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fsbrain (version 0.7.0)

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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475

Version

0.7.0

License

MIT + file LICENSE

Issues

2

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0

Stars

77

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15

Maintainer

Tim Schc3<a4>fer

Last Published

August 23rd, 2026

Functions in fsbrain (0.7.0)

annot.outline

Compute outline vertex colors from annotation.
arrange.brainview.images.grid

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

Perform alpha blending for pairs of RGBA colors.
arrange.brainview.images

Combine several brainview images into a new figure.
apply.style.alpha

Extract the alpha value from resolved style parameters
apply.transform

Apply matmult transformation to input.
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.
boxcoords.from.bbox

Compute the coordinates of the 8 corners of a 3D box.
brainview.t9

Visualize a list of colored meshes from nine angles.
brainviews

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

Visualize a list of colored meshes from four angles.
can.plot.colorbar.from.coloredmeshes

Determine whether colorbar can be plotted with given coloredmeshes.
brain

Create fsbrain instance from 2 coloredmeshes.
brainview.si

Visualize a list of colored meshes from a single viewpoint, interactively.
brainview.sr

Visualize a list of colored meshes, rotating the camera around them.
brainview.sd

Visualize a list of colored meshes from a single defined angle.
can.plot.colorbar

Determine whether colorbar can be plotted with given metadata.
check.subjects.files

Report subjects missing files
cm.heat

Return the standard fsbrain heat colormap.
cm.qual

Return the standard fsbrain qualitative colormap.
cm.div

Return the standard fsbrain diverging colormap.
collayer.bg.atlas

Compute atlas or annotation surface color layer.
clip_fun

Get data clipping function.
clip.data

Clip data at quantiles to remove outliers.
cm.cbry

Get cyan blue red yellow colormap function.
collayer.bg

Compute binarized mean curvature surface color layer.
cm.seq

Return the standard fsbrain sequential colormap.
check.subjectslist

Check whether the subjects_list looks good, warn if not.
collayer.bg.meancurv

Compute binarized mean curvature surface color layer.
collayer.from.mask.data

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

Compute binarized sulcal depth surface color layer.
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.
color_to_rgba

Convert an R color to an RGBA float vector
coloredmesh.from.annot

Create a coloredmesh from an annotation of an atlas.
collayer.from.annot

Compute surface color layer from annotation or atlas data.
collayer.from.annotdata

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

Create a coloredmesh from a mesh and pre-defined colors.
coloredmesh_to_scimesh

Convert a single fs.coloredmesh to a scimesh mesh descriptor
coloredmeshes.from.color

Create coloredmeshes for both hemis using pre-defined colors.
coloredmesh.from.preloaded.data

Generate coloredmesh from loaded data.
coloredmesh.from.morphdata

Create a coloredmesh from arbitrary data.
coloredmesh.plot.colorbar.separate

Draw colorbar for coloredmeshes in separate 2D plot.
coloredmesh.from.morph.native

Create a coloredmesh from native space morphometry data.
coloredmesh.from.label

Create a coloredmesh from a label.
coloredmesh.from.morph.standard

Create a coloredmesh from standard space morphometry data.
coloredmesh.from.mask

Create a coloredmesh from a mask.
coloredmeshes.combined.data.range

Retrieve combined data range from hemilist of coloredmeshes.
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.
common.makecmap.range

Get cmap and colorlayer from data and makecmap_options.
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.
colorlist.brain.clusters

Return diverging color list
coloredmeshes.get.md

Retrieve metadata from hemilist of coloredmeshes.
coloredmeshes_to_scimesh

Convert a hemilist of fs.coloredmeshes to a list of scimesh mesh descriptors
combine.colorbar.with.brainview.image.vertical

Combine a vertical colorbar and a brainview image into a new figure.
compute.surface.contour.slices

Compute surface contour slice images (internal).
cubes3D.tris

Vectorized version of cube3D.tris
desaturate

Perform simple desaturation or grayscale conversion of RGBA colors.
constant.pervertexdata

Get vertex data for a single fs.surface or a hemilist of surfaces.
demographics.to.qdec.table.dat

Convert a dataframe containing demographics data to a qdec.table.dat file and related files.
demo

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

Delete all data in the package cache.
cube3D.tris

Return triangles for a 3D cube or cuboid.
deg2rad

Convert degree to radians
demographics.to.fsgd.file

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

Write deepcopy list for longitudinal subjects.
download_fsaverage3

Download the FreeSurfer v6 low-resolution fsaverage3 subject.
download_fsaverage_minimal

