arrange.brainview.images.grid
Combine several brainview images as a grid into a new figure.
Compute surface color layer from morph-like data.
Report subjects missing files
Check whether the subjects_list looks good, warn if not.
coloredmesh.from.morph.native
Create a coloredmesh from native space morphometry data.
Return the standard fsbrain sequential colormap.
Compute binarized mean curvature surface color layer.
coloredmesh.from.morph.standard
Create a coloredmesh from standard space morphometry data.
Vectorized version of cube3D.tris
Find the FREESURFER_HOME directory on disk.
Return triangles for a 3D cube or cuboid.
Perform simple desaturation or grayscale conversion of RGBA colors.
Download the FreeSurfer v6 fsaverage subject.
Find the subject directory containing the fsaverage subject (or others) on disk.
Check for the given color strings whether they have transparency, i.e., an alpha channel value != fully opaque.
Given a list of path coordinates, create matrix containing only the first and last point of each path.
Delete all data in the package cache.
combine.colorbar.with.brainview.animation
Combine a colorbar and a brain animation in gif format into a new animation.
Export a coloredmeshes with vertexcolors in PLY format.
Show demo visualization to test whether fsbrain is setup correctly.
Change data to ensure requested data_range.
annot.outline.border.vertices
Compute the border vertices for each region in an annot.
Get subject names from sub directories of FreeSurfer long directory.
Load a label from file and apply it to morphometry data.
Get an rgl tmesh3d instance from a brain surface mesh.
fs.surface.vertex.neighbors
Compute vertex neighborhoods or the full adjacency list for a mesh using the Rvcg or igraph library.
Recursive computation of neighborhoods, see surf.sphere.dist
Compute atlas or annotation surface color layer.
Find completely run FreeSurfer long subjects in a recon-all long output folder.
Visualize a list of colored meshes from four angles.
Visualize a list of colored meshes, rotating the camera around them.
Compute binarized mean curvature surface color layer.
Produce the named list of style parameters from style definition.
Determine atlas region names from a subject.
Create a coloredmesh from a label.
Create a coloredmesh from a mask.
Get the default visualization style parameters as a named list.
Aggregate standard space morphometry data over brain atlas regions and subjects for a group of subjects.
group.morph.agg.standard.vertex
Aggregate standard space morphometry data over subjects.
Aggregate native space morphometry data over brain atlas regions and subjects for a group of subjects.
Retrieve native space morphometry data for a group of subjects.
Create coloredmeshes for both hemis using pre-defined colors.
Write deepcopy list for longitudinal subjects.
Retrieve metadata from hemilist of coloredmeshes.
group.multimorph.agg.native
Aggregate native space morphometry data for multiple measures over hemispheres for a group of subjects.
get.rglstyle.semitransparent
Get the semi-transparent visualization style parameters as a named list.
download_optional_paper_data
Download extra data to reproduce the figures from the fsbrain paper.
Convert degree to radians
title Ensure an key for a hemilist exists.
Wrap data into a named hemi list.
highlight.vertices.on.subject
Highlight vertices given by index on a subject's meshes by coloring faces.
Draw small 3D spheres at given points.
group.multimorph.agg.standard
Aggregate standard space (fsaverage) morphometry data for multiple measures over hemispheres for a group of subjects.
Compute max width and height of magick images.
Annotate image with text.
Draw coloredbar into background of current plot.
Enumerate all edges of the given faces or mesh.
fs.surface.as.adjacencylist
Turn surface mesh into a igraph and return its adjacency list representation.
Try to extract a 3D volume from the input argument.
Create igraph undirected graph from a brain surface mesh.
geod.patches.color.overlay
Generate color overlay from geodesic patches around several vertices.
geod.patches.color.overlay.singlehemi
Generate color overlay from geodesic patches around several vertices for a single hemi.
Perform alpha blending for pairs of RGBA colors.
Check whether object is an fs.coloredmesh (S3)
Get file names available in package cache.
Check whether object is an fs.coloredvoxels instance (S3)
Arrange a multi-frame ImageMagick image into a grid.
pervertexdata.smoothnn.compute.fwhm
Compute expected FWHM from given number of neighborhood smoothing iterations.
Transform surfaces indices which go over two surfaces to per-hemi indices.
Compute slopes of paths relative to axes.
Simple internal wrapper around Rvcg::vcgDijkstra with function check.
Compute geodesic path from a source vertex to one or more target vertices.
pervertexdata.smoothnn.compute.numiter
Compute number of neighborhood smoothing iterations to reach requested fwhm.
Perform data quality check based on computed region stats.
Construct FSGD Class name from group and non-continuous covariate columns.
Perform data quality check based on a dataframe containing aggregated region-wise data.
A simple colormap function for binary colors.
Get data limiting function.
