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fsbrain (version 0.6.0)

Managing and Visualizing Brain Surface Data

Description

Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.

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install.packages('fsbrain')

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Version

0.6.0

License

MIT + file LICENSE

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2

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76

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15

Maintainer

Tim Schc3<a4>fer

Last Published

July 8th, 2026

Functions in fsbrain (0.6.0)

brain

Create fsbrain instance from 2 coloredmeshes.
apply.label.to.morphdata

Load a label from file and apply it to morphometry data.
arrange.brainview.images.grid

Combine several brainview images as a grid into a new figure.
arrange.brainview.images

Combine several brainview images into a new figure.
brainview.sr

Visualize a list of colored meshes, rotating the camera around them.
apply.labeldata.to.morphdata

Apply a label to morphometry data.
annot.outline

Compute outline vertex colors from annotation.
brainviews

Show one or more views of the given meshes in rgl windows.
brainview.t4

Visualize a list of colored meshes from four angles.
brainview.t9

Visualize a list of colored meshes from nine angles.
collayer.bg.atlas

Compute atlas or annotation surface color layer.
cm.heat

Return the standard fsbrain heat colormap.
check.subjectslist

Check whether the subjects_list looks good, warn if not.
check.subjects.files

Report subjects missing files
can.plot.colorbar

Determine whether colorbar can be plotted with given metadata.
can.plot.colorbar.from.coloredmeshes

Determine whether colorbar can be plotted with given coloredmeshes.
collayer.bg

Compute binarized mean curvature surface color layer.
cm.seq

Return the standard fsbrain sequential colormap.
cm.div

Return the standard fsbrain diverging colormap.
cm.cbry

Get cyan blue red yellow colormap function.
collayer.bg.meancurv

Compute binarized mean curvature surface color layer.
cm.qual

Return the standard fsbrain qualitative colormap.
collayers.merge

Merge two or more color layers based on their transparency values.
collayer.from.morphlike.data

Compute surface color layer from morph-like data.
collayer.bg.sulc

Compute binarized sulcal depth surface color layer.
clip_fun

Get data clipping function.
clip.data

Clip data at quantiles to remove outliers.
collayer.from.annot

Compute surface color layer from annotation or atlas data.
brainview.sd

Visualize a list of colored meshes from a single defined angle.
coloredmesh.from.mask

Create a coloredmesh from a mask.
coloredmesh.from.label

Create a coloredmesh from a label.
brainview.si

Visualize a list of colored meshes from a single viewpoint, interactively.
colors.are.grayscale

Check for the given color strings whether they represent gray scale colors.
colorlist.brain.clusters

Return diverging color list
coloredmesh.from.annot

Create a coloredmesh from an annotation of an atlas.
coloredmesh.from.color

Create a coloredmesh from a mesh and pre-defined colors.
collayer.from.annotdata

Compute surface color layer from annotation or atlas data.
coloredmesh.from.morphdata

Create a coloredmesh from arbitrary data.
coloredmesh.from.preloaded.data

Generate coloredmesh from loaded data.
coloredmeshes.from.color

Create coloredmeshes for both hemis using pre-defined colors.
coloredmeshes.get.md

Retrieve metadata from hemilist of coloredmeshes.
deepcopylist.long

Write deepcopy list for longitudinal subjects.
colors.have.transparency

Check for the given color strings whether they have transparency, i.e., an alpha channel value != fully opaque.
collayer.from.mask.data

Compute surface color layer from morph-like data.
coloredmesh.from.morph.standard

Create a coloredmesh from standard space morphometry data.
coloredmesh.from.morph.native

Create a coloredmesh from native space morphometry data.
constant.pervertexdata

Get vertex data for a single fs.surface or a hemilist of surfaces.
common.makecmap.range

Get cmap and colorlayer from data and makecmap_options.
cubes3D.tris

Vectorized version of cube3D.tris
download_optional_data

Download optional data for this package if required.
download_fsaverage_minimal

Download only essential FreeSurfer v6 fsaverage files for quick visualization.
cube3D.tris

