{ "_id": "6ad78ff20d12c08e591b9221", "Package": "freesurferformats", "Type": "Package", "Title": "Read and Write 'FreeSurfer' Neuroimaging File Formats", "Version": "1.1.2", "Authors@R": "c(\nperson(\"Tim\", \"Schäfer\", role = c(\"aut\", \"cre\"), email = \"ts+code@rcmd.org\", comment = c(ORCID = \"0000-0002-3683-8070\")),\nperson(\"Van Essen Lab\", role = \"cph\", comment = \"Copyright holder of the Conte69 template and HCP group-average data files that can OPTIONALLY be downloaded via download_opt_data().\"),\nperson(\"Montreal Neurological Institute (MNI)\", role = \"cph\", comment = \"Copyright holder of the MNI152/avg152T1 template that can OPTIONALLY be downloaded via download_opt_data().\"))", "Maintainer": "Tim Schäfer ", "Description": "Provides functions to read and write neuroimaging data in\nvarious file formats, with a focus on 'FreeSurfer' formats.\nThis includes, but is not limited to, the following file\nformats: 1) MGH/MGZ/NIFTI format files, which can contain\nmulti-dimensional images or other data. Typically they contain\ntime-series of three-dimensional brain scans acquired by\nmagnetic resonance imaging (MRI). They can also contain\nvertex-wise measures of surface morphometry data. The MGH\nformat is named after the Massachusetts General Hospital, and\nthe MGZ format is a compressed version of the same format. 2)\n'FreeSurfer' morphometry data files in binary 'curv' format.\nThese contain vertex-wise surface measures, i.e., one scalar\nvalue for each vertex of a brain surface mesh. These are\ntypically values like the cortical thickness or brain surface\narea at each vertex. 3) Annotation file format. This contains a\nbrain surface parcellation derived from a cortical atlas. 4)\nSurface file format. Contains a brain surface mesh, given by a\nlist of vertices and a list of faces.", "License": "MIT + file LICENSE", "Copyright": "Tim Schäfer (package code); the optional data files that can\nbe downloaded at runtime are owned by their respective\ncopyright holders, see 'inst/COPYRIGHTS'.", "Encoding": "UTF-8", "URL": "https://github.com/dfsp-spirit/freesurferformats,\nhttps://dfsp-spirit.github.io/freesurferformats/", "BugReports": "https://github.com/dfsp-spirit/freesurferformats/issues", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libxml2-dev libssl-dev", "Repository": "https://dfsp-spirit.r-universe.dev", "Date/Publication": "2026-10-20 14:17:01 UTC", "RemoteUrl": "https://github.com/dfsp-spirit/freesurferformats", "RemoteRef": "v1.1.2", "RemoteSha": "dc2a5a8beee529392bf4e336256078f474468b6b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-20 15:51:43 UTC", "User": "root" }, "Author": "Tim Schäfer [aut, cre] (ORCID: ),\nVan Essen Lab [cph] (Copyright holder of the Conte69 template and HCP\ngroup-average data files that can OPTIONALLY be downloaded via\ndownload_opt_data().),\nMontreal Neurological Institute (MNI) [cph] (Copyright holder of the\nMNI152/avg152T1 template that can OPTIONALLY be downloaded via\ndownload_opt_data().)", "_user": "dfsp-spirit", "_type": "src", "_file": "freesurferformats_1.1.2.tar.gz", "_fileid": "https://r2.ropensci.org/311d4f81d851f3f69cfa4cb4fc8bde90c3f6ce65905916ed6a545b3a1e43821d", "_filesize": 4846582, "_sha256": "311d4f81d851f3f69cfa4cb4fc8bde90c3f6ce65905916ed6a545b3a1e43821d", "_expires": "2027-01-28T15:59:43.000Z", "_created": "2026-10-20T15:51:43.000Z", "_published": "2026-10-20T15:59:46.032Z", "_upstream": "https://github.com/dfsp-spirit/freesurferformats", "_status": "success", "_maintainer": { "name": "Tim Schäfer", "email": "ts+code@rcmd.org", "login": "dfsp-spirit", "orcid": "0000-0002-3683-8070", "description": "Research Software Engineer at Max Planck Institute for Empirical Aesthetics", "uuid": 1061893 }, "_jobs": [ { "job": 118730322625, "time": 205, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12278088477" }, { "job": 118730322666, "time": 204, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12278728429" }, { "job": 118730322608, "time": 177, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12278018898" }, { "job": 118730322479, "time": 208, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12278908696" }, { "job": 118728165926, "time": 244, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12278908005" }, { "job": 118730322345, "time": 97, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12279122601" }, { "job": 118730322488, "time": 202, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12278982896" }, { "job": 118730322508, "time": 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"version": ">= 0.9", "role": "Suggests" }, { "package": "gifti", "version": ">= 0.7.5", "role": "Suggests" }, { "package": "cifti", "version": ">= 0.4.5", "role": "Suggests" } ], "_owner": "dfsp-spirit", "_selfowned": true, "_usedby": 10, "_updates": [ { "week": "2026-27", "n": 5 }, { "week": "2026-28", "n": 27 }, { "week": "2026-31", "n": 6 }, { "week": "2026-32", "n": 1 }, { "week": "2026-35", "n": 2 }, { "week": "2026-36", "n": 4 }, { "week": "2026-37", "n": 13 }, { "week": "2026-38", "n": 11 }, { "week": "2026-39", "n": 26 }, { "week": "2026-40", "n": 2 }, { "week": "2026-43", "n": 2 } ], "_tags": [ { "name": "nitestdata-v1", "date": "2026-07-07" }, { "name": "v1.0.1", "date": "2026-07-08" }, { "name": "v1.0.2", "date": "2026-09-08" }, { "name": "v1.1.0", "date": "2026-09-22" }, { "name": "v1.1.1", "date": "2026-09-30" }, { "name": "v1.1.2", "date": "2026-10-20" } ], "_topics": [ "brain", "brain-atlas", "brain-surfaces", "curv", "dti", "fileformats", "freesurfer", "label", "mesh", "mgh", "mri", "neuroimaging", "parcellation", "research", "surface", "voxel" ], "_stars": 23, "_contributors": [ { "user": "dfsp-spirit", "count": 943, "uuid": 1061893 }, { "user": "dipterix", "count": 5, "uuid": 8163576 }, { "user": "fbrockmeyer", "count": 4, "uuid": 74774192 }, { "user": "andrewlawrence", "count": 1, "uuid": 4668209 } ], "_userbio": { "uuid": 1061893, "type": "user", "name": "Tim Schäfer", "followers": 77, "description": "Research