A simple colormap function for binary colors.
Create labeldata from a mask.
Return recommended 'makecmap_options' for diverging cluster data.
Compute outline vertex colors from annotation.
Visualize a list of colored meshes from nine angles.
Get list of valid view angle names.
Load annotations for a group of subjects.
Return the standard fsbrain heat colormap.
Show one or more views of the given meshes in rgl windows.
Return the standard fsbrain qualitative colormap.
Return recommended 'makecmap_options' for diverging data.
Print description of fs.coloredvoxels (S3).
Print description of an fsbrain (S3).
group.concat.measures.native
Concatenate native space data for a group of subjects.
Read subjects file
Retrieve standard space morphometry data for a group of subjects.
Read combined data for a group from a single file.
Compute lobe labels for a single hemi from aparc atlas.
read.md.subjects.from.fsgd
Read subjects list from an FSGD file.
Compute average distance from the origin to each vertex.
Get pre-computed center for fsaverage white surface.
Compute vertex neighborhoods on a sphere based on the given max distance along the sphere.
collayer.from.morphlike.data
Compute surface color layer from morph-like data.
Create a hemilist from lh and rh data.
Recycle parameters or whatever.
Extent all images to the width of the image with maximal width.
coloredmesh.plot.colorbar.separate
Draw colorbar for coloredmeshes in separate 2D plot.
Merge two or more color layers based on their transparency values.
demographics.to.qdec.table.dat
Convert a dataframe containing demographics data to a qdec.table.dat file and related files.
coloredmeshes.combined.data.range
Retrieve combined data range from hemilist of coloredmeshes.
demographics.to.fsgd.file
Write FreeSurfer Group Descriptor (FSGD) file from demographics dataframe.
Give suggestions for regions to ignore for an atlas.
Visualize native space data on a group of subjects.
Create rglactions list, suitable to be passed as parameter to vis functions.
surf.sphere.gaussianweights
Compute Gaussian weights
apply.labeldata.to.morphdata
Apply a label to morphometry data.
Check for a key in names of rglactions.
Check whether object is a Triangles3D instance
spread.values.over.subject
Spread the values in the region_value_list and return them for one hemisphere.
vis.data.on.group.standard
Visualize standard space data for a group on template.
Compute 3D bounding box of a volume.
Ensure the mesh is a tmesh3d instance. Will convert fs.surfaces to one automatically.
Apply matmult transformation to input.
Load an annotation for a subject.
Return recommended 'makecmap_options' for sequential data.
Extract a region from an annotation as a label.
Merge several labels into an annotation
Perform rglactions, like taking screenshots.
Return recommended 'makecmap_options' for sequential data with heatmap style.
Compute annot border vertices.
Filter QDEC long table for subjects.
Perform NA mapping for transparency
Apply a boundary box to a volume, returning the inner volume part
Plot x, y and z axes in R,G,B.
Visualize a list of colored meshes from a single viewpoint, interactively.
Visualize a list of colored meshes from a single defined angle.
Get cyan blue red yellow colormap function.
Export high-quality brainview image with a colorbar.
Print a demographics report
Generate skeleton dataframe for FreeSurfer QDEC long file from subjects list.
rotation.matrix.for.axis.rot
Get rotation matrix for a 3D rotation around an axis.
write.group.morph.standard.sf
Reshape and write combined per-vertex data for a group to a single MGH file.
geod.patches.pervertexdata
Generate per-vertex distance data from geodesic patches around several vertices.
Write data aggregated over regions to morphometry file for group.
Return the standard fsbrain diverging colormap.
write.group.morph.standard.singlehemi
Write single hemi per-vertex data for a group of subjects to given file names.
Aggregate morphometry data over brain atlas regions for a subject.
Write one value per atlas region for a subject.
Read a brain volume.
Compute the coordinates of the 8 corners of a 3D box.
Create a submesh including only the given vertices.
Perform tests for group differences on paired or 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.
Create fsbrain instance from 2 coloredmeshes.
Create a coloredmesh from an annotation of an atlas.
Create a coloredmesh from a mesh and pre-defined colors.
Download optional demo data if needed and return its path.
Visualize pre-defined vertex colors on a subject.
Shift hemis apart if indicated in rglactions
Scale given values to range 0..1.
Return diverging color list
Get the mesh edges visualization style parameters as a named list.
geod.patches.pervertexdata.singlehemi
Generate per-vertex distance data from geodesic patches around several vertices for a single hemi.
vol.overlay.colors.from.activation
Generate colors for a 3D volume, based on the activation data and a colormap.
Get the default visualization style parameters as a named list.
Determine whether colorbar can be plotted with given metadata.
Get cmap and colorlayer from data and makecmap_options.
Check for the given color strings whether they represent gray scale colors.
can.plot.colorbar.from.coloredmeshes
Determine whether colorbar can be plotted with given coloredmeshes.
