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fsbrain (version 0.4.2)

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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465

Version

0.4.2

License

MIT + file LICENSE

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Repository

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

Maintainer

Tim Schc3<a4>fer

Last Published

March 28th, 2021

Functions in fsbrain (0.4.2)

arrange.brainview.images

Combine several brainview images into a new figure.

apply.transform

Apply matmult transformation to input.

boxcoords.from.bbox

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

arrange.brainview.images.grid

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

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.

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

Perform alpha blending for pairs of RGBA colors.

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

can.plot.colorbar

Determine whether colorbar can be plotted with given metadata.

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

Get cyan blue red yellow colormap function.

Visualize a list of colored meshes from four angles.

Compute outline vertex colors from annotation.

Return the standard fsbrain sequential colormap.

Compute binarized mean curvature surface color layer.

can.plot.colorbar.from.coloredmeshes

Determine whether colorbar can be plotted with given coloredmeshes.

Return the standard fsbrain diverging colormap.

coloredmesh.from.label

Create a coloredmesh from a label.

Return the standard fsbrain heat colormap.

Return the standard fsbrain qualitative colormap.

coloredmesh.from.mask

Create a coloredmesh from a mask.

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.sulc

Compute binarized sulcal depth surface color layer.

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

Visualize a list of colored meshes from nine angles.

collayer.bg.atlas

Compute atlas or annotation surface color layer.

check.subjectslist

Check whether the subjects_list looks good, warn if not.

Clip data at quantiles to remove outliers.

collayer.from.annot

Compute surface color layer from annotation or atlas data.

coloredmesh.from.morphdata

Create a coloredmesh from arbitrary data.

coloredmesh.from.annot

Create a coloredmesh from an annotation of an atlas.

coloredmesh.from.morph.native

Create a coloredmesh from native space morphometry data.

coloredmesh.from.color

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

collayer.bg.meancurv

Compute binarized mean curvature surface color layer.

coloredmesh.from.morph.standard

Create a coloredmesh from standard space morphometry data.

get.rglstyle.edges

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

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.

delete_all_optional_data

Delete all data in the package cache.

get.rglstyle.parameters

Produce the named list of style parameters from style definition.

coloredmesh.plot.colorbar.separate

Draw colorbar for coloredmeshes in separate 2D plot.

coloredmeshes.from.color

Create coloredmeshes for both hemis using pre-defined colors.

download_fsaverage

Download the FreeSurfer v6 fsaverage subject.

Perform simple desaturation or grayscale conversion of RGBA colors.

coloredmeshes.get.md

Retrieve metadata from hemilist of coloredmeshes.

collayer.from.morphlike.data

Compute surface color layer from morph-like data.

Enumerate all edges of the given faces or mesh.

demographics.to.fsgd.file

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

Change data to ensure requested data_range.

coloredmesh.from.preloaded.data

Generate coloredmesh from loaded data.

get.slice.indices

Compute slice indices from slice definition.

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.

get.subject.class

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

coloredmeshes.combined.data.range

Retrieve combined data range from hemilist of coloredmeshes.

collayers.merge

Merge two or more color layers based on their transparency values.

hemilist.derive.hemi

Derive 'hemi' string from the data in a hemilist

hemilist.get.combined.data

Get combined data of hemi list

find.freesurferhome

Find the FREESURFER_HOME directory on disk.

group.agg.atlas.native

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

get_optional_data_filepath

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

is.fs.coloredmesh

Check whether object is an fs.coloredmesh (S3)

Transform first character of a string to uppercase.

fsbrain.set.default.figsize

Set default figure size for fsbrain visualization functions.

fs.coloredmesh constructor

combine.colorbar.with.brainview.image

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

Convert degree to radians

Return triangles for a 3D cube or cuboid.

Vectorized version of cube3D.tris

Return FreeSurfer path.

is.fs.coloredvoxels

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

common.makecmap.range

Get cmap and colorlayer from data and makecmap_options.

group.label.from.annot

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

hemilist.unwrap

Unwrap hemi data from a named hemi list.

get.rglstyle.semitransparent

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

get.rglstyle.shiny

Get a shiny visualization style.

labeldata.from.mask

Create labeldata from a mask.

Get data limiting function.

Return recommended 'makecmap_options' for sequential data.

