cdata                   Create CDATA element string from string.
colortable.from.annot   Extract color lookup table (LUT) from
                        annotation.
delete_all_opt_data     Delete all data in the package cache.
download_opt_data       Download optional data for the
                        freesurferformats package.
faces.quad.to.tris      Convert quadrangular faces or polygons to
                        triangular ones.
flip2D                  Flip a 2D matrix.
flip3D                  Flip a 3D array along an axis.
fs.get.morph.file.ext.for.format
                        Determine morphometry file extension from
                        format
fs.get.morph.file.format.from.filename
                        Determine morphometry file format from filename
fs.patch                Constructor for fs.patch
get_opt_data_filepath   Access a single file from the package cache by
                        its file name.
gifti_writer            Write data to a gifti file.
gifti_xml               Get GIFTI XML representation of data.
gifti_xml_add_global_metadata
                        Add metadata to GIFTI XML tree.
gifti_xml_write         Write XML tree to a gifti file.
giftixml_add_labeltable_from_annot
                        Add a label tabel from an annotation to a GIFTI
                        XML tree.
is.fs.annot             Check whether object is an fs.annot
is.fs.label             Check whether object is an fs.label
is.fs.surface           Check whether object is an fs.surface
is.fs.volume            Check whether object is an fs.volume
list_opt_data           Get file names available in package cache.
mghheader.centervoxelRAS.from.firstvoxelRAS
                        Compute RAS coords of center voxel.
mghheader.crs.orientation
                        Compute MGH volume orientation string.
mghheader.is.conformed
                        Determine whether an MGH volume is conformed.
mghheader.is.ras.valid
                        Check whether header contains valid ras
                        information
mghheader.primary.slice.direction
                        Compute MGH primary slice direction
mghheader.ras2vox       Compute ras2vox matrix from basic MGH header
                        fields.
mghheader.ras2vox.tkreg
                        Compute ras2vox-tkreg matrix from basic MGH
                        header fields.
mghheader.scanner2tkreg
                        Compute scanner-RAS 2 tkreg-RAS matrix from
                        basic MGH header fields.
mghheader.tkreg2scanner
                        Compute tkreg-RAS to scanner-RAS matrix from
                        basic MGH header fields.
mghheader.update.from.vox2ras
                        Update mghheader fields from vox2ras matrix.
mghheader.vox2ras       Compute vox2ras matrix from basic MGH header
                        fields.
mghheader.vox2ras.tkreg
                        Compute vox2ras-tkreg matrix from basic MGH
                        header fields.
mghheader.vox2vox       Compute vox2vox matrix between two volumes.
print.fs.annot          Print description of a brain atlas or
                        annotation.
print.fs.label          Print description of a brain surface label.
print.fs.patch          Print description of a brain surface patch.
print.fs.surface        Print description of a brain surface.
print.fs.volume         Print description of a brain volume.
read.fs.annot           Read file in FreeSurfer annotation format
read.fs.annot.gii       Read an annotation or label in GIFTI format.
read.fs.colortable      Read colortable file in FreeSurfer ASCII LUT
                        format.
read.fs.curv            Read file in FreeSurfer curv format
read.fs.label           Read file in FreeSurfer label format
read.fs.label.gii       Read a label from a GIFTI label/annotation
                        file.
read.fs.mgh             Read file in FreeSurfer MGH or MGZ format
read.fs.morph           Read morphometry data file in any FreeSurfer
                        format.
read.fs.morph.gii       Read morphometry data file in GIFTI format.
read.fs.patch           Read FreeSurfer binary or ASCII patch file.
read.fs.patch.asc       Read FreeSurfer ASCII format patch.
read.fs.surface         Read file in FreeSurfer surface format or
                        various mesh formats.
read.fs.surface.asc     Read FreeSurfer ASCII format surface.
read.fs.surface.byu     Read mesh in BYU format.
read.fs.surface.gii     Read GIFTI format mesh as surface.
read.fs.surface.mz3     Read surface mesh in mz3 format, used by
                        Surf-Ice.
read.fs.surface.ply     Read Stanford PLY format mesh as surface.
read.fs.surface.stl     Read mesh in STL format, auto-detecting ASCII
                        versus binary format version.
read.fs.surface.stl.bin
                        Read surface mesh in STL binary format.
read.fs.surface.vtk     Read VTK ASCII format mesh as surface.
read.fs.transform       Load transformation matrix from a file.
read.fs.volume          Read volume file in MGH, MGZ or NIFTI format
read.fs.volume.nii      Turn a 3D or 4D 'oro.nifti' instance into an
                        'fs.volume' instance with complete header.
read.fs.weight          Read file in FreeSurfer weight or w format
read_nisurface          Read a surface, based on the file path without
                        extension.
read_nisurfacefile      S3 method to read a neuroimaging surface file.
read_nisurfacefile.fsascii
                        Read a FreeSurfer ASCII surface file.
read_nisurfacefile.fsnative
                        Read a FreeSurfer ASCII surface file.
read_nisurfacefile.gifti
                        Read a gifti file as a surface.
readable.files          Find files with the given base name and
                        extensions that exist.
rotate2D                Rotate a 2D matrix in 90 degree steps.
rotate3D                Rotate a 3D array in 90 degree steps.
write.fs.annot          Write annotation to binary file.
write.fs.annot.gii      Write annotation to GIFTI file.
write.fs.colortable     Write colortable file in FreeSurfer ASCII LUT
                        format.
write.fs.curv           Write file in FreeSurfer curv format
write.fs.label          Write vertex indices to file in FreeSurfer
                        label format
write.fs.label.gii      Write a binary surface label in GIFTI format.
write.fs.mgh            Write file in FreeSurfer MGH or MGZ format
write.fs.morph          Write morphometry data in a format derived from
                        the given file name.
write.fs.morph.gii      Write morphometry data in GIFTI format.
write.fs.patch          Write a surface patch
write.fs.surface        Write mesh to file in FreeSurfer binary surface
                        format
write.fs.surface.asc    Write mesh to file in FreeSurfer ASCII surface
                        format
write.fs.surface.byu    Write mesh to file in BYU ASCII format.
write.fs.surface.gii    Write mesh to file in GIFTI surface format
write.fs.surface.mz3    Write mesh to file in mz3 binary format.
write.fs.surface.obj    Write mesh to file in Wavefront object (.obj)
                        format
write.fs.surface.off    Write mesh to file in Object File Format (.off)
write.fs.surface.ply    Write mesh to file in PLY format (.ply)
write.fs.surface.ply2   Write mesh to file in PLY2 File Format (.ply2)
write.fs.surface.vtk    Write mesh to file in VTK ASCII format
write.fs.weight         Write file in FreeSurfer weight format
xml_node_gifti_coordtransform
                        Create XML GIFTI
                        CoordinateSystemTransformMatrix node.
