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fsbrain (version 0.0.2)

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

0.0.2

License

MIT + file LICENSE

Issues

13

Pull Requests

0

Stars

71

Forks

13

Maintainer

Tim Schc3<a4>fer

Last Published

November 8th, 2019

Functions in fsbrain (0.0.2)

clip.data

Clip data at quantiles to remove outliers.
get.rglstyle.shiny

Get a shiny visualization style.
group.annot

Load annotations for a group of subjects.
download_fsaverage

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

Concatenate native space data for a group of subjects.
brainviews

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

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

Create a coloredmesh from native space morphometry data.
brainview.sr

Visualize a list of colored meshes, rotating the camera around them.
coloredmesh.from.morph.standard

Create a coloredmesh from standard space morphometry data.
get_optional_data_filepath

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

Extract a region from an annotation as a label.
read.md.demographics

Read demographics file
group.multimorph.agg.standard

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

Perform rglactions, like taking screenshots.
spread.values.over.hemi

Spread the values in the region_value_list and return them for one hemisphere.
group.concat.measures.standard

Concatenate standard space data for a group of subjects.
spread.values.over.subject

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

Retrieve standard space morphometry data for a group of subjects.
combine.coloredmeshes.data

Combine the data from the coloredmeshes, if any.
coloredmesh.from.morphdata

Create a coloredmesh from arbitrary data.
check.for.coloredmeshes.colormap

Return the colormap function from the meshes, if any.
group.label

Retrieve label data for a group of subjects.
mask.from.labeldata.for.hemi

Create a binary mask from labels.
brainview.t4

Visualize a list of colored meshes from four angles.
brainview.t9

Visualize a list of colored meshes from nine angles.
find.subjectsdir.of

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

Create a coloredmesh from an annotation of an atlas.
draw.colorbar

Draw a coloredbar into the current plot.
download_optional_data

Download optional data for this package if required.
coloredmesh.from.mask

Create a coloredmesh from a mask.
fs.value.list.from.agg.res

Create a named value list from a dataframe.
test.numerical.meandiff

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

Merge the annotations from two hemispheres into one annot.
subject.filepath.morph.native

Construct filepath of native space morphometry data file.
subject.filepath.any

Construct filepath of any freesurfer file.
vis.coloredmesh

Draw a coloredmesh using a style.
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.
group.morph.agg.standard

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

Transform first character of a string to uppercase.
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.coloredmeshes

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

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

Get the default visualization style parameters as a named list.
regions.to.ignore

Give suggestions for regions to ignore for an atlas.
read.md.subjects

Read subjects file
get.atlas.region.names

Determine atlas region names from a subject.
group.multimorph.agg.native

Aggregate native space morphometry data for multiple measures over hemispheres for a group of subjects.
vis.subject.annot

Visualize an annotation for a subject.
write.region.values.fsaverage

Write one value per atlas region for a template subject.
rglactions.has.key

Check for a key in names of rglactions.
vis.rotated.coloredmeshes

Rotate and visualize coloredmeshes, applying a style.
report.on.demographics

Print a demographics report
group.label.from.annot

Extract a region from an atlas annotation as a label for a group of subjects.
sort.coloredmeshes.by.hemi

Sort coloredmeshes into 2 lists by their 'hemi' property.
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.
vis.region.values.on.subject

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

Visualize a label for a subject.
spread.values.over.annot

Spread a single value for a region to all region vertices.
get.rglstyle.default

Get the default visualization style parameters as a named list.
unify.coloredmeshes.colormaps

Recompute the colormaps in the meshes, using data from all meshes.
subject.annot

Load an annotation for a subject.
write.region.aggregated

Write data aggregated over regions to morphometry file for group.
group.morph.agg.native

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

Create labeldata from a mask.
write.region.values

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

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

Construct filepath of standard space morphometry data file.
vis.subject.morph.native

Visualize native space morphometry data for a subject.
subject.atlas.agg

Aggregate morphometry data over brain atlas regions for a subject.
vis.subject.morph.standard

Visualize native space morphometry data for a subject.
subject.label

Retrieve label data for a single subject.
list_optional_data

Get file names available in package cache.
subject.morph.standard

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

Retrieve native space morphometry data for a single subject.
subject.surface

Load a surface for a subject.
vis.coloredmeshes.rotating

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

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

Create a coloredmesh from an annotation of an atlas.
delete_all_optional_data

Delete all data in the package cache.