| Perform alpha blending for pairs of RGBA colors. | alphablend |
| Compute outline vertex colors from annotation. | annot.outline |
| Compute the border vertices for each region in an annot. | annot.outline.border.vertices |
| Load a label from file and apply it to morphometry data. | apply.label.to.morphdata |
| Apply a label to morphometry data. | apply.labeldata.to.morphdata |
| Apply matmult transformation to input. | apply.transform |
| Combine several brainview images into a new figure. | arrange.brainview.images |
| Combine several brainview images as a grid into a new figure. | arrange.brainview.images.grid |
| Show one or more views of the given meshes in rgl windows. | brainviews |
| Get data clipping function. | clip_fun |
| Clip data at quantiles to remove outliers. | clip.data |
| Get cyan blue red yellow colormap function. | cm.cbry |
| Return the standard fsbrain diverging colormap. | cm.div |
| Return the standard fsbrain heat colormap. | cm.heat |
| Return the standard fsbrain qualitative colormap. | cm.qual |
| Return the standard fsbrain sequential colormap. | cm.seq |
| Compute binarized mean curvature surface color layer. | collayer.bg |
| Compute atlas or annotation surface color layer. | collayer.bg.atlas |
| Compute binarized mean curvature surface color layer. | collayer.bg.meancurv |
| Compute binarized sulcal depth surface color layer. | collayer.bg.sulc |
| Compute surface color layer from annotation or atlas data. | collayer.from.annot |
| Compute surface color layer from annotation or atlas data. | collayer.from.annotdata |
| Compute surface color layer from morph-like data. | collayer.from.mask.data |
| Compute surface color layer from morph-like data. | collayer.from.morphlike.data |
| Merge two or more color layers based on their transparency values. | collayers.merge |
| Create a coloredmesh from an annotation of an atlas. | coloredmesh.from.annot |
| Create a coloredmesh from a label. | coloredmesh.from.label |
| Create a coloredmesh from a mask. | coloredmesh.from.mask |
| Create a coloredmesh from native space morphometry data. | coloredmesh.from.morph.native |
| Create a coloredmesh from standard space morphometry data. | coloredmesh.from.morph.standard |
| Create a coloredmesh from arbitrary data. | coloredmesh.from.morphdata |
| Generate coloredmesh from loaded data. | coloredmesh.from.preloaded.data |
| Draw colorbar for coloredmeshes in separate 2D plot. | coloredmesh.plot.colorbar.separate |
| Create coloredmeshes for both hemis using pre-defined colors. | coloredmeshes.from.color |
| Return diverging color list | colorlist.brain.clusters |
| Check for the given color strings whether they represent gray scale colors. | colors.are.grayscale |
| Check for the given color strings whether they have transparency, i.e., an alpha channel value != fully opaque. | colors.have.transparency |
| Combine a colorbar and a brain animation in gif format into a new animation. | combine.colorbar.with.brainview.animation |
| Combine a colorbar and a brainview image into a new figure. | combine.colorbar.with.brainview.image |
| Get vertex data for a single fs.surface or a hemilist of surfaces. | constant.pervertexdata |
| Return triangles for a 3D cube or cuboid. | cube3D.tris |
| Vectorized version of cube3D.tris | cubes3D.tris |
| Delete all data in the package cache. | delete_all_optional_data |
| Write FreeSurfer Group Descriptor (FSGD) file from demographics dataframe. | demographics.to.fsgd.file |
| Convert a dataframe containing demographics data to a qdec.table.dat file and related files. | demographics.to.qdec.table.dat |
| Perform simple desaturation or grayscale conversion of RGBA colors. | desaturate |
| Download the FreeSurfer v6 fsaverage subject. | download_fsaverage |
| Download the FreeSurfer v6 low-resolution fsaverage3 subject. | download_fsaverage3 |
| Download optional data for this package if required. | download_optional_data |
| Download extra data to reproduce the figures from the fsbrain paper. | download_optional_paper_data |
| Export high-quality brainview image with a colorbar. | export |
| Export a coloredmeshes with vertexcolors in PLY format. | export.coloredmesh.ply |
| Enumerate all edges of the given faces or mesh. | face.edges |
| Find the FREESURFER_HOME directory on disk. | find.freesurferhome |
| Find the subject directory containing the fsaverage subject (or others) on disk. | find.subjectsdir.of |
| fs.coloredmesh constructor | fs.coloredmesh |
| Return FreeSurfer path. | fs.home |
