Man pages for fsbrain
Managing and Visualizing Brain Surface Data

alphablendPerform alpha blending for pairs of RGBA colors.
annot.outlineCompute outline vertex colors from annotation.
apply.labeldata.to.morphdataApply a label to morphometry data.
apply.label.to.morphdataLoad a label from file and apply it to morphometry data.
apply.transformApply matmult transformation to input.
arrange.brainview.imagesCombine several brainview images into a new figure.
arrange.brainview.images.gridCombine several brainview images as a grid into a new figure.
boxcoords.from.bboxCompute the coordinates of the 8 corners of a 3D box.
brainviewsShow one or more views of the given meshes in rgl windows.
brainview.sdVisualize a list of colored meshes from a single defined...
brainview.siVisualize a list of colored meshes from a single viewpoint,...
brainview.srVisualize a list of colored meshes, rotating the camera...
brainview.t4Visualize a list of colored meshes from four angles.
brainview.t9Visualize a list of colored meshes from nine angles.
can.plot.colorbarDetermine whether colorbar can be plotted with given...
can.plot.colorbar.from.coloredmeshesDetermine whether colorbar can be plotted with given...
check.subjectslistCheck whether the subjects_list looks good, warn if not.
clip.dataClip data at quantiles to remove outliers.
cm.cbryGet cyan blue red yellow colormap function.
cm.divReturn the standard fsbrain diverging colormap.
cm.heatReturn the standard fsbrain heat colormap.
cm.qualReturn the standard fsbrain qualitative colormap.
cm.seqReturn the standard fsbrain sequential colormap.
collayer.bgCompute binarized mean curvature surface color layer.
collayer.bg.atlasCompute atlas or annotation surface color layer.
collayer.bg.meancurvCompute binarized mean curvature surface color layer.
collayer.bg.sulcCompute binarized sulcal depth surface color layer.
collayer.from.annotCompute surface color layer from annotation or atlas data.
collayer.from.annotdataCompute surface color layer from annotation or atlas data.
collayer.from.mask.dataCompute surface color layer from morph-like data.
collayer.from.morphlike.dataCompute surface color layer from morph-like data.
collayers.mergeMerge two or more color layers based on their transparency...
coloredmeshes.combined.data.rangeRetrieve combined data range from hemilist of coloredmeshes.
coloredmeshes.from.colorCreate coloredmeshes for both hemis using pre-defined colors.
coloredmeshes.get.mdRetrieve metadata from hemilist of coloredmeshes.
coloredmesh.from.annotCreate a coloredmesh from an annotation of an atlas.
coloredmesh.from.colorCreate a coloredmesh from a mesh and pre-defined colors.
coloredmesh.from.labelCreate a coloredmesh from a label.
coloredmesh.from.maskCreate a coloredmesh from a mask.
coloredmesh.from.morphdataCreate a coloredmesh from arbitrary data.
coloredmesh.from.morph.nativeCreate a coloredmesh from native space morphometry data.
coloredmesh.from.morph.standardCreate a coloredmesh from standard space morphometry data.
coloredmesh.from.preloaded.dataGenerate coloredmesh from loaded data.
coloredmesh.plot.colorbar.separateDraw colorbar for coloredmeshes in separate 2D plot.
colorlist.brain.clustersReturn diverging color list
combine.colorbar.with.brainview.animationCombine a colorbar and a brain animation in gif format into a...
combine.colorbar.with.brainview.imageCombine a colorbar and a brainview image into a new figure.
combine.colorbar.with.brainview.image.verticalCombine a vertical colorbar and a brainview image into a new...
common.makecmap.rangeGet cmap and colorlayer from data and makecmap_options.
cube3D.trisReturn triangles for a 3D cube or cuboid.
cubes3D.trisVectorized version of cube3D.tris
deg2radConvert degree to radians
delete_all_optional_dataDelete all data in the package cache.
demographics.to.fsgd.fileWrite FreeSurfer Group Descriptor (FSGD) file from...
desaturatePerform simple desaturation or grayscale conversion of RGBA...
download_fsaverageDownload the FreeSurfer v6 fsaverage subject.
download_fsaverage3Download the FreeSurfer v6 low-resolution fsaverage3 subject.
download_optional_dataDownload optional data for this package if required.
download_optional_paper_dataDownload extra data to reproduce the figures from the fsbrain...
