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"Get an rgl tmesh3d instance from a brain surface mesh.", "topics": [ "fs.surface.to.tmesh3d" ] }, { "page": "fs.surface.vertex.neighbors", "title": "Compute vertex neighborhoods or the full adjacency list for a mesh using the Rvcg or igraph library.", "topics": [ "fs.surface.vertex.neighbors" ] }, { "page": "fsaverage.path", "title": "Return path to fsaverage dir.", "topics": [ "fsaverage.path" ] }, { "page": "fsbrain.set.default.figsize", "title": "Set default figure size for fsbrain visualization functions.", "topics": [ "fsbrain.set.default.figsize" ] }, { "page": "fup", "title": "Transform first character of a string to uppercase.", "topics": [ "fup" ] }, { "page": "gen.test.volume", "title": "Generate test 3D volume of integers. The volume has an outer background area (intensity value 'bg') and an inner foreground areas (intensity value 200L).", "topics": [ "gen.test.volume" ] }, { "page": "geod.patches.color.overlay", "title": "Generate color overlay from geodesic patches around several vertices.", "topics": [ "geod.patches.color.overlay" ] }, { "page": "geod.vert.neighborhood", "title": "Compute all vertices within given geodesic distance on the mesh.", "topics": [ "geod.vert.neighborhood" ] }, { "page": "geodesic.circles", "title": "Compute geodesic circles and ball stats for given vertices.", "topics": [ "geodesic.circles" ] }, { "page": "geodesic.dists.to.vertex", "title": "Simple internal wrapper around 'Rvcg::vcgDijkstra' with function check.", "topics": [ "geodesic.dists.to.vertex" ] }, { "page": "geodesic.path", "title": "Compute geodesic path from a source vertex to one or more target vertices.", "topics": [ "geodesic.path" ] }, { "page": "get_optional_data_filepath", "title": "Access a single file from the package cache by its file name.", "topics": [ "get_optional_data_filepath" ] }, { "page": "get.atlas.region.names", "title": "Determine atlas region names from a subject.", "concept": [ "atlas functions" ], "topics": [ "get.atlas.region.names" ] }, { "page": "get.rglstyle", "title": "Get the default visualization style parameters as a named list.", "topics": [ "get.rglstyle" ] }, { "page": "get.view.angle.names", "title": "Get list of valid view angle names.", "topics": [ "get.view.angle.names" ] }, { "page": "getIn", "title": "Retrieve values from nested named lists", "topics": [ "getIn" ] }, { "page": "group.agg.atlas.native", "title": "Aggregate native space morphometry data over brain atlas regions and subjects for a group of subjects.", "concept": [ "aggregation functions", "atlas functions" ], "topics": [ "group.agg.atlas.native" ] }, { "page": "group.agg.atlas.standard", "title": "Aggregate standard space morphometry data over brain atlas regions and subjects for a group of subjects.", "concept": [ "aggregation functions", "atlas functions" ], "topics": [ "group.agg.atlas.standard" ] }, { "page": "group.annot", "title": "Load annotations for a group of subjects.", "concept": [ "atlas functions" ], "topics": [ "group.annot" ] }, { "page": "group.concat.measures.native", "title": "Concatenate native space data for a group of subjects.", "concept": [ "concatination functions" ], "topics": [ "group.concat.measures.native" ] }, { "page": "group.concat.measures.standard", "title": "Concatenate standard space data for a group of subjects.", "concept": [ "concatination functions" ], "topics": [ "group.concat.measures.standard" ] }, { "page": "group.label", "title": "Retrieve label data for a group of subjects.", "concept": [ "label data functions" ], "topics": [ "group.label" ] }, { "page": "group.label.from.annot", "title": "Extract a region from an atlas annotation as a label for a group of subjects.", "concept": [ "atlas functions" ], "topics": [ "group.label.from.annot" ] }, { "page": "group.morph.agg.native", "title": "Aggregate native space morphometry data over one hemisphere for a group of subjects.", "concept": [ "global aggregation functions" ], "topics": [ "group.morph.agg.native" ] }, { "page": "group.morph.agg.standard", "title": "Aggregate standard space (fsaverage) morphometry data over one hemisphere for a group of subjects.", "concept": [ "global aggregation functions" ], "topics": [ "group.morph.agg.standard" ] }, { "page": "group.morph.agg.standard.vertex", "title": "Aggregate standard space morphometry data over subjects.", "concept": [ "aggregation functions" ], "topics": [ "group.morph.agg.standard.vertex" ] }, { "page": "group.morph.native", "title": "Retrieve native space morphometry data for a group of subjects.", "concept": [ "morphometry data functions" ], "topics": [ "group.morph.native" ] }, { "page": "group.morph.standard", "title": "Retrieve standard space morphometry data for a group of subjects.", "concept": [ "morphometry data functions" ], "topics": [ "group.morph.standard" ] }, { "page": "group.morph.standard.sf", "title": "Read combined data for a group from a single file.", "topics": [ "group.morph.standard.sf" ] }, { "page": "group.multimorph.agg.native", "title": "Aggregate native space morphometry data for multiple measures over hemispheres for a group of subjects.", "concept": [ "global aggregation functions" ], "topics": [ "group.multimorph.agg.native" ] }, { "page": "group.multimorph.agg.standard", "title": "Aggregate standard space (fsaverage) morphometry data for multiple measures over hemispheres for a group of subjects.", "concept": [ "global aggregation functions" ], "topics": [ "group.multimorph.agg.standard" ] }, { "page": "group.surface", "title": "Retrieve surface mesh data for a group of subjects.", "concept": [ "mesh data functions" ], "topics": [ "group.surface" ] }, { "page": "groupmorph.split.hemilist", "title": "Split a per-vertex group data matrix for both hemispheres into a hemilist at given index.", "topics": [ "groupmorph.split.hemilist" ] }, { "page": "hasIn", "title": "Check for values in nested named lists", "topics": [ "hasIn" ] }, { "page": "hemilist", "title": "Create a hemilist from lh and rh data.", "concept": [ "hemilist functions" ], "topics": [ "hemilist" ] }, { "page": "hemilist.derive.hemi", "title": "Derive 'hemi' string from the data in a hemilist", "concept": [ "hemilist functions" ], "topics": [ "hemilist.derive.hemi" ] }, { "page": "hemilist.from.prefixed.list", "title": "Create a hemilist from a named list with keys prefixed with 'lh_' and 'rh_'.", "concept": [ "hemilist functions" ], "topics": [ "hemilist.from.prefixed.list" ] }, { "page": "hemilist.get.combined.data", "title": "Get combined data of hemi list", "concept": [ "hemilist functions" ], "topics": [ "hemilist.get.combined.data" ] }, { "page": "hemilist.unwrap", "title": "Unwrap hemi data from a named hemi list.", "concept": [ "hemilist functions" ], "topics": [ "hemilist.unwrap" ] }, { "page": "hemilist.wrap", "title": "Wrap data into a named hemi list.", "concept": [ "hemilist functions" ], "topics": [ "hemilist.wrap" ] }, { "page": "highlight.points.spheres", "title": "Draw small 3D spheres at given points.", "concept": [ "3d utility functions" ], "topics": [ "highlight.points.spheres" ] }, { "page": "highlight.vertices.on.subject", "title": "Highlight vertices given by index on a subject's meshes by coloring faces.", "concept": [ "surface visualization functions", "visualization functions" ], "topics": [ "highlight.vertices.on.subject" ] }, { "page": "highlight.vertices.on.subject.spheres", "title": "Highlight vertices given by index on a subject's meshes by coloring faces.", "concept": [ "surface visualization functions", "visualization functions" ], "topics": [ "highlight.vertices.on.subject.spheres" ] }, { "page": "highlight.vertices.spheres", "title": "Draw small 3D spheres at given brain mesh vertices. Supports full brain (2 meshes) as well.", "concept": [ "3d utility functions" ], "topics": [ "highlight.vertices.spheres" ] }, { "page": "images.dimmax", "title": "Compute max width and height of magick images.", "topics": [ "images.dimmax" ] }, { "page": "is.fs.coloredmesh", "title": "Check whether object is an fs.coloredmesh (S3)", "topics": [ "is.fs.coloredmesh" ] }, { "page": "is.fs.coloredvoxels", "title": "Check whether object is an fs.coloredvoxels instance (S3)", "topics": [ "is.fs.coloredvoxels" ] }, { "page": "is.fsbrain", "title": "Check whether object is an fsbrain (S3)", "topics": [ "is.fsbrain" ] }, { "page": "is.hemilist", "title": "Check whether x is a hemilist", "concept": [ "hemilist functions" ], "topics": [ "is.hemilist" ] }, { "page": "label.border", "title": "Compute