Normalize data.

read.md.subjects

Read subjects file

read.md.subjects.from.fsgd

Read subjects list from an FSGD file.

group.morph.agg.native

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

Wrap data into a named hemi list.

hull.retain.along.axis

Copy the first *n* foreground voxel values.

group.multimorph.agg.standard

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

Get the default visualization style parameters as a named list.

group.data.to.array

Convert group 1D data to array format.

get.rglstyle.default

Get the default visualization style parameters as a named list.

fs.value.list.from.agg.res

Create a named value list from a dataframe.

spread.values.over.annot

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

Get data limiting function to NA.

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

Retrieve label data for a group of subjects.

download_optional_paper_data

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

limit_fun_na_inside

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

images.annotate

Annotate image with text.

combine.colorbar.with.brainview.image.vertical

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

Retrieve surface mesh data for a group of subjects.

images.rescale.to.max.canvas

Rescale all images canvas to match the largest one.

Draw coloredbar into background of current plot.

path.colors.from.orientation

Compute path color from its orientation.

mask.from.labeldata.for.hemi

Create a binary mask from labels.

plot.fsbrain.colorbar

Draw a simple colorbar from colors.

makecmakeopts.merge

Create final `makecmap_options` list

Check whether object is a Triangles3D instance

Pretty-print a named list or vector.

report.on.demographics

Print a demographics report

vis.coloredmeshes

Visualize a list of colored meshes in a single scene.

vis.group.morph.standard

Plot standard space morphometry data for a group of subjects.

rgl.coord.lines

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

vis.coloredmesh

Draw a coloredmesh using a style.

download_fsaverage3

Download the FreeSurfer v6 low-resolution fsaverage3 subject.

print.fs.coloredvoxels

Print description of fs.coloredvoxels (S3).

Compute slopes of paths relative to axes.

Perform data quality check based on computed region stats.

Recycle parameters or whatever.

vis.labeldata.on.subject

Visualize a label on the surface of a subject.

spread.values.over.subject

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

subject.filepath.morph.standard

Construct filepath of standard space morphometry data file.

spread.values.over.hemi

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

Retrieve label data for a single subject.

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

Compute simple version of center and radius of 2 meshes.

regions.to.ignore

Give suggestions for regions to ignore for an atlas.

vis.subject.annot

Visualize an annotation for a subject.

shift.hemis.apart

Shift hemispheres apart.

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

shape.descriptors

Computes geometric curvature-based descriptors.

rglactions.has.key

Check for a key in names of rglactions.

vis.coloredmeshes.rotating

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

Given data, compute symmetric range around zero.

subject.label.from.annot

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

vis.subject.label

Visualize a binary label for a subject.

export.coloredmesh.ply

Export a coloredmeshes with vertexcolors in PLY format.

fsbrain.renderable

Check whether object can be rendered by fsbrain

Return path to fsaverage dir.

Load annotations 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.morph.native

Retrieve native space morphometry data for a group of subjects.

Check for values in nested named lists

group.morph.standard

Retrieve standard space morphometry data for a group of subjects.

hemi.lobe.labels

Compute lobe labels for a single hemi from aparc atlas.

Get indices of the axes defining the given plane.

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).

find.subjectsdir.of

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

download_optional_data

Download optional data for this package if required.

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

Visualize many paths.

vis.colortable.legend

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

label.colFn.inv

A simple colormap function for binary colors.

A simple colormap function for binary colors.

Load labels representing brain lobes.

get.atlas.region.names

Determine atlas region names from a subject.

label.from.annotdata

Extract a region from an annotation as a label.

test.numerical.meandiff

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

vis.region.values.on.subject

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

Translate names and indices of planes.

vol.mask.from.segmentation

Extract subset from a volume by value.

vis.group.coloredmeshes

Plot coloredmeshes for a group of subjects.

vis.data.on.group.standard

Visualize standard space data for a group on template.

Visualize a renderable object

vis.data.on.subject

Visualize arbitrary data on the surface of any subject.

vis.group.morph.native

Plot native space morphometry data for a group of subjects.

Merge background volume and overlay to new colors.

