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