Return triangles for a 3D cube or cuboid.
combine.colorbar.with.brainview.animation

Combine a colorbar and a brain animation in gif format into a new animation.
download_fsaverage3

Download the FreeSurfer v6 low-resolution fsaverage3 subject.
deg2rad

Convert degree to radians
demographics.to.qdec.table.dat

Convert a dataframe containing demographics data to a qdec.table.dat file and related files.
coloredmesh.plot.colorbar.separate

Draw colorbar for coloredmeshes in separate 2D plot.
demographics.to.fsgd.file

Write FreeSurfer Group Descriptor (FSGD) file from demographics dataframe.
export

Export high-quality brainview image with a colorbar.
export.coloredmesh.ply

Export a coloredmeshes with vertexcolors in PLY format.
coloredmeshes.combined.data.range

Retrieve combined data range from hemilist of coloredmeshes.
demo

Show demo visualization to test whether fsbrain is setup correctly.
delete_all_optional_data

Delete all data in the package cache.
download_fsaverage

Download the FreeSurfer v6 fsaverage subject.
desaturate

Perform simple desaturation or grayscale conversion of RGBA colors.
download_optional_paper_data

Download extra data to reproduce the figures from the fsbrain paper.
face.edges

Enumerate all edges of the given faces or mesh.
eeg_coords

Internal function to get some demo EEG electrode coordinates. Will be removed from public API. Do not use this.
ensure.fs.surface

Check whether parameter is an fs.surface instance.
ensure.tmesh3d

Ensure the mesh is a tmesh3d instance. Will convert fs.surfaces to one automatically.
draw.segments.on.image

Draw contour segments onto a magick image.
find.subjectsdir.of

Find the subject directory containing the fsaverage subject (or others) on disk.
force.to.range

Change data to ensure requested data_range.
draw.colorbar

Draw colorbar into background of current plot.
fslong.subjects.finished

Find completely run FreeSurfer long subjects in a recon-all long output folder.
flc

Given a list of path coordinates, create matrix containing only the first and last point of each path.
fsbrain.set.default.figsize

Set default figure size for fsbrain visualization functions.
fup

Transform first character of a string to uppercase.
geodesic.path

Compute geodesic path from a source vertex to one or more target vertices.
fs.surface.vertex.neighbors

Compute vertex neighborhoods or the full adjacency list for a mesh using the Rvcg or igraph library.
fs.value.list.from.agg.res

Create a named value list from a dataframe.
download_fsaverage6

Download the FreeSurfer v6 fsaverage6 subject.
find.freesurferhome

Find the FREESURFER_HOME directory on disk.
extract.volume.3D

Try to extract a 3D volume from the input argument.
get.atlas.region.names

Determine atlas region names from a subject.
extend_neighbors

Recursive computation of neighborhoods, see surf.sphere.dist
fs.coloredmesh

fs.coloredmesh constructor
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).
fs.home

Return FreeSurfer path.
fs.surface.as.adjacencylist

Turn surface mesh into a igraph and return its adjacency list representation.
geod.patches.color.overlay

Generate color overlay from geodesic patches around several vertices.
get.rglstyle.glass2

Get the glass2 visualization style parameters as a named list.
geodesic.circles

Compute geodesic circles and ball stats for given vertices.
combine.colorbar.with.brainview.image

Combine a colorbar and a brainview image into a new figure.
combine.colorbar.with.brainview.image.vertical

Combine a vertical colorbar and a brainview image into a new figure.
geodesic.dists.to.vertex

Simple internal wrapper around Rvcg::vcgDijkstra with function check.
get.rglstyle.edges

Get the mesh edges visualization style parameters as a named list.
get.rglstyle.glass

Get the glass visualization style parameters as a named list.
fs.surface.to.igraph

Create igraph undirected graph from a brain surface mesh.
group.concat.measures.native

Concatenate native space data for a group of subjects.
geod.patches.color.overlay.singlehemi

