alphablend | Perform alpha blending for pairs of RGBA colors. |
annot.outline | Compute outline vertex colors from annotation. |
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. |
apply.transform | Apply matmult transformation to input. |
arrange.brainview.images | Combine several brainview images into a new figure. |
brainviews | Show one or more views of the given meshes in rgl windows. |
clip.data | Clip data at quantiles to remove outliers. |
collayer.bg | Compute binarized mean curvature surface color layer. |
collayer.bg.atlas | Compute atlas or annotation surface color layer. |
collayer.bg.meancurv | Compute binarized mean curvature surface color layer. |
collayer.bg.sulc | Compute binarized sulcal depth surface color layer. |
collayer.from.annot | Compute surface color layer from annotation or atlas data. |
collayer.from.annotdata | Compute surface color layer from annotation or atlas data. |
collayer.from.mask.data | Compute surface color layer from morph-like data. |
collayer.from.morphlike.data | Compute surface color layer from morph-like data. |
collayers.merge | Merge two or more color layers based on their transparency values. |
coloredmesh.from.mask | Create a coloredmesh from a mask. |
coloredmesh.from.morph.native | Create a coloredmesh from native space morphometry data. |
coloredmesh.plot.colorbar.separate | Draw colorbar for coloredmeshes in separate 2D plot. |
coloredmeshes.from.color | Create coloredmeshes for both hemis using pre-defined colors. |
colorlist.brain.clusters | Return diverging color list |
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. |
cube3D.tris | Return triangles for a 3D cube or cuboid. |
cubes3D.tris | Vectorized version of cube3D.tris |
delete_all_optional_data | Delete all data in the package cache. |
desaturate | Perform simple desaturation or grayscale conversion of RGBA colors. |
download_fsaverage | Download the FreeSurfer v6 fsaverage subject. |
download_optional_data | Download optional data for this package if required. |
face.edges | Enumerate all edges of the given faces or mesh. |
find.freesurferhome | Find the FREESURFER_HOME directory on disk. |
find.subjectsdir.of | Find the subject directory containing the fsaverage subject (or others) on disk. |
flip3D | Flip a 3D array along an axis. |
fs.coloredmesh | fs.coloredmesh constructor |
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. |
getIn | Retrieve values from nested named lists |
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. |
hasIn | Check for values in nested named lists |
hemilist.derive.hemi | Derive 'hemi' string from the data in a hemilist |
hemilist.get.combined.data | Get combined data of hemi list |
hemilist.unwrap | Unwrap hemi data from a named hemi list. |
hemilist.wrap | Wrap data into a named hemi list. |
is.fs.coloredmesh | Check whether object is an fs.coloredmesh (S3) |
is.fs.coloredvoxels | Check whether object is an fs.coloredvoxels instance (S3) |
is.hemilist | Check whether x is a hemilist |
label.border | Compute border of a label. |
label.from.annotdata | Extract a region from an annotation as a label. |
label.to.annot | Merge several labels into an annotation |
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 neighborhood of a vertex |
print.fs.coloredmesh | Print description of a brain coloredmesh (S3). |
print.fs.coloredvoxels | Print description of fs.coloredvoxels (S3). |
ras2vox_tkr | The FreeSurfer default ras2vox_tkr matrix. |
read.colorcsv | Read colors from CSV file. |
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 |
rglvoxels | Draw 3D boxes at locations using rgl. |
rotate3D | Rotate a 3D array in 90 degree steps. |
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.mask | Compute a mask 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. |
subject.volume | Read a brain volume. |
vis.color.on.subject | Visualize pre-defined vertex colors on a subject. |
vis.coloredmeshes | Visualize a list of colored meshes in a single scene. |
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.path.along.verts | Draw a 3D line from vertex to vertex |
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 binary 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. |
vis.symmetric.data.on.subject | Visualize clusters or activation data on the surface of any subject. |
vislayout.from.coloredmeshes | Visualize coloredmeshes from several angles and combine the images into a new figure. |
vol.boundary.box | Compute 3D bounding box of a volume. |
vol.boundary.box.apply | Apply a boundary box to a volume, returning the inner volume part |
vol.hull | Retain only the outer hull voxels of the foreground. |
vol.imagestack | Turn volume into an ImageMagick image stack. |
vol.intensity.to.color | Convert integer intensity image to RGB color string form. |
vol.mask.from.segmentation | Extract subset from a volume by value. |
vol.merge | Merge background volume and overlay to new colors. |
vol.overlay.colors.from.activation | Generate colors for a 3D volume, based on the activation data and a colormap. |
vol.overlay.colors.from.colortable | Compute voxel colors based on colortable. |
vol.planes | Translate names and indices of planes. |
vol.slice | Extract a slice of a 3D image stack. |
vol.vox.from.crs | Compute R voxel index for FreeSurfer CRS voxel index. |
volvis.contour | Visualize contour of a volume. |
volvis.lightbox | Draw a lightbox view from volume slices. |
volvis.voxels | Voxel-based visualization of volume mask at surface RAS positions. |
vox2ras_tkr | The FreeSurfer default vox2ras_tkr matrix. |
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. |