Software Engineer at Max Planck Institute for Empirical Aesthetics" }, "_downloads": { "count": 2135, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/freesurferformats" }, "_devurl": "https://github.com/dfsp-spirit/freesurferformats", "_pkgdown": "https://dfsp-spirit.github.io/freesurferformats/", "_searchresults": 64, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/freesurferformats.html", "extra/manual.pdf", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/dfsp-spirit/freesurferformats", "_realowner": "dfsp-spirit", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2019-09-04" }, { "version": "0.1.1", "date": "2019-09-13" }, { "version": "0.1.2", "date": "2019-10-02" }, { "version": "0.1.3", "date": "2019-10-15" }, { "version": "0.1.4", "date": "2019-11-06" }, { "version": "0.1.5", "date": "2019-11-12" }, { "version": "0.1.6", "date": "2019-11-27" }, { "version": "0.1.7", "date": "2020-01-07" }, { "version": "0.1.8", "date": "2020-02-17" }, { "version": "0.1.9", "date": "2020-04-14" }, { "version": "0.1.10", "date": "2020-05-13" }, { "version": "0.1.11", "date": "2020-06-17" }, { "version": "0.1.12", "date": "2020-08-26" }, { "version": "0.1.13", "date": "2020-09-21" }, { "version": "0.1.14", "date": "2021-01-17" }, { "version": "0.1.15", "date": "2021-05-25" }, { "version": "0.1.16", "date": "2021-11-07" }, { "version": "0.1.17", "date": 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You will have to adapt it for your use case.", "topics": [ "analyzeheader.template" ] }, { "page": "annot.max.region.idx", "title": "Get max region index of an fs.annot instance.", "topics": [ "annot.max.region.idx" ] }, { "page": "as.fs.tracts", "title": "Convert a collection of tracts to an fs.tracts instance.", "topics": [ "as.fs.tracts" ] }, { "page": "as.list.fs.tracts", "title": "Convert an fs.tracts instance to a plain list of tracts.", "topics": [ "as.list.fs.tracts" ] }, { "page": "atlas.from.lut.and.csv", "title": "Construct a brain atlas from a colortable (LUT) file and a per-vertex label file.", "concept": [ "atlas functions" ], "topics": [ "atlas.from.lut.and.csv" ] }, { "page": "bvsmp", "title": "Create new bvsmp instance encoding morph data for Brainvoyager.", "topics": [ "bvsmp" ] }, { "page": "cdata", "title": "Create CDATA element string from string.", "topics": [ "cdata" ] }, { "page": "cifti.axis.brain.models", "title": "Create a CIFTI-2 axis for brain models.", "concept": [ "cifti functions" ], "topics": [ "cifti.axis.brain.models" ] }, { "page": "cifti.axis.from.template", "title": "Create a CIFTI-2 axis from a template file.", "concept": [ "cifti functions" ], "topics": [ "cifti.axis.from.template" ] }, { "page": "cifti.axis.labels", "title": "Create a CIFTI-2 axis for label maps.", "concept": [ "cifti functions" ], "topics": [ "cifti.axis.labels" ] }, { "page": "cifti.axis.parcels", "title": "Create a CIFTI-2 axis for parcels.", "concept": [ "cifti functions" ], "topics": [ "cifti.axis.parcels" ] }, { "page": "cifti.axis.parcels.from.annot", "title": "Create a CIFTI-2 parcels axis from brain surface annotations.", "concept": [ "cifti functions" ], "topics": [ "cifti.axis.parcels.from.annot" ] }, { "page": "cifti.axis.scalars", "title": "Create a CIFTI-2 axis for scalar or label maps.", "concept": [ "cifti functions" ], "topics": [ "cifti.axis.scalars" ] }, { "page": "cifti.axis.series", "title": "Create a CIFTI-2 axis for a series.", "concept": [ "cifti functions" ], "topics": [ "cifti.axis.series" ] }, { "page": "cifti.brain.model.surface", "title": "Create a CIFTI-2 brain model entry for a surface.", "concept": [ "cifti functions" ], "topics": [ "cifti.brain.model.surface" ] }, { "page": "cifti.brain.model.volume", "title": "Create a CIFTI-2 brain model entry for volume voxels.", "concept": [ "cifti functions" ], "topics": [ "cifti.brain.model.volume" ] }, { "page": "cifti.dim.labels", "title": "Get axis labels for a matrix dimension of a CIFTI-2 file.", "concept": [ "cifti functions" ], "topics": [ "cifti.dim.labels" ] }, { "page": "cifti.file.type.for.axes", "title": "Get the standard CIFTI-2 file type for a set of axes.", "concept": [ "cifti functions" ], "topics": [ "cifti.file.type.for.axes" ] }, { "page": "cifti.grayordinates", "title": "Get the brainordinate table of a CIFTI-2 file.", "concept": [ "cifti functions" ], "topics": [ "cifti.grayordinates" ] }, { "page": "cifti.header.from.axes", "title": "Create the CIFTI-2 XML metadata for a set of axes.", "concept": [ "cifti functions" ], "topics": [ "cifti.header.from.axes" ] }, { "page": "cifti.label.table", "title": "Get a label table from a CIFTI-2 label file.", "concept": [ "cifti functions" ], "topics": [ "cifti.label.table" ] }, { "page": "cifti.parcel", "title": "Create a CIFTI-2 parcel.", "concept": [ "cifti functions" ], "topics": [ "cifti.parcel" ] }, { "page": "cifti.parcels", "title": "Get the parcel table of a CIFTI-2 file.", "concept": [ "cifti functions" ], "topics": [ "cifti.parcels" ] }, { "page": "cifti.series.info", "title": "Get the series information of a CIFTI-2 file.", "concept": [ "cifti functions" ], "topics": [ "cifti.series.info" ] }, { "page": "cifti.structure.data", "title": "Extract the data of one brain structure from a CIFTI-2 file.", "concept": [ "cifti functions" ], "topics": [ "cifti.structure.data" ] }, { "page": "cifti.structures", "title": "Get the brain model table of a CIFTI-2 file.", "concept": [ "cifti functions" ], "topics": [ "cifti.structures" ] }, { "page": "cifti.volume", "title": "Create a CIFTI-2 axis for a volume.", "concept": [ "cifti functions" ], "topics": [ "cifti.volume" ] }, { "page": "closest.vert.to.point", "title": "Find vertex index closest to given query coordinate using Euclidean distance.", "concept": [ "Euclidean distance util functions" ], "topics": [ "closest.vert.to.point" ] }, { "page": "colortable.from.annot", "title": "Extract color lookup table (LUT) from annotation.", "concept": [ "atlas functions", "colorLUT functions" ], "topics": [ "colortable.from.annot" ] }, { "page": "delete_all_opt_data", "title": "Delete all data in the package cache.", "topics": [ "delete_all_opt_data" ] }, { "page": "doapply.transform.mtx", "title": "Apply a spatial transformation matrix to the given coordinates.", "topics": [ "doapply.transform.mtx" ] }, { "page": "download_opt_data", "title": "Download optional data for the freesurferformats package.", "topics": [ "download_opt_data" ] }, { "page": "dti.track.bbox", "title": "Compute the bounding box of all tract coordinates in a file.", "topics": [ "dti.track.bbox" ] }, { "page": "dti.track.count", "title": "Count the tracts in a DTI tract file.", "topics": [ "dti.track.count" ] }, { "page": "dti.track.iterator", "title": "Create an iterator over the tracts of a DTI tract file.", "topics": [ "dti.track.iterator" ] }, { "page": "faces.quad.to.tris", "title": "Convert quadrangular faces or polygons to triangular ones.", "concept": [ "mesh functions" ], "topics": [ "faces.quad.to.tris" ] }, { "page": "faces.tris.to.quad", "title": "Convert tris faces to quad faces by simple merging.", "topics": [ "faces.tris.to.quad" ] }, { "page": "flip2D", "title": "Flip a 2D matrix.", "topics": [ "flip2D" ] }, { "page": "flip3D", "title": "Flip a 3D array along an axis.", "concept": [ "volume math" ], "topics": [ "flip3D" ] }, { "page": "fs.get.morph.file.ext.for.format", "title": "Determine morphometry file extension from format", "concept": [ "morphometry functions" ], "topics": [ "fs.get.morph.file.ext.for.format" ] }, { "page": "fs.get.morph.file.format.from.filename", "title": "Determine morphometry file format from filename", "concept": [ "morphometry functions" ], "topics": [ "fs.get.morph.file.format.from.filename" ] }, { "page": "fs.patch", "title": "Constructor for fs.patch", "concept": [ "patch functions" ], "topics": [ "fs.patch" ] }, { "page": "fs.surface.to.tmesh3d", "title": "Get an rgl tmesh3d instance from a brain surface mesh.", "topics": [ "fs.surface.to.tmesh3d" ] }, { "page": "fs.tracts", "title": "Create an fs.tracts instance from a compact tract representation.", "topics": [ "fs.tracts" ] }, { "page": "fs.tracts.coords", "title": "Get the concatenated coordinates of fs.tracts instances.", "topics": [ "fs.tracts.coords" ] }, { "page": "fs.tracts.lengths", "title": "Get the number of points of each tract.", "topics": [ "fs.tracts.lengths" ] }, { "page": "get_opt_data_filepath", "title": "Access a single file from the package cache by its file name.", "topics": [ "get_opt_data_filepath" ] }, { "page": "gifti_writer", "title": "Write data to a gifti file.", "topics": [ "gifti_writer" ] }, { "page": "gifti_xml", "title": "Get GIFTI XML representation of data.", "topics": [ "gifti_xml" ] }, { "page": "gifti_xml_add_global_metadata", "title": "Add metadata to GIFTI XML tree.", "topics": [ "gifti_xml_add_global_metadata" ] }, { "page": "gifti_xml_write", "title": "Write XML tree to a gifti file.", "topics": [ "gifti_xml_write" ] }, { "page": "giftixml_add_labeltable_from_annot", "title": "Add a label tabel from an annotation to a GIFTI XML tree.", "topics": [ "giftixml_add_labeltable_from_annot" ] }, { "page": "invert.fs.transform", "title": "Invert a transformation.", "concept": [ "header coordinate space" ], "topics": [ "invert.fs.transform" ] }, { "page": "is.analyze.file", "title": "Check whether a file is an ANALYZE 7.5 file.", "topics": [ "is.analyze.file" ] }, { "page": "is.bvsmp", "title": "Check whether object is a bvsmp instance.", "topics": [ "is.bvsmp" ] }, { "page": "is.fs.annot", "title": "Check whether object is an fs.annot", "topics": [ "is.fs.annot" ] }, { "page": "is.fs.label", "title": "Check whether object is an fs.label", "topics": [ "is.fs.label" ] }, { "page": "is.fs.surface", "title": "Check whether object is an fs.surface", "topics": [ "is.fs.surface" ] }, { "page": "is.fs.tracts", "title": "Check whether an object is an fs.tracts instance.", "topics": [ "is.fs.tracts" ] }, { "page": "is.fs.transform", "title": "Check whether an object is an fs.transform instance.", "concept": [ "header coordinate space" ], "topics": [ "is.fs.transform" ] }, { "page": "is.fs.volume", "title": "Check whether object is an fs.volume", "topics": [ "is.fs.volume" ] }, { "page": "is.mghheader", "title": "Check whether object is an mghheader", "topics": [ "is.mghheader" ] }, { "page": "length.fs.tracts", "title": "Number of tracts in an fs.tracts instance.", "topics": [ "length.fs.tracts" ] }, { "page": "list_opt_data", "title": "Get file names available in package cache.", "topics": [ "list_opt_data" ] }, { "page": "mghheader.centervoxelRAS.from.firstvoxelRAS", "title": "Compute RAS coords of center voxel.", "topics": [ "mghheader.centervoxelRAS.from.firstvoxelRAS" ] }, { "page": "mghheader.crs.orientation", "title": "Compute MGH volume orientation string.", "topics": [ "mghheader.crs.orientation" ] }, { "page": "mghheader.is.conformed", "title": "Determine whether an MGH volume is conformed.", "topics": [ "mghheader.is.conformed" ] }, { "page": "mghheader.is.ras.valid", "title": "Check whether header contains valid ras information", "concept": [ "header coordinate space" ], "topics": [ "mghheader.is.ras.valid" ] }, { "page": "mghheader.primary.slice.direction", "title": "Compute MGH primary slice direction", "topics": [ "mghheader.primary.slice.direction" ] }, { "page": "mghheader.ras2vox", "title": "Compute ras2vox matrix from basic MGH header fields.", "concept": [ "header coordinate space" ], "topics": [ "mghheader.ras2vox" ] }, { "page": "mghheader.ras2vox.tkreg", "title": "Compute ras2vox-tkreg matrix from basic MGH header fields.", "concept": [ "header coordinate space" ], "topics": [ "mghheader.ras2vox.tkreg" ] }, { "page": "mghheader.scanner2tkreg", "title": "Compute scanner-RAS 2 tkreg-RAS matrix from basic MGH header fields.", "concept": [ "header coordinate space" ], "topics": [ "mghheader.scanner2tkreg" ] }, { "page": "mghheader.tkreg2scanner", "title": "Compute tkreg-RAS to scanner-RAS matrix from basic