| alphablend | Perform alpha blending for pairs of RGBA colors. |
| annot.outline | Compute outline vertex colors from annotation. |
| annot.outline.border.vertices | Compute the border vertices for each region in an annot. |
| apply.labeldata.to.morphdata | Apply a label to morphometry data. |
| apply.label.to.morphdata | Load a label from file and apply it to morphometry data. |
| apply.transform | Apply matmult transformation to input. |
| arrange.brainview.images | Combine several brainview images into a new figure. |
| arrange.brainview.images.grid | Combine several brainview images as a grid into a new figure. |
| boxcoords.from.bbox | Compute the coordinates of the 8 corners of a 3D box. |
| brain | Create fsbrain instance from 2 coloredmeshes. |
| brainviews | Show one or more views of the given meshes in rgl windows. |
| brainview.sd | Visualize a list of colored meshes from a single defined... |
| brainview.si | Visualize a list of colored meshes from a single viewpoint,... |
| brainview.sr | Visualize a list of colored meshes, rotating the camera... |
| brainview.t4 | Visualize a list of colored meshes from four angles. |
| brainview.t9 | Visualize a list of colored meshes from nine angles. |
| can.plot.colorbar | Determine whether colorbar can be plotted with given... |
| can.plot.colorbar.from.coloredmeshes | Determine whether colorbar can be plotted with given... |
| check.subjects.files | Report subjects missing files |
| check.subjectslist | Check whether the subjects_list looks good, warn if not. |
| clip.data | Clip data at quantiles to remove outliers. |
| clip_fun | Get data clipping function. |
| cm.cbry | Get cyan blue red yellow colormap function. |
| cm.div | Return the standard fsbrain diverging colormap. |
| cm.heat | Return the standard fsbrain heat colormap. |
| cm.qual | Return the standard fsbrain qualitative colormap. |
| cm.seq | Return the standard fsbrain sequential colormap. |
| 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... |
| coloredmeshes.combined.data.range | Retrieve combined data range from hemilist of coloredmeshes. |
| coloredmeshes.from.color | Create coloredmeshes for both hemis using pre-defined colors. |
| coloredmeshes.get.md | Retrieve metadata from hemilist of coloredmeshes. |
| coloredmesh.from.annot | Create a coloredmesh from an annotation of an atlas. |
| coloredmesh.from.color | Create a coloredmesh from a mesh and pre-defined colors. |
| coloredmesh.from.label | Create a coloredmesh from a label. |
| coloredmesh.from.mask | Create a coloredmesh from a mask. |
| coloredmesh.from.morphdata | Create a coloredmesh from arbitrary data. |
| coloredmesh.from.morph.native | Create a coloredmesh from native space morphometry data. |
| coloredmesh.from.morph.standard | Create a coloredmesh from standard space morphometry data. |
| coloredmesh.from.preloaded.data | Generate coloredmesh from loaded data. |
| coloredmesh.plot.colorbar.separate | Draw colorbar for coloredmeshes in separate 2D plot. |
| colorlist.brain.clusters | Return diverging color list |
| colors.are.grayscale | Check for the given color strings whether they represent gray... |
| colors.have.transparency | Check for the given color strings whether they have... |
| combine.colorbar.with.brainview.animation | Combine a colorbar and a brain animation in gif format into a... |
| combine.colorbar.with.brainview.image | Combine a colorbar and a brainview image into a new figure. |
| combine.colorbar.with.brainview.image.vertical | Combine a vertical colorbar and a brainview image into a new... |
| common.makecmap.range | Get cmap and colorlayer from data and makecmap_options. |
| constant.pervertexdata | Get vertex data for a single fs.surface or a hemilist of... |
| cube3D.tris | Return triangles for a 3D cube or cuboid. |
| cubes3D.tris | Vectorized version of cube3D.tris |
| deepcopylist.long | Write deepcopy list for longitudinal subjects. |
| deg2rad | Convert degree to radians |
| delete_all_optional_data | Delete all data in the package cache. |
| demo | Show demo visualization to test whether fsbrain is setup... |
| demographics.to.fsgd.file | Write FreeSurfer Group Descriptor (FSGD) file from... |
| demographics.to.qdec.table.dat | Convert a dataframe containing demographics data to a... |
| desaturate | Perform simple desaturation or grayscale conversion of RGBA... |
| download_fsaverage | Download the FreeSurfer v6 fsaverage subject. |
| download_fsaverage3 | Download the FreeSurfer v6 low-resolution fsaverage3 subject. |
