alphablend              Perform alpha blending for pairs of RGBA
                        colors.
annot.outline           Compute outline vertex colors from annotation.
annot.outline.border.vertices
                        Compute the border vertices for each region in
                        an annot.
apply.label.to.morphdata
                        Load a label from file and apply it to
                        morphometry data.
apply.labeldata.to.morphdata
                        Apply a label to morphometry data.
apply.transform         Apply matmult transformation to input.
arrange.brainview.images
                        Combine several brainview images into a new
                        figure.
arrange.brainview.images.grid
                        Combine several brainview images as a grid into
                        a new figure.
brainviews              Show one or more views of the given meshes in
                        rgl windows.
clip.data               Clip data at quantiles to remove outliers.
clip_fun                Get data clipping function.
cm.cbry                 Get cyan blue red yellow colormap function.
cm.div                  Return the standard fsbrain diverging colormap.
cm.heat                 Return the standard fsbrain heat colormap.
cm.qual                 Return the standard fsbrain qualitative
                        colormap.
cm.seq                  Return the standard fsbrain sequential
                        colormap.
collayer.bg             Compute binarized mean curvature surface color
                        layer.
collayer.bg.atlas       Compute atlas or annotation surface color
                        layer.
collayer.bg.meancurv    Compute binarized mean curvature surface color
                        layer.
collayer.bg.sulc        Compute binarized sulcal depth surface color
                        layer.
collayer.from.annot     Compute surface color layer from annotation or
                        atlas data.
collayer.from.annotdata
                        Compute surface color layer from annotation or
                        atlas data.
collayer.from.mask.data
                        Compute surface color layer from morph-like
                        data.
collayer.from.morphlike.data
                        Compute surface color layer from morph-like
                        data.
collayers.merge         Merge two or more color layers based on their
                        transparency values.
coloredmesh.from.annot
                        Create a coloredmesh from an annotation of an
                        atlas.
coloredmesh.from.label
                        Create a coloredmesh from a label.
coloredmesh.from.mask   Create a coloredmesh from a mask.
coloredmesh.from.morph.native
                        Create a coloredmesh from native space
                        morphometry data.
coloredmesh.from.morph.standard
                        Create a coloredmesh from standard space
                        morphometry data.
coloredmesh.from.morphdata
                        Create a coloredmesh from arbitrary data.
coloredmesh.from.preloaded.data
                        Generate coloredmesh from loaded data.
coloredmesh.plot.colorbar.separate
                        Draw colorbar for coloredmeshes in separate 2D
                        plot.
coloredmeshes.from.color
                        Create coloredmeshes for both hemis using
                        pre-defined colors.
colorlist.brain.clusters
                        Return diverging color list
colors.are.grayscale    Check for the given color strings whether they
                        represent gray scale colors.
colors.have.transparency
                        Check for the given color strings whether they
                        have transparency, i.e., an alpha channel value
                        != fully opaque.
combine.colorbar.with.brainview.animation
                        Combine a colorbar and a brain animation in gif
                        format into a new animation.
combine.colorbar.with.brainview.image
                        Combine a colorbar and a brainview image into a
                        new figure.
constant.pervertexdata
                        Get vertex data for a single fs.surface or a
                        hemilist of surfaces.
cube3D.tris             Return triangles for a 3D cube or cuboid.
cubes3D.tris            Vectorized version of cube3D.tris
delete_all_optional_data
                        Delete all data in the package cache.
demographics.to.fsgd.file
                        Write FreeSurfer Group Descriptor (FSGD) file
                        from demographics dataframe.
demographics.to.qdec.table.dat
                        Convert a dataframe containing demographics
                        data to a qdec.table.dat file and related
                        files.
desaturate              Perform simple desaturation or grayscale
                        conversion of RGBA colors.
download_fsaverage      Download the FreeSurfer v6 fsaverage subject.
download_fsaverage3     Download the FreeSurfer v6 low-resolution
                        fsaverage3 subject.
download_fsaverage6     Download the FreeSurfer v6 fsaverage6 subject.
download_optional_data
                        Download optional data for this package if
                        required.
download_optional_paper_data
                        Download extra data to reproduce the figures
                        from the fsbrain paper.
export                  Export high-quality brainview image with a
                        colorbar.
export.coloredmesh.ply
                        Export a coloredmeshes with vertexcolors in PLY
                        format.
face.edges              Enumerate all edges of the given faces or mesh.
find.freesurferhome     Find the FREESURFER_HOME directory on disk.
find.subjectsdir.of     Find the subject directory containing the
                        fsaverage subject (or others) on disk.
