Managing and Visualizing Brain Surface Data
Perform alpha blending for pairs of RGBA colors.
Compute the border vertices for each region in an annot.
Compute outline vertex colors from annotation.
Load a label from file and apply it to morphometry data.
Apply a label to morphometry data.
Apply matmult transformation to input.
Combine several brainview images as a grid into a new figure.
Combine several brainview images into a new figure.
Compute the coordinates of the 8 corners of a 3D box.
Create fsbrain instance from 2 coloredmeshes.
Visualize a list of colored meshes from a single defined angle.
Visualize a list of colored meshes from a single viewpoint, interactiv...
Visualize a list of colored meshes, rotating the camera around them.
Visualize a list of colored meshes from four angles.
Visualize a list of colored meshes from nine angles.
Show one or more views of the given meshes in rgl windows.
Determine whether colorbar can be plotted with given coloredmeshes.
Determine whether colorbar can be plotted with given metadata.
Report subjects missing files
Check whether the subjects_list looks good, warn if not.
Get data clipping function.
Clip data at quantiles to remove outliers.
Get cyan blue red yellow colormap function.
Return the standard fsbrain diverging colormap.
Return the standard fsbrain heat colormap.
Return the standard fsbrain qualitative colormap.
Return the standard fsbrain sequential colormap.
Compute atlas or annotation surface color layer.
Compute binarized mean curvature surface color layer.
Compute binarized mean curvature surface color layer.
Compute binarized sulcal depth surface color layer.
Compute surface color layer from annotation or atlas data.
Compute surface color layer from annotation or atlas data.
Compute surface color layer from morph-like data.
Compute surface color layer from morph-like data.
Merge two or more color layers based on their transparency values.
Create a coloredmesh from an annotation of an atlas.
Create a coloredmesh from a mesh and pre-defined colors.
Create a coloredmesh from a label.
Create a coloredmesh from a mask.
Create a coloredmesh from native space morphometry data.
Create a coloredmesh from standard space morphometry data.
Create a coloredmesh from arbitrary data.
Generate coloredmesh from loaded data.
Draw colorbar for coloredmeshes in separate 2D plot.
Retrieve combined data range from hemilist of coloredmeshes.
Create coloredmeshes for both hemis using pre-defined colors.
Retrieve metadata from hemilist of coloredmeshes.
Return diverging color list
Check for the given color strings whether they represent gray scale co...
Check for the given color strings whether they have transparency, i.e....
Combine a colorbar and a brain animation in gif format into a new anim...
Combine a colorbar and a brainview image into a new figure.
Combine a vertical colorbar and a brainview image into a new figure.
Get cmap and colorlayer from data and makecmap_options.
Get vertex data for a single fs.surface or a hemilist of surfaces.
Return triangles for a 3D cube or cuboid.
Vectorized version of cube3D.tris
Write deepcopy list for longitudinal subjects.
Convert degree to radians
Delete all data in the package cache.
Show demo visualization to test whether fsbrain is setup correctly.
Write FreeSurfer Group Descriptor (FSGD) file from demographics datafr...
Convert a dataframe containing demographics data to a qdec.table.dat f...
Perform simple desaturation or grayscale conversion of RGBA colors.
Download the FreeSurfer v6 fsaverage subject.
Download the FreeSurfer v6 low-resolution fsaverage3 subject.
Download the FreeSurfer v6 fsaverage6 subject.
Download optional data for this package if required.
Download extra data to reproduce the figures from the fsbrain paper.
Draw colorbar into background of current plot.
Internal function to get some demo EEG electrode coordinates. Will be ...
Check whether parameter is an fs.surface instance.
Ensure the mesh is a tmesh3d instance. Will convert fs.surfaces to one...
Export a coloredmeshes with vertexcolors in PLY format.
Export high-quality brainview image with a colorbar.
Recursive computation of neighborhoods, see surf.sphere.dist
Try to extract a 3D volume from the input argument.
Enumerate all edges of the given faces or mesh.
Find the FREESURFER_HOME directory on disk.