draw.colorbarDraw coloredbar into background of current plot.
eeg_coordsInternal function to get some demo EEG electrode coordinates....
export.coloredmesh.plyExport a coloredmeshes with vertexcolors in PLY format.
face.edgesEnumerate all edges of the given faces or mesh.
find.freesurferhomeFind the FREESURFER_HOME directory on disk.
find.subjectsdir.ofFind the subject directory containing the fsaverage subject...
flcGiven a list of path coordinates, create matrix containing...
force.to.rangeChange data to ensure requested data_range.
fsaverage.pathReturn path to fsaverage dir.
fsbrain.renderableCheck whether object can be rendered by fsbrain
fsbrain.set.default.figsizeSet default figure size for fsbrain visualization functions.
fs.coloredmeshfs.coloredmesh constructor
fs.homeReturn FreeSurfer path.
fs.value.list.from.agg.resCreate a named value list from a dataframe.
fupTransform first character of a string to uppercase.
gen.test.volumeGenerate test 3D volume of integers. The volume has an outer...
get.atlas.region.namesDetermine atlas region names from a subject.
getInRetrieve values from nested named lists
get_optional_data_filepathAccess a single file from the package cache by its file name.
get.rglstyleGet the default visualization style parameters as a named...
get.rglstyle.defaultGet the default visualization style parameters as a named...
get.rglstyle.edgesGet the mesh edges visualization style parameters as a named...
get.rglstyle.parametersProduce the named list of style parameters from style...
get.rglstyle.semitransparentGet the semi-transparent visualization style parameters as a...
get.rglstyle.shinyGet a shiny visualization style.
get.slice.indicesCompute slice indices from slice definition.
get.subject.classConstruct FSGD Class name from group and non-continuous...
get.view.angle.namesGet list of valid view angle names.
group.agg.atlas.nativeAggregate native space morphometry data over brain atlas...
group.agg.atlas.standardAggregate standard space morphometry data over brain atlas...
group.annotLoad annotations for a group of subjects.
group.concat.measures.nativeConcatenate native space data for a group of subjects.
group.concat.measures.standardConcatenate standard space data for a group of subjects.
group.data.to.arrayConvert group 1D data to array format.
group.labelRetrieve label data for a group of subjects.
group.label.from.annotExtract a region from an atlas annotation as a label for a...
group.morph.agg.nativeAggregate native space morphometry data over one hemisphere...
group.morph.agg.standardAggregate standard space (fsaverage) morphometry data over...
group.morph.agg.standard.vertexAggregate standard space morphometry data over subjects.
group.morph.nativeRetrieve native space morphometry data for a group of...
group.morph.standardRetrieve standard space morphometry data for a group of...
group.morph.standard.sfRead combined data for a group from a single file.
group.multimorph.agg.nativeAggregate native space morphometry data for multiple measures...
group.multimorph.agg.standardAggregate standard space (fsaverage) morphometry data for...
group.surfaceRetrieve surface mesh data for a group of subjects.
hasInCheck for values in nested named lists
hemilist.derive.hemiDerive 'hemi' string from the data in a hemilist
hemilist.get.combined.dataGet combined data of hemi list
hemilist.unwrapUnwrap hemi data from a named hemi list.
hemilist.wrapWrap data into a named hemi list.
hemi.lobe.labelsCompute lobe labels for a single hemi from aparc atlas.
highlight.vertices.on.subjectHighlight vertices given by index on a subject's meshes.
hull.retain.along.axisCopy the first *n* foreground voxel values.
image.remap.colorRemap a color in an image, typically used to set the...
images.annotateAnnotate image with text.
images.dimmaxCompute max width and height of magick images.
images.rescale.to.max.canvasRescale all images canvas to match the largest one.
images.same.heightExtent all images to the height of the image with maximal...
images.same.widthExtent all images to the width of the image with maximal...
is.fs.coloredmeshCheck whether object is an fs.coloredmesh (S3)
is.fs.coloredvoxelsCheck whether object is an fs.coloredvoxels instance (S3)
is.hemilistCheck whether x is a hemilist
is.Triangles3DCheck whether object is a Triangles3D instance
label.borderCompute border of a label.
label.colFnA simple colormap function for binary colors.
label.colFn.invA simple colormap function for binary colors.
labeldata.from.maskCreate labeldata from a mask.