fs.coloredmesh          fs.coloredmesh constructor
fs.home                 Return FreeSurfer path.
fs.surface.as.adjacencylist
                        Turn surface mesh into a igraph and return its
                        adjacency list representation.
fs.surface.to.igraph    Create igraph undirected graph from a brain
                        surface mesh.
fs.surface.to.tmesh3d   Get an rgl tmesh3d instance from a brain
                        surface mesh.
fs.surface.vertex.neighbors
                        Compute vertex neighborhoods or the full
                        adjacency list for a mesh using the Rvcg or
                        igraph library.
fsaverage.path          Return path to fsaverage dir.
fsbrain.set.default.figsize
                        Set default figure size for fsbrain
                        visualization functions.
fup                     Transform first character of a string to
                        uppercase.
gen.test.volume         Generate test 3D volume of integers. The volume
                        has an outer background area (intensity value
                        'bg') and an inner foreground areas (intensity
                        value 200L).
geod.patches.color.overlay
                        Generate color overlay from geodesic patches
                        around several vertices.
geod.vert.neighborhood
                        Compute all vertices within given geodesic
                        distance on the mesh.
geodesic.circles        Compute geodesic circles and ball stats for
                        given vertices.
geodesic.dists.to.vertex
                        Simple internal wrapper around
                        'Rvcg::vcgDijkstra' with function check.
geodesic.path           Compute geodesic path from a source vertex to
                        one or more target vertices.
get.atlas.region.names
                        Determine atlas region names from a subject.
get.rglstyle            Get the default visualization style parameters
                        as a named list.
get.view.angle.names    Get list of valid view angle names.
getIn                   Retrieve values from nested named lists
get_optional_data_filepath
                        Access a single file from the package cache by
                        its file name.
group.agg.atlas.native
                        Aggregate native space morphometry data over
                        brain atlas regions and subjects for a group of
                        subjects.
group.agg.atlas.standard
                        Aggregate standard space morphometry data over
                        brain atlas regions and subjects for a group of
                        subjects.
group.annot             Load annotations for a group of subjects.
group.concat.measures.native
                        Concatenate native space data for a group of
                        subjects.
group.concat.measures.standard
                        Concatenate standard space data for a group of
                        subjects.
group.label             Retrieve label data for a group of subjects.
group.label.from.annot
                        Extract a region from an atlas annotation as a
                        label for a group of subjects.
group.morph.agg.native
                        Aggregate native space morphometry data over
                        one hemisphere for a group of subjects.
group.morph.agg.standard
                        Aggregate standard space (fsaverage)
                        morphometry data over one hemisphere for a
                        group of subjects.
group.morph.agg.standard.vertex
                        Aggregate standard space morphometry data over
                        subjects.
group.morph.native      Retrieve native space morphometry data for a
                        group of subjects.
group.morph.standard    Retrieve standard space morphometry data for a
                        group of subjects.
group.morph.standard.sf
                        Read combined data for a group from a single
                        file.
group.multimorph.agg.native
                        Aggregate native space morphometry data for
                        multiple measures over hemispheres for a group
                        of subjects.
group.multimorph.agg.standard
                        Aggregate standard space (fsaverage)
                        morphometry data for multiple measures over
                        hemispheres for a group of subjects.
group.surface           Retrieve surface mesh data for a group of
                        subjects.
groupmorph.split.hemilist
                        Split a per-vertex group data matrix for both
                        hemispheres into a hemilist at given index.
hasIn                   Check for values in nested named lists
hemilist                Create a hemilist from lh and rh data.
hemilist.derive.hemi    Derive 'hemi' string from the data in a
                        hemilist
hemilist.from.prefixed.list
                        Create a hemilist from a named list with keys
                        prefixed with 'lh_' and 'rh_'.
hemilist.get.combined.data
                        Get combined data of hemi list
hemilist.unwrap         Unwrap hemi data from a named hemi list.
hemilist.wrap           Wrap data into a named hemi list.
highlight.points.spheres
                        Draw small 3D spheres at given points.
highlight.vertices.on.subject
                        Highlight vertices given by index on a
                        subject's meshes by coloring faces.
highlight.vertices.on.subject.spheres
                        Highlight vertices given by index on a
                        subject's meshes by coloring faces.
highlight.vertices.spheres
                        Draw small 3D spheres at given brain mesh
                        vertices. Supports full brain (2 meshes) as
                        well.
images.dimmax           Compute max width and height of magick images.