MGH header fields.", "concept": [ "header coordinate space" ], "topics": [ "mghheader.tkreg2scanner" ] }, { "page": "mghheader.update.from.vox2ras", "title": "Update mghheader fields from vox2ras matrix.", "topics": [ "mghheader.update.from.vox2ras" ] }, { "page": "mghheader.vox2ras", "title": "Compute vox2ras matrix from basic MGH header fields.", "concept": [ "header coordinate space" ], "topics": [ "mghheader.vox2ras" ] }, { "page": "mghheader.vox2ras.tkreg", "title": "Compute vox2ras-tkreg matrix from basic MGH header fields.", "concept": [ "header coordinate space" ], "topics": [ "mghheader.vox2ras.tkreg" ] }, { "page": "mghheader.vox2vox", "title": "Compute vox2vox matrix between two volumes.", "topics": [ "mghheader.vox2vox" ] }, { "page": "mni152reg", "title": "Get fsaverage (MNI305) to MNI152 transformation matrix.", "topics": [ "mni152reg" ] }, { "page": "ni1header.for.data", "title": "Create NIFTI v1 header suitable for given data.", "topics": [ "ni1header.for.data" ] }, { "page": "ni1header.template", "title": "Create a template NIFTI v1 header. You will have to adapt it for your use case.", "topics": [ "ni1header.template" ] }, { "page": "ni2header.for.data", "title": "Create NIFTI v2 header suitable for given data.", "topics": [ "ni2header.for.data" ] }, { "page": "ni2header.template", "title": "Create a template NIFTI v2 header. You will have to adapt it for your use case.", "topics": [ "ni2header.template" ] }, { "page": "nifti.datadim.from.dimfield", "title": "Compute data dimensions from the 'dim' field of the NIFTI (v1 or v2) header.", "concept": [ "NIFTI helper functions" ], "topics": [ "nifti.datadim.from.dimfield" ] }, { "page": "nifti.datadim.to.dimfield", "title": "Compute NIFTI dim field for data dimension.", "concept": [ "NIFTI helper functions" ], "topics": [ "nifti.datadim.to.dimfield" ] }, { "page": "nifti.file.uses.fshack", "title": "Determine whether a NIFTI file uses the FreeSurfer hack.", "topics": [ "nifti.file.uses.fshack" ] }, { "page": "nifti.file.version", "title": "Determine NIFTI file version information and whether file is a NIFTI file.", "topics": [ "nifti.file.version" ] }, { "page": "nifti.header.check", "title": "Perform basic sanity checks on NIFTI header data. These are in no way meant to be exhaustive.", "topics": [ "nifti.header.check" ] }, { "page": "nifti2.extension", "title": "Create a NIFTI v2 header extension.", "concept": [ "nifti2 extensions" ], "topics": [ "nifti2.extension" ] }, { "page": "nifti2.extension.text", "title": "Get the payload of a NIFTI v2 header extension as text.", "concept": [ "nifti2 extensions" ], "topics": [ "nifti2.extension.text" ] }, { "page": "nifti2.get.extension", "title": "Get a NIFTI v2 header extension by code.", "concept": [ "nifti2 extensions" ], "topics": [ "nifti2.get.extension" ] }, { "page": "nii1header.for.mgh", "title": "Create a NIFTI v1 header from the header information contained in an fs.volume instance.", "concept": [ "nifti1 writers" ], "topics": [ "nii1header.for.mgh" ] }, { "page": "print.dti.track.iterator", "title": "Print a tract file iterator.", "topics": [ "print.dti.track.iterator" ] }, { "page": "print.fs.annot", "title": "Print description of a brain atlas or annotation.", "topics": [ "print.fs.annot" ] }, { "page": "print.fs.cifti", "title": "Print an fs.cifti instance.", "concept": [ "cifti functions" ], "topics": [ "print.fs.cifti" ] }, { "page": "print.fs.cifti.data", "title": "Print an fs.cifti.data instance.", "concept": [ "cifti functions" ], "topics": [ "print.fs.cifti.data" ] }, { "page": "print.fs.connectome", "title": "Print an fs.connectome instance.", "concept": [ "cifti functions" ], "topics": [ "print.fs.connectome" ] }, { "page": "print.fs.label", "title": "Print description of a brain surface label.", "topics": [ "print.fs.label" ] }, { "page": "print.fs.patch", "title": "Print description of a brain surface patch.", "topics": [ "print.fs.patch" ] }, { "page": "print.fs.surface", "title": "Print description of a brain surface.", "topics": [ "print.fs.surface" ] }, { "page": "print.fs.tracts", "title": "Print an fs.tracts instance.", "topics": [ "print.fs.tracts" ] }, { "page": "print.fs.transform", "title": "Print an fs.transform instance.", "concept": [ "header coordinate space" ], "topics": [ "print.fs.transform" ] }, { "page": "print.fs.volume", "title": "Print description of a brain volume.", "topics": [ "print.fs.volume" ] }, { "page": "ras.to.surfaceras", "title": "Translate RAS coordinates, as used in volumes by applying vox2ras, to surface RAS.", "topics": [ "ras.to.surfaceras" ] }, { "page": "ras.to.talairachras", "title": "Compute MNI talairach coordinates from RAS coords.", "topics": [ "ras.to.talairachras" ] }, { "page": "read_nisurface", "title": "Read a surface, based on the file path without extension.", "concept": [ "mesh functions" ], "topics": [ "read_nisurface" ] }, { "page": "read_nisurfacefile", "title": "S3 method to read a neuroimaging surface file.", "concept": [ "mesh functions" ], "topics": [ "read_nisurfacefile" ] }, { "page": "read_nisurfacefile.fsascii", "title": "Read a FreeSurfer ASCII surface file.", "topics": [ "read_nisurfacefile.fsascii" ] }, { "page": "read_nisurfacefile.fsnative", "title": "Read a FreeSurfer ASCII surface file.", "topics": [ "read_nisurfacefile.fsnative" ] }, { "page": "read_nisurfacefile.gifti", "title": "Read a gifti file as a surface.", "topics": [ "read_nisurfacefile.gifti" ] }, { "page": "read.analyze.data", "title": "Read ANALYZE 7.5 data from file.", "topics": [ "read.analyze.data" ] }, { "page": "read.analyze.header", "title": "Read ANALYZE 7.5 header from file.", "topics": [ "read.analyze.header" ] }, { "page": "read.cifti", "title": "Read a CIFTI-2 file.", "concept": [ "cifti functions" ], "topics": [ "read.cifti" ] }, { "page": "read.cifti.header", "title": "Read CIFTI-2 header (XML metadata).", "concept": [ "cifti functions" ], "topics": [ "read.cifti.header" ] }, { "page": "read.cifti.rows", "title": "Read selected