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fsbrain (version 0.2.1)

Managing and Visualizing Brain Surface Data

Description

Provides high-level access to 'FreeSurfer' neuroimaging data 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 results directly in 'R'.

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install.packages('fsbrain')

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446

Version

0.2.1

License

MIT + file LICENSE

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Repository

https://github.com/dfsp-spirit/fsbrain

Maintainer

Tim Schc3<a4>fer

Last Published

May 27th, 2020

Functions in fsbrain (0.2.1)

apply.labeldata.to.morphdata

Apply a label to morphometry data.

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

Perform alpha blending for pairs of RGBA colors.

Compute outline vertex colors from annotation.

apply.transform

Apply matmult transformation to input.

apply.label.to.morphdata

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

arrange.brainview.images

Combine several brainview images into a new figure.

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

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

boxcoords.from.bbox

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

collayer.from.annotdata

Compute surface color layer from annotation or atlas data.

Clip data at quantiles to remove outliers.

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

Return the standard fsbrain diverging colormap.

Return the standard fsbrain qualitative colormap.

Return the standard fsbrain heat colormap.

collayer.bg.atlas

Compute atlas or annotation surface color layer.

Perform simple desaturation or grayscale conversion of RGBA colors.

collayer.bg.meancurv

Compute binarized mean curvature surface color layer.

download_fsaverage

Download the FreeSurfer v6 fsaverage subject.

can.plot.colorbar

Determine whether colorbar can be plotted with given metadata.

collayer.from.mask.data

Compute surface color layer from morph-like data.

Return the standard fsbrain sequential colormap.

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.

Visualize a list of colored meshes from four angles.

Compute binarized mean curvature surface color layer.

coloredmeshes.combined.data.range

Retrieve combined data range from hemilist of coloredmeshes.

coloredmeshes.from.color

Create coloredmeshes for both hemis using pre-defined colors.

Flip a 2D matrix.

coloredmesh.from.annot

Create a coloredmesh from an annotation of an atlas.

coloredmeshes.get.md

Retrieve metadata from hemilist of coloredmeshes.

coloredmesh.from.morphdata

Create a coloredmesh from arbitrary data.

coloredmesh.plot.colorbar.separate

Draw colorbar for coloredmeshes in separate 2D plot.

Return triangles for a 3D cube or cuboid.

fs.coloredmesh constructor

combine.colorbar.with.brainview.image.vertical

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

coloredmesh.from.color

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

Transform first character of a string to uppercase.

get.atlas.region.names

Determine atlas region names from a subject.

fs.value.list.from.agg.res

Create a named value list from a dataframe.

combine.colorbar.with.brainview.image

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

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.

fsbrain.renderable

Check whether object can be rendered by fsbrain

export.coloredmesh.ply

Export a coloredmeshes with vertexcolors in PLY format.

group.concat.measures.native

Concatenate native space data for a group of subjects.

Get the default visualization style parameters as a named list.

coloredmesh.from.mask

Create a coloredmesh from a mask.

download_optional_data

Download optional data for this package if required.

coloredmesh.from.label

Create a coloredmesh from a label.

get.rglstyle.parameters

Produce the named list of style parameters from style definition.

Draw coloredbar into background of current plot.

collayer.bg.sulc

Compute binarized sulcal depth surface color layer.

get.rglstyle.semitransparent

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

find.freesurferhome

Find the FREESURFER_HOME directory on disk.

find.subjectsdir.of

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

group.agg.atlas.standard

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

coloredmesh.from.morph.native

Create a coloredmesh from native space morphometry data.

collayer.from.annot

Compute surface color layer from annotation or atlas data.

get.rglstyle.default

Get the default visualization style parameters as a named list.

group.concat.measures.standard

Concatenate standard space data for a group of subjects.

Load annotations for a group of subjects.

Compute border of a label.

Check whether x is a hemilist

Visualize a list of colored meshes from nine angles.

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.

mesh.vertex.included.faces

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

get.rglstyle.shiny

Get a shiny visualization style.

mesh.vertex.neighbors

Compute neighborhood of a vertex

coloredmesh.from.morph.standard

Create a coloredmesh from standard space morphometry data.

Retrieve label data for a group of subjects.

labeldata.from.mask

Create labeldata from a mask.

plot.fsbrain.colorbar

Draw a simple colorbar from colors.

Vectorized version of cube3D.tris

group.morph.native

Retrieve native space morphometry data for a group of subjects.

get.slice.indices

Compute slice indices from slice definition.

Enumerate all edges of the given faces or mesh.

Draw 3D boxes at locations using rgl.

print.fs.coloredmesh

Print description of a brain coloredmesh (S3).

group.label.from.annot

Extract a region from an atlas annotation as a label for a group of subjects.

get_optional_data_filepath

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

delete_all_optional_data

Delete all data in the package cache.

group.morph.standard

Retrieve standard space morphometry data for a group of subjects.

hemilist.derive.hemi

Derive 'hemi' string from the data in a hemilist

group.agg.atlas.native

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

Rotate a 2D matrix in 90 degree steps.