Download only essential FreeSurfer v6 fsaverage files for quick visualization.
download_fsaverage6

Download the FreeSurfer v6 fsaverage6 subject.
download_optional_data

Download optional data for this package if required.
download_fsaverage

Download the FreeSurfer v6 fsaverage subject.
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.
draw.colorbar

Draw colorbar into background of current plot.
draw.segments.on.image

Draw contour segments onto a magick image.
download_optional_paper_data

Download extra data to reproduce the figures from the fsbrain paper.
export.coloredmesh.ply

Export a coloredmeshes with vertexcolors in PLY format.
find.freesurferhome

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

Try to extract a 3D volume from the input argument.
face.edges

Enumerate all edges of the given faces or mesh.
find.subjectsdir.of

Find the subject directory containing the fsaverage subject (or others) on disk.
flc

Given a list of path coordinates, create matrix containing only the first and last point of each path.
extend_neighbors

Recursive computation of neighborhoods, see surf.sphere.dist
filter_scene_by_view

Filter a scimesh scene to the meshes visible from a given view
export

Export high-quality brainview image with a colorbar.
ensure.tmesh3d

Ensure the mesh is a tmesh3d instance. Will convert fs.surfaces to one automatically.
fs.surface.to.igraph

Create igraph undirected graph from a brain surface mesh.
fsbrain.renderable

Check whether object can be rendered by fsbrain
fs.surface.to.tmesh3d

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

fs.coloredmesh constructor
fsaverage.path

Return path to fsaverage dir.
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.
fup

Transform first character of a string to uppercase.
geod.patches.color.overlay

Generate color overlay from geodesic patches around several vertices.
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).
fsbrain.set.default.figsize

Set default figure size for fsbrain visualization functions.
fs.home

Return FreeSurfer path.
get.rglstyle

Get the default visualization style parameters as a named list.
fs.surface.as.adjacencylist

Turn surface mesh into a igraph and return its adjacency list representation.
force.to.range

Change data to ensure requested data_range.
geodesic.dists.to.vertex

Simple internal wrapper around Rvcg::vcgDijkstra with function check.
get.atlas.region.names

Determine atlas region names from a subject.
get.fsbrain.renderer.backend

Get the current fsbrain renderer backend
fslong.subjects.detect

Get subject names from sub directories of FreeSurfer long directory.
geod.patches.color.overlay.singlehemi

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

Find completely run FreeSurfer long subjects in a recon-all long output folder.
get.fsbrain.scimesh.output.dims

Get the output image dimensions for the scimesh backend
geodesic.average.distance

Compute the average (pseudo-) geodesic distance on the mesh from each vertex to all other vertices.
geod.vert.neighborhood

Compute all vertices within given geodesic distance on the mesh.
geodesic.path

Compute geodesic path from a source vertex to one or more target vertices.
geodesic.ballstats

Compute geodesic ball area and perimeter at location defined by geodists for all radii.
get.view.angle.names

Get list of valid view angle names.
get.rglstyle.edges

Get the mesh edges visualization style parameters as a named list.
geod.patches.pervertexdata

Generate per-vertex distance data from geodesic patches around several vertices.
get.rglstyle.default

Get the default visualization style parameters as a named list.
geod.patches.pervertexdata.singlehemi

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

Compute geodesic circles and ball stats for given vertices.
fsbrain_style_to_scimesh_options

Map an fsbrain rendering style to scimesh render options
get.rglstyle.glass

Get the glass visualization style parameters as a named list.
get.slice.indices

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

Construct FSGD Class name from group and non-continuous covariate columns.
get.rglstyle.shiny

Get a shiny visualization style.
get.rglstyle.glass2

Get the glass2 visualization style parameters as a named list.
get.rglstyle.parameters

Produce the named list of style parameters from style definition.
getIn

Retrieve values from nested named lists
get.rglstyle.semitransparent

Get the semi-transparent visualization style parameters as a named list.
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.label

Retrieve label data for a group of subjects.
group.annot

Load annotations for a group of subjects.
group.concat.measures.standard

Concatenate standard space 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.concat.measures.native

Concatenate native space data for a group of subjects.
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.standard.sf

Read combined data for a group from a single file.
group.morph.agg.native

Aggregate native space morphometry data over one hemisphere for a group of subjects.
group.surface