matrix rows of a CIFTI-2 file without loading the whole matrix.", "concept": [ "cifti functions" ], "topics": [ "read.cifti.rows" ] }, { "page": "read.dti.bval", "title": "Read b-values from a FSL-style bvals file.", "concept": [ "dti functions" ], "topics": [ "read.dti.bval" ] }, { "page": "read.dti.bvec", "title": "Read b-vectors from a FSL-style bvecs file.", "concept": [ "dti functions" ], "topics": [ "read.dti.bvec" ] }, { "page": "read.dti.grad", "title": "Read a gradient table in MRtrix3 format.", "concept": [ "dti functions" ], "topics": [ "read.dti.grad" ] }, { "page": "read.dti.gradients", "title": "Read and validate a diffusion MRI gradient table.", "concept": [ "dti functions" ], "topics": [ "read.dti.gradients" ] }, { "page": "read.dti.tck", "title": "Read DTI tracking data from file in MRtrix 'TCK' format.", "topics": [ "read.dti.tck" ] }, { "page": "read.dti.tck.header", "title": "Read the header of a file in MRtrix 'TCK' or 'TSF' format.", "topics": [ "read.dti.tck.header" ] }, { "page": "read.dti.trk", "title": "Read fiber tracks from Diffusion Toolkit in trk format.", "topics": [ "read.dti.trk" ] }, { "page": "read.dti.trk.header", "title": "Read the header of a TrackVis TRK file.", "topics": [ "read.dti.trk.header" ] }, { "page": "read.dti.tsf", "title": "Read DTI tracking per-coord data from file in MRtrix 'TSF' format.", "topics": [ "read.dti.tsf" ] }, { "page": "read.dti.tsf.header", "title": "Read the header of a file in MRtrix 'TSF' format.", "topics": [ "read.dti.tsf.header" ] }, { "page": "read.fs.annot", "title": "Read file in FreeSurfer annotation format", "concept": [ "atlas functions" ], "topics": [ "read.fs.annot" ] }, { "page": "read.fs.annot.gii", "title": "Read an annotation or label in GIFTI format.", "concept": [ "gifti readers" ], "topics": [ "read.fs.annot.gii" ] }, { "page": "read.fs.colortable", "title": "Read colortable file in FreeSurfer ASCII LUT format.", "concept": [ "atlas functions", "colorLUT functions" ], "topics": [ "read.fs.colortable" ] }, { "page": "read.fs.connectome.cifti", "title": "Read a CIFTI-2 connectome file.", "concept": [ "cifti functions" ], "topics": [ "read.fs.connectome.cifti" ] }, { "page": "read.fs.curv", "title": "Read file in FreeSurfer curv format", "concept": [ "morphometry functions" ], "topics": [ "read.fs.curv" ] }, { "page": "read.fs.gca", "title": "Read FreeSurfer GCA file.", "topics": [ "read.fs.gca" ] }, { "page": "read.fs.label", "title": "Read a label file.", "concept": [ "label functions" ], "topics": [ "read.fs.label" ] }, { "page": "read.fs.label.gii", "title": "Read a label from a GIFTI label/annotation file.", "concept": [ "gifti readers", "label functions" ], "topics": [ "read.fs.label.gii" ] }, { "page": "read.fs.label.native", "title": "Read file in FreeSurfer label format", "concept": [ "label functions" ], "topics": [ "read.fs.label.native" ] }, { "page": "read.fs.mgh", "title": "Read file in FreeSurfer MGH or MGZ format", "concept": [ "morphometry functions" ], "topics": [ "read.fs.mgh" ] }, { "page": "read.fs.morph", "title": "Read morphometry data file in any FreeSurfer format.", "concept": [ "morphometry functions" ], "topics": [ "read.fs.morph" ] }, { "page": "read.fs.morph.asc", "title": "Read morphometry data from ASCII curv format file", "topics": [ "read.fs.morph.asc" ] }, { "page": "read.fs.morph.bvsmp", "title": "Read Brainvoyager vertex-wise statistical surface data from SMP file.", "topics": [ "read.fs.morph.bvsmp" ] }, { "page": "read.fs.morph.cifti", "title": "Read surface morphometry data from CIFTI dscalar files.", "topics": [ "read.fs.morph.cifti" ] }, { "page": "read.fs.morph.gii", "title": "Read morphometry data file in GIFTI format.", "concept": [ "gifti readers", "morphometry functions" ], "topics": [ "read.fs.morph.gii" ] }, { "page": "read.fs.morph.ni1", "title": "Read morphometry data from FreeSurfer NIFTI v1 format files.", "topics": [ "read.fs.morph.ni1" ] }, { "page": "read.fs.morph.ni2", "title": "Read morphometry data from FreeSurfer NIFTI v2 format files.", "topics": [ "read.fs.morph.ni2" ] }, { "page": "read.fs.morph.nii", "title": "Read morphometry data from FreeSurfer NIFTI format files, determine NIFTI version automatically.", "topics": [ "read.fs.morph.nii" ] }, { "page": "read.fs.morph.txt", "title": "Read morphometry data from plain text file", "topics": [ "read.fs.morph.txt" ] }, { "page": "read.fs.parcellation.cifti", "title": "Read surface parcellation data from CIFTI dlabel files.", "topics": [ "read.fs.parcellation.cifti" ] }, { "page": "read.fs.patch", "title": "Read FreeSurfer binary or ASCII patch file.", "concept": [ "patch functions" ], "topics": [ "read.fs.patch" ] }, { "page": "read.fs.patch.asc", "title": "Read FreeSurfer ASCII format patch.", "concept": [ "patch functions" ], "topics": [ "read.fs.patch.asc" ] }, { "page": "read.fs.series.cifti", "title": "Read surface time series data from CIFTI dtseries files.", "topics": [ "read.fs.series.cifti" ] }, { "page": "read.fs.surface", "title": "Read file in FreeSurfer surface format or various mesh formats.", "concept": [ "mesh functions" ], "topics": [ "read.fs.surface" ] }, { "page": "read.fs.surface.asc", "title": "Read FreeSurfer ASCII format surface.", "concept": [ "mesh functions" ], "topics": [ "read.fs.surface.asc" ] }, { "page": "read.fs.surface.bvsrf", "title": "Read Brainvoyager srf format (.srf) mesh as surface.", "concept": [ "mesh functions" ], "topics": [ "read.fs.surface.bvsrf" ] }, { "page": "read.fs.surface.byu", "title": "Read mesh in BYU format.", "topics": [ "read.fs.surface.byu" ] }, { "page": "read.fs.surface.geo", "title": "Read GEO format mesh as surface.", "concept": [ "mesh functions" ], "topics": [ "read.fs.surface.geo" ] }, { "page": "read.fs.surface.gii", "title": "Read GIFTI format mesh as surface.", "concept": [ "gifti readers", "mesh functions" ], "topics": [ "read.fs.surface.gii" ] }, { "page": "read.fs.surface.ico", "title": "Read ICO format mesh as surface.", "concept": [ "mesh