border of a label.", "concept": [ "surface mesh functions" ], "topics": [ "label.border" ] }, { "page": "label.colFn", "title": "A simple colormap function for binary colors.", "topics": [ "label.colFn" ] }, { "page": "label.colFn.inv", "title": "A simple colormap function for binary colors.", "topics": [ "label.colFn.inv" ] }, { "page": "label.from.annotdata", "title": "Extract a region from an annotation as a label.", "concept": [ "atlas functions" ], "topics": [ "label.from.annotdata" ] }, { "page": "label.to.annot", "title": "Merge several labels into an annotation", "concept": [ "atlas functions" ], "topics": [ "label.to.annot" ] }, { "page": "labeldata.from.mask", "title": "Create labeldata from a mask.", "concept": [ "label data functions" ], "topics": [ "labeldata.from.mask" ] }, { "page": "limit_fun", "title": "Get data limiting function.", "topics": [ "limit_fun" ] }, { "page": "limit_fun_na", "title": "Get data limiting function to NA.", "topics": [ "limit_fun_na" ] }, { "page": "limit_fun_na_inside", "title": "Get data limiting function, setting values inside range to NA.", "topics": [ "limit_fun_na_inside" ] }, { "page": "list_optional_data", "title": "Get file names available in package cache.", "topics": [ "list_optional_data" ] }, { "page": "mask.from.labeldata.for.hemi", "title": "Create a binary mask from labels.", "concept": [ "label data functions", "mask functions" ], "topics": [ "mask.from.labeldata.for.hemi" ] }, { "page": "mesh.vertex.neighbors", "title": "Compute neighborhood of a vertex", "concept": [ "surface mesh functions" ], "topics": [ "mesh.vertex.neighbors" ] }, { "page": "mkco.cluster", "title": "Return recommended 'makecmap_options' for diverging cluster data.", "topics": [ "mkco.cluster" ] }, { "page": "mkco.div", "title": "Return recommended 'makecmap_options' for diverging data.", "topics": [ "mkco.div" ] }, { "page": "mkco.heat", "title": "Return recommended 'makecmap_options' for sequential data with heatmap style.", "topics": [ "mkco.heat" ] }, { "page": "mkco.seq", "title": "Return recommended 'makecmap_options' for sequential data.", "topics": [ "mkco.seq" ] }, { "page": "numverts.lh", "title": "Determine vertex count of left hemi from hemilist of surfaces or the count itself.", "topics": [ "numverts.lh" ] }, { "page": "numverts.rh", "title": "Determine vertex count of right hemi from hemilist of surfaces or the count itself.", "topics": [ "numverts.rh" ] }, { "page": "principal.curvatures", "title": "Computes principal curvatures according to 2 definitions from raw k1 and k2 values.", "topics": [ "principal.curvatures" ] }, { "page": "print.fs.coloredmesh", "title": "Print description of a brain coloredmesh (S3).", "topics": [ "print.fs.coloredmesh" ] }, { "page": "print.fs.coloredvoxels", "title": "Print description of fs.coloredvoxels (S3).", "topics": [ "print.fs.coloredvoxels" ] }, { "page": "print.fsbrain", "title": "Print description of an fsbrain (S3).", "topics": [ "print.fsbrain" ] }, { "page": "qc.for.group", "title": "Perform data quality check based on computed region stats.", "concept": [ "quality check functions" ], "topics": [ "qc.for.group" ] }, { "page": "qc.from.regionwise.df", "title": "Perform data quality check based on a dataframe containing aggregated region-wise data.", "concept": [ "quality check functions" ], "topics": [ "qc.from.regionwise.df" ] }, { "page": "qc.from.segstats.tables", "title": "Perform data quality check based on a segstats table.", "topics": [ "qc.from.segstats.tables" ] }, { "page": "qc.vis.failcount.by.region", "title": "Visualize the number of outlier subjects per region in your dataset.", "topics": [ "qc.vis.failcount.by.region" ] }, { "page": "qdec.table.skeleton", "title": "Generate skeleton dataframe for FreeSurfer QDEC long file from subjects list.", "topics": [ "qdec.table.skeleton" ] }, { "page": "ras2vox_tkr", "title": "The FreeSurfer default ras2vox_tkr matrix.", "concept": [ "surface and volume coordinates" ], "topics": [ "ras2vox_tkr" ] }, { "page": "read.colorcsv", "title": "Read colors from CSV file.", "topics": [ "read.colorcsv" ] }, { "page": "read.md.demographics", "title": "Read demographics file", "concept": [ "metadata functions" ], "topics": [ "read.md.demographics" ] }, { "page": "read.md.subjects", "title": "Read subjects file", "concept": [ "metadata functions" ], "topics": [ "read.md.subjects" ] }, { "page": "read.md.subjects.from.fsgd", "title": "Read subjects list from an FSGD file.", "topics": [ "read.md.subjects.from.fsgd" ] }, { "page": "regions.to.ignore", "title": "Give suggestions for regions to ignore for an atlas.", "concept": [ "atlas functions" ], "topics": [ "regions.to.ignore" ] }, { "page": "report.on.demographics", "title": "Print a demographics report", "concept": [ "metadata functions" ], "topics": [ "report.on.demographics" ] }, { "page": "rglactions", "title": "Create rglactions list, suitable to be passed as parameter to vis functions.", "topics": [ "rglactions" ] }, { "page": "rglo", "title": "Get rgloptions and consider global options.", "topics": [ "rglo" ] }, { "page": "rglot", "title": "Get rgloptions for testing.", "topics": [ "rglot" ] }, { "page": "rglvoxels", "title": "Draw 3D boxes at locations using rgl.", "topics": [ "rglvoxels" ] }, { "page": "scale01", "title": "Scale given values to range 0..1.", "topics": [ "scale01" ] }, { "page": "shape.descriptor.names", "title": "Get all shape descriptor names.", "topics": [ "shape.descriptor.names" ] }, { "page": "shape.descriptors", "title": "Computes geometric curvature-based descriptors.", "topics": [ "shape.descriptors" ] }, { "page": "shift.hemis.apart", "title": "Shift hemispheres apart.", "topics": [ "shift.hemis.apart" ] }, { "page": "sjd.demo", "title": "Download optional demo data if needed and return its path.", "topics": [ "sjd.demo" ] }, { "page": "sjld", "title": "Get subjects list from subjects.txt file in dir.", "topics": [ "sjld" ] }, { "page": "spread.values.over.annot", "title": "Spread a single value for a region to all region vertices.", "concept": [ "atlas functions" ], "topics": [ "spread.values.over.annot" ] }, { "page": "spread.values.over.hemi", "title": "Spread the values in the region_value_list and return them for one hemisphere.", "concept": [ "atlas functions" ], "topics": [ "spread.values.over.hemi" ] }, { "page": "spread.values.over.subject", "title": "Spread the values in the region_value_list and return them for one hemisphere.", "concept": [ "atlas functions" ], "topics": [ "spread.values.over.subject" ] }, { "page": "subject.annot", "title": "Load an annotation for a subject.", "concept": [ "atlas functions" ], "topics": [ "subject.annot" ] }, { "page": "subject.annot.border", "title": "Compute annot border vertices.", "topics": [ "subject.annot.border" ] }, { "page": "subject.atlas.agg", "title": "Aggregate morphometry data over brain atlas regions for a subject.", "concept": [ "aggregation functions", "atlas functions" ], "topics": [ "subject.atlas.agg" ] }, { "page": "subject.filepath.morph.native", "title": "Construct filepath of native space morphometry data file.", "topics": [ "subject.filepath.morph.native" ] }, { "page": "subject.filepath.morph.standard", "title": "Construct filepath of standard space morphometry data file.", "topics": [ "subject.filepath.morph.standard" ] }, { "page": "subject.label", "title": "Retrieve label data for a single subject.", "concept": [ "label data functions" ], "topics": [ "subject.label" ] }, { "page": "subject.label.from.annot", "title": "Extract a region from an atlas annotation as a label for a subject.", "concept": [ "atlas functions" ], "topics": [ "subject.label.from.annot" ] }, { "page": "subject.lobes", "title": "Load labels representing brain lobes.", "concept": [ "atlas functions", "label functions" ], "topics": [ "subject.lobes" ] }, { "page": "subject.mask", "title": "Compute a mask for a subject.", "concept": [ "label functions" ], "topics": [ "subject.mask" ] }, { "page": "subject.morph.native", "title": "Retrieve native space morphometry data for a single subject.", "concept": [ "morphometry data functions" ], "topics": [ "subject.morph.native" ] }, { "page": "subject.morph.standard", "title": "Retrieve standard space morphometry data for a single subject.", "concept": [ "morphometry data functions" ], "topics": [ "subject.morph.standard" ] }, { "page": "subject.num.verts", "title": "Get subjects vertex count.", "topics": [ "subject.num.verts" ] }, { "page": "subject.surface", "title": "Load