| Turn surface mesh into a igraph and return its adjacency list representation. | fs.surface.as.adjacencylist |
| Create igraph undirected graph from a brain surface mesh. | fs.surface.to.igraph |
| Get an rgl tmesh3d instance from a brain surface mesh. | fs.surface.to.tmesh3d |
| Compute vertex neighborhoods or the full adjacency list for a mesh using the Rvcg or igraph library. | fs.surface.vertex.neighbors |
| Return path to fsaverage dir. | fsaverage.path |
| Set default figure size for fsbrain visualization functions. | fsbrain.set.default.figsize |
| Transform first character of a string to uppercase. | fup |
| Generate test 3D volume of integers. The volume has an outer background area (intensity value 'bg') and an inner foreground areas (intensity value 200L). | gen.test.volume |
| Generate color overlay from geodesic patches around several vertices. | geod.patches.color.overlay |
| Compute all vertices within given geodesic distance on the mesh. | geod.vert.neighborhood |
| Compute geodesic circles and ball stats for given vertices. | geodesic.circles |
| Simple internal wrapper around 'Rvcg::vcgDijkstra' with function check. | geodesic.dists.to.vertex |
| Compute geodesic path from a source vertex to one or more target vertices. | geodesic.path |
| Access a single file from the package cache by its file name. | get_optional_data_filepath |
| Determine atlas region names from a subject. | get.atlas.region.names |
| Get the default visualization style parameters as a named list. | get.rglstyle |
| Get list of valid view angle names. | get.view.angle.names |
| Retrieve values from nested named lists | getIn |
| Aggregate native space morphometry data over brain atlas regions and subjects for a group of subjects. | group.agg.atlas.native |
| Aggregate standard space morphometry data over brain atlas regions and subjects for a group of subjects. | group.agg.atlas.standard |
| Load annotations for a group of subjects. | group.annot |
| Concatenate native space data for a group of subjects. | group.concat.measures.native |
| Concatenate standard space data for a group of subjects. | group.concat.measures.standard |
| Retrieve label data for a group of subjects. | group.label |
| Extract a region from an atlas annotation as a label for a group of subjects. | group.label.from.annot |
| Aggregate native space morphometry data over one hemisphere for a group of subjects. | group.morph.agg.native |
| Aggregate standard space (fsaverage) morphometry data over one hemisphere for a group of subjects. | group.morph.agg.standard |
| Aggregate standard space morphometry data over subjects. | group.morph.agg.standard.vertex |
| Retrieve native space morphometry data for a group of subjects. | group.morph.native |
| Retrieve standard space morphometry data for a group of subjects. | group.morph.standard |
| Read combined data for a group from a single file. | group.morph.standard.sf |
| Aggregate native space morphometry data for multiple measures over hemispheres for a group of subjects. | group.multimorph.agg.native |
| Aggregate standard space (fsaverage) morphometry data for multiple measures over hemispheres for a group of subjects. | group.multimorph.agg.standard |
| Retrieve surface mesh data for a group of subjects. | group.surface |
| Split a per-vertex group data matrix for both hemispheres into a hemilist at given index. | groupmorph.split.hemilist |
| Check for values in nested named lists | hasIn |
| Create a hemilist from lh and rh data. | hemilist |
| Derive 'hemi' string from the data in a hemilist | hemilist.derive.hemi |
| Create a hemilist from a named list with keys prefixed with 'lh_' and 'rh_'. | hemilist.from.prefixed.list |
| Get combined data of hemi list | hemilist.get.combined.data |
| Unwrap hemi data from a named hemi list. | hemilist.unwrap |
| Wrap data into a named hemi list. | hemilist.wrap |
| Draw small 3D spheres at given points. | highlight.points.spheres |
| Highlight vertices given by index on a subject's meshes by coloring faces. | highlight.vertices.on.subject |
| Highlight vertices given by index on a subject's meshes by coloring faces. | highlight.vertices.on.subject.spheres |
| Draw small 3D spheres at given brain mesh vertices. Supports full brain (2 meshes) as well. | highlight.vertices.spheres |
| Compute max width and height of magick images. | images.dimmax |
| Check whether object is an fs.coloredmesh (S3) | is.fs.coloredmesh |
| Check whether object is an fs.coloredvoxels instance (S3) | is.fs.coloredvoxels |
| Check whether object is an fsbrain (S3) | is.fsbrain |
| Check whether x is a hemilist | is.hemilist |
