fsbrain v0.0.2

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Managing and Visualizing Brain Surface Data

Provides high-level access to 'FreeSurfer' <http://freesurfer.net/> 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'.

Functions in fsbrain

Name Description
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.
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Vignettes of fsbrain

Name
fsbrain.Rmd
fsbrain_aparc.jpg
fsbrain_ct.jpg
fsbrain_vis_surfaces.jpg
fsbrain_vis_views.jpg
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Details

Type Package
License MIT + file LICENSE
Encoding UTF-8
LazyData true
URL https://github.com/dfsp-spirit/fsbrain
BugReports https://github.com/dfsp-spirit/fsbrain/issues
VignetteBuilder knitr
RoxygenNote 6.1.1
NeedsCompilation no
Packaged 2019-11-08 13:42:52 UTC; spirit
Repository CRAN
Date/Publication 2019-11-08 14:10:03 UTC

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