Return recommended 'makecmap_options' for diverging data.

test.numerical.meandiff.paired

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

vis.rotated.coloredmeshes

Rotate and visualize coloredmeshes, applying a style.

get.view.angle.names

Get list of valid view angle names.

vol.intensity.to.color

Convert integer intensity image to RGB color string form.

volvis.lightbox

Draw a lightbox view from volume slices.

Visualize contour of a volume.

Turn volume into an ImageMagick image stack.

group.morph.agg.standard.vertex

Aggregate standard space morphometry data over subjects.

Retrieve values from nested named lists

group.multimorph.agg.native

Aggregate native space 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.sf

Read combined data for a group from a single file.

Check whether x is a hemilist

Compute border of a label.

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

Merge several labels into an annotation

write.group.morph.standard.sf

Write combined data for a group to a single MGH file.

perform.na.mapping

Perform NA mapping for transparency

perform.rglactions

Perform rglactions, like taking screenshots.

Read colors from CSV file.

list_optional_data

Get file names available in package cache.

mesh.vertex.neighbors

Compute neighborhood of a vertex

Arrange a multi-frame ImageMagick image into a grid.

read.md.demographics

Read demographics file

write.region.aggregated

Write data aggregated over regions to morphometry file for group.

rglactions.transform

Apply data transformation rglactions.

write.region.values.fsaverage

Write one value per atlas region for a template subject.

Get rgloptions and consider global options.

write.region.values

Write one value per atlas region for a subject.

subject.filepath.any

Construct filepath of any freesurfer file.

merge.hemi.annots

Merge the annotations from two hemispheres into one annot.

subject.filepath.morph.native

Construct filepath of native space morphometry data file.

surf.radius.fsaverage

Get pre-computed radius for fsaverage white surface.

surf.center.fsaverage

Get pre-computed center for fsaverage white surface.

vis.color.on.subject

Visualize pre-defined vertex colors on a subject.

vdata.split.by.hemi

Split morph data vector at hemisphere boundary.

Return recommended 'makecmap_options' for diverging cluster data.

vol.overlay.colors.from.colortable

Compute voxel colors based on colortable.

vis.export.from.coloredmeshes

Export high-quality brainview image with horizontal colorbar.

Visualize DTI tracks from Diffusion Toolkit/TrackVis TRK format file.

vol.overlay.colors.from.activation

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

qc.from.segstats.tables

Perform data quality check based on a segstats table.

qc.from.regionwise.df

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

mesh.vertex.included.faces

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

Get rgloptions for testing.

qc.vis.failcount.by.region

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

qc.from.segstats.table

Perform data quality check based on a segstats table.

Draw 3D boxes at locations using rgl.

principal.curvatures

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

Convert raduians to degree

print.fs.coloredmesh

Print description of a brain coloredmesh (S3).

The FreeSurfer default ras2vox_tkr matrix.

shape.descriptor.names

Get all shape descriptor names.

sort.coloredmeshes.by.hemi

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

subject.num.verts

Get subjects vertex count.

subject.morph.standard

Retrieve standard space morphometry data for a single subject.

shift.hemis.rglactions

Shift hemis apart if indicated in rglactions

scale.to.range.zero.one

Scale given values to range 0..1.

Load an annotation for a subject.

Compute a mask for a subject.

subject.atlas.agg

Aggregate morphometry data over brain atlas regions for a subject.

subject.morph.native

Retrieve native space morphometry data for a single subject.

test.numerical.meandiff.unpaired

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

vis.path.along.verts

Draw a 3D line from vertex to vertex

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.

vis.subject.morph.native

Visualize native space morphometry data for a subject.

vis.mask.on.subject

Visualize a vertex mask on the surface of a subject.

subject.surface

Load a surface for a subject.

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

vis.subject.morph.standard

Visualize native space morphometry data for a subject or a group.

Read a brain volume.

vol.boundary.mask

Compute foreground pixels over the whole 3D imagestack.

Retain only the outer hull voxels of the foreground.

vis.group.annot

Plot atlas annotations for a group of subjects.

vislayout.from.coloredmeshes

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

vis.symmetric.data.on.subject

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

Visualize fs.surface mesh

Extract a slice of a 3D image stack.

vol.vox.from.crs

Compute R voxel index for FreeSurfer CRS voxel index.

vol.boundary.box.apply

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

The FreeSurfer default vox2ras_tkr matrix.

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

vol.boundary.box

Compute 3D bounding box of a volume.