label.from.annotdataExtract a region from an annotation as a label.
label.to.annotMerge several labels into an annotation
limit_funGet data limiting function.
limit_fun_naGet data limiting function to NA.
limit_fun_na_insideGet data limiting function, setting values inside range to...
list_optional_dataGet file names available in package cache.
magick.gridArrange a multi-frame ImageMagick image into a grid.
makecmakeopts.mergeCreate final 'makecmap_options' list
mask.from.labeldata.for.hemiCreate a binary mask from labels.
merge.hemi.annotsMerge the annotations from two hemispheres into one annot.
mesh.vertex.included.facesReturn all faces which are made up completely of the listed...
mesh.vertex.neighborsCompute neighborhood of a vertex
mkco.clusterReturn recommended 'makecmap_options' for diverging cluster...
mkco.divReturn recommended 'makecmap_options' for diverging data.
mkco.heatReturn recommended 'makecmap_options' for sequential data...
mkco.seqReturn recommended 'makecmap_options' for sequential data.
normalizeNormalize data.
path.colors.from.orientationCompute path color from its orientation.
path.slopesCompute slopes of paths relative to axes.
perform.na.mappingPerform NA mapping for transparency
perform.rglactionsPerform rglactions, like taking screenshots.
plot.fsbrain.colorbarDraw a simple colorbar from colors.
pp.named.listPretty-print a named list or vector.
principal.curvaturesComputes principal curvatures according to 2 definitions from...
print.fs.coloredmeshPrint description of a brain coloredmesh (S3).
print.fs.coloredvoxelsPrint description of fs.coloredvoxels (S3).
qc.for.groupPerform data quality check based on computed region stats.
qc.from.regionwise.dfPerform data quality check based on a dataframe containing...
qc.from.segstats.tablePerform data quality check based on a segstats table.
qc.from.segstats.tablesPerform data quality check based on a segstats table.
qc.vis.failcount.by.regionVisualize the number of outlier subjects per region in your...
rad2degConvert raduians to degree
ras2vox_tkrThe FreeSurfer default ras2vox_tkr matrix.
read.colorcsvRead colors from CSV file.
read.md.demographicsRead demographics file
read.md.subjectsRead subjects file
read.md.subjects.from.fsgdRead subjects list from an FSGD file.
recycleRecycle parameters or whatever.
regions.to.ignoreGive suggestions for regions to ignore for an atlas.
report.on.demographicsPrint a demographics report
rglactionsCreate rglactions list, suitable to be passed as parameter to...
rglactions.has.keyCheck for a key in names of rglactions.
rglactions.transformApply data transformation rglactions.
rgl.coord.linesPlot x, y and z axes in R,G,B.
rgloGet rgloptions and consider global options.
rglotGet rgloptions for testing.
rglvoxelsDraw 3D boxes at locations using rgl.
scale.to.range.zero.oneScale given values to range 0..1.
shape.descriptor.namesGet all shape descriptor names.
shape.descriptorsComputes geometric curvature-based descriptors.
shift.hemis.apartShift hemispheres apart.
shift.hemis.rglactionsShift hemis apart if indicated in rglactions
sort.coloredmeshes.by.hemiSort coloredmeshes into 2 lists by their 'hemi' property.
sph2fsTransform spherical coordinates to FreeSurfer surface space...
spread.values.over.annotSpread a single value for a region to all region vertices.
spread.values.over.hemiSpread the values in the region_value_list and return them...
spread.values.over.subjectSpread the values in the region_value_list and return them...
subject.annotLoad an annotation for a subject.
subject.atlas.aggAggregate morphometry data over brain atlas regions for a...
subject.filepath.anyConstruct filepath of any freesurfer file.
subject.filepath.morph.nativeConstruct filepath of native space morphometry data file.
subject.filepath.morph.standardConstruct filepath of standard space morphometry data file.
subject.labelRetrieve label data for a single subject.
subject.label.from.annotExtract a region from an atlas annotation as a label for a...
subject.lobesLoad labels representing brain lobes.
subject.maskCompute a mask for a subject.
subject.morph.nativeRetrieve native space morphometry data for a single subject.
subject.morph.standardRetrieve standard space morphometry data for a single...
subject.num.vertsGet subjects vertex count.
subject.surfaceLoad a surface for a subject.
subject.volumeRead a brain volume.
surf.center.fsaverageGet pre-computed center for fsaverage white surface.