Generate color overlay from geodesic patches around several vertices for a single hemi.
fslong.subjects.detect

Get subject names from sub directories of FreeSurfer long directory.
geod.patches.pervertexdata

Generate per-vertex distance data from geodesic patches around several vertices.
get.slice.indices

Compute slice indices from slice definition.
get.subject.class

Construct FSGD Class name from group and non-continuous covariate columns.
group.concat.measures.standard

Concatenate standard space data for a group of subjects.
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.
geod.patches.pervertexdata.singlehemi

Generate per-vertex distance data from geodesic patches around several vertices for a single hemi.
get.rglstyle.parameters

Produce the named list of style parameters from style definition.
fs.surface.to.tmesh3d

Get an rgl tmesh3d instance from a brain surface mesh.
fsaverage.path

Return path to fsaverage dir.
fsbrain.renderable

Check whether object can be rendered by fsbrain
geodesic.average.distance

Compute the average (pseudo-) geodesic distance on the mesh from each vertex to all other vertices.
group.label

Retrieve label data 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.
geod.vert.neighborhood

Compute all vertices within given geodesic distance on the mesh.
group.annot

Load annotations for a group of subjects.
get.rglstyle.shiny

Get a shiny visualization style.
group.data.to.array

Convert group 2D data (1 vector per subject) to 4D array format.
group.morph.agg.standard.vertex

Aggregate standard space morphometry data over subjects.
group.morph.agg.standard

Aggregate standard space (fsaverage) morphometry data over one hemisphere for a group of subjects.
get.rglstyle.semitransparent

Get the semi-transparent visualization style parameters as a named list.
group.morph.standard

Retrieve standard space morphometry data for a group of subjects.
group.morph.native

Retrieve native space morphometry data for a group of subjects.
geodesic.ballstats

Compute geodesic ball area and perimeter at location defined by geodists for all radii.
hemilist.unwrap

Unwrap hemi data from a named hemi list.
hemilist.wrap

Wrap data into a named hemi list.
get.rglstyle.default

Get the default visualization style parameters as a named list.
get.rglstyle

Get the default visualization style parameters as a named list.
group.multimorph.agg.native

Aggregate native space morphometry data for multiple measures over hemispheres for a group of subjects.
group.morph.standard.sf

Read combined data for a group from a single file.
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
getIn

Retrieve values from nested named lists
group.label.from.annot

Extract a region from an atlas annotation as a label for a group of subjects.
get.view.angle.names

Get list of valid view angle names.
group.morph.agg.native

Aggregate native space morphometry data over one hemisphere for a group of subjects.
groupmorph.split.hemilist

Split a per-vertex group data matrix for both hemispheres into a hemilist at given index.
image.remap.color

Remap a color in an image, typically used to set the background color to transparent.
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.
is.fs.coloredvoxels

Check whether object is an fs.coloredvoxels instance (S3)
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.
hemilist

Create a hemilist from lh and rh data.
handle.rglactions.highlight.points

Highlight requested points (if any), but apply given view rotation before doing so.
label.border.fast

Compute border vertices of a label using Rvcg.
label.colFn

A simple colormap function for binary colors.
hull.retain.along.axis

Copy the first n foreground voxel values.
images.same.height

Extent all images to the height of the image with maximal height.
hemilist.derive.hemi

Derive 'hemi' string from the data in a hemilist
images.annotate

Annotate image with text.
is.Triangles3D

Check whether object is a Triangles3D instance
hasIn

Check for values in nested named lists
images.rescale.to.max.canvas

Rescale all images canvas to match the largest one.
hemi.lobe.labels

Compute lobe labels for a single hemi from aparc atlas.
images.dimmax

Compute max width and height of magick images.
limit_fun_na

Get data limiting function to NA.
limit_fun

Get data limiting function.
hemlist.ensure.contains

title Ensure an key for a hemilist exists.
mkco.heat

Return recommended 'makecmap_options' for sequential data with heatmap style.
is.fsbrain