a surface for a subject.", "concept": [ "surface mesh functions" ], "topics": [ "subject.surface" ] }, { "page": "subject.volume", "title": "Read a brain volume.", "topics": [ "subject.volume" ] }, { "page": "surface.curvatures", "title": "Compute the k1 and k2 principal curvatures of a mesh.", "topics": [ "surface.curvatures" ] }, { "page": "tmesh3d.to.fs.surface", "title": "Get an fs.surface brain mesh from an rgl tmesh3d instance.", "topics": [ "tmesh3d.to.fs.surface" ] }, { "page": "vdata.split.by.hemi", "title": "Split morph data vector at hemisphere boundary.", "topics": [ "vdata.split.by.hemi" ] }, { "page": "vertex.coords", "title": "Return coordinates for vertices, supporting entire brain via hemilist.", "concept": [ "3d utility functions" ], "topics": [ "vertex.coords" ] }, { "page": "vertex.hemis", "title": "Return the proper hemi string ('lh' or 'rh') for each vertex.", "topics": [ "vertex.hemis" ] }, { "page": "vis.color.on.subject", "title": "Visualize pre-defined vertex colors on a subject.", "concept": [ "surface visualization functions", "visualization functions" ], "topics": [ "vis.color.on.subject" ] }, { "page": "vis.coloredmeshes", "title": "Visualize a list of colored meshes in a single scene.", "topics": [ "vis.coloredmeshes" ] }, { "page": "vis.coloredmeshes.rotating", "title": "Visualize a list of colored meshes in a single scene and rotate them, movie-style.", "topics": [ "vis.coloredmeshes.rotating" ] }, { "page": "vis.colortable.legend", "title": "Create a separate legend plot for a colortable or an annotation.", "topics": [ "vis.colortable.legend" ] }, { "page": "vis.data.on.fsaverage", "title": "Visualize arbitrary data on the fsaverage template subject, if available.", "concept": [ "morphometry visualization functions", "visualization functions" ], "topics": [ "vis.data.on.fsaverage" ] }, { "page": "vis.data.on.group.native", "title": "Visualize native space data on a group of subjects.", "concept": [ "group visualization functions" ], "topics": [ "vis.data.on.group.native" ] }, { "page": "vis.data.on.group.standard", "title": "Visualize standard space data for a group on template.", "concept": [ "group visualization functions" ], "topics": [ "vis.data.on.group.standard" ] }, { "page": "vis.data.on.subject", "title": "Visualize arbitrary data on the surface of any subject.", "concept": [ "morphometry visualization functions", "visualization functions" ], "topics": [ "vis.data.on.subject" ] }, { "page": "vis.dti.trk", "title": "Visualize DTI tracks from Diffusion Toolkit/TrackVis TRK format file.", "topics": [ "vis.dti.trk" ] }, { "page": "vis.export.from.coloredmeshes", "title": "Export high-quality brainview image with a colorbar.", "topics": [ "vis.export.from.coloredmeshes" ] }, { "page": "vis.fs.surface", "title": "Visualize fs.surface mesh", "topics": [ "vis.fs.surface" ] }, { "page": "vis.group.annot", "title": "Plot atlas annotations for a group of subjects.", "concept": [ "group visualization functions" ], "topics": [ "vis.group.annot" ] }, { "page": "vis.group.coloredmeshes", "title": "Plot coloredmeshes for a group of subjects.", "concept": [ "group visualization functions" ], "topics": [ "vis.group.coloredmeshes" ] }, { "page": "vis.group.morph.native", "title": "Plot native space morphometry data for a group of subjects.", "concept": [ "group visualization functions" ], "topics": [ "vis.group.morph.native" ] }, { "page": "vis.group.morph.standard", "title": "Plot standard space morphometry data for a group of subjects.", "concept": [ "group visualization functions" ], "topics": [ "vis.group.morph.standard" ] }, { "page": "vis.labeldata.on.subject", "title": "Visualize a label on the surface of a subject.", "concept": [ "label functions", "visualization functions" ], "topics": [ "vis.labeldata.on.subject" ] }, { "page": "vis.mask.on.subject", "title": "Visualize a vertex mask on the surface of a subject.", "concept": [ "mask functions", "visualization functions" ], "topics": [ "vis.mask.on.subject" ] }, { "page": "vis.path.along.verts", "title": "Draw a 3D line from vertex to vertex", "concept": [ "surface mesh functions" ], "topics": [ "vis.path.along.verts" ] }, { "page": "vis.paths", "title": "Visualize many paths.", "topics": [ "vis.paths" ] }, { "page": "vis.paths.along.verts", "title": "Visualize several paths in different colors.", "topics": [ "vis.paths.along.verts" ] }, { "page": "vis.region.values.on.subject", "title": "Visualize arbitrary data, one value per atlas region, on the surface of any subject (including template subjects).", "concept": [ "region-based visualization functions", "visualization functions" ], "topics": [ "vis.region.values.on.subject" ] }, { "page": "vis.seg.legend", "title": "Plot legend for a brain volume segmentation based on colorLUT.", "topics": [ "vis.seg.legend" ] }, { "page": "vis.subject.annot", "title": "Visualize an annotation for a subject.", "concept": [ "region-based visualization functions", "visualization functions" ], "topics": [ "vis.subject.annot" ] }, { "page": "vis.subject.label", "title": "Visualize a binary label for a subject.", "concept": [ "label functions", "visualization functions" ], "topics": [ "vis.subject.label" ] }, { "page": "vis.subject.morph.native", "title": "Visualize native space morphometry data for a subject.", "concept": [ "morphometry visualization functions", "visualization functions" ], "topics": [ "vis.subject.morph.native" ] }, { "page": "vis.subject.morph.standard", "title": "Visualize native space morphometry data for a subject or a group.", "concept": [ "morphometry visualization functions", "visualization functions" ], "topics": [ "vis.subject.morph.standard" ] }, { "page": "vis.subject.pre", "title": "Visualize pre-loaded data.", "concept": [ "visualization functions" ], "topics": [ "vis.subject.pre" ] }, { "page": "vis.symmetric.data.on.subject", "title": "Visualize clusters or activation data on the surface of any subject.", "concept": [ "morphometry visualization functions", "visualization functions" ], "topics": [ "vis.symmetric.data.on.subject" ] }, { "page": "vislayout.from.coloredmeshes", "title": "Visualize coloredmeshes from several angles and combine the images into a new figure.", "concept": [ "visualization functions" ], "topics": [ "vislayout.from.coloredmeshes" ] }, { "page": "vol.boundary.box", "title": "Compute 3D bounding box of a volume.", "concept": [ "volume utility" ], "topics": [ "vol.boundary.box" ] }, { "page": "vol.boundary.box.apply", "title": "Apply a boundary box to a volume, returning the inner volume part", "topics": [ "vol.boundary.box.apply" ] }, { "page": "vol.hull", "title": "Retain only the outer hull voxels of the foreground.", "topics": [ "vol.hull" ] }, { "page": "vol.imagestack", "title": "Turn volume into an ImageMagick image stack.", "concept": [ "volume utility" ], "topics": [ "vol.imagestack" ] }, { "page": "vol.intensity.to.color", "title": "Convert integer intensity image to RGB color string form.", "topics": [ "vol.intensity.to.color" ] }, { "page": "vol.mask.from.segmentation", "title": "Extract subset from a volume by value.", "topics": [ "vol.mask.from.segmentation" ] }, { "page": "vol.merge", "title": "Merge background volume and overlay to new colors.", "concept": [ "volume utility" ], "topics": [ "vol.merge" ] }, { "page": "vol.overlay.colors.from.activation", "title": "Generate colors for a 3D volume, based on the activation data and a colormap.", "concept": [ "volume utility" ], "topics": [ "vol.overlay.colors.from.activation" ] }, { "page": "vol.overlay.colors.from.colortable", "title": "Compute voxel colors based on colortable.", "topics": [ "vol.overlay.colors.from.colortable" ] }, { "page": "vol.planes", "title": "Translate names and indices of planes.", "concept": [ "volume utility" ], "topics": [ "vol.planes" ] }, { "page": "vol.slice", "title": "Extract a slice of a 3D image stack.", "concept": [ "volume utility" ], "topics": [ "vol.slice" ] }, { "page": "vol.vox.from.crs", "title": "Compute R voxel index for FreeSurfer CRS voxel index.", "topics": [ "vol.vox.from.crs" ] }, { "page": "volvis.contour", "title": "Visualize contour of a volume.", "topics": [ "volvis.contour" ] }, { "page": "volvis.lb", "title": "Show continuous 3D voxel/volume data as a lightbox, optionally with a background brain volume and colormap.", "concept": [ "volume visualization" ], "topics": [ "volvis.lb" ] }, { "page": "volvis.lightbox", "title": "Draw a lightbox view from volume slices.", "concept": [ "volume