| download_fsaverage6 | Download the FreeSurfer v6 fsaverage6 subject. |
| download_optional_data | Download optional data for this package if required. |
| download_optional_paper_data | Download extra data to reproduce the figures from the fsbrain... |
| draw.colorbar | Draw colorbar into background of current plot. |
| eeg_coords | Internal function to get some demo EEG electrode coordinates.... |
| ensure.fs.surface | Check whether parameter is an fs.surface instance. |
| ensure.tmesh3d | Ensure the mesh is a tmesh3d instance. Will convert... |
| export | Export high-quality brainview image with a colorbar. |
| export.coloredmesh.ply | Export a coloredmeshes with vertexcolors in PLY format. |
| extend_neighbors | Recursive computation of neighborhoods, see surf.sphere.dist |
| extract.volume.3D | Try to extract a 3D volume from the input argument. |
| 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... |
| flc | Given a list of path coordinates, create matrix containing... |
| force.to.range | Change data to ensure requested data_range. |
| fsaverage.path | Return path to fsaverage dir. |
| fsbrain.renderable | Check whether object can be rendered by fsbrain |
| fsbrain.set.default.figsize | Set default figure size for fsbrain visualization functions. |
| fs.coloredmesh | fs.coloredmesh constructor |
| fs.home | Return FreeSurfer path. |
| fslong.subjects.detect | Get subject names from sub directories of FreeSurfer long... |
| fslong.subjects.finished | Find completely run FreeSurfer long subjects in a recon-all... |
| fs.surface.as.adjacencylist | Turn surface mesh into a igraph and return its adjacency list... |
| fs.surface.to.igraph | Create igraph undirected graph from a brain surface mesh. |
| fs.surface.to.tmesh3d | Get an rgl tmesh3d instance from a brain surface mesh. |
| fs.surface.vertex.neighbors | Compute vertex neighborhoods or the full adjacency list for a... |
| fs.value.list.from.agg.res | Create a named value list from a dataframe. |
| fup | Transform first character of a string to uppercase. |
| gen.test.volume | Generate test 3D volume of integers. The volume has an outer... |
| geodesic.average.distance | Compute the average (pseudo-) geodesic distance on the mesh... |
| geodesic.ballstats | Compute geodesic ball area and perimeter at location defined... |
| geodesic.circles | Compute geodesic circles and ball stats for given vertices. |
| geodesic.dists.to.vertex | Simple internal wrapper around 'Rvcg::vcgDijkstra' with... |
| geodesic.path | Compute geodesic path from a source vertex to one or more... |
| geod.patches.color.overlay | Generate color overlay from geodesic patches around several... |
| geod.patches.color.overlay.singlehemi | Generate color overlay from geodesic patches around several... |
| geod.patches.pervertexdata | Generate per-vertex distance data from geodesic patches... |
| geod.patches.pervertexdata.singlehemi | Generate per-vertex distance data from geodesic patches... |
| geod.vert.neighborhood | Compute all vertices within given geodesic distance on the... |
| get.atlas.region.names | Determine atlas region names from a subject. |
| getIn | Retrieve values from nested named lists |
| get_optional_data_filepath | Access a single file from the package cache by its file name. |
| get.rglstyle | Get the default visualization style parameters as a named... |
| get.rglstyle.default | Get the default visualization style parameters as a named... |
| get.rglstyle.edges | Get the mesh edges visualization style parameters as a named... |
| get.rglstyle.glass | Get the glass visualization style parameters as a named list. |
| get.rglstyle.glass2 | Get the glass2 visualization style parameters as a named... |
| get.rglstyle.parameters | Produce the named list of style parameters from style... |
| get.rglstyle.semitransparent | Get the semi-transparent visualization style parameters as a... |
| get.rglstyle.shiny | Get a shiny visualization style. |
| get.slice.indices | Compute slice indices from slice definition. |
| get.subject.class | Construct FSGD Class name from group and non-continuous... |
| get.view.angle.names | Get list of valid view angle names. |
| group.agg.atlas.native | Aggregate native space morphometry data over brain atlas... |
| group.agg.atlas.standard | Aggregate standard space morphometry data over brain atlas... |
| 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.data.to.array | Convert group 2D data (1 vector per subject) to 4D array... |
