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fsbrain (version 0.8.0)

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

0.8.0

License

MIT + file LICENSE

Issues

2

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77

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15

Maintainer

Tim Schc3<a4>fer

Last Published

September 14th, 2026

Functions in fsbrain (0.8.0)

clip.data

Clip data at quantiles to remove outliers.
clip_fun

Get data clipping function.
check.subjects.files

Report subjects missing files
cm.div

Return the standard fsbrain diverging colormap.
cm.seq

Return the standard fsbrain sequential colormap.
collayer.from.mask.data

Compute surface color layer from morph-like data.
collayer.from.annotdata

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

Compute atlas or annotation surface color layer.
collayer.bg.sulc

Compute binarized sulcal depth surface color layer.
collayer.bg.meancurv

Compute binarized mean curvature surface color layer.
check.subjectslist

Check whether the subjects_list looks good, warn if not.
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.
coloredmesh.from.morph.standard

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

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

Create a coloredmesh from a label.
coloredmesh.from.annot

Create a coloredmesh from an annotation of an atlas.
coloredmesh.from.morph.native

Create a coloredmesh from native space morphometry data.
combine.colorbar.with.brainview.animation

Combine a colorbar and a brain animation in gif format into a new animation.
coloredmesh.from.mask

Create a coloredmesh from a mask.
coloredmesh.from.morphdata

Create a coloredmesh from arbitrary data.
collayer.bg

Compute binarized mean curvature surface color layer.
color_to_rgba

Convert an R color to an RGBA float vector
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.image

Combine a colorbar and a brainview image into a new figure.
colors.are.grayscale

Check for the given color strings whether they represent gray scale colors.
collayer.from.annot

Compute surface color layer from annotation or atlas 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.
coloredmeshes.combined.data.range

Retrieve combined data range from hemilist of coloredmeshes.
demo

Show demo visualization to test whether fsbrain is setup correctly.
compute.surface.contour.slices

Compute surface contour slice images (internal).
delete_all_optional_data

Delete all data in the package cache.
constant.pervertexdata

Get vertex data for a single fs.surface or a hemilist of surfaces.
colorlist.brain.clusters

Return diverging color list
coloredmeshes.get.md

Retrieve metadata from hemilist of coloredmeshes.
cube3D.tris

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

Combine a vertical colorbar and a brainview image into a new figure.
coloredmeshes_to_scimesh

Convert a hemilist of fs.coloredmeshes to a list of scimesh mesh descriptors
coloredmesh_to_scimesh

Convert a single fs.coloredmesh to a scimesh mesh descriptor
download_fs_LR_32_atlases

Download atlas files for the fs_LR 32k template.
demographics.to.fsgd.file

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

Perform simple desaturation or grayscale conversion of RGBA colors.
demographics.to.qdec.table.dat

Convert a dataframe containing demographics data to a qdec.table.dat file and related files.
export.coloredmesh.ply

Export a coloredmeshes with vertexcolors in PLY format.
common.makecmap.range

Get cmap and colorlayer from data and makecmap_options.
draw.colorbar

Draw colorbar into background of current plot.
download_fsaverage_minimal

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

Export high-quality brainview image with a colorbar.
cubes3D.tris

Vectorized version of cube3D.tris
download_fsaverage6

Download the FreeSurfer v6 fsaverage6 subject.
download_optional_data

Download optional data for this package if required.
download_fsaverage3

Download the FreeSurfer v6 low-resolution fsaverage3 subject.
download_optional_paper_data

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

fs.coloredmesh constructor
fs.surface.vertex.neighbors

Compute vertex neighborhoods or the full adjacency list for a mesh using the Rvcg or igraph library.
fs.home

Return FreeSurfer path.
find.subjectsdir.of

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

Download atlas files for the fsaverage template subject.
deepcopylist.long

Write deepcopy list for longitudinal subjects.
extract.volume.3D

Try to extract a 3D volume from the input argument.
fs.value.list.from.agg.res

Create a named value list from a dataframe.
draw.segments.on.image

Draw contour segments onto a magick image.
deg2rad

Convert degree to radians
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.
force.to.range