| Compute border of a label. | label.border |
| A simple colormap function for binary colors. | label.colFn |
| A simple colormap function for binary colors. | label.colFn.inv |
| Extract a region from an annotation as a label. | label.from.annotdata |
| Merge several labels into an annotation | label.to.annot |
| Create labeldata from a mask. | labeldata.from.mask |
| Get data limiting function. | limit_fun |
| Get data limiting function to NA. | limit_fun_na |
| Get data limiting function, setting values inside range to NA. | limit_fun_na_inside |
| Get file names available in package cache. | list_optional_data |
| Create a binary mask from labels. | mask.from.labeldata.for.hemi |
| Compute neighborhood of a vertex | mesh.vertex.neighbors |
| Return recommended 'makecmap_options' for diverging cluster data. | mkco.cluster |
| Return recommended 'makecmap_options' for diverging data. | mkco.div |
| Return recommended 'makecmap_options' for sequential data with heatmap style. | mkco.heat |
| Return recommended 'makecmap_options' for sequential data. | mkco.seq |
| Determine vertex count of left hemi from hemilist of surfaces or the count itself. | numverts.lh |
| Determine vertex count of right hemi from hemilist of surfaces or the count itself. | numverts.rh |
| Computes principal curvatures according to 2 definitions from raw k1 and k2 values. | principal.curvatures |
| Print description of a brain coloredmesh (S3). | print.fs.coloredmesh |
| Print description of fs.coloredvoxels (S3). | print.fs.coloredvoxels |
| Print description of an fsbrain (S3). | print.fsbrain |
| Perform data quality check based on computed region stats. | qc.for.group |
| Perform data quality check based on a dataframe containing aggregated region-wise data. | qc.from.regionwise.df |
| Perform data quality check based on a segstats table. | qc.from.segstats.tables |
| Visualize the number of outlier subjects per region in your dataset. | qc.vis.failcount.by.region |
| Generate skeleton dataframe for FreeSurfer QDEC long file from subjects list. | qdec.table.skeleton |
| The FreeSurfer default ras2vox_tkr matrix. | ras2vox_tkr |
| Read colors from CSV file. | read.colorcsv |
| Read demographics file | read.md.demographics |
| Read subjects file | read.md.subjects |
| Read subjects list from an FSGD file. | read.md.subjects.from.fsgd |
| Give suggestions for regions to ignore for an atlas. | regions.to.ignore |
| Print a demographics report | report.on.demographics |
| Create rglactions list, suitable to be passed as parameter to vis functions. | rglactions |
| Get rgloptions and consider global options. | rglo |
| Get rgloptions for testing. | rglot |
| Draw 3D boxes at locations using rgl. | rglvoxels |
| Scale given values to range 0..1. | scale01 |
| Get all shape descriptor names. | shape.descriptor.names |
| Computes geometric curvature-based descriptors. | shape.descriptors |
| Shift hemispheres apart. | shift.hemis.apart |
| Download optional demo data if needed and return its path. | sjd.demo |
| Get subjects list from subjects.txt file in dir. | sjld |
| Spread a single value for a region to all region vertices. | spread.values.over.annot |
| Spread the values in the region_value_list and return them for one hemisphere. | spread.values.over.hemi |
| Spread the values in the region_value_list and return them for one hemisphere. | spread.values.over.subject |
| Load an annotation for a subject. | subject.annot |
| Compute annot border vertices. | subject.annot.border |
| Aggregate morphometry data over brain atlas regions for a subject. | subject.atlas.agg |
| Construct filepath of native space morphometry data file. | subject.filepath.morph.native |
| Construct filepath of standard space morphometry data file. | subject.filepath.morph.standard |
| Retrieve label data for a single subject. | subject.label |
| Extract a region from an atlas annotation as a label for a subject. | subject.label.from.annot |
| Load labels representing brain lobes. | subject.lobes |
| Compute a mask for a subject. | subject.mask |
| Retrieve native space morphometry data for a single subject. | subject.morph.native |
| Retrieve standard space morphometry data for a single subject. | subject.morph.standard |
| Get subjects vertex count. | subject.num.verts |
| Load a surface for a subject. | subject.surface |
| Read a brain volume. | subject.volume |
| Compute the k1 and k2 principal curvatures of a mesh. | surface.curvatures |
| Get an fs.surface brain mesh from an rgl tmesh3d instance. | tmesh3d.to.fs.surface |