Compute binarized sulcal depth surface color layer.
Compute surface color layer from annotation or atlas data.
Create a separate legend plot for a colortable or an annotation.
Load labels representing brain lobes.
get_optional_data_filepath
Access a single file from the package cache by its file name.
Retrieve values from nested named lists
Aggregate native space morphometry data over one hemisphere for a group of subjects.
Get vertex data for a single fs.surface or a hemilist of surfaces.
coloredmesh.from.morphdata
Create a coloredmesh from arbitrary data.
highlight.vertices.on.subject.spheres
Highlight vertices given by index on a subject's meshes by coloring faces.
hemilist.get.combined.data
Get combined data of hemi list
Aggregate standard space (fsaverage) morphometry data over one hemisphere for a group of subjects.
Unwrap hemi data from a named hemi list.
Compute the k1 and k2 principal curvatures of a mesh.
Download optional data for this package if required.
Download the FreeSurfer v6 low-resolution fsaverage3 subject.
Internal function to get some demo EEG electrode coordinates. Will be removed from public API. Do not use this.
Return path to fsaverage dir.
Check whether parameter is an fs.surface instance.
fs.value.list.from.agg.res
Create a named value list from a dataframe.
Visualize arbitrary data on the fsaverage template subject, if available.
Transform first character of a string to uppercase.
Plot atlas annotations for a group of subjects.
Generate test 3D volume of integers. The volume has an outer background area (intensity value 'bg') and an inner foreground areas (intensity value 200L).
Compute all vertices within given geodesic distance on the mesh.
geodesic.average.distance
Compute the average (pseudo-) geodesic distance on the mesh from each vertex to all other vertices.
Compute a mask for a subject.
Retain only the outer hull voxels of the foreground.
surf.sphere.spatialfilter
Apply spatial filter to surface data.
Visualize a label on the surface of a subject.
Plot coloredmeshes for a group of subjects.
coloredmesh.from.preloaded.data
Generate coloredmesh from loaded data.
Get the glass visualization style parameters as a named list.
Compute border of a label.
highlight.vertices.spheres
Draw small 3D spheres at given brain mesh vertices. Supports full brain (2 meshes) as well.
Visualize a vertex mask on the surface of a subject.
Compute border vertices of a label using Rvcg.
Get the glass2 visualization style parameters as a named list.
group.concat.measures.standard
Concatenate standard space data for a group of subjects.
Visualize a renderable object
mask.from.labeldata.for.hemi
Create a binary mask from labels.
vis.subject.morph.standard
Visualize native space morphometry data for a subject or a group.
Merge the annotations from two hemispheres into one annot.
Visualize pre-loaded data.
Convert group 2D data (1 vector per subject) to 4D array format.
handle.rglactions.highlight.points
Highlight requested points (if any), but apply given view rotation before doing so.
Draw a coloredmesh using a style.
Plot standard space morphometry data for a group of subjects.
Plot native space morphometry data for a group of subjects.
vol.overlay.colors.from.colortable
Compute voxel colors based on colortable.
combine.colorbar.with.brainview.image.vertical
Combine a vertical colorbar and a brainview image into a new figure.
combine.colorbar.with.brainview.image
Combine a colorbar and a brainview image into a new figure.
Compute R voxel index for FreeSurfer CRS voxel index.
Extract a slice of a 3D image stack.
Draw a lightbox view from volume slices.
Voxel-based visualization of volume mask at surface RAS positions.
Check for values in nested named lists
vis.rotated.coloredmeshes
Rotate and visualize coloredmeshes, applying a style.
Print description of a brain coloredmesh (S3).
write.region.values.fsaverage
Write one value per atlas region for a template subject.
Compute foreground pixels over the whole 3D imagestack.
Computes principal curvatures according to 2 definitions from raw k1 and k2 values.
fs.coloredmesh constructor
Derive 'hemi' string from the data in a hemilist
Return FreeSurfer path.
Check whether object can be rendered by fsbrain
fsbrain.set.default.figsize
Set default figure size for fsbrain visualization functions.
Perform data quality check based on a segstats table.
Perform data quality check based on a segstats table.
Compute geodesic circles and ball stats for given vertices.
hemilist.from.prefixed.list
Create a hemilist from a named list with keys prefixed with 'lh_' and 'rh_'.
Compute geodesic ball area and perimeter at location defined by geodists for all radii.
Extract a region from an atlas annotation as a label for a group of subjects.
Compute slice indices from slice definition.
Retrieve surface mesh data for a group of subjects.
Retrieve label data for a group of subjects.
Get a shiny visualization style.
Copy the first *n* foreground voxel values.
groupmorph.split.hemilist
Split a per-vertex group data matrix for both hemispheres into a hemilist at given index.
images.rescale.to.max.canvas
Rescale all images canvas to match the largest one.