Find the subject directory containing the fsaverage subject (or others...
Given a list of path coordinates, create matrix containing only the fi...
Change data to ensure requested data_range.
fs.coloredmesh constructor
Return FreeSurfer path.
Turn surface mesh into a igraph and return its adjacency list represen...
Create igraph undirected graph from a brain surface mesh.
Get an rgl tmesh3d instance from a brain surface mesh.
Compute vertex neighborhoods or the full adjacency list for a mesh usi...
Create a named value list from a dataframe.
Return path to fsaverage dir.
Check whether object can be rendered by fsbrain
Set default figure size for fsbrain visualization functions.
Get subject names from sub directories of FreeSurfer long directory.
Find completely run FreeSurfer long subjects in a recon-all long outpu...
Transform first character of a string to uppercase.
Generate test 3D volume of integers. The volume has an outer backgroun...
Generate color overlay from geodesic patches around several vertices.
Generate color overlay from geodesic patches around several vertices f...
Generate per-vertex distance data from geodesic patches around several...
Generate per-vertex distance data from geodesic patches around several...
Compute all vertices within given geodesic distance on the mesh.
Compute the average (pseudo-) geodesic distance on the mesh from each ...
Compute geodesic ball area and perimeter at location defined by geodis...
Compute geodesic circles and ball stats for given vertices.
Simple internal wrapper around Rvcg::vcgDijkstra with function check...
Compute geodesic path from a source vertex to one or more target verti...
Access a single file from the package cache by its file name.
Determine atlas region names from a subject.
Get the default visualization style parameters as a named list.
Get the mesh edges visualization style parameters as a named list.
Get the glass visualization style parameters as a named list.
Get the glass2 visualization style parameters as a named list.
Produce the named list of style parameters from style definition.
Get the default visualization style parameters as a named list.
Get the semi-transparent visualization style parameters as a named lis...
Get a shiny visualization style.
Compute slice indices from slice definition.
Construct FSGD Class name from group and non-continuous covariate colu...
Get list of valid view angle names.
Retrieve values from nested named lists
Aggregate native space morphometry data over brain atlas regions and s...
Aggregate standard space morphometry data over brain atlas regions and...
Load annotations for a group of subjects.
Concatenate native space data for a group of subjects.
Concatenate standard space data for a group of subjects.
Convert group 2D data (1 vector per subject) to 4D array format.
Extract a region from an atlas annotation as a label for a group of su...
Retrieve label data for a group of subjects.
Aggregate native space morphometry data over one hemisphere for a grou...
Aggregate standard space (fsaverage) morphometry data over one hemisph...
Aggregate standard space morphometry data over subjects.
Retrieve native space morphometry data for a group of subjects.
Retrieve standard space morphometry data for a group of subjects.
Read combined data for a group from a single file.
Aggregate native space morphometry data for multiple measures over hem...
Aggregate standard space (fsaverage) morphometry data for multiple mea...
Retrieve surface mesh data for a group of subjects.
Split a per-vertex group data matrix for both hemispheres into a hemil...
Highlight requested points (if any), but apply given view rotation bef...
Check for values in nested named lists
Compute lobe labels for a single hemi from aparc atlas.
Derive 'hemi' string from the data in a hemilist
Create a hemilist from a named list with keys prefixed with 'lh_' and ...
Get combined data of hemi list
Create a hemilist from lh and rh data.
Unwrap hemi data from a named hemi list.
Wrap data into a named hemi list.
title Ensure an key for a hemilist exists.
Draw small 3D spheres at given points.
Highlight vertices given by index on a subject's meshes by coloring fa...
Highlight vertices given by index on a subject's meshes by coloring fa...
Draw small 3D spheres at given brain mesh vertices. Supports full brai...
Copy the first n foreground voxel values.
Remap a color in an image, typically used to set the background color ...
Annotate image with text.
Compute max width and height of magick images.
Rescale all images canvas to match the largest one.
Extent all images to the height of the image with maximal height.
Extent all images to the width of the image with maximal width.
