fsbrain v0.0.2

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by Tim Schc3<a4>fer View Source

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

imports	dplyr , fields , freesurferformats (>= 0.1.4) , ggplot2 , pkgfilecache (>= 0.1.1) , reshape , reshape2 , rgl , squash
suggests	knitr , magick , rmarkdown , testthat (>= 2.1.0)
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