annot.max.region.idx    Get max region index of an fs.annot instance.
bvsmp                   Create new bvsmp instance encoding morph data
                        for Brainvoyager.
cdata                   Create CDATA element string from string.
closest.vert.to.point   Find vertex index closest to given query
                        coordinate using Euclidean distance.
colortable.from.annot   Extract color lookup table (LUT) from
                        annotation.
delete_all_opt_data     Delete all data in the package cache.
doapply.transform.mtx   Apply a spatial transformation matrix to the
                        given coordinates.
download_opt_data       Download optional data for the
                        freesurferformats package.
faces.quad.to.tris      Convert quadrangular faces or polygons to
                        triangular ones.
faces.tris.to.quad      Convert tris faces to quad faces by simple
                        merging.
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
fs.surface.to.tmesh3d   Get an rgl tmesh3d instance from a brain
                        surface mesh.
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.bvsmp                Check whether object is a bvsmp instance.
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
is.mghheader            Check whether object is an mghheader
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.
mni152reg               Get fsaverage (MNI305) to MNI152 transformation
                        matrix.
ni1header.for.data      Create NIFTI v1 header suitable for given data.
ni1header.template      Create a template NIFTI v1 header. You will
                        have to adapt it for your use case.
ni2header.for.data      Create NIFTI v2 header suitable for given data.
ni2header.template      Create a template NIFTI v2 header. You will
                        have to adapt it for your use case.
nifti.datadim.from.dimfield
                        Compute data dimensions from the 'dim' field of
                        the NIFTI (v1 or v2) header.
nifti.datadim.to.dimfield
                        Compute NIFTI dim field for data dimension.
nifti.file.uses.fshack
                        Determine whether a NIFTI file uses the
                        FreeSurfer hack.
nifti.file.version      Determine NIFTI file version information and
                        whether file is a NIFTI file.
nifti.header.check      Perform basic sanity checks on NIFTI header
                        data. These are in no way meant to be
                        exhaustive.
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.
ras.to.surfaceras       Translate RAS coordinates, as used in volumes
                        by applying vox2ras, to surface RAS.
ras.to.talairachras     Compute MNI talairach coordinates from RAS
                        coords.
read.dti.tck            Read DTI tracking data from file in MRtrix
                        'TCK' format.
read.dti.trk            Read fiber tracks from Diffusion Toolkit in trk
                        format.
read.dti.tsf            Read DTI tracking per-coord data from file in
                        MRtrix 'TSF' format.
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.gca             Read FreeSurfer GCA file.
read.fs.label           Read a label file.
read.fs.label.gii       Read a label from a GIFTI label/annotation
                        file.
read.fs.label.native    Read file in FreeSurfer label format
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.asc       Read morphometry data from ASCII curv format
                        file
read.fs.morph.bvsmp     Read Brainvoyager vertex-wise statistical
                        surface data from SMP file.
read.fs.morph.cifti     Read surface morphometry data from CIFTI
                        dscalar files.
read.fs.morph.gii       Read morphometry data file in GIFTI format.
read.fs.morph.ni1       Read morphometry data from FreeSurfer NIFTI v1
                        format files.
read.fs.morph.ni2       Read morphometry data from FreeSurfer NIFTI v2
                        format files.
read.fs.morph.nii       Read morphometry data from FreeSurfer NIFTI
                        format files, determine NIFTI version
                        automatically.
read.fs.morph.txt       Read morphometry data from plain text file
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.bvsrf   Read Brainvoyager srf format (.srf) mesh as
                        surface.
read.fs.surface.byu     Read mesh in BYU format.
read.fs.surface.geo     Read GEO format mesh as surface.
read.fs.surface.gii     Read GIFTI format mesh as surface.
read.fs.surface.ico     Read ICO format mesh as surface.
read.fs.surface.mz3     Read surface mesh in mz3 format, used by
                        Surf-Ice.
read.fs.surface.obj     Read OBJ format mesh as surface.
read.fs.surface.off     Read Object File Format (OFF) mesh as surface.
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.transform.dat   Load transformation matrix from a tkregister
                        dat file.
read.fs.transform.lta   Load transformation matrix from a FreeSurfer
                        linear transform array (LTA) file.
read.fs.transform.xfm   Load transformation matrix from an XFM 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.mesh.brainvoyager
                        Read Brainvoyager srf format (.srf) mesh.
read.nifti1.data        Read raw NIFTI v1 data from file (which may
                        contain the FreeSurfer hack).
read.nifti1.header      Read NIFTI v1 header from file (which may
                        contain the FreeSurfer hack).
read.nifti2.data        Read raw data from NIFTI v2 file.
read.nifti2.header      Read NIFTI v2 header from file.
read.smp.brainvoyager   Read Brainvoyager statistical surface results
                        from SMP file.
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.
sm0to1                  Adapt spatial transformation matrix for 1-based
                        indices.
sm1to0                  Adapt spatial transformation matrix for 0-based
                        indices.
surfaceras.to.ras       Translate surface RAS coordinates, as used in
                        surface vertices and surface labels, to volume
                        RAS.
surfaceras.to.talairach
                        Compute Talairach RAS for surface RAS (e.g.,
                        vertex coordinates).
talairachras.to.ras     Compute MNI talairach coordinates from RAS
                        coords.
vertex.euclid.dist      Compute Euclidean distance between two vertices
                        v1 and v2.
vertexdists.to.point    Compute Euclidean distance from all mesh
                        vertices to given point.
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.asc      Write file in FreeSurfer ASCII curv format
write.fs.morph.gii      Write morphometry data in GIFTI format.
write.fs.morph.ni1      Write morphometry data in NIFTI v1 format.
write.fs.morph.ni2      Write morphometry data in NIFTI v2 format.
write.fs.morph.smp      Write morphometry data in Brainvoyager SMP
                        format.
write.fs.morph.txt      Write curv data to file in simple text 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.bvsrf
                        Write surface to Brainvoyager SRF file.
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
write.fs.weight.asc     Write file in FreeSurfer weight ASCII format
write.nifti1            Write header and data to a file in NIFTI v1
                        format.
write.nifti2            Write header and data to a file in NIFTI v2
                        format.
write.smp.brainvoyager
                        Write a brainvoyager SMP file.
xml_node_gifti_coordtransform
                        Create XML GIFTI
                        CoordinateSystemTransformMatrix node.