Check whether object is an fsbrain (S3)
labeldata.from.mask

Create labeldata from a mask.
label.colFn.inv

A simple colormap function for binary colors.
label.to.annot

Merge several labels into an annotation
label.from.annotdata

Extract a region from an annotation as a label.
images.same.width

Extent all images to the width of the image with maximal width.
mkco.div

Return recommended 'makecmap_options' for diverging data.
mesh.vertex.included.faces

Return all faces which are made up completely of the listed vertices.
mesh.slice.intersection

Compute intersection of a triangular surface mesh with an axis-aligned plane.
limit_fun_na_inside

Get data limiting function, setting values inside range to NA.
is.hemilist

Check whether x is a hemilist
label.border

Compute border of a label.
mergehemi.annots

Merge the annotations from two hemispheres into one annot.
highlight.points.spheres

Draw small 3D spheres at given points.
list_optional_data

Get file names available in package cache.
mkco.seq

Return recommended 'makecmap_options' for sequential data.
mesh.vertex.neighbors

Compute neighborhood of a vertex
mkco.cluster

Return recommended 'makecmap_options' for diverging cluster data.
normalize

Normalize data.
is.fs.coloredmesh

Check whether object is an fs.coloredmesh (S3)
mask.from.labeldata.for.hemi

Create a binary mask from labels.
pervertexdata.smoothnn.compute.numiter

Compute number of neighborhood smoothing iterations to reach requested fwhm.
magick.grid

Arrange a multi-frame ImageMagick image into a grid.
plot.fsbrain.colorbar

Draw a simple colorbar from colors.
rad2deg

Convert raduians to degree
ras2vox_tkr

The FreeSurfer default ras2vox_tkr matrix.
path.colors.from.orientation

Compute path color from its orientation.
path.slopes

Compute slopes of paths relative to axes.
numverts.rh

Determine vertex count of right hemi from hemilist of surfaces or the count itself.
numverts.lh

Determine vertex count of left hemi from hemilist of surfaces or the count itself.
read.md.subjects

Read subjects file
read.md.subjects.from.fsgd

Read subjects list from an FSGD file.
print.fs.coloredvoxels

Print description of fs.coloredvoxels (S3).
qc.from.segstats.tables

Perform data quality check based on a segstats table.
print.fs.coloredmesh

Print description of a brain coloredmesh (S3).
qc.fslong.checkidenticaldata

Check whether subjects for FS longitudinal pipeline contain data that is identical between time points.
pp.named.list

Pretty-print a named list or vector.
mesh.ras2crs

Transform surface vertices from surface RAS to 0-based volume CRS space.
pervertexdata.smoothnn

Perform iterative nearest-neighbor smoothing of per-vertex data.
pervertexdata.smoothnn.compute.fwhm

Compute expected FWHM from given number of neighborhood smoothing iterations.
per.hemi.vertex.indices

Transform surfaces indices which go over two surfaces to per-hemi indices.
perform.na.mapping

Perform NA mapping for transparency
recycle

Recycle parameters or whatever.
perform.rglactions

Perform rglactions, like taking screenshots.
scale01

Scale given values to range 0..1.
regions.to.ignore

Give suggestions for regions to ignore for an atlas.
shape.descriptor.names

Get all shape descriptor names.
pervertexdata.smoothgaussian

Perform Gaussian smoothing
qc.from.regionwise.df

Perform data quality check based on a dataframe containing aggregated region-wise data.
report.on.demographics

Print a demographics report
qc.from.segstats.table

Perform data quality check based on a segstats table.
read.colorcsv

Read colors from CSV file.
read.md.demographics

Read demographics file
qdec.table.skeleton

Generate skeleton dataframe for FreeSurfer QDEC long file from subjects list.
print.fsbrain

Print description of an fsbrain (S3).
rglo

Get rgloptions and consider global options.
qc.for.group

Perform data quality check based on computed region stats.
principal.curvatures

Computes principal curvatures according to 2 definitions from raw k1 and k2 values.
rgl.coord.lines

