Algorithm",
      "topics": [
        "mri_normalize"
      ]
    },
    {
      "page": "mri_normalize.help",
      "title": "MRI Normalize Help",
      "topics": [
        "mri_normalize.help"
      ]
    },
    {
      "page": "mri_segment",
      "title": "Use Freesurfers MRI Segmentation Algorithm",
      "topics": [
        "mri_segment",
        "mri_segment.help"
      ]
    },
    {
      "page": "mri_surf2surf",
      "title": "Resample Cortical Surface Data with FreeSurfer",
      "topics": [
        "mri_surf2surf",
        "mri_surf2surf.help"
      ]
    },
    {
      "page": "mri_synthstrip",
      "title": "Use Freesurfers MRI SynthStrip",
      "topics": [
        "mri_synthstrip",
        "synthstrip"
      ]
    },
    {
      "page": "mri_synthstrip.help",
      "title": "MRI Normalize Help",
      "topics": [
        "mri_synthstrip.help"
      ]
    },
    {
      "page": "mri_watershed",
      "title": "Use Freesurfers MRI Watershed Algorithm",
      "topics": [
        "mri_watershed",
        "mri_watershed.help"
      ]
    },
    {
      "page": "mris_convert",
      "title": "Convert Cortical Surface File Formats with FreeSurfer",
      "topics": [
        "mris_convert",
        "mris_convert.help",
        "mris_convert_annot",
        "mris_convert_curv",
        "mris_convert_normals",
        "mris_convert_vertex"
      ]
    },
    {
      "page": "mris_euler_number",
      "title": "MRIs Euler Number",
      "topics": [
        "mris_euler_number"
      ]
    },
    {
      "page": "mris_euler_number.help",
      "title": "MRI Euler Number Help",
      "topics": [
        "mris_euler_number.help"
      ]
    },
    {
      "page": "nii2mnc",
      "title": "Convert NIfTI to MNC",
      "topics": [
        "nii2mnc",
        "nii2mnc.help"
      ]
    },
    {
      "page": "nu_correct",
      "title": "Use FreeSurfer's Non-Uniformity Correction",
      "topics": [
        "nu_correct",
        "nu_correct.help"
      ]
    },
    {
      "page": "read_annotation",
      "title": "Read Freesurfer annotation file",
      "topics": [
        "read_annotation"
      ]
    },
    {
      "page": "read_aseg_stats",
      "title": "Read FreeSurfer Anatomical Segmentation Statistics",
      "topics": [
        "read_aseg_stats"
      ]
    },
    {
      "page": "read_fs_label",
      "title": "Read Label File",
      "topics": [
        "read_fs_label"
      ]
    },
    {
      "page": "read_fs_table",
      "title": "Read FreeSurfer Table Output",
      "topics": [
        "read_fs_table",
        "read_stats_table"
      ]
    },
    {
      "page": "read_mgz",
      "title": "Read MGH or MGZ File",
      "topics": [
        "readmgh",
        "readmgz",
        "read_mgh",
        "read_mgz"
      ]
    },
    {
      "page": "read_mnc",
      "title": "Read MNC File",
      "topics": [
        "read_mnc"
      ]
    },
    {
      "page": "recon",
      "title": "FreeSurfer Reconstruction Pipeline Functions",
      "topics": [
        "recon",
        "recon_all",
        "recon_steps"
      ]
    },
    {
      "page": "recon_manual",
      "title": "Manual Freesurfer Reconstruction Workflow",
      "topics": [
        "autorecon1",
        "autorecon2",
        "autorecon3",
        "recon_con1",
        "recon_con2",
        "recon_con3",
        "recon_manual"
      ]
    },
    {
      "page": "reconner",
      "title": "Reconstruction Helper for FreeSurfer's recon-all",
      "topics": [
        "reconner"
      ]
    },
    {
      "page": "stats2table",
      "title": "Generalized Stats to Table",
      "topics": [
        "aparcstats2table",
        "aparcstats2table.help",
        "asegstats2table",
        "asegstats2table.help",
        "stats2table"
      ]
    },
    {
      "page": "surf_convert",
      "title": "Convert Surface Data to ASCII",
      "topics": [
        "surf_convert"
      ]
    },
    {
      "page": "surface_to_obj",
      "title": "Convert Freesurfer Surface to Wavefront OBJ",
      "topics": [
        "surface_to_obj"
      ]
    },
    {
      "page": "surface_to_triangles",
      "title": "Convert Freesurfer Surface to Triangles",
      "topics": [
        "surface_to_triangles"
      ]
    },
    {
      "page": "temp_file",
      "title": "Create a Temporary File with a Newly Created Directory",
      "topics": [
        "temp_file"
      ]
    },
    {
      "page": "trac",
      "title": "FreeSurfer Diffusion Tractography Pipeline",
      "topics": [
        "trac",
        "tracker",
        "tracker.help",
        "trac_all",
        "trac_bedpost",
        "trac_path",
        "trac_prep"
      ]
    }
  ],
  "_readme": "https://github.com/drmowinckels/freesurfer/raw/refactor/README.md",
  "_rundeps": [
    "abind",
    "bitops",
    "cli",
    "lifecycle",
    "matrixStats",
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