surf.radius.fsaverageGet pre-computed radius for fsaverage white surface.
surfs.propsCompute simple version of center and radius of 2 meshes.
symmrangeGiven data, compute symmetric range around zero.
test.numerical.meandiffPerform tests for group differences on paired or unpaired...
test.numerical.meandiff.pairedPerform tests for group differences on paired data (repeated...
test.numerical.meandiff.unpairedPerform tests for group differences on unpaired data for two...
track.lengthCompute the total length of a path given by the coordinates...
vdata.split.by.hemiSplit morph data vector at hemisphere boundary.
vis.coloredmeshDraw a coloredmesh using a style.
vis.coloredmeshesVisualize a list of colored meshes in a single scene.
vis.coloredmeshes.rotatingVisualize a list of colored meshes in a single scene and...
vis.color.on.subjectVisualize pre-defined vertex colors on a subject.
vis.colortable.legendCreate a separate legend plot for a colortable or an...
vis.data.on.fsaverageVisualize arbitrary data on the fsaverage template subject,...
vis.data.on.group.nativeVisualize native space data on a group of subjects.
vis.data.on.group.standardVisualize standard space data for a group on template.
vis.data.on.subjectVisualize arbitrary data on the surface of any subject.
vis.dti.trkVisualize DTI tracks from Diffusion Toolkit/TrackVis TRK...
vis.export.from.coloredmeshesExport high-quality brainview image with a colorbar.
vis.fs.surfaceVisualize fs.surface mesh
vis.group.annotPlot atlas annotations for a group of subjects.
vis.group.coloredmeshesPlot coloredmeshes for a group of subjects.
vis.group.morph.nativePlot native space morphometry data for a group of subjects.
vis.group.morph.standardPlot standard space morphometry data for a group of subjects.
vis.labeldata.on.subjectVisualize a label on the surface of a subject.
vislayout.from.coloredmeshesVisualize coloredmeshes from several angles and combine the...
vis.mask.on.subjectVisualize a vertex mask on the surface of a subject.
vis.path.along.vertsDraw a 3D line from vertex to vertex
vis.pathsVisualize many paths.
vis.region.values.on.subjectVisualize arbitrary data, one value per atlas region, on the...
vis.renderableVisualize a renderable object
vis.rotated.coloredmeshesRotate and visualize coloredmeshes, applying a style.
vis.subject.annotVisualize an annotation for a subject.
vis.subject.labelVisualize a binary label for a subject.
vis.subject.morph.nativeVisualize native space morphometry data for a subject.
vis.subject.morph.standardVisualize native space morphometry data for a subject or a...
vis.symmetric.data.on.subjectVisualize clusters or activation data on the surface of any...
vol.boundary.boxCompute 3D bounding box of a volume.
vol.boundary.box.applyApply a boundary box to a volume, returning the inner volume...
vol.boundary.maskCompute foreground pixels over the whole 3D imagestack.
vol.hullRetain only the outer hull voxels of the foreground.
vol.imagestackTurn volume into an ImageMagick image stack.
vol.intensity.to.colorConvert integer intensity image to RGB color string form.
vol.mask.from.segmentationExtract subset from a volume by value.
vol.mergeMerge background volume and overlay to new colors.
vol.overlay.colors.from.activationGenerate colors for a 3D volume, based on the activation data...
vol.overlay.colors.from.colortableCompute voxel colors based on colortable.
vol.plane.axesGet indices of the axes defining the given plane.
vol.planesTranslate names and indices of planes.
vol.sliceExtract a slice of a 3D image stack.
volvis.contourVisualize contour of a volume.
volvis.lightboxDraw a lightbox view from volume slices.
volvis.voxelsVoxel-based visualization of volume mask at surface RAS...
vol.vox.from.crsCompute R voxel index for FreeSurfer CRS voxel index.
vox2ras_tkrThe FreeSurfer default vox2ras_tkr matrix.
wrapped.image.appendWrapper around magick::image_append that allows specifying...
write.group.morph.standard.sfWrite combined data for a group to a single MGH file.
write.region.aggregatedWrite data aggregated over regions to morphometry file for...
write.region.valuesWrite one value per atlas region for a subject.
write.region.values.fsaverageWrite one value per atlas region for a template subject.
fsbrain documentation built on May 12, 2021, 5:06 p.m.