Retrieve values from nested named lists

hemi.lobe.labels

Compute lobe labels for a single hemi from aparc atlas.

Check for values in nested named lists

get.view.angle.names

Get list of valid view angle names.

A simple colormap function for binary colors.

label.colFn.inv

A simple colormap function for binary colors.

subject.surface

Load a surface for a subject.

group.morph.agg.native

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

Read a brain volume.

vis.rotated.coloredmeshes

Rotate and visualize coloredmeshes, applying a style.

hemilist.get.combined.data

Get combined data of hemi list

list_optional_data

Get file names available in package cache.

mask.from.labeldata.for.hemi

Create a binary mask from labels.

Check whether object is a Triangles3D instance

is.fs.coloredmesh

Check whether object is an fs.coloredmesh (S3)

group.morph.agg.standard

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

is.fs.coloredvoxels

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

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

Return recommended 'makecmap_options' for diverging data.

hull.retain.along.axis

Copy the first *n* foreground voxel values.

merge.hemi.annots

Merge the annotations from two hemispheres into one annot.

hemilist.unwrap

Unwrap hemi data from a named hemi list.

Rotate 2D matrix clockwise in 90 degree steps.

vis.subject.annot

Visualize an annotation for a subject.

Translate names and indices of planes.

Extract a slice of a 3D image stack.

The FreeSurfer default ras2vox_tkr matrix.

subject.atlas.agg

Aggregate morphometry data over brain atlas regions for a subject.

sort.coloredmeshes.by.hemi

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

Read colors from CSV file.

Wrap data into a named hemi list.

subject.filepath.any

Construct filepath of any freesurfer file.

label.from.annotdata

Extract a region from an annotation as a label.

Arrange a multi-frame ImageMagick image into a grid.

vis.color.on.subject

Visualize pre-defined vertex colors on a subject.

subject.label.from.annot

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

Retrieve label data for a single subject.

perform.na.mapping

Perform NA mapping for transparency

perform.rglactions

Perform rglactions, like taking screenshots.

vis.coloredmesh

Draw a coloredmesh using a style.

readable.volume

Find files with the given base name and extensions that exist.

subject.morph.native

Retrieve native space morphometry data for a single subject.

vol.intensity.to.color

Convert integer intensity image to RGB color string form.

vol.mask.from.segmentation

Extract subset from a volume by value.

vis.colortable.legend

Create a separate legend plot for a colortable or an annotation.

subject.morph.standard

Retrieve standard space morphometry data for a single subject.

vis.subject.morph.standard

Visualize native space morphometry data for a subject.

vis.data.on.fsaverage

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

vis.symmetric.data.on.subject

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

Retain only the outer hull voxels of the foreground.

makecmakeopts.merge

Create final `makecmap_options` list

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.

Turn volume into an ImageMagick image stack.

Merge several labels into an annotation

Load labels representing brain lobes.

Load an annotation for a subject.

spread.values.over.subject

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

regions.to.ignore

Give suggestions for regions to ignore for an atlas.

Compute a mask for a subject.

volvis.lightbox

Draw a lightbox view from volume slices.

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

vis.mask.on.subject

Visualize a vertex mask on the surface of a subject.

Return recommended 'makecmap_options' for sequential data.

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).

print.fs.coloredvoxels

Print description of fs.coloredvoxels (S3).

Normalize data.

vol.overlay.colors.from.colortable

Compute voxel colors based on colortable.

Visualize a renderable object

qc.from.segstats.table

Perform data quality check based on a segstats table.

read.md.subjects

Read subjects file

read.md.demographics

Read demographics file

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.

Get rgl_options for testing.

rglactions.transform

Apply data transformation rglactions.

subject.filepath.morph.standard

Construct filepath of standard space morphometry data file.

report.on.demographics

Print a demographics report

subject.filepath.morph.native

Construct filepath of native space morphometry data file.

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.

Get indices of the axes defining the given plane.

rglactions.has.key

Check for a key in names of rglactions.

Visualize contour of a volume.

vol.vox.from.crs

Compute R voxel index for FreeSurfer CRS voxel index.

vis.data.on.subject

Visualize arbitrary data on the surface of any subject.

vis.subject.label

Visualize a binary label for a subject.

vis.labeldata.on.subject

Visualize a label on the surface of a subject.

Merge background volume and overlay to new colors.

vis.subject.morph.native

Visualize native space morphometry data for a subject.

vol.overlay.colors.from.activation

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

Given data, compute symmetric range around zero.

The FreeSurfer default vox2ras_tkr matrix.

write.region.aggregated

Write data aggregated over regions to morphometry file for group.

test.numerical.meandiff

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

vis.coloredmeshes

Visualize a list of colored meshes in a single scene.

vis.coloredmeshes.rotating

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

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.boundary.mask

Compute foreground pixels over the whole 3D imagestack.