| Split morph data vector at hemisphere boundary. | vdata.split.by.hemi |
| Return coordinates for vertices, supporting entire brain via hemilist. | vertex.coords |
| Return the proper hemi string ('lh' or 'rh') for each vertex. | vertex.hemis |
| Visualize pre-defined vertex colors on a subject. | vis.color.on.subject |
| Visualize a list of colored meshes in a single scene. | vis.coloredmeshes |
| Visualize a list of colored meshes in a single scene and rotate them, movie-style. | vis.coloredmeshes.rotating |
| Create a separate legend plot for a colortable or an annotation. | vis.colortable.legend |
| Visualize arbitrary data on the fsaverage template subject, if available. | vis.data.on.fsaverage |
| Visualize native space data on a group of subjects. | vis.data.on.group.native |
| Visualize standard space data for a group on template. | vis.data.on.group.standard |
| Visualize arbitrary data on the surface of any subject. | vis.data.on.subject |
| Visualize DTI tracks from Diffusion Toolkit/TrackVis TRK format file. | vis.dti.trk |
| Export high-quality brainview image with a colorbar. | vis.export.from.coloredmeshes |
| Visualize fs.surface mesh | vis.fs.surface |
| Plot atlas annotations for a group of subjects. | vis.group.annot |
| Plot coloredmeshes for a group of subjects. | vis.group.coloredmeshes |
| Plot native space morphometry data for a group of subjects. | vis.group.morph.native |
| Plot standard space morphometry data for a group of subjects. | vis.group.morph.standard |
| Visualize a label on the surface of a subject. | vis.labeldata.on.subject |
| Visualize a vertex mask on the surface of a subject. | vis.mask.on.subject |
| Draw a 3D line from vertex to vertex | vis.path.along.verts |
| Visualize many paths. | vis.paths |
| Visualize several paths in different colors. | vis.paths.along.verts |
| Visualize arbitrary data, one value per atlas region, on the surface of any subject (including template subjects). | vis.region.values.on.subject |
| Plot legend for a brain volume segmentation based on colorLUT. | vis.seg.legend |
| Visualize an annotation for a subject. | vis.subject.annot |
| Visualize a binary label for a subject. | vis.subject.label |
| Visualize native space morphometry data for a subject. | vis.subject.morph.native |
| Visualize native space morphometry data for a subject or a group. | vis.subject.morph.standard |
| Visualize pre-loaded data. | vis.subject.pre |
| Visualize clusters or activation data on the surface of any subject. | vis.symmetric.data.on.subject |
| Visualize coloredmeshes from several angles and combine the images into a new figure. | vislayout.from.coloredmeshes |
| Compute 3D bounding box of a volume. | vol.boundary.box |
| Apply a boundary box to a volume, returning the inner volume part | vol.boundary.box.apply |
| Retain only the outer hull voxels of the foreground. | vol.hull |
| Turn volume into an ImageMagick image stack. | vol.imagestack |
| Convert integer intensity image to RGB color string form. | vol.intensity.to.color |
| Extract subset from a volume by value. | vol.mask.from.segmentation |
| Merge background volume and overlay to new colors. | vol.merge |
| Generate colors for a 3D volume, based on the activation data and a colormap. | vol.overlay.colors.from.activation |
| Compute voxel colors based on colortable. | vol.overlay.colors.from.colortable |
| Translate names and indices of planes. | vol.planes |
| Extract a slice of a 3D image stack. | vol.slice |
| Compute R voxel index for FreeSurfer CRS voxel index. | vol.vox.from.crs |
| Visualize contour of a volume. | volvis.contour |
| Show continuous 3D voxel/volume data as a lightbox, optionally with a background brain volume and colormap. | volvis.lb |
| Draw a lightbox view from volume slices. | volvis.lightbox |
| Voxel-based visualization of volume mask at surface RAS positions. | volvis.voxels |
| The FreeSurfer default vox2ras_tkr matrix. | vox2ras_tkr |
| Write standard space group data to a standard FreeSurfer directory stucture. | write.group.morph.standard |
| Write per-vertex standard space data for a group of subjects to given file names. | write.group.morph.standard.mf |
| Reshape and write combined per-vertex data for a group to a single MGH file. | write.group.morph.standard.sf |
| Write data aggregated over regions to morphometry file for group. | write.region.aggregated |
| Write one value per atlas region for a subject. | write.region.values |
| Write one value per atlas region for a template subject. | write.region.values.fsaverage |