Extent all images to the height of the image with maximal height.
Remap a color in an image, typically used to set the background color to transparent.
Get data limiting function, setting values inside range to NA.
Get data limiting function to NA.
Convert raduians to degree
Determine vertex count of right hemi from hemilist of surfaces or the count itself.
Check whether object is an fsbrain (S3)
Check whether x is a hemilist
path.colors.from.orientation
Compute path color from its orientation.
The FreeSurfer default ras2vox_tkr matrix.
Draw a simple colorbar from colors.
mesh.vertex.included.faces
Return all faces which are made up completely of the listed vertices.
Get rgloptions for testing.
Draw 3D boxes at locations using rgl.
Spread a single value for a region to all region vertices.
Compute neighborhood of a vertex
Spread the values in the region_value_list and return them for one hemisphere.
subject.descriptor.geodesic.average.distance
Compute mean geodesic distance descriptor for a subject.
qc.fslong.checkidenticaldata
Check whether subjects for FS longitudinal pipeline contain data that is identical between time points.
Pretty-print a named list or vector.
qc.vis.failcount.by.region
Visualize the number of outlier subjects per region in your dataset.
write.group.morph.standard.mf
Write per-vertex standard space data for a group of subjects to given file names.
Scale given values to range 0..1.
Read colors from CSV file.
Read demographics file
vis.export.from.coloredmeshes
Export high-quality brainview image with a colorbar.
Construct filepath of any freesurfer file.
Determine vertex count of left hemi from hemilist of surfaces or the count itself.
Return coordinates for vertices, supporting entire brain via hemilist.
Compute metric surface properties.
Normalize data.
Get pre-computed radius for fsaverage white surface.
pervertexdata.smoothgaussian
Perform Gaussian smoothing
Get all shape descriptor names.
Computes geometric curvature-based descriptors.
subject.filepath.morph.native
Construct filepath of native space morphometry data file.
Visualize a list of colored meshes in a single scene.
vol.mask.from.segmentation
Extract subset from a volume by value.
Shift hemispheres apart.
subject.filepath.morph.standard
Construct filepath of standard space morphometry data file.
test.numerical.meandiff.unpaired
Perform tests for group differences on unpaired data for two groups.
Get subjects vertex count.
Get an fs.surface brain mesh from an rgl tmesh3d instance.
Load a surface for a subject.
Compute the total length of a path given by the coordinates of its points.
Perform iterative nearest-neighbor smoothing of per-vertex data.
Get rgloptions and consider global options.
Apply data transformation rglactions.
Plot legend for a brain volume segmentation based on colorLUT.
vis.coloredmeshes.rotating
Visualize a list of colored meshes in a single scene and rotate them, movie-style.
Get indices of the axes defining the given plane.
Transform spherical coordinates to FreeSurfer surface space to plot things around a brain.
sort.coloredmeshes.by.hemi
Sort coloredmeshes into 2 lists by their 'hemi' property.
Visualize an annotation for a subject.
write.group.morph.standard
Write standard space group data to a standard FreeSurfer directory stucture.
Visualize fs.surface mesh
Merge background volume and overlay to new colors.
Split morph data vector at hemisphere boundary.
Visualize arbitrary data on the surface of any subject.
Visualize DTI tracks from Diffusion Toolkit/TrackVis TRK format file.
Retrieve label data for a single subject.
Translate names and indices of planes.
Extract a region from an atlas annotation as a label for a subject.
Retrieve native space morphometry data for a single subject.
Visualize a binary label for a subject.
Retrieve standard space morphometry data for a single subject.
Compute simple version of center and radius of 2 meshes.
Draw a 3D line from vertex to vertex
Visualize many paths.
Given data, compute symmetric range around zero.
Visualize several paths in different colors.
vislayout.from.coloredmeshes
Visualize coloredmeshes from several angles and combine the images into a new figure.
vis.symmetric.data.on.subject
Visualize clusters or activation data on the surface of any subject.
Show continuous 3D voxel/volume data as a lightbox, optionally with a background brain volume and colormap.
Return the proper hemi string ('lh' or 'rh') for each vertex.
Visualize native space morphometry data for a subject.
Wrapper around magick::image_append that allows specifying the background color when working with images of different width/height.
vis.region.values.on.subject
Visualize arbitrary data, one value per atlas region, on the surface of any subject (including template subjects).
The FreeSurfer default vox2ras_tkr matrix.
Turn volume into an ImageMagick image stack.
Convert integer intensity image to RGB color string form.
Visualize contour of a volume.
Combine several brainview images into a new figure.
Compute surface color layer from annotation or atlas data.
Clip data at quantiles to remove outliers.
Get data clipping function.