Change data to ensure requested data_range.
fsbrain_style_to_scimesh_options

Map an fsbrain rendering style to scimesh render options
eeg_coords

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

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

Download the FreeSurfer v6 fsaverage subject.
download_fs_LR_32_meshes

Download surface meshes for the fs_LR 32k template.
extend_neighbors

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

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

Return path to fsaverage dir.
fs.surface.as.adjacencylist

Turn surface mesh into a igraph and return its adjacency list representation.
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.vert.neighborhood

Compute all vertices within given geodesic distance on the mesh.
geod.patches.color.overlay.singlehemi

Generate color overlay from geodesic patches around several vertices for a single hemi.
fsbrain.renderable

Check whether object can be rendered by fsbrain
geod.patches.color.overlay

Generate color overlay from geodesic patches around several vertices.
geodesic.dists.to.vertex

Simple internal wrapper around Rvcg::vcgDijkstra with function check.
filter_scene_by_view

Filter a scimesh scene to the meshes visible from a given view
geodesic.average.distance

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

Compute geodesic path from a source vertex to one or more target vertices.
fsbrain.set.default.figsize

Set default figure size for fsbrain visualization functions.
geod.patches.pervertexdata

Generate per-vertex distance data from geodesic patches around several vertices.
face.edges

Enumerate all edges of the given faces or mesh.
get.fsbrain.renderer.backend

Get the current fsbrain renderer backend
get.atlas.region.names

Determine atlas region names from a subject.
get.rglstyle.shiny

Get a shiny visualization style.
find.freesurferhome

Find the FREESURFER_HOME directory on disk.
get.rglstyle

Get the default visualization style parameters as a named list.
fs.surface.to.tmesh3d

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

Create igraph undirected graph from a brain surface mesh.
geod.patches.pervertexdata.singlehemi

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

Get subject names from sub directories of FreeSurfer long directory.
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
get.rglstyle.default

Get the default visualization style parameters as a named list.
geodesic.ballstats

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

Compute geodesic circles and ball stats for given vertices.
get.rglstyle.glass

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

Compute slice indices from slice definition.
group.agg.atlas.standard

Aggregate standard space morphometry data over brain atlas regions and subjects for a group of subjects.
group.agg.atlas.native

Aggregate native space morphometry data over brain atlas regions and subjects for a group of subjects.
get.rglstyle.glass2

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

Construct FSGD Class name from group and non-continuous covariate columns.
get.view.angle.names

Get list of valid view angle names.
group.annot

Load annotations for a group of subjects.
group.morph.native

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

Aggregate standard space morphometry data over subjects.
get_optional_data_filepath

Access a single file from the package cache by its file name.
getIn

Retrieve values from nested named lists
group.concat.measures.standard

Concatenate standard space data for a group of subjects.
get.rglstyle.semitransparent

Get the semi-transparent visualization style parameters as a named list.
group.data.to.array

Convert group 2D data (1 vector per subject) to 4D array format.
get.rglstyle.edges

Get the mesh edges visualization style parameters as a named list.
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.standard.sf

Read combined data for a group from a single file.
groupmorph.split.hemilist

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

Retrieve standard space morphometry data for a group of subjects.
get.rglstyle.parameters

Produce the named list of style parameters from style definition.
group.surface

Retrieve surface mesh data for a group of subjects.
group.concat.measures.native

Concatenate native space data for a group of subjects.
highlight.points.spheres

Draw small 3D spheres at given points.
hemilist

Create a hemilist from lh and rh data.
hemi.lobe.labels

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

Convert a vector of hex colors to an Nx4 RGBA float matrix
group.multimorph.agg.standard

Aggregate standard space (fsaverage) morphometry data for multiple measures over hemispheres for a group of subjects.
group.multimorph.agg.native

Aggregate native space morphometry data for multiple measures over hemispheres for a group of subjects.
hex_to_rgba

Convert hex color string to RGBA float vector
group.morph.agg.standard

Aggregate standard space (fsaverage) morphometry data over one hemisphere for a group of subjects.
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.
handle.rglactions.highlight.points

Highlight requested points (if any), for camera-based views.
hemilist.get.combined.data

