# Managing and Visualizing Brain Surface Data

## Documentation for package ‘fsbrain’ version 0.0.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.
arrange.brainview.images | Combine several brainview images into a new figure.
clip.data | Clip data at quantiles to remove outliers.
coloredmesh.from.mask | Create a coloredmesh from a mask.
coloredmesh.plot.colorbar.separate | Draw colorbar for coloredmeshes in separate 2D plot.
combine.colorbar.with.brainview.animation | Combine a colorbar and a brain animation in gif format into a new animation.
combine.colorbar.with.brainview.image | Combine a colorbar and a brainview image into a new figure.
delete_all_optional_data | Delete all data in the package cache.
download_fsaverage | Download the FreeSurfer v6 fsaverage subject.
download_optional_data | Download optional data for this package if required.
find.subjectsdir.of | Find the subject directory containing the fsaverage subject (or others) on disk.
fup | Transform first character of a string to uppercase.
get.atlas.region.names | Determine atlas region names from a subject.
get.view.angle.names | Get list of valid view angle names.
get_optional_data_filepath | Access a single file from the package cache by its file name.
group.agg.atlas.native | Aggregate native space morphometry data over brain atlas regions and subjects 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.annot | Load annotations for a group of subjects.
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.
group.label | Retrieve label data for a group of subjects.
group.label.from.annot | Extract a region from an atlas annotation as a label for a group of subjects.
group.morph.agg.native | Aggregate native space morphometry data over one hemisphere 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.native | Retrieve native space morphometry data for a group of subjects.
group.morph.standard | Retrieve standard space morphometry data for a group of subjects.
group.multimorph.agg.native | Aggregate native space morphometry data for multiple measures over hemispheres for a group of subjects.
group.multimorph.agg.standard | Aggregate standard space (fsaverage) morphometry data for multiple measures over hemispheres for a group of subjects.
label.from.annotdata | Extract a region from an annotation as a label.
labeldata.from.mask | Create labeldata from a mask.
list_optional_data | Get file names available in package cache.
mask.from.labeldata.for.hemi | Create a binary mask from labels.
mesh.vertex.neighbors | Compute neighbors of a vertex
read.md.demographics | Read demographics file
read.md.subjects | Read subjects file
regions.to.ignore | Give suggestions for regions to ignore for an atlas.
report.on.demographics | Print a demographics report
spread.values.over.annot | Spread a single value for a region to all region vertices.
spread.values.over.hemi | Spread the values in the region_value_list and return them for one hemisphere.
spread.values.over.subject | Spread the values in the region_value_list and return them for one hemisphere.
subject.annot | Load an annotation for a subject.
subject.atlas.agg | Aggregate morphometry data over brain atlas regions for a subject.
subject.filepath.morph.native | Construct filepath of native space morphometry data file.
subject.filepath.morph.standard | Construct filepath of standard space morphometry data file.
subject.label | Retrieve label data for a single subject.
subject.label.from.annot | Extract a region from an atlas annotation as a label for a subject.
subject.morph.native | Retrieve native space morphometry data for a single subject.
subject.morph.standard | Retrieve standard space morphometry data for a single subject.
subject.surface | Load a surface for a subject.
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.
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.
vis.region.values.on.subject | Visualize arbitrary data, one value per atlas region, on the surface of any subject (including template subjects).
vis.subject.annot | Visualize an annotation for a subject.
vis.subject.label | Visualize a label for a subject.
vis.subject.morph.native | Visualize native space morphometry data for a subject.
vis.subject.morph.standard | Visualize native space morphometry data for a subject.
vislayout.from.coloredmeshes | Visualize coloredmeshes from several angles and combine the images into a new figure.
write.region.aggregated | Write data aggregated over regions to morphometry file for group.
write.region.values | Write one value per atlas region for a subject.
write.region.values.fsaverage | Write one value per atlas region for a template subject.