| 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.morph.agg.native | Aggregate native space morphometry data over one hemisphere... |
| group.morph.agg.standard | Aggregate standard space (fsaverage) morphometry data over... |
| group.morph.agg.standard.vertex | Aggregate standard space morphometry data over subjects. |
| group.morph.native | Retrieve native space morphometry data for a group of... |
| groupmorph.split.hemilist | Split a per-vertex group data matrix for both hemispheres... |
| group.morph.standard | Retrieve standard space morphometry data for a group of... |
| group.morph.standard.sf | Read combined data for a group from a single file. |
| group.multimorph.agg.native | Aggregate native space morphometry data for multiple measures... |
| group.multimorph.agg.standard | Aggregate standard space (fsaverage) morphometry data for... |
| group.surface | Retrieve surface mesh data for a group of subjects. |
| handle.rglactions.highlight.points | Highlight requested points (if any), but apply given view... |
| hasIn | Check for values in nested named lists |
| hemilist | Create a hemilist from lh and rh data. |
| hemilist.derive.hemi | Derive 'hemi' string from the data in a hemilist |
| hemilist.from.prefixed.list | Create a hemilist from a named list with keys prefixed with... |
| 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. |
| hemi.lobe.labels | Compute lobe labels for a single hemi from aparc atlas. |
| hemlist.ensure.contains | title Ensure an key for a hemilist exists. |
| highlight.points.spheres | Draw small 3D spheres at given points. |
| highlight.vertices.on.subject | Highlight vertices given by index on a subject's meshes by... |
| highlight.vertices.on.subject.spheres | Highlight vertices given by index on a subject's meshes by... |
| highlight.vertices.spheres | Draw small 3D spheres at given brain mesh vertices. Supports... |
| hull.retain.along.axis | Copy the first *n* foreground voxel values. |
| image.remap.color | Remap a color in an image, typically used to set the... |
| images.annotate | Annotate image with text. |
| images.dimmax | Compute max width and height of magick images. |
| images.rescale.to.max.canvas | Rescale all images canvas to match the largest one. |
| images.same.height | Extent all images to the height of the image with maximal... |
| images.same.width | Extent all images to the width of the image with maximal... |
| is.fsbrain | Check whether object is an fsbrain (S3) |
| 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 |
| is.Triangles3D | Check whether object is a Triangles3D instance |
| label.border | Compute border of a label. |
| label.border.fast | Compute border vertices of a label using Rvcg. |
| label.colFn | A simple colormap function for binary colors. |
| label.colFn.inv | A simple colormap function for binary colors. |
| labeldata.from.mask | Create labeldata from a mask. |
| label.from.annotdata | Extract a region from an annotation as a label. |
| label.to.annot | Merge several labels into an annotation |
| limit_fun | Get data limiting function. |
| limit_fun_na | Get data limiting function to NA. |
| limit_fun_na_inside | Get data limiting function, setting values inside range to... |
| list_optional_data | Get file names available in package cache. |
| magick.grid | Arrange a multi-frame ImageMagick image into a grid. |
| mask.from.labeldata.for.hemi | Create a binary mask from labels. |
| mergehemi.annots | Merge the annotations from two hemispheres into one annot. |
| mesh.vertex.included.faces | Return all faces which are made up completely of the listed... |
| mesh.vertex.neighbors | Compute neighborhood of a vertex |
| mkco.cluster | Return recommended 'makecmap_options' for diverging cluster... |
| mkco.div | Return recommended 'makecmap_options' for diverging data. |
| mkco.heat | Return recommended 'makecmap_options' for sequential data... |
| mkco.seq | Return recommended 'makecmap_options' for sequential data. |
| normalize | Normalize data. |
| numverts.lh | Determine vertex count of left hemi from hemilist of surfaces... |
| numverts.rh | Determine vertex count of right hemi from hemilist of... |
| path.colors.from.orientation | Compute path color from its orientation. |
| path.slopes | Compute slopes of paths relative to axes. |
| perform.na.mapping | Perform NA mapping for transparency |
| perform.rglactions | Perform rglactions, like taking screenshots. |
| per.hemi.vertex.indices | Transform surfaces indices which go over two surfaces to... |
| pervertexdata.smoothgaussian | Perform Gaussian smoothing |