is.fs.coloredmesh       Check whether object is an fs.coloredmesh (S3)
is.fs.coloredvoxels     Check whether object is an fs.coloredvoxels
                        instance (S3)
is.fsbrain              Check whether object is an fsbrain (S3)
is.hemilist             Check whether x is a hemilist
label.border            Compute border of a label.
label.colFn             A simple colormap function for binary colors.
label.colFn.inv         A simple colormap function for binary colors.
label.from.annotdata    Extract a region from an annotation as a label.
label.to.annot          Merge several labels into an annotation
labeldata.from.mask     Create labeldata from a mask.
limit_fun               Get data limiting function.
limit_fun_na            Get data limiting function to NA.
limit_fun_na_inside     Get data limiting function, setting values
                        inside range to NA.
list_optional_data      Get file names available in package cache.
mask.from.labeldata.for.hemi
                        Create a binary mask from labels.
mesh.vertex.neighbors   Compute neighborhood of a vertex
mkco.cluster            Return recommended 'makecmap_options' for
                        diverging cluster data.
mkco.div                Return recommended 'makecmap_options' for
                        diverging data.
mkco.heat               Return recommended 'makecmap_options' for
                        sequential data with heatmap style.
mkco.seq                Return recommended 'makecmap_options' for
                        sequential data.
numverts.lh             Determine vertex count of left hemi from
                        hemilist of surfaces or the count itself.
numverts.rh             Determine vertex count of right hemi from
                        hemilist of surfaces or the count itself.
principal.curvatures    Computes principal curvatures according to 2
                        definitions from raw k1 and k2 values.
print.fs.coloredmesh    Print description of a brain coloredmesh (S3).
print.fs.coloredvoxels
                        Print description of fs.coloredvoxels (S3).
print.fsbrain           Print description of an fsbrain (S3).
qc.for.group            Perform data quality check based on computed
                        region stats.
qc.from.regionwise.df   Perform data quality check based on a dataframe
                        containing aggregated region-wise data.
qc.from.segstats.tables
                        Perform data quality check based on a segstats
                        table.
qc.vis.failcount.by.region
                        Visualize the number of outlier subjects per
                        region in your dataset.
qdec.table.skeleton     Generate skeleton dataframe for FreeSurfer QDEC
                        long file from subjects list.
ras2vox_tkr             The FreeSurfer default ras2vox_tkr matrix.
read.colorcsv           Read colors from CSV file.
read.md.demographics    Read demographics file
read.md.subjects        Read subjects file
read.md.subjects.from.fsgd
                        Read subjects list from an FSGD file.
regions.to.ignore       Give suggestions for regions to ignore for an
                        atlas.
report.on.demographics
                        Print a demographics report
rglactions              Create rglactions list, suitable to be passed
                        as parameter to vis functions.
rglo                    Get rgloptions and consider global options.
rglot                   Get rgloptions for testing.
rglvoxels               Draw 3D boxes at locations using rgl.
scale01                 Scale given values to range 0..1.
shape.descriptor.names
                        Get all shape descriptor names.
shape.descriptors       Computes geometric curvature-based descriptors.
shift.hemis.apart       Shift hemispheres apart.
sjd.demo                Download optional demo data if needed and
                        return its path.
sjld                    Get subjects list from subjects.txt file in
                        dir.
spread.values.over.annot
                        Spread a single value for a region to all
                        region vertices.
spread.values.over.hemi
                        Spread the values in the region_value_list and
                        return them for one hemisphere.
spread.values.over.subject
                        Spread the values in the region_value_list and
                        return them for one hemisphere.
subject.annot           Load an annotation for a subject.
subject.annot.border    Compute annot border vertices.
subject.atlas.agg       Aggregate morphometry data over brain atlas
                        regions for a subject.
subject.filepath.morph.native
                        Construct filepath of native space morphometry
                        data file.
subject.filepath.morph.standard
                        Construct filepath of standard space
                        morphometry data file.
subject.label           Retrieve label data for a single subject.
subject.label.from.annot
                        Extract a region from an atlas annotation as a
                        label for a subject.
subject.lobes           Load labels representing brain lobes.
subject.mask            Compute a mask for a subject.
subject.morph.native    Retrieve native space morphometry data for a
                        single subject.
subject.morph.standard
                        Retrieve standard space morphometry data for a
                        single subject.
subject.num.verts       Get subjects vertex count.
subject.surface         Load a surface for a subject.
subject.volume          Read a brain volume.
surface.curvatures      Compute the k1 and k2 principal curvatures of a
                        mesh.
tmesh3d.to.fs.surface   Get an fs.surface brain mesh from an rgl
                        tmesh3d instance.
vdata.split.by.hemi     Split morph data vector at hemisphere boundary.
vertex.coords           Return coordinates for vertices, supporting
                        entire brain via hemilist.
vertex.hemis            Return the proper hemi string ('lh' or 'rh')
                        for each vertex.
vis.color.on.subject    Visualize pre-defined vertex colors on a
                        subject.
vis.coloredmeshes       Visualize a list of colored meshes in a single
                        scene.
vis.coloredmeshes.rotating
                        Visualize a list of colored meshes in a single
                        scene and rotate them, movie-style.
vis.colortable.legend   Create a separate legend plot for a colortable
                        or an annotation.
vis.data.on.fsaverage   Visualize arbitrary data on the fsaverage
                        template subject, if available.
vis.data.on.group.native
                        Visualize native space data on a group of
                        subjects.
vis.data.on.group.standard
                        Visualize standard space data for a group on
                        template.
vis.data.on.subject     Visualize arbitrary data on the surface of any
                        subject.
vis.dti.trk             Visualize DTI tracks from Diffusion
                        Toolkit/TrackVis TRK format file.
vis.export.from.coloredmeshes
                        Export high-quality brainview image with a
                        colorbar.
vis.fs.surface          Visualize fs.surface mesh
vis.group.annot         Plot atlas annotations for a group of subjects.
vis.group.coloredmeshes
                        Plot coloredmeshes for a group of subjects.
vis.group.morph.native
                        Plot native space morphometry data for a group
                        of subjects.
vis.group.morph.standard
                        Plot standard space morphometry data for a
                        group of subjects.
vis.labeldata.on.subject
                        Visualize a label on the surface of a subject.
vis.mask.on.subject     Visualize a vertex mask on the surface of a
                        subject.
vis.path.along.verts    Draw a 3D line from vertex to vertex
vis.paths               Visualize many paths.
vis.paths.along.verts   Visualize several paths in different colors.
vis.region.values.on.subject
                        Visualize arbitrary data, one value per atlas
                        region, on the surface of any subject
                        (including template subjects).
vis.seg.legend          Plot legend for a brain volume segmentation
                        based on colorLUT.
vis.subject.annot       Visualize an annotation for a subject.
vis.subject.label       Visualize a binary label for a subject.
vis.subject.morph.native
                        Visualize native space morphometry data for a
                        subject.
vis.subject.morph.standard
                        Visualize native space morphometry data for a
                        subject or a group.
vis.subject.pre         Visualize pre-loaded data.
vis.symmetric.data.on.subject
                        Visualize clusters or activation data on the
                        surface of any subject.
vislayout.from.coloredmeshes
                        Visualize coloredmeshes from several angles and
                        combine the images into a new figure.
vol.boundary.box        Compute 3D bounding box of a volume.
vol.boundary.box.apply
                        Apply a boundary box to a volume, returning the
                        inner volume part
vol.hull                Retain only the outer hull voxels of the
                        foreground.
vol.imagestack          Turn volume into an ImageMagick image stack.
vol.intensity.to.color
                        Convert integer intensity image to RGB color
                        string form.
vol.mask.from.segmentation
                        Extract subset from a volume by value.
vol.merge               Merge background volume and overlay to new
                        colors.
vol.overlay.colors.from.activation
                        Generate colors for a 3D volume, based on the
                        activation data and a colormap.
vol.overlay.colors.from.colortable
                        Compute voxel colors based on colortable.
vol.planes              Translate names and indices of planes.
vol.slice               Extract a slice of a 3D image stack.
vol.vox.from.crs        Compute R voxel index for FreeSurfer CRS voxel
                        index.
volvis.contour          Visualize contour of a volume.
volvis.lb               Show continuous 3D voxel/volume data as a
                        lightbox, optionally with a background brain
                        volume and colormap.
volvis.lightbox         Draw a lightbox view from volume slices.
volvis.voxels           Voxel-based visualization of volume mask at
                        surface RAS positions.
vox2ras_tkr             The FreeSurfer default vox2ras_tkr matrix.
write.group.morph.standard
                        Write standard space group data to a standard
                        FreeSurfer directory stucture.
write.group.morph.standard.mf
                        Write per-vertex standard space data for a
                        group of subjects to given file names.
write.group.morph.standard.sf
                        Reshape and write combined per-vertex data for
                        a group to a single MGH file.
write.region.aggregated
                        Write data aggregated over regions to
                        morphometry file for group.
write.region.values     Write one value per atlas region for a subject.
write.region.values.fsaverage
                        Write one value per atlas region for a template
                        subject.