Retrieve surface mesh data for a group of subjects.
group.multimorph.agg.native

Aggregate native space morphometry data for multiple measures over hemispheres for a group of subjects.
groupmorph.split.hemilist

Split a per-vertex group data matrix for both hemispheres into a hemilist at given index.
group.morph.native

Retrieve native space morphometry data 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.morph.agg.standard

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

Retrieve standard space morphometry data for a group of subjects.
handle.rglactions.highlight.points

Highlight requested points (if any), but apply given view rotation before doing so.
hemilist.wrap

Wrap data into a named hemi list.
hasIn

Check for values in nested named lists
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.unwrap

Unwrap hemi data from a named hemi list.
hemilist.get.combined.data

Get combined data of hemi list
hemlist.ensure.contains

title Ensure an key for a hemilist exists.
hemi.lobe.labels

Compute lobe labels for a single hemi from aparc atlas.
hemilist

Create a hemilist from lh and rh data.
highlight_points_to_scimesh

Convert highlight points (rglactions) to scimesh sphere meshes
highlight.vertices.on.subject.spheres

Highlight vertices given by index on a subject's meshes by coloring faces.
highlight.vertices.on.subject

Highlight vertices given by index on a subject's meshes by coloring faces.
highlight.points.spheres

Draw small 3D spheres at given points.
highlight.vertices.spheres

Draw small 3D spheres at given brain mesh vertices. Supports full brain (2 meshes) as well.
images.annotate

Annotate image with text.
hex_to_rgba

Convert hex color string to RGBA float vector
images.dimmax

Compute max width and height of magick images.
hex_colors_to_rgba_matrix

Convert a vector of hex colors to an Nx4 RGBA float matrix
hull.retain.along.axis

Copy the first n foreground voxel values.
is.fsbrain

Check whether object is an fsbrain (S3)
label.border

Compute border of a label.
is.hemilist

Check whether x is a hemilist
label.border.fast

Compute border vertices of a label using Rvcg.
is.fs.coloredvoxels

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

Check whether object is an fs.coloredmesh (S3)
label.colFn

A simple colormap function for binary colors.
labeldata.from.mask

Create labeldata from a mask.
images.same.height

Extent all images to the height of the image with maximal height.
is.Triangles3D

Check whether object is a Triangles3D instance
images.same.width

Extent all images to the width of the image with maximal width.
limit_fun_na

Get data limiting function to NA.
label.colFn.inv

A simple colormap function for binary colors.
images.rescale.to.max.canvas

Rescale all images canvas to match the largest one.
label.to.annot

Merge several labels into an annotation
label.from.annotdata

Extract a region from an annotation as a label.
list_optional_data

Get file names available in package cache.
limit_fun

Get data limiting function.
magick.grid

Arrange a multi-frame ImageMagick image into a grid.
mkco.heat

Return recommended 'makecmap_options' for sequential data with heatmap style.
mesh.vertex.included.faces

Return all faces which are made up completely of the listed vertices.
mesh.ras2crs

Transform surface vertices from surface RAS to 0-based volume CRS space.
mesh.vertex.neighbors

Compute neighborhood of a vertex
limit_fun_na_inside

Get data limiting function, setting values inside range to NA.
mkco.seq

Return recommended 'makecmap_options' for sequential data.
mkco.cluster

Return recommended 'makecmap_options' for diverging cluster data.
mkco.div

Return recommended 'makecmap_options' for diverging data.
mesh.slice.intersection

Compute intersection of a triangular surface mesh with an axis-aligned plane.
mask.from.labeldata.for.hemi

Create a binary mask from labels.
normalize

Normalize data.
mergehemi.annots

Merge the annotations from two hemispheres into one annot.
path.slopes

Compute slopes of paths relative to axes.
perform.na.mapping

Perform NA mapping for transparency
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.
path.colors.from.orientation

Compute path color from its orientation.
perform.rglactions

Perform rglactions, like taking screenshots.
per.hemi.vertex.indices

Transform surfaces indices which go over two surfaces to per-hemi indices.
pervertexdata.smoothnn

Perform iterative nearest-neighbor smoothing of per-vertex data.
pervertexdata.smoothgaussian

Perform Gaussian smoothing
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.
print.fs.coloredmesh

Print description of a brain coloredmesh (S3).
principal.curvatures

Computes principal curvatures according to 2 definitions from raw k1 and k2 values.
pervertexdata.smoothnn.compute.numiter