visualization" ], "topics": [ "volvis.lightbox" ] }, { "page": "volvis.voxels", "title": "Voxel-based visualization of volume mask at surface RAS positions.", "topics": [ "volvis.voxels" ] }, { "page": "vox2ras_tkr", "title": "The FreeSurfer default vox2ras_tkr matrix.", "concept": [ "surface and volume coordinates" ], "topics": [ "vox2ras_tkr" ] }, { "page": "write.group.morph.standard", "title": "Write standard space group data to a standard FreeSurfer directory stucture.", "topics": [ "write.group.morph.standard" ] }, { "page": "write.group.morph.standard.mf", "title": "Write per-vertex standard space data for a group of subjects to given file names.", "topics": [ "write.group.morph.standard.mf" ] }, { "page": "write.group.morph.standard.sf", "title": "Reshape and write combined per-vertex data for a group to a single MGH file.", "topics": [ "write.group.morph.standard.sf" ] }, { "page": "write.region.aggregated", "title": "Write data aggregated over regions to morphometry file for group.", "concept": [ "output functions" ], "topics": [ "write.region.aggregated" ] }, { "page": "write.region.values", "title": "Write one value per atlas region for a subject.", "concept": [ "output functions" ], "topics": [ "write.region.values" ] }, { "page": "write.region.values.fsaverage", "title": "Write one value per atlas region for a template subject.", "concept": [ "output functions" ], "topics": [ "write.region.values.fsaverage" ] } ], "_readme": "https://github.com/dfsp-spirit/fsbrain/raw/HEAD/README.md", "_rundeps": [ "base64enc", "bslib", "cachem", "cli", "cpp11", "curl", "data.table", "digest", "dotCall64", "downloader", "evaluate", "farver", "fastmap", "fields", "fontawesome", "freesurferformats", "fs", "ggplot2", "glue", "gridExtra", "gtable", "highr", "htmltools", "htmlwidgets", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lifecycle", "magick", "magrittr", "maps", "memoise", "mime", "pkgfilecache", "plyr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "reshape", "rgl", "rlang", "rmarkdown", "S7", "sass", "scales", "spam", "squash", "tinytex", "vctrs", "viridis", "viridisLite", "withr", "xfun", "xml2", "yaml" ], "_vignettes": [ { "source": "fsbrain_vol.Rmd", "filename": "fsbrain_vol.html", "title": "Brain volume visualization with fsbrain", "engine": "knitr::rmarkdown", "headings": [ "Example data used in this document", "Loading volume data", "Volume visualization", "Basic Lightbox view for raw MRI data", "Advanced lightbox view", "Raw 3D voxel visualization" ], "created": "2020-04-07 17:05:34", "modified": "2021-09-10 07:44:57", "commits": 9 }, { "source": "fsbrain.Rmd", "filename": "fsbrain.html", "title": "fsbrain: Managing and Visualizing Structural Neuroimaging Data in GNU R", "engine": "knitr::rmarkdown", "headings": [ "Example data used in this document", "Accessing group data", "Subjects list and demographics", "Morphometry data for groups", "Automatically masking the medial wall when accessing morphometry data", "Faster access to group data", "Labels for groups", "Labels and masks", "Annotations for groups", "Aggregating morphometry data", "Aggregating group data over entire hemispheres", "A single morphometry measure in native space", "A single morphometry measure in standard space", "Several measures over several hemispheres in native space", "Several measures over several hemispheres in standard space", "Automatically masking the medial wall when aggregating", "Aggregating over atlas regions", "Native space", "Standard space", "Working with atlas data", "Creating a label from an atlas region", "Mapping one result value to each brain atlas region", "Data visualization", "Visualizing different types of data", "Visualizing annotations (brain parcellations based on an atlas)", "Visualizing morphometry data", "Visualizing labels", "Visualizing arbitrary vertices", "Visualizing masks", "Visualizing results of region-based analyses", "Full control: visualizing vertex colors and color layers", "General visualization options", "Figure size", "Different views", "Changing the visualisation surface", "Changing the resolution of figures (or other rgloptions)", "Using backgrounds when visualizing data", "Saving screenshots and creating GIF movies (and other rglactions)", "Example: Creating a GIF