functions" ], "topics": [ "read.fs.surface.ico" ] }, { "page": "read.fs.surface.mz3", "title": "Read surface mesh in mz3 format, used by Surf-Ice.", "topics": [ "read.fs.surface.mz3" ] }, { "page": "read.fs.surface.obj", "title": "Read OBJ format mesh as surface.", "concept": [ "mesh functions" ], "topics": [ "read.fs.surface.obj" ] }, { "page": "read.fs.surface.off", "title": "Read Object File Format (OFF) mesh as surface.", "concept": [ "mesh functions" ], "topics": [ "read.fs.surface.off" ] }, { "page": "read.fs.surface.ply", "title": "Read Stanford PLY format mesh as surface.", "concept": [ "mesh functions" ], "topics": [ "read.fs.surface.ply" ] }, { "page": "read.fs.surface.stl", "title": "Read mesh in STL format, auto-detecting ASCII versus binary format version.", "topics": [ "read.fs.surface.stl" ] }, { "page": "read.fs.surface.stl.bin", "title": "Read surface mesh in STL binary format.", "topics": [ "read.fs.surface.stl.bin" ] }, { "page": "read.fs.surface.vtk", "title": "Read VTK legacy format mesh as surface.", "concept": [ "mesh functions" ], "topics": [ "read.fs.surface.vtk" ] }, { "page": "read.fs.tracts.vtk", "title": "Read VTK legacy format streamlines as tracts.", "topics": [ "read.fs.tracts.vtk" ] }, { "page": "read.fs.transform", "title": "Load transformation matrix from a file.", "concept": [ "header coordinate space" ], "topics": [ "read.fs.transform" ] }, { "page": "read.fs.transform.dat", "title": "Load transformation matrix from a tkregister dat file.", "concept": [ "header coordinate space" ], "topics": [ "read.fs.transform.dat" ] }, { "page": "read.fs.transform.fslmat", "title": "Read a transformation matrix from an FSL matrix file.", "concept": [ "header coordinate space" ], "topics": [ "read.fs.transform.fslmat" ] }, { "page": "read.fs.transform.itk", "title": "Read a transformation matrix from an ITK text transform file.", "concept": [ "header coordinate space" ], "topics": [ "read.fs.transform.itk" ] }, { "page": "read.fs.transform.lta", "title": "Load transformation matrix from a FreeSurfer linear transform array (LTA) file.", "concept": [ "header coordinate space" ], "topics": [ "read.fs.transform.lta" ] }, { "page": "read.fs.transform.xfm", "title": "Load transformation matrix from an XFM file.", "concept": [ "header coordinate space" ], "topics": [ "read.fs.transform.xfm" ] }, { "page": "read.fs.volume", "title": "Read volume file in MGH, MGZ or NIFTI format", "concept": [ "morphometry functions" ], "topics": [ "read.fs.volume" ] }, { "page": "read.fs.volume.analyze", "title": "Read an ANALYZE 7.5 or NIFTI v1 pair file as an fs.volume.", "topics": [ "read.fs.volume.analyze" ] }, { "page": "read.fs.volume.nii", "title": "Read a 3D or 4D NIFTI file into an 'fs.volume' instance with complete header.", "topics": [ "read.fs.volume.nii" ] }, { "page": "read.fs.volume.nrrd", "title": "Read volume data from a file in NRRD format.", "topics": [ "read.fs.volume.nrrd" ] }, { "page": "read.fs.weight", "title": "Read file in FreeSurfer weight or w format", "concept": [ "morphometry functions" ], "topics": [ "read.fs.weight" ] }, { "page": "read.mesh.brainvoyager", "title": "Read Brainvoyager srf format (.srf) mesh.", "concept": [ "mesh functions" ], "topics": [ "read.mesh.brainvoyager" ] }, { "page": "read.nifti1.data", "title": "Read raw NIFTI v1 data from file (which may contain the FreeSurfer hack).", "topics": [ "read.nifti1.data" ] }, { "page": "read.nifti1.header", "title": "Read NIFTI v1 header from file (which may contain the FreeSurfer hack).", "topics": [ "read.nifti1.header" ] }, { "page": "read.nifti2.data", "title": "Read raw data from NIFTI v2 file.", "topics": [ "read.nifti2.data" ] }, { "page": "read.nifti2.header", "title": "Read NIFTI v2 header from file.", "topics": [ "read.nifti2.header" ] }, { "page": "read.nrrd.header", "title": "Read the header of a file in NRRD format.", "topics": [ "read.nrrd.header" ] }, { "page": "read.smp.brainvoyager", "title": "Read Brainvoyager statistical surface results from SMP file.", "topics": [ "read.smp.brainvoyager" ] }, { "page": "readable.files", "title": "Find files with the given base name and extensions that exist.", "topics": [ "readable.files" ] }, { "page": "rotate2D", "title": "Rotate a 2D matrix in 90 degree steps.", "topics": [ "rotate2D" ] }, { "page": "rotate3D", "title": "Rotate a 3D array in 90 degree steps.", "concept": [ "volume math" ], "topics": [ "rotate3D" ] }, { "page": "sm0to1", "title": "Adapt spatial transformation matrix for 1-based indices.", "concept": [ "header coordinate space" ], "topics": [ "sm0to1" ] }, { "page": "sm1to0", "title": "Adapt spatial transformation matrix for 0-based indices.", "concept": [ "header coordinate space" ], "topics": [ "sm1to0" ] }, { "page": "summary.fs.transform", "title": "Summarize an fs.transform instance.", "concept": [ "header coordinate space" ], "topics": [ "summary.fs.transform" ] }, { "page": "surfaceras.to.ras", "title": "Translate surface RAS coordinates, as used in surface vertices and surface labels, to volume RAS.", "topics": [ "surfaceras.to.ras" ] }, { "page": "surfaceras.to.talairach", "title": "Compute Talairach RAS for surface RAS (e.g., vertex coordinates).", "topics": [ "surfaceras.to.talairach" ] }, { "page": "talairachras.to.ras", "title": "Compute MNI talairach coordinates from RAS coords.", "topics": [ "talairachras.to.ras" ] }, { "page": "transform2lps", "title": "Convert a transformation to LPS world coordinates.", "concept": [ "header coordinate space" ], "topics": [ "transform2lps" ] }, { "page": "transform2ras", "title": "Convert a transformation to RAS world coordinates.", "concept": [ "header coordinate space" ], "topics": [ "transform2ras" ] }, { "page": "transform2voxel", "title": "Convert a transformation to voxel coordinates.", "concept": [ "header coordinate space" ], "topics": [ "transform2voxel" ] }, { "page": "transform2world", "title": "Convert a transformation to the world (RAS) coordinate space.", "concept": [ "header coordinate space" ], "topics": [ "transform2world" ] }, { "page": "vertex.euclid.dist", "title": "Compute Euclidean distance between two vertices v1 and v2.", "concept": [ "Euclidean distance util functions" ], "topics": [ "vertex.euclid.dist" ] }, { "page": "vertexdists.to.point", "title": "Compute Euclidean distance from all mesh vertices to given point.", "concept": [ "Euclidean distance util functions" ], "topics": [ "vertexdists.to.point" ] }, { "page": "write.analyze", "title": "Write data to a file in ANALYZE 7.5 format.", "topics": [ "write.analyze" ] }, { "page": "write.atlas.to.lut.and.csv", "title": "Write a brain atlas to a colortable (LUT) file and a per-vertex label file.", "concept": [ "atlas functions" ], "topics": [ "write.atlas.to.lut.and.csv" ] }, { "page": "write.cifti", "title": "Write a CIFTI-2 file.", "concept": [ "cifti functions" ], "topics": [ "write.cifti" ] }, { "page": "write.dti.bval", "title": "Write b-values to a FSL-style bvals file.", "concept": [ "dti functions" ], "topics": [ "write.dti.bval" ] }, { "page": "write.dti.bvec", "title": "Write b-vectors to a FSL-style bvecs file.", "concept": [ "dti functions" ], "topics": [ "write.dti.bvec" ] }, { "page": "write.dti.grad", "title": "Write a gradient table in MRtrix3 format.", "concept": [ "dti functions" ], "topics": [ "write.dti.grad" ] }, { "page": "write.dti.tck", "title": "Write tracks to a file in MRtrix TCK format.", "topics": [ "write.dti.tck" ] }, { "page": "write.dti.trk", "title": "Write tracks to a file in TrackVis TRK format.", "topics": [ "write.dti.trk" ] }, { "page": "write.dti.tsf", "title": "Write per-point track values to a file in MRtrix TSF format.", "topics": [ "write.dti.tsf" ] }, { "page": "write.fs.annot", "title": "Write annotation to binary file.", "concept": [ "atlas functions" ], "topics": [ "write.fs.annot" ] }, { "page": "write.fs.annot.gii", "title": "Write annotation to GIFTI file.", "concept": [ "atlas functions", "gifti writers" ], "topics": [ "write.fs.annot.gii" ] }, { "page": "write.fs.colortable", "title": "Write colortable file in FreeSurfer ASCII LUT format.", "concept": [ "atlas functions", "colorLUT functions" ], "topics": [ "write.fs.colortable" ] }, { "page": "write.fs.connectome.cifti", "title": "Write a CIFTI-2 connectome file.", "concept": [ "cifti functions" ], "topics": [ "write.fs.connectome.cifti" ] }, { "page": "write.fs.curv", "title": "Write file in FreeSurfer curv format", "concept": [ "morphometry functions" ], "topics": [ "write.fs.curv" ] }, { "page": "write.fs.label", "title": "Write vertex indices to file in FreeSurfer label format", "concept": [ "label functions" ], "topics": [ "write.fs.label" ] }, { "page": "write.fs.label.gii", "title": "Write a binary surface label in GIFTI format.", "concept": [ "gifti writers", "morphometry functions" ], "topics": [ "write.fs.label.gii" ] }, { "page": "write.fs.mgh", "title": "Write file in FreeSurfer MGH or MGZ format", "concept": [ "morphometry functions" ], "topics": [ "write.fs.mgh" ] }, { "page": "write.fs.morph", "title": "Write morphometry data in a format derived from the given file name.", "concept": [ "morphometry functions" ], "topics": [ "write.fs.morph" ] }, { "page": "write.fs.morph.asc", "title": "Write file in FreeSurfer ASCII curv format", "concept": [ "morphometry functions" ], "topics": [ "write.fs.morph.asc" ] }, { "page": "write.fs.morph.cifti", "title": "Write morphometry data to a CIFTI-2 '.dscalar' file.", "concept": [ "cifti functions" ], "topics": [ "write.fs.morph.cifti" ] }, { "page": "write.fs.morph.gii", "title": "Write morphometry data in GIFTI format.", "concept": [ "gifti writers", "morphometry functions" ], "topics": [ "write.fs.morph.gii" ] }, { "page": "write.fs.morph.ni1", "title": "Write morphometry data in NIFTI v1 format.", "concept": [ "morphometry functions", "nifti1 writers" ], "topics": [ "write.fs.morph.ni1" ] }, { "page": "write.fs.morph.ni2", "title": "Write morphometry data in NIFTI v2 format.", "concept": [ "morphometry functions", "nifti2 writers" ], "topics": [ "write.fs.morph.ni2" ] }, { "page": "write.fs.morph.smp", "title": "Write morphometry data in Brainvoyager SMP format.", "concept": [ "morphometry functions" ], "topics": [ "write.fs.morph.smp" ] }, { "page": "write.fs.morph.txt", "title": "Write curv data to file in simple text format", "concept": [ "morphometry functions" ], "topics": [ "write.fs.morph.txt" ] }, { "page": "write.fs.parcellated.cifti", "title": "Write a CIFTI-2 parcellated map or series file.", "concept": [ "cifti functions" ], "topics": [ "write.fs.parcellated.cifti" ] }, { "page": "write.fs.parcellation.cifti", "title": "Write a parcellation to a CIFTI-2 '.dlabel' file.", "concept": [ "cifti functions" ], "topics": [ "write.fs.parcellation.cifti" ] }, { "page": "write.fs.patch", "title": "Write a surface patch", "concept": [ "patch functions" ], "topics": [ "write.fs.patch" ] }, { "page": "write.fs.series.cifti", "title": "Write time series data to a CIFTI-2 '.dtseries' file.", "concept": [ "cifti functions" ], "topics": [ "write.fs.series.cifti" ] }, { "page": "write.fs.surface", "title": "Write mesh to file in FreeSurfer binary surface format", "concept": [ "mesh export functions", "mesh functions" ], "topics": [ "write.fs.surface" ] }, { "page": "write.fs.surface.asc", "title": "Write mesh to file in FreeSurfer ASCII surface format", "concept": [ "mesh functions" ], "topics": [ "write.fs.surface.asc" ] }, { "page": "write.fs.surface.bvsrf", "title": "Write surface to Brainvoyager SRF file.", "topics": [ "write.fs.surface.bvsrf" ] }, { "page": "write.fs.surface.byu", "title": "Write mesh to file in BYU ASCII format.", "concept": [ "mesh functions" ], "topics": [ "write.fs.surface.byu" ] }, { "page": "write.fs.surface.gii", "title": "Write mesh to file in GIFTI surface format", "concept": [ "gifti writers", "mesh functions" ], "topics": [ "write.fs.surface.gii" ] }, { "page": "write.fs.surface.mz3", "title": "Write mesh to file in mz3 binary format.", "concept": [ "mesh