Compute number of neighborhood smoothing iterations to reach requested fwhm.
pp.named.list

Pretty-print a named list or vector.
pervertexdata.smoothnn.compute.fwhm

Compute expected FWHM from given number of neighborhood smoothing iterations.
qc.from.regionwise.df

Perform data quality check based on a dataframe containing aggregated region-wise data.
qdec.table.skeleton

Generate skeleton dataframe for FreeSurfer QDEC long file from subjects list.
qc.from.segstats.table

Perform data quality check based on a segstats table.
ras2vox_tkr

The FreeSurfer default ras2vox_tkr matrix.
qc.vis.failcount.by.region

Visualize the number of outlier subjects per region in your dataset.
qc.report.html

Create visual quality check report from QC result.
read.md.demographics

Read demographics file
qdec.table.filter

Filter QDEC long table for subjects.
read.colorcsv

Read colors from CSV file.
qc.from.segstats.tables

Perform data quality check based on a segstats table.
rglactions

Create rglactions list, suitable to be passed as parameter to vis functions.
qc.fslong.checkidenticaldata

Check whether subjects for FS longitudinal pipeline contain data that is identical between time points.
read.md.subjects

Read subjects file
rad2deg

Convert raduians to degree
rglactions.has.key

Check for a key in names of rglactions.
report.on.demographics

Print a demographics report
read.md.subjects.from.fsgd

Read subjects list from an FSGD file.
rglo

Get rgloptions and consider global options.
regions.to.ignore

Give suggestions for regions to ignore for an atlas.
recycle

Recycle parameters or whatever.
rglactions.transform

Apply data transformation rglactions.
shift.hemis.apart

Shift hemispheres apart.
scale01

Scale given values to range 0..1.
shape.descriptor.names

Get all shape descriptor names.
rotation.matrix

Build a 4x4 rotation matrix (Rodrigues formula).
safe.image.trim

Safe wrapper around magick::image_trim that handles blank images.
rgl.coord.lines

Plot x, y and z axes in R,G,B.
rglot

Get rgloptions for testing.
shape.descriptors

Computes geometric curvature-based descriptors.
rglvoxels

Draw 3D boxes at locations using rgl.
rotation.matrix.for.axis.rot

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

Shift hemis apart if indicated in rglactions
subject.annot.border

Compute annot border vertices.
subject.atlas.agg

Aggregate morphometry data over brain atlas regions for a subject.
subject.annot

Load an annotation for a subject.
spread.values.over.hemi

Spread the values in the region_value_list and return them for one hemisphere.
sjld

Get subjects list from subjects.txt file in dir.
sph2fs

Transform spherical coordinates to FreeSurfer surface space to plot things around a brain.
sjd.demo

Download optional demo data if needed and return its path.
spread.values.over.subject

Spread the values in the region_value_list and return them for one hemisphere.
spread.values.over.annot

Spread a single value for a region to all region vertices.
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.lobes

Load labels representing brain lobes.
subject.morph.standard

Retrieve standard space morphometry data for a single subject.
subject.label

Retrieve label data for a single subject.
subject.descriptor.geodesic.average.distance

Compute mean geodesic distance descriptor for a subject.
subject.label.from.annot

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

Compute a mask for a subject.
subject.morph.native

Retrieve native space morphometry data for a single subject.
subject.filepath.morph.standard

Construct filepath of standard space morphometry data file.
subject.filepath.any

Construct filepath of any freesurfer file.
subject.volume

Read a brain volume.
subject.report.html

Create visual quality check report from QC result.
subject.num.verts

Get subjects vertex count.
surf.center.fsaverage

Get pre-computed center for fsaverage white surface.
surf.sphere.dist

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

Get pre-computed radius for fsaverage white surface.
surf.metric.properties

Compute metric surface properties.
surf.avg.vertexradius

Compute average distance from the origin to each vertex.
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.
subject.surface

Load a surface for a subject.
vdata.split.by.hemi

Split morph data vector at hemisphere boundary.
vertex.coords

Return coordinates for vertices, supporting entire brain via hemilist.
vis.color.on.subject

Visualize pre-defined vertex colors on a subject.
vertex.hemis

Return the proper hemi string ('lh' or 'rh') for each vertex.
vis.coloredmeshes.rotating

Visualize a list of colored meshes in a single scene and rotate them, movie-style.
vis.coloredmeshes