Plot x, y and z axes in R,G,B.
rotation.matrix.for.axis.rot

Get rotation matrix for a 3D rotation around an axis.
rglactions.transform

Apply data transformation rglactions.
qdec.table.filter

Filter QDEC long table for subjects.
shape.descriptors

Computes geometric curvature-based descriptors.
shift.hemis.apart

Shift hemispheres apart.
qc.report.html

Create visual quality check report from QC result.
subject.annot

Load an annotation for a subject.
sph2fs

Transform spherical coordinates to FreeSurfer surface space to plot things around a brain.
subject.filepath.any

Construct filepath of any freesurfer file.
subject.atlas.agg

Aggregate morphometry data over brain atlas regions for a subject.
subject.descriptor.geodesic.average.distance

Compute mean geodesic distance descriptor for a subject.
subject.annot.border

Compute annot border vertices.
rglvoxels

Draw 3D boxes at locations using rgl.
sjld

Get subjects list from subjects.txt file in dir.
rglot

Get rgloptions for testing.
sortcoloredmeshes.by.hemi

Sort coloredmeshes into 2 lists by their 'hemi' property.
subject.filepath.morph.native

Construct filepath of native space morphometry data file.
subject.surface

Load a surface for a subject.
subject.report.html

Create visual quality check report from QC result.
subject.morph.standard

Retrieve standard space morphometry data for a single subject.
subject.num.verts

Get subjects vertex count.
surf.sphere.dist

Compute vertex neighborhoods on a sphere based on the given max distance along the sphere.
surf.sphere.gaussianweights

Compute Gaussian weights
rglactions

Create rglactions list, suitable to be passed as parameter to vis functions.
qc.vis.failcount.by.region

Visualize the number of outlier subjects per region in your dataset.
surface.curvatures

Compute the k1 and k2 principal curvatures of a mesh.
rglactions.has.key

Check for a key in names of rglactions.
surf.sphere.spatialfilter

Apply spatial filter to surface data.
subject.label.from.annot

Extract a region from an atlas annotation as a label for a subject.
subject.lobes

Load labels representing brain lobes.
sjd.demo

Download optional demo data if needed and return its path.
shift.hemis.rglactions

Shift hemis apart if indicated in rglactions
test.numerical.meandiff

Perform tests for group differences on paired or unpaired data for two groups.
spread.values.over.hemi

Spread the values in the region_value_list and return them for one hemisphere.
vis.data.on.group.native

Visualize native space data on a group of subjects.
scale.to.range.zero.one

Scale given values to range 0..1.
surf.metric.properties

Compute metric surface properties.
spread.values.over.subject

Spread the values in the region_value_list and return them for one hemisphere.
test.numerical.meandiff.paired

Perform tests for group differences on paired data (repeated measurements) for two conditions or time points.
subject.morph.native

Retrieve native space morphometry data for a single subject.
subject.volume

Read a brain volume.
subject.mask

Compute a mask for a subject.
vis.color.on.subject

Visualize pre-defined vertex colors on a subject.
vis.data.on.subject

Visualize arbitrary data on the surface of any subject.
tmesh3d.to.fs.surface

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

Return coordinates for vertices, supporting entire brain via hemilist.
test.numerical.meandiff.unpaired

Perform tests for group differences on unpaired data for two groups.
submesh.vertex

Create a submesh including only the given vertices.
vis.coloredmesh

Draw a coloredmesh using a style.
vis.data.on.group.standard

Visualize standard space data for a group on template.
vis.group.coloredmeshes

Plot coloredmeshes for a group of subjects.
vis.group.annot

Plot atlas annotations for a group of subjects.
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.mask.on.subject

Visualize a vertex mask on the surface of a subject.
vertex.hemis

Return the proper hemi string ('lh' or 'rh') for each vertex.
surf.avg.vertexradius

Compute average distance from the origin to each vertex.
vis.labeldata.on.subject

