Managing and Visualizing Brain Surface Data

Documentation for package ‘fsbrain’ version 0.5.5

Help Pages

-- A --

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.

-- B --

brainviews

Show one or more views of the given meshes in rgl windows.

-- C --

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

-- D --

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_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.

-- E --

export	Export high-quality brainview image with a colorbar.
export.coloredmesh.ply	Export a coloredmeshes with vertexcolors in PLY format.

-- F --

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.

-- G --

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.

-- H --

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.

-- I --

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

-- L --

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.

-- M --

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.

-- N --

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.

-- P --

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).

-- Q --

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.

-- R --

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.

-- S --

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.

-- T --

tmesh3d.to.fs.surface

Get an fs.surface brain mesh from an rgl tmesh3d instance.

-- V --

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.

-- W --

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.