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

Map an fsbrain view angle to a scimesh camera
view.angle.to.hemi.filter

Get the hemisphere filter for a view angle
test.numerical.meandiff

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

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

Draw a coloredmesh using a style.
symmrange

Given data, compute symmetric range around zero.
take.screenshot

Take screenshot of rgl scene, with fallback for systems without X11.
surf.sphere.spatialfilter

Apply spatial filter to surface data.
surfs.props

Compute simple version of center and radius of 2 meshes.
track.length

Compute the total length of a path given by the coordinates of its points.
surf.sphere.gaussianweights

Compute Gaussian weights
vis.data.on.group.standard

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

Export high-quality brainview image with a colorbar.
test.numerical.meandiff.unpaired

Perform tests for group differences on unpaired data for two groups.
test.numerical.meandiff.paired

Perform tests for group differences on paired data (repeated measurements) for two conditions or time points.
vis.fs.surface

Visualize fs.surface mesh
vis.dti.trk

Visualize DTI tracks from Diffusion Toolkit/TrackVis TRK format file.
vis.data.on.subject

Visualize arbitrary data on the surface of any subject.
vis.group.coloredmeshes

Plot coloredmeshes for a group of subjects.
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.colortable.legend

Create a separate legend plot for a colortable or an annotation.
vis.group.annot

Plot atlas annotations for a group of subjects.
vis.group.morph.standard

Plot standard space morphometry data for a group of subjects.
vis.path.along.verts

Draw a 3D line from vertex to vertex
vis.renderable

Visualize a renderable object
vis.group.morph.native

Plot native space morphometry data for a group of subjects.
vis.mask.on.subject

Visualize a vertex mask on the surface of a subject.
vis.paths

Visualize many paths.
vis.labeldata.on.subject

Visualize a label on the surface of a subject.
vis.paths.along.verts

Visualize several paths in different colors.
vis.rglwidget

Visualize coloredmeshes as an interactive rgl WebGL widget for use in R Shiny apps and RMarkdown documents.
vis.region.values.on.subject

Visualize arbitrary data, one value per atlas region, on the surface of any subject (including template subjects).
vis.subject.morph.standard

Visualize native space morphometry data for a subject or a group.
vis.volume.on.surface

Visualize a brain volume overlaid on a cortical surface in 3D.
vis.seg.legend

Plot legend for a brain volume segmentation based on colorLUT.
vislayout.from.coloredmeshes

Visualize coloredmeshes from several angles and combine the images into a new figure.
vis.subject.annot

Visualize an annotation for a subject.
vis.subject.pre

Visualize pre-loaded data.
vis.subject.label

Visualize a binary label for a subject.
vis.symmetric.data.on.subject

Visualize clusters or activation data on the surface of any subject.
vis.rotated.coloredmeshes

Rotate and visualize coloredmeshes, applying a style.
vis.subject.morph.native

Visualize native space morphometry data for a subject.
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.
vol.intensity.to.color

Convert integer intensity image to RGB color string form.
vol.overlay.colors.from.colortable

Compute voxel colors based on colortable.
vol.imagestack

Turn volume into an ImageMagick image stack.
vol.boundary.mask

Compute foreground pixels over the whole 3D imagestack.
vol.overlay.colors.from.activation

Generate colors for a 3D volume, based on the activation data and a colormap.
vol.hull

Retain only the outer hull voxels of the foreground.
vol.mask.from.segmentation

Extract subset from a volume by value.
vol.merge

Merge background volume and overlay to new colors.
volvis.slices.with.surface

Export individual volume slices with surface contours to image files.
volvis.lightbox

Draw a lightbox view from volume slices.
vol.planes

Translate names and indices of planes.
volvis.lb

Show continuous 3D voxel/volume data as a lightbox, optionally with a background brain volume and colormap.
volvis.contour

Visualize contour of a volume.
vol.vox.from.crs

Compute R voxel index for FreeSurfer CRS voxel index.
volvis.lb.with.surface

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

Extract a slice of a 3D image stack.
volvis.voxels

Voxel-based visualization of volume mask at surface RAS positions.
vol.plane.axes

Get indices of the axes defining the given plane.
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.group.morph.standard.singlehemi

Write single hemi per-vertex 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.
vox2ras_tkr

The FreeSurfer default vox2ras_tkr matrix.
write.region.values.fsaverage

Write one value per atlas region for a template subject.
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.
wrapped.image.append

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