animation (movie)", "Postprocessing the movies", "Drawing colorbars", "Plotting a colorbar in the background of a 3D plot", "Plotting a colorbar to a separate 2D plot", "Exporting publication quality plots", "Visualizing groups of subjects" ], "created": "2019-10-25 11:36:46", "modified": "2021-09-16 07:15:14", "commits": 28 }, { "source": "fsbrain_faq.Rmd", "filename": "fsbrain_faq.html", "title": "The fsbrain FAQ", "engine": "knitr::rmarkdown", "headings": [ "Input data", "Q: What kind of input data do I need for fsbrain?", "Q: Which file formats are supported?", "Q: I want to load a single file that is somewhere on my harddisk, i.e., not within a standard recon-all output directory structure. How can I load it?", "Q: Can I use fsbrain to visualize data from SPM12 / CAT12 or other software packages?", "What is the best way to visualize data computed in R (or from arbitrary files that do not follow the FreeSurfer recon-all directory layout)?", "Can I used fsbrain to visualize surface data from BrainSuite surfaces in DFS format?", "Visualization", "How can I set the output image resolution?", "How can I save high quality figures to PNG images?", "Can I save fsbrain figures as vector images (like PDF, EPS, SVG)?", "A journal requires me to submit a vector graphics file, what to do?", "When visualizing data with outliers and long tails, the colors are not helpful. What to do?", "Can I limit the data range, including the min and max values displayed on the color bar?", "How can I enforce fixed colorbar settings (i.e., one color should represent the same value) across several images?", "How can I change the colormap for the plots?", "What are the best colormaps for my data?", "I am using a diverging colormap. When plotting the colorbar (legend), the neutral value is not at zero. How to fix it?", "The colorbar shows only very few different colors, why is that and how can I change it?", "Can I set a custom color for NA values in the plot, like the masked medial wall?", "Can I get a color legend when plotting atlas regions from an annotation? I want to know the region names for the colors.", "Can I get a color legend when plotting a segmentation/parcellation (different brain regions), based on a color lookup table (like the FreeSurferColorLUT.txt file)?", "There is too much whitespace between the different views of the brain. How can I reduce it?", "Can I export PNG images with transparent (instead of white) background?", "When visualizing data on the inflated surface, the left and right hemisphere overlap and look garbled. How to fix that?", "When plotting several views, can I have the subplots arranged in a horizontal strip (rather than 2x2 tiles)?", "Various topics", "Can I integrate the plots produced by fsbrain into an R Markdown document (the R equivalent of a Python Jupyter notebook)?", "Can I use fsbrain to visualize arbitrary triangular meshes in R?", "Technical problems", "I am getting the error 'invalid value specified for graphical parameter plt', why?", "I am getting the error 'Error in squash::cmap, found x values outside map range'", "I am getting the warning 'RGL: unable to open X11 display' when loading fsbrain", "How can I plot on a machine that does not have X11?", "I am trying to plot a very large image with fsbrain, but the output is not as large as expected. Why?", "What to do about the error 'lazy-load database is corrupt' when loading fsbrain?", "I see no output image after running a vis function, and also get no error message. What to do?" ], "created": "2020-05-01 08:58:01", "modified": "2023-06-26 07:37:36", "commits": 38 } ], "_score": 7.073938190635253, "_indexed": true, "_nocasepkg": "fsbrain", "_universes": [ "dfsp-spirit" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.5.6", "date": "2026-05-12T09:31:09.000Z", "distro": "noble", "commit": "4a8ed444d01f0e7a9124701862539eca7c5e6a53", "fileid": "9490ffa65e748c678515d9c7fefbc7f75b6ae05a65b832ec70479c25d79414c1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dfsp-spirit/actions/runs/25725518811" }, { "r": "4.6.0", "os": "linux", "version": "0.5.6", "date": "2026-05-12T09:31:12.000Z", "distro": "noble", "commit": "4a8ed444d01f0e7a9124701862539eca7c5e6a53", "fileid": "d706d8120be831f4914fabc479be1ac1b18822b99786ec3c1ccