Managing and Visualizing Brain Surface Data

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Documentation for package ‘fsbrain’ version 0.1.0

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A B C D F G H I L M P R S V W

-- A --

alphablend Perform alpha blending for pairs of RGBA colors.
annot.outline Compute outline vertex colors from annotation.
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.

-- B --

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

-- C --

clip.data Clip data at quantiles to remove outliers.
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.mask Create a coloredmesh from a mask.
coloredmesh.from.morph.native Create a coloredmesh from native space morphometry 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
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.
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.
desaturate Perform simple desaturation or grayscale conversion of RGBA colors.
download_fsaverage Download the FreeSurfer v6 fsaverage subject.
download_optional_data Download optional data for this package if required.

-- 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.
flip3D Flip a 3D array along an axis.
fs.coloredmesh fs.coloredmesh constructor
fup Transform first character of a string to uppercase.

-- G --

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

-- H --

hasIn Check for values in nested named lists
hemilist.derive.hemi Derive 'hemi' string from the data in a hemilist
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.

-- I --

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

-- L --

label.border Compute border of a label.
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.
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

-- P --

print.fs.coloredmesh Print description of a brain coloredmesh (S3).
print.fs.coloredvoxels Print description of fs.coloredvoxels (S3).

-- 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
regions.to.ignore Give suggestions for regions to ignore for an atlas.
report.on.demographics Print a demographics report
rglvoxels Draw 3D boxes at locations using rgl.
rotate3D Rotate a 3D array in 90 degree steps.

-- S --

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.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.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.surface Load a surface for a subject.
subject.volume Read a brain volume.

-- V --

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.data.on.fsaverage Visualize arbitrary data on the fsaverage template subject, if available.
vis.data.on.subject Visualize arbitrary data on the surface of any subject.
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.region.values.on.subject Visualize arbitrary data, one value per atlas region, on the surface of any subject (including template subjects).
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.
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.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.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.