Check whether object is an fs.coloredmesh (S3)
Check whether object is an fs.coloredvoxels instance (S3)
Check whether object is an fsbrain (S3)
Check whether x is a hemilist
Check whether object is a Triangles3D instance
Compute border vertices of a label using Rvcg.
Compute border of a label.
A simple colormap function for binary colors.
A simple colormap function for binary colors.
Extract a region from an annotation as a label.
Merge several labels into an annotation
Create labeldata from a mask.
Get data limiting function, setting values inside range to NA.
Get data limiting function to NA.
Get data limiting function.
Get file names available in package cache.
Arrange a multi-frame ImageMagick image into a grid.
Create a binary mask from labels.
Merge the annotations from two hemispheres into one annot.
Return all faces which are made up completely of the listed vertices.
Compute neighborhood of a vertex
Return recommended 'makecmap_options' for diverging cluster data.
Return recommended 'makecmap_options' for diverging data.
Return recommended 'makecmap_options' for sequential data with heatmap...
Return recommended 'makecmap_options' for sequential data.
Normalize data.
Determine vertex count of left hemi from hemilist of surfaces or the c...
Determine vertex count of right hemi from hemilist of surfaces or the ...
Compute path color from its orientation.
Compute slopes of paths relative to axes.
Transform surfaces indices which go over two surfaces to per-hemi indi...
Perform NA mapping for transparency
Perform rglactions, like taking screenshots.
Perform Gaussian smoothing
Compute expected FWHM from given number of neighborhood smoothing iter...
Compute number of neighborhood smoothing iterations to reach requested...
Perform iterative nearest-neighbor smoothing of per-vertex data.
Draw a simple colorbar from colors.
Pretty-print a named list or vector.
Computes principal curvatures according to 2 definitions from raw k1 a...
Print description of a brain coloredmesh (S3).
Print description of fs.coloredvoxels (S3).
Print description of an fsbrain (S3).
Perform data quality check based on computed region stats.
Perform data quality check based on a dataframe containing aggregated ...
Perform data quality check based on a segstats table.
Perform data quality check based on a segstats table.
Check whether subjects for FS longitudinal pipeline contain data that ...
Create visual quality check report from QC result.
Visualize the number of outlier subjects per region in your dataset.
Filter QDEC long table for subjects.
Generate skeleton dataframe for FreeSurfer QDEC long file from subject...
Convert raduians to degree
The FreeSurfer default ras2vox_tkr matrix.
Read colors from CSV file.
Read demographics file
Read subjects list from an FSGD file.
Read subjects file
Recycle parameters or whatever.
Give suggestions for regions to ignore for an atlas.
Print a demographics report
Plot x, y and z axes in R,G,B.
Check for a key in names of rglactions.
Create rglactions list, suitable to be passed as parameter to vis func...
Apply data transformation rglactions.
Get rgloptions and consider global options.
Get rgloptions for testing.
Draw 3D boxes at locations using rgl.
Get rotation matrix for a 3D rotation around an axis.
Scale given values to range 0..1.
Scale given values to range 0..1.
Get all shape descriptor names.
Computes geometric curvature-based descriptors.
Shift hemispheres apart.
Shift hemis apart if indicated in rglactions
Download optional demo data if needed and return its path.
Get subjects list from subjects.txt file in dir.
Sort coloredmeshes into 2 lists by their 'hemi' property.
Transform spherical coordinates to FreeSurfer surface space to plot th...
Spread a single value for a region to all region vertices.
Spread the values in the region_value_list and return them for one hem...
Spread the values in the region_value_list and return them for one hem...
Compute annot border vertices.
Load an annotation for a subject.
Aggregate morphometry data over brain atlas regions for a subject.
Compute mean geodesic distance descriptor for a subject.
Construct filepath of any freesurfer file.
Construct filepath of native space morphometry data file.
Construct filepath of standard space morphometry data file.
Extract a region from an atlas annotation as a label for a subject.
Retrieve label data for a single subject.
Load labels representing brain lobes.
Compute a mask for a subject.