functions" ], "topics": [ "write.fs.surface.mz3" ] }, { "page": "write.fs.surface.obj", "title": "Write mesh to file in Wavefront object (.obj) format", "concept": [ "mesh export functions" ], "topics": [ "write.fs.surface.obj" ] }, { "page": "write.fs.surface.off", "title": "Write mesh to file in Object File Format (.off)", "concept": [ "mesh export functions" ], "topics": [ "write.fs.surface.off" ] }, { "page": "write.fs.surface.ply", "title": "Write mesh to file in PLY format (.ply)", "concept": [ "mesh export functions" ], "topics": [ "write.fs.surface.ply" ] }, { "page": "write.fs.surface.ply2", "title": "Write mesh to file in PLY2 File Format (.ply2)", "concept": [ "mesh export functions" ], "topics": [ "write.fs.surface.ply2" ] }, { "page": "write.fs.surface.stl", "title": "Write mesh to file in STL format (ASCII or binary).", "concept": [ "mesh export functions" ], "topics": [ "write.fs.surface.stl" ] }, { "page": "write.fs.surface.vtk", "title": "Write mesh to file in VTK legacy format", "concept": [ "mesh export functions", "mesh functions" ], "topics": [ "write.fs.surface.vtk" ] }, { "page": "write.fs.transform", "title": "Write a transformation matrix to a file.", "concept": [ "header coordinate space" ], "topics": [ "write.fs.transform" ] }, { "page": "write.fs.transform.dat", "title": "Write a tkregister dat file.", "concept": [ "header coordinate space" ], "topics": [ "write.fs.transform.dat" ] }, { "page": "write.fs.transform.fslmat", "title": "Write a transformation matrix in FSL format.", "concept": [ "header coordinate space" ], "topics": [ "write.fs.transform.fslmat" ] }, { "page": "write.fs.transform.itk", "title": "Write an ITK text transform file.", "concept": [ "header coordinate space" ], "topics": [ "write.fs.transform.itk" ] }, { "page": "write.fs.transform.lta", "title": "Write a FreeSurfer linear transform array (LTA) file.", "concept": [ "header coordinate space" ], "topics": [ "write.fs.transform.lta" ] }, { "page": "write.fs.transform.xfm", "title": "Write an MNI transform (xfm) file.", "concept": [ "header coordinate space" ], "topics": [ "write.fs.transform.xfm" ] }, { "page": "write.fs.volume", "title": "Write an fs.volume instance to a file in MGH, MGZ or NIFTI v1 format.", "concept": [ "volume export functions" ], "topics": [ "write.fs.volume" ] }, { "page": "write.fs.weight", "title": "Write file in FreeSurfer weight format", "concept": [ "morphometry functions" ], "topics": [ "write.fs.weight" ] }, { "page": "write.fs.weight.asc", "title": "Write file in FreeSurfer weight ASCII format", "concept": [ "morphometry functions" ], "topics": [ "write.fs.weight.asc" ] }, { "page": "write.nifti1", "title": "Write header and data to a file in NIFTI v1 format.", "concept": [ "nifti1 writers" ], "topics": [ "write.nifti1" ] }, { "page": "write.nifti2", "title": "Write header and data to a file in NIFTI v2 format.", "concept": [ "nifti2 writers" ], "topics": [ "write.nifti2" ] }, { "page": "write.smp.brainvoyager", "title": "Write a brainvoyager SMP file.", "topics": [ "write.smp.brainvoyager" ] }, { "page": "xml_node_gifti_coordtransform", "title": "Create XML GIFTI CoordinateSystemTransformMatrix node.", "topics": [ "xml_node_gifti_coordtransform" ] } ], "_readme": "https://github.com/dfsp-spirit/freesurferformats/raw/v1.1.2/README.md", "_rundeps": [ "cli", "curl", "pkgfilecache", "rappdirs", "rlang", "xml2" ], "_vignettes": [ { "source": "freesurferformats_header.Rmd", "filename": "freesurferformats_header.html", "title": "Computing volume header data with freesurferformats", "engine": "knitr::rmarkdown", "headings": [ "About the MGH header", "Getting access to the header data in MGH or MGZ files", "Computing more information from the header", "Transformation matrices", "Primary slice direction and volume CRS orientation", "Check whether the volume is conformed" ], "created": "2020-02-11 16:02:19", "modified": "2026-07-30 05:52:21", "commits": 3 }, { "source": "freesurferformats.Rmd", "filename": "freesurferformats.html", "title": "Reading FreeSurfer neuroimaging data with freesurferformats", "engine": "knitr::rmarkdown", "headings": [ "Reading FreeSurfer neuroimaging data with freesurferformats", "Background", "Reading MGH and MGZ format files", "Accessing metadata from the MGH header", "A second MGH example", "Hint: Further image processing and visualization for volumes", "Reading 'curv' format files", "Reading morphometry data, no matter the format", "Reading morphometry data for a subset of vertices from weight, paint or w files", "Reading annotation files", "Working with annotation data", "Reading surface files (meshes)", "Reading arbitrary triangular meshes and converting to rgl mesh3d", "Reading labels", "Reading color lookup tables (LUT files)", "Computing the unique color codes", "References", "Alternatives, similar and related Packages" ], "created": "2019-08-21 12:54:44", "modified": "2026-07-30 05:52:21", "commits": 26 }, { "source": "freesurferformats_write.Rmd", "filename": "freesurferformats_write.html", "title": "Writing FreeSurfer neuroimaging data with freesurferformats", "engine": "knitr::rmarkdown", "headings": [ "Writing FreeSurfer neuroimaging data with freesurferformats", "Writing 1D morphometry data or other per-vertex information (in MGH, MGZ or curv format)", "Writing MGH and MGZ format files with full control over the header", "MGH data types", "Writing 'curv' format files (morphometry data)", "Writing surface format files", "Writing label files", "Writing color lookup table (LUT) files in ASCII format" ], "created": "2019-09-13 08:13:42", "modified": "2026-07-30 05:52:21", "commits": 6 } ], "_score": 9.669032143015755, "_indexed": true, "_nocasepkg": "freesurferformats", "_universes": [ "dfsp-spirit" ], "_previous": "1.1.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.2", "date": "2026-10-20T15:54:23.000Z", "distro": "resolute", "commit": "dc2a5a8beee529392bf4e336256078f474468b6b", "fileid": 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