Get combined data of hemi list
hasIn

Check for values in nested named lists
hemilist.derive.hemi

Derive 'hemi' string from the data in a hemilist
group.morph.agg.native

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

Wrap data into a named hemi list.
hemlist.ensure.contains

title Ensure an key for a hemilist exists.
highlight_points_to_scimesh

Convert highlight points (rglactions) to scimesh sphere meshes
hull.retain.along.axis

Copy the first n foreground voxel values.
images.annotate

Annotate image with text.
images.same.height

Extent all images to the height of the image with maximal height.
images.same.width

Extent all images to the width of the image with maximal width.
images.rescale.to.max.canvas

Rescale all images canvas to match the largest one.
is.fs.coloredmesh

Check whether object is an fs.coloredmesh (S3)
highlight.vertices.on.subject.spheres

Highlight vertices given by index on a subject's meshes by coloring faces.
is.fs.coloredvoxels

Check whether object is an fs.coloredvoxels instance (S3)
highlight.vertices.spheres

Draw small 3D spheres at given brain mesh vertices. Supports full brain (2 meshes) as well.
label.from.annotdata

Extract a region from an annotation as a label.
label.to.annot

Merge several labels into an annotation
highlight.vertices.on.subject

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

A simple colormap function for binary colors.
label.colFn.inv

A simple colormap function for binary colors.
images.dimmax

Compute max width and height of magick images.
mesh.ras2crs

Transform surface vertices from surface RAS to 0-based volume CRS space.
mask.from.labeldata.for.hemi

Create a binary mask from labels.
mergehemi.annots

Merge the annotations from two hemispheres into one annot.
mesh.slice.intersection

Compute intersection of a triangular surface mesh with an axis-aligned plane.
is.Triangles3D

Check whether object is a Triangles3D instance
mkco.heat

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

Check whether object is an fsbrain (S3)
is.hemilist

Check whether x is a hemilist
mesh.vertex.neighbors

Compute neighborhood of a vertex
magick.grid

Arrange a multi-frame ImageMagick image into a grid.
mesh.vertex.included.faces

Return all faces which are made up completely of the listed vertices.
mkco.div

Return recommended 'makecmap_options' for diverging data.
limit_fun_na_inside

Get data limiting function, setting values inside range to NA.
label.border

Compute border of a label.
limit_fun_na

Get data limiting function to NA.
mkco.cluster

Return recommended 'makecmap_options' for diverging cluster data.
labeldata.from.mask

Create labeldata from a mask.
principal.curvatures

Computes principal curvatures according to 2 definitions from raw k1 and k2 values.
numverts.lh

Determine vertex count of left hemi from hemilist of surfaces or the count itself.
pervertexdata.smoothnn.compute.fwhm

Compute expected FWHM from given number of neighborhood smoothing iterations.
label.border.fast

Compute border vertices of a label using Rvcg.
pervertexdata.smoothnn.compute.numiter

Compute number of neighborhood smoothing iterations to reach requested fwhm.
qc.from.segstats.tables

Perform data quality check based on a segstats table.
pp.named.list

Pretty-print a named list or vector.
normalize

Normalize data.
numverts.rh

Determine vertex count of right hemi from hemilist of surfaces or the count itself.
print.fs.coloredmesh

Print description of a brain coloredmesh (S3).
limit_fun

Get data limiting function.
print.fs.coloredvoxels

Print description of fs.coloredvoxels (S3).
qc.fslong.checkidenticaldata

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

Perform rglactions, like taking screenshots.
perform.na.mapping

Perform NA mapping for transparency
per.hemi.vertex.indices

Transform surfaces indices which go over two surfaces to per-hemi indices.
path.slopes

Compute slopes of paths relative to axes.
qc.vis.failcount.by.region

Visualize the number of outlier subjects per region in your dataset.
qc.from.regionwise.df

Perform data quality check based on a dataframe containing aggregated region-wise data.
path.colors.from.orientation

Compute path color from its orientation.
qc.report.html

Create visual quality check report from QC result.
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.
rglactions.transform

Apply data transformation rglactions.
recycle

Recycle parameters or whatever.
ras2vox_tkr

The FreeSurfer default ras2vox_tkr matrix.
rad2deg

Convert raduians to degree
read.colorcsv

Read colors from CSV file.
read.md.subjects

Read subjects file
read.md.demographics

Read demographics file
rotation.matrix

Build a 4x4 rotation matrix (Rodrigues formula).
rglot

Get rgloptions for testing.
qdec.table.skeleton

Generate skeleton dataframe for FreeSurfer QDEC long file from subjects list.
sjd.demo

Download optional demo data if needed and return its path.
rglvoxels

Draw 3D boxes at locations using rgl.
report.on.demographics

Print a demographics report
qc.from.segstats.table

Perform data quality check based on a segstats table.
qdec.table.filter

Filter QDEC long table for subjects.
shape.descriptor.names

Get all shape descriptor names.
shift.hemis.apart

Shift hemispheres apart.
subject.annot.border

Compute annot border vertices.
shift.hemis.rglactions

Shift hemis apart if indicated in rglactions
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.
scale01

Scale given values to range 0..1.
spread.values.over.annot

Spread a single value for a region to all region vertices.
subject.descriptor.geodesic.average.distance

Compute mean geodesic distance descriptor for a subject.
rgl.coord.lines

Plot x, y and z axes in R,G,B.
subject.filepath.any

Construct filepath of any freesurfer file.
mkco.seq

Return recommended 'makecmap_options' for sequential 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.
list_optional_data

Get file names available in package cache.
subject.num.verts

Get subjects vertex count.
subject.label

Retrieve label data for a single subject.
shape.descriptors

Computes geometric curvature-based descriptors.
safe.image.trim

Safe wrapper around magick::image_trim that handles blank images.
subject.annot

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

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

Create rglactions list, suitable to be passed as parameter to vis functions.
print.fsbrain

Print description of an fsbrain (S3).
subject.surface

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

Create visual quality check report from QC result.
rotation.matrix.for.axis.rot

Get rotation matrix for a 3D rotation around an axis.
sortcoloredmeshes.by.hemi

Sort coloredmeshes into 2 lists by their 'hemi' property.
pervertexdata.smoothgaussian

Perform Gaussian smoothing
pervertexdata.smoothnn

Perform iterative nearest-neighbor smoothing of per-vertex data.
subject.atlas.agg

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

Compute a mask for a subject.
surf.sphere.spatialfilter

Apply spatial filter to surface data.
surf.radius.fsaverage

Get pre-computed radius for fsaverage white surface.
surf.sphere.gaussianweights

Compute Gaussian weights
surf.sphere.dist

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

Get pre-computed center for fsaverage white surface.
surf.avg.vertexradius

Compute average distance from the origin to each vertex.
submesh.vertex

Create a submesh including only the given vertices.
subject.volume

Read a brain volume.
tmesh3d.to.fs.surface

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

Return the proper hemi string ('lh' or 'rh') for each vertex.
vertex.coords

Return coordinates for vertices, supporting entire brain via hemilist.
qc.for.group

Perform data quality check based on computed region stats.
test.numerical.meandiff.unpaired

Perform tests for group differences on unpaired data for two groups.
surface.curvatures

Compute the k1 and k2 principal curvatures of a mesh.
surf.metric.properties

Compute metric surface properties.
track.length

Compute the total length of a path given by the coordinates of its points.
rglactions.has.key

Check for a key in names of rglactions.
subject.filepath.morph.native

Construct filepath of native space morphometry data file.
vis.coloredmesh

Draw a coloredmesh using a style.
test.numerical.meandiff

Perform tests for group differences on paired or 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.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.group.native

Visualize native space data on a group of subjects.
vis.data.on.fsaverage

Visualize arbitrary data on the fsaverage template subject, if available.
sph2fs

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

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

Take screenshot of rgl scene, with fallback for systems without X11.
vdata.split.by.hemi

Split morph data vector at hemisphere boundary.
vis.dti.trk

Visualize DTI tracks from Diffusion Toolkit/TrackVis TRK format file.
view.angle.to.hemi.filter

Get the hemisphere filter for a view angle
view_angle_to_scimesh_camera

Map an fsbrain view angle to a scimesh camera
vis.export.from.coloredmeshes

Export high-quality brainview image with a colorbar.
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.coloredmeshes

Visualize a list of colored meshes in a single scene.
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.mask.on.subject

Visualize a vertex mask on the surface of a subject.
vis.seg.legend

Plot legend for a brain volume segmentation based on colorLUT.
vis.fs.surface

Visualize fs.surface mesh
vis.group.annot

Plot atlas annotations for a group of subjects.
vis.renderable

Visualize a renderable object
vis.region.values.on.subject

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

Retrieve standard space morphometry data for a single subject.
vis.group.morph.standard

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

Visualize several paths in different colors.
vis.paths

Visualize many paths.
vis.labeldata.on.subject

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

Retrieve native space morphometry data for a single subject.
vis.subject.annot

Visualize an annotation for a subject.
vis.color.on.subject

Visualize pre-defined vertex colors on a subject.
subject.filepath.morph.standard

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

Visualize coloredmeshes as an interactive rgl WebGL widget for use in R Shiny apps and RMarkdown documents.
surfs.props

Compute simple version of center and radius of 2 meshes.
view_label3d

Draw a view label at a position, compensating for the camera rotation.
vis.path.along.verts

Draw a 3D line from vertex to vertex
vis.subject.morph.standard

Visualize native space morphometry data for a subject or a group.
vol.boundary.box.apply

Apply a boundary box to a volume, returning the inner volume part
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.
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.subject.morph.native

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

Visualize pre-loaded data.
vis.rotated.coloredmeshes

Rotate and visualize coloredmeshes, applying a style.
vis.view

Render renderables for a static view and orient the camera (camera-based).
vis.volume.on.surface

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

Merge background volume and overlay to new colors.
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.mask.from.segmentation

Extract subset from a volume by value.
vol.plane.axes

Get indices of the axes defining the given plane.
vol.planes

Translate names and indices of planes.
vol.imagestack

Turn volume into an ImageMagick image stack.
volvis.contour

Visualize contour of a volume.
wrapped.image.append

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

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

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

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

Voxel-based visualization of volume mask at surface RAS positions.
vox2ras_tkr

The FreeSurfer default vox2ras_tkr matrix.
volvis.lightbox

Draw a lightbox view from volume slices.
volvis.slices.with.surface

Export individual volume slices with surface contours to image files.
vol.slice

Extract a slice of a 3D image stack.
write.group.morph.standard.sf

Reshape and write combined per-vertex data for a group to a single MGH file.
write.region.values

Write one value per atlas region for a subject.
write.group.morph.standard.mf

Write per-vertex standard space data for a group of subjects to given file names.
write.region.values.fsaverage

Write one value per atlas region for a template 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

Write standard space group data to a standard FreeSurfer directory stucture.
write.region.aggregated

Write data aggregated over regions to morphometry file for group.
Triangles3D.to.coloredmesh

Convert a misc3d Triangles3D iso-surface to a coloredmesh.
agg.res.long.to.wide

Reshape aggregated region data from long to wide format.
apply.transform

Apply matmult transformation to input.
arrange.brainview.images

Combine several brainview images into a new figure.
apply.label.to.morphdata

Load a label from file and apply it to morphometry data.
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.labeldata.to.morphdata

Apply a label to morphometry data.
apply.style.alpha

Extract the alpha value from resolved style parameters
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.
brainview.sr

Visualize a list of colored meshes, rotating the camera around them.
brainview.t9

Visualize a list of colored meshes from nine angles.
bounding_sphere

Compute the bounding sphere of a set of 3D vertices.
brain

Create fsbrain instance from 2 coloredmeshes.
brainview.t4

Visualize a list of colored meshes from four angles.
boxcoords.from.bbox

Compute the coordinates of the 8 corners of a 3D box.
cm.cbry

Get cyan blue red yellow colormap function.
cm.qual

Return the standard fsbrain qualitative colormap.
cm.heat

Return the standard fsbrain heat colormap.
can.plot.colorbar.from.coloredmeshes

Determine whether colorbar can be plotted with given coloredmeshes.
brainview.sd

Visualize a list of colored meshes from a single defined angle.
brainview.si

Visualize a list of colored meshes from a single viewpoint, interactively.
can.plot.colorbar

Determine whether colorbar can be plotted with given metadata.