Retrieve native space morphometry data for a single subject.
Retrieve standard space morphometry data for a single subject.
Get subjects vertex count.
Create visual quality check report from QC result.
Load a surface for a subject.
Read a brain volume.
Create a submesh including only the given vertices.
Compute average distance from the origin to each vertex.
Get pre-computed center for fsaverage white surface.
Compute metric surface properties.
Get pre-computed radius for fsaverage white surface.
Compute vertex neighborhoods on a sphere based on the given max distan...
Compute Gaussian weights
Apply spatial filter to surface data.
Compute the k1 and k2 principal curvatures of a mesh.
Compute simple version of center and radius of 2 meshes.
Given data, compute symmetric range around zero.
Perform tests for group differences on paired data (repeated measureme...
Perform tests for group differences on paired or unpaired data for two...
Perform tests for group differences on unpaired data for two groups.
Get an fs.surface brain mesh from an rgl tmesh3d instance.
Compute the total length of a path given by the coordinates of its poi...
Split morph data vector at hemisphere boundary.
Return coordinates for vertices, supporting entire brain via hemilist.
Return the proper hemi string ('lh' or 'rh') for each vertex.
Visualize pre-defined vertex colors on a subject.
Draw a coloredmesh using a style.
Visualize a list of colored meshes in a single scene.
Visualize a list of colored meshes in a single scene and rotate them, ...
Create a separate legend plot for a colortable or an annotation.
Visualize arbitrary data on the fsaverage template subject, if availab...
Visualize native space data on a group of subjects.
Visualize standard space data for a group on template.
Visualize arbitrary data on the surface of any subject.
Visualize DTI tracks from Diffusion Toolkit/TrackVis TRK format file.
Export high-quality brainview image with a colorbar.
Visualize fs.surface mesh
Plot atlas annotations for a group of subjects.
Plot coloredmeshes for a group of subjects.
Plot native space morphometry data for a group of subjects.
Plot standard space morphometry data for a group of subjects.
Visualize a label on the surface of a subject.
Visualize a vertex mask on the surface of a subject.
Draw a 3D line from vertex to vertex
Visualize several paths in different colors.
Visualize many paths.
Visualize arbitrary data, one value per atlas region, on the surface o...
Visualize a renderable object
Rotate and visualize coloredmeshes, applying a style.
Plot legend for a brain volume segmentation based on colorLUT.
Visualize an annotation for a subject.
Visualize a binary label for a subject.
Visualize native space morphometry data for a subject.
Visualize native space morphometry data for a subject or a group.
Visualize pre-loaded data.
Visualize clusters or activation data on the surface of any subject.
Visualize coloredmeshes from several angles and combine the images int...
Apply a boundary box to a volume, returning the inner volume part
Compute 3D bounding box of a volume.
Compute foreground pixels over the whole 3D imagestack.
Retain only the outer hull voxels of the foreground.
Turn volume into an ImageMagick image stack.
Convert integer intensity image to RGB color string form.
Extract subset from a volume by value.
Merge background volume and overlay to new colors.
Generate colors for a 3D volume, based on the activation data and a co...
Compute voxel colors based on colortable.
Get indices of the axes defining the given plane.
Translate names and indices of planes.
Extract a slice of a 3D image stack.
Compute R voxel index for FreeSurfer CRS voxel index.
Visualize contour of a volume.
Show continuous 3D voxel/volume data as a lightbox, optionally with a ...
Draw a lightbox view from volume slices.
Voxel-based visualization of volume mask at surface RAS positions.
The FreeSurfer default vox2ras_tkr matrix.
Wrapper around magick::image_append that allows specifying the backgro...
Write per-vertex standard space data for a group of subjects to given ...
Write standard space group data to a standard FreeSurfer directory stu...
Reshape and write combined per-vertex data for a group to a single MGH...
Write single hemi per-vertex data for a group of subjects to given fil...
Write data aggregated over regions to morphometry file for group.
Write one value per atlas region for a template subject.
Write one value per atlas region for a subject.
Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.