| pervertexdata.smoothnn | Perform iterative nearest-neighbor smoothing of per-vertex... |
| pervertexdata.smoothnn.compute.fwhm | Compute expected FWHM from given number of neighborhood... |
| pervertexdata.smoothnn.compute.numiter | Compute number of neighborhood smoothing iterations to reach... |
| plot.fsbrain.colorbar | Draw a simple colorbar from colors. |
| pp.named.list | Pretty-print a named list or vector. |
| principal.curvatures | Computes principal curvatures according to 2 definitions from... |
| print.fsbrain | Print description of an fsbrain (S3). |
| print.fs.coloredmesh | Print description of a brain coloredmesh (S3). |
| print.fs.coloredvoxels | Print description of fs.coloredvoxels (S3). |
| qc.for.group | Perform data quality check based on computed region stats. |
| qc.from.regionwise.df | Perform data quality check based on a dataframe containing... |
| qc.from.segstats.table | Perform data quality check based on a segstats table. |
| qc.from.segstats.tables | Perform data quality check based on a segstats table. |
| qc.fslong.checkidenticaldata | Check whether subjects for FS longitudinal pipeline contain... |
| qc.report.html | Create visual quality check report from QC result. |
| qc.vis.failcount.by.region | Visualize the number of outlier subjects per region in your... |
| qdec.table.filter | Filter QDEC long table for subjects. |
| qdec.table.skeleton | Generate skeleton dataframe for FreeSurfer QDEC long file... |
| rad2deg | Convert raduians to degree |
| 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 |
| read.md.subjects.from.fsgd | Read subjects list from an FSGD file. |
| recycle | Recycle parameters or whatever. |
| regions.to.ignore | Give suggestions for regions to ignore for an atlas. |
| report.on.demographics | Print a demographics report |
| rglactions | Create rglactions list, suitable to be passed as parameter to... |
| rglactions.has.key | Check for a key in names of rglactions. |
| rglactions.transform | Apply data transformation rglactions. |
| rgl.coord.lines | Plot x, y and z axes in R,G,B. |
| rglo | Get rgloptions and consider global options. |
| rglot | Get rgloptions for testing. |
| rglvoxels | Draw 3D boxes at locations using rgl. |
| rotation.matrix.for.axis.rot | Get rotation matrix for a 3D rotation around an axis. |
| scale01 | Scale given values to range 0..1. |
| scale.to.range.zero.one | Scale given values to range 0..1. |
| shape.descriptor.names | Get all shape descriptor names. |
| shape.descriptors | Computes geometric curvature-based descriptors. |
| shift.hemis.apart | Shift hemispheres apart. |
| shift.hemis.rglactions | Shift hemis apart if indicated in rglactions |
| sjd.demo | Download optional demo data if needed and return its path. |
| sjld | Get subjects list from subjects.txt file in dir. |
| sortcoloredmeshes.by.hemi | Sort coloredmeshes into 2 lists by their 'hemi' property. |
| sph2fs | Transform spherical coordinates to FreeSurfer surface space... |
| 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... |
| spread.values.over.subject | Spread the values in the region_value_list and return them... |
| subject.annot | Load an annotation for a subject. |
| subject.annot.border | Compute annot border vertices. |
| subject.atlas.agg | Aggregate morphometry data over brain atlas regions for a... |
| subject.descriptor.geodesic.average.distance | Compute mean geodesic distance descriptor for a subject. |
| subject.filepath.any | Construct filepath of any freesurfer file. |
| 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.lobes | Load labels representing brain lobes. |
| 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.num.verts | Get subjects vertex count. |
| subject.report.html | Create visual quality check report from QC result. |
| subject.surface | Load a surface for a subject. |
| subject.volume | Read a brain volume. |
| submesh.vertex | Create a submesh including only the given vertices. |
| surface.curvatures | Compute the k1 and k2 principal curvatures of a mesh. |
| surf.avg.vertexradius | Compute average distance from the origin to each vertex. |
| surf.center.fsaverage | Get pre-computed center for fsaverage white surface. |
| surf.metric.properties | Compute metric surface properties. |
| surf.radius.fsaverage | Get pre-computed radius for fsaverage white surface. |
| surf.sphere.dist | Compute vertex neighborhoods on a sphere based on the given... |
| surf.sphere.gaussianweights | Compute Gaussian weights |