Visualize a label on the surface of a subject.
subject.label

Retrieve label data for a single subject.
spread.values.over.annot

Spread a single value for a region to all region vertices.
subject.filepath.morph.standard

Construct filepath of standard space morphometry data file.
vis.coloredmeshes

Visualize a list of colored meshes in a single scene.
symmrange

Given data, compute symmetric range around zero.
vis.subject.annot

Visualize an annotation for a subject.
surf.center.fsaverage

Get pre-computed center for fsaverage white surface.
surfs.props

Compute simple version of center and radius of 2 meshes.
vis.paths

Visualize many paths.
vis.path.along.verts

Draw a 3D line from vertex to vertex
vis.seg.legend

Plot legend for a brain volume segmentation based on colorLUT.
vis.rotated.coloredmeshes

Rotate and visualize coloredmeshes, applying a style.
vis.subject.label

Visualize a binary label for a subject.
vis.coloredmeshes.rotating

Visualize a list of colored meshes in a single scene and rotate them, movie-style.
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.group.morph.native

Plot native space morphometry data for a group of subjects.
track.length

Compute the total length of a path given by the coordinates of its points.
vis.colortable.legend

Create a separate legend plot for a colortable or an annotation.
vdata.split.by.hemi

Split morph data vector at hemisphere boundary.
vis.data.on.fsaverage

Visualize arbitrary data on the fsaverage template subject, if available.
vis.group.morph.standard

Plot standard space morphometry data for a group of subjects.
vis.subject.morph.native

Visualize native space morphometry data for a subject.
vis.rglwidget

Visualize coloredmeshes as an interactive rgl WebGL widget for use in R Shiny apps and RMarkdown documents.
vol.boundary.mask

Compute foreground pixels over the whole 3D imagestack.
vis.renderable

Visualize a renderable object
vis.subject.morph.standard

Visualize native space morphometry data for a subject or a group.
surf.radius.fsaverage

Get pre-computed radius for fsaverage white surface.
vol.hull

Retain only the outer hull voxels of the foreground.
vol.boundary.box.apply

Apply a boundary box to a volume, returning the inner volume part
vol.boundary.box

Compute 3D bounding box of a volume.
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.
vis.volume.on.surface

Visualize a brain volume overlaid on a cortical surface in 3D.
vol.imagestack

Turn volume into an ImageMagick image stack.
vol.intensity.to.color

Convert integer intensity image to RGB color string form.
vol.slice

Extract a slice of a 3D image stack.
vol.vox.from.crs

Compute R voxel index for FreeSurfer CRS voxel index.
vol.planes

Translate names and indices of planes.
vol.plane.axes

Get indices of the axes defining the given plane.
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.
volvis.contour

Visualize contour of a volume.
write.group.morph.standard

Write standard space group data to a standard FreeSurfer directory stucture.
volvis.voxels

Voxel-based visualization of volume mask at surface RAS positions.
write.group.morph.standard.mf

Write per-vertex standard space data for a group of subjects to given file names.
wrapped.image.append

Wrapper around magick::image_append that allows specifying the background color when working with images of different width/height.
volvis.lb.with.surface

Visualize volume slices with surface mesh contours overlaid in lightbox view.
volvis.lightbox

Draw a lightbox view from volume slices.
write.region.values.fsaverage

Write one value per atlas region for a template subject.
write.region.values

Write one value per atlas region for a subject.
volvis.lb

Show continuous 3D voxel/volume data as a lightbox, optionally with a background brain volume and colormap.
write.group.morph.standard.singlehemi

Write single hemi per-vertex data for a group of subjects to given file names.
vox2ras_tkr

The FreeSurfer default vox2ras_tkr matrix.
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.
boxcoords.from.bbox

Compute the coordinates of the 8 corners of a 3D box.
annot.outline.border.vertices

Compute the border vertices for each region in an annot.
alphablend

Perform alpha blending for pairs of RGBA colors.
apply.transform

Apply matmult transformation to input.