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fsbrain (version 0.0.3)

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 the results directly in 'R'.

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Install

install.packages('fsbrain')

Monthly Downloads

496

Version

0.0.3

License

MIT + file LICENSE

Issues

13

Pull Requests

0

Stars

71

Forks

13

Maintainer

Tim Schc3<a4>fer

Last Published

December 1st, 2019

Functions in fsbrain (0.0.3)

coloredmesh.from.morphdata

Create a coloredmesh from arbitrary data.
coloredmesh.from.morph.native

Create a coloredmesh from native space morphometry data.
download_optional_data

Download optional data for this package if required.
brainview.t9

Visualize a list of colored meshes from nine angles.
subject.label.from.annot

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

Create a coloredmesh from standard space morphometry data.
download_fsaverage

Download the FreeSurfer v6 fsaverage subject.
group.concat.measures.standard

Concatenate standard space data for a group of subjects.
coloredmesh.plot.colorbar.separate

Draw colorbar for coloredmeshes in separate 2D plot.
draw.colorbar

Draw coloredbar into background of current plot.
coloredmesh.from.mask

Create a coloredmesh from a mask.
get.atlas.region.names

Determine atlas region names from a subject.
clip.data

Clip data at quantiles to remove outliers.
get.rglstyle

Get the default visualization style parameters as a named list.
group.agg.atlas.standard

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

Visualize a label for a subject.
label.from.annotdata

Extract a region from an annotation as a label.
coloredmesh.from.label

Create a coloredmesh from an annotation of an atlas.
group.agg.atlas.native

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

Get file names available in package cache.
combine.coloredmeshes.data

Combine the data from the coloredmeshes, if any.
delete_all_optional_data

Delete all data in the package cache.
write.region.values.fsaverage

Write one value per atlas region for a template subject.
coloredmesh.from.annot

Create a coloredmesh from an annotation of an atlas.
spread.values.over.hemi

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

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

Get a shiny visualization style.
find.subjectsdir.of

Find the subject directory containing the fsaverage subject (or others) on disk.
group.multimorph.agg.native

Aggregate native space morphometry data for multiple measures over hemispheres for a group of subjects.
get.view.angle.names

Get list of valid view angle names.
combine.colorbar.with.brainview.animation

Combine a colorbar and a brain animation in gif format into a new animation.
subject.surface

Load a surface for a subject.
vis.subject.annot

Visualize an annotation for a subject.
group.multimorph.agg.standard

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

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

Create a binary mask from labels.
combine.colorbar.with.brainview.image

Combine a colorbar and a brainview image into a new figure.
subject.filepath.any

Construct filepath of any freesurfer file.
merge.hemi.annots

Merge the annotations from two hemispheres into one annot.
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.
mesh.vertex.neighbors

Compute neighbors of a vertex
vis.coloredmeshes.rotating

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

Print a demographics report
regions.to.ignore

Give suggestions for regions to ignore for an atlas.
get_optional_data_filepath

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

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

Construct filepath of native space morphometry data file.
group.morph.agg.native

Aggregate native space morphometry data over one hemisphere for a group of subjects.
subject.filepath.morph.standard

Construct filepath of standard space morphometry data file.
group.label.from.annot

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

Retrieve standard space morphometry data for a group of subjects.
fs.value.list.from.agg.res

Create a named value list from a dataframe.
fup

Transform first character of a string to uppercase.
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.
labeldata.from.mask

Create labeldata from a mask.
subject.morph.standard

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

Retrieve label data for a group of subjects.
write.region.aggregated

Write data aggregated over regions to morphometry file for group.
vislayout.from.coloredmeshes

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

Perform rglactions, like taking screenshots.
read.md.demographics

Read demographics file
rglactions.has.key

Check for a key in names of rglactions.
group.annot

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

Concatenate native space data for a group of subjects.
group.morph.agg.standard

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

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

Retrieve label data for a single subject.
vis.coloredmesh

Draw a coloredmesh using a style.
unify.coloredmeshes.colormaps

Recompute the colormaps in the meshes, using data from all meshes.
vis.subject.morph.standard

Visualize native space morphometry data for a subject.
read.md.subjects

Read subjects file
vis.region.values.on.subject

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

Visualize a list of colored meshes in a single scene.
group.morph.native

Retrieve native space morphometry data for a group of subjects.
spread.values.over.subject

Spread the values in the region_value_list and return them for one hemisphere.
sort.coloredmeshes.by.hemi

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

Load an annotation for a subject.
test.numerical.meandiff

Perform tests for group differences on paired or unpaired data for two groups.
vis.subject.morph.native

Visualize native space morphometry data for a subject.
write.region.values

Write one value per atlas region for a subject.
vis.rotated.coloredmeshes

Rotate and visualize coloredmeshes, applying a style.
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.
brainview.sr

Visualize a list of colored meshes, rotating the camera around them.
check.for.coloredmeshes.colormap

Return the colormap function from the meshes, if any.
brainview.sd

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

Show one or more views of the given meshes in rgl windows.
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.
apply.labeldata.to.morphdata

Apply a label to morphometry data.
brainview.si

Visualize a list of colored meshes from a single viewpoint, interactively.
brainview.t4

Visualize a list of colored meshes from four angles.