| surf.sphere.spatialfilter | Apply spatial filter to surface data. |
| surfs.props | Compute simple version of center and radius of 2 meshes. |
| symmrange | Given data, compute symmetric range around zero. |
| test.numerical.meandiff | Perform tests for group differences on paired or unpaired... |
| test.numerical.meandiff.paired | Perform tests for group differences on paired data (repeated... |
| test.numerical.meandiff.unpaired | Perform tests for group differences on unpaired data for two... |
| tmesh3d.to.fs.surface | Get an fs.surface brain mesh from an rgl tmesh3d instance. |
| track.length | Compute the total length of a path given by the coordinates... |
| vdata.split.by.hemi | Split morph data vector at hemisphere boundary. |
| vertex.coords | Return coordinates for vertices, supporting entire brain via... |
| vertex.hemis | Return the proper hemi string ('lh' or 'rh') for each vertex. |
| vis.coloredmesh | Draw a coloredmesh using a style. |
| vis.coloredmeshes | Visualize a list of colored meshes in a single scene. |
| vis.coloredmeshes.rotating | Visualize a list of colored meshes in a single scene and... |
| vis.color.on.subject | Visualize pre-defined vertex colors on a subject. |
| vis.colortable.legend | Create a separate legend plot for a colortable or an... |
| vis.data.on.fsaverage | Visualize arbitrary data on the fsaverage template subject,... |
| vis.data.on.group.native | Visualize native space data on a group of subjects. |
| vis.data.on.group.standard | Visualize standard space data for a group on template. |
| vis.data.on.subject | Visualize arbitrary data on the surface of any subject. |
| vis.dti.trk | Visualize DTI tracks from Diffusion Toolkit/TrackVis TRK... |
| vis.export.from.coloredmeshes | Export high-quality brainview image with a colorbar. |
| vis.fs.surface | Visualize fs.surface mesh |
| vis.group.annot | Plot atlas annotations for a group of subjects. |
| vis.group.coloredmeshes | Plot coloredmeshes for a group of subjects. |
| vis.group.morph.native | Plot native space morphometry data for a group of subjects. |
| vis.group.morph.standard | Plot standard space morphometry data for a group of subjects. |
| vis.labeldata.on.subject | Visualize a label on the surface of a subject. |
| vislayout.from.coloredmeshes | Visualize coloredmeshes from several angles and combine the... |
| 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.paths | Visualize many paths. |
| vis.paths.along.verts | Visualize several paths in different colors. |
| vis.region.values.on.subject | Visualize arbitrary data, one value per atlas region, on the... |
| vis.renderable | Visualize a renderable object |
| vis.rotated.coloredmeshes | Rotate and visualize coloredmeshes, applying a style. |
| vis.seg.legend | Plot legend for a brain volume segmentation based on... |
| 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 or a... |
| vis.subject.pre | Visualize pre-loaded data. |
| vis.symmetric.data.on.subject | Visualize clusters or activation data on the surface of any... |
| 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... |
| vol.boundary.mask | Compute foreground pixels over the whole 3D imagestack. |
| 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... |
| vol.overlay.colors.from.colortable | Compute voxel colors based on colortable. |
| vol.plane.axes | Get indices of the axes defining the given plane. |
| vol.planes | Translate names and indices of planes. |
| vol.slice | Extract a slice of a 3D image stack. |
| volvis.contour | Visualize contour of a volume. |
| volvis.lb | Show continuous 3D voxel/volume data as a lightbox,... |
| volvis.lightbox | Draw a lightbox view from volume slices. |
| volvis.voxels | Voxel-based visualization of volume mask at surface RAS... |
| vol.vox.from.crs | Compute R voxel index for FreeSurfer CRS voxel index. |
| vox2ras_tkr | The FreeSurfer default vox2ras_tkr matrix. |
| wrapped.image.append | Wrapper around magick::image_append that allows specifying... |
| write.group.morph.standard | Write standard space group data to a standard FreeSurfer... |
| write.group.morph.standard.mf | Write per-vertex standard space data for a group of subjects... |
| write.group.morph.standard.sf | Reshape and write combined per-vertex data for a group to a... |
| write.group.morph.standard.singlehemi | Write single hemi per-vertex data for a group of subjects to... |
| write.region.aggregated | Write data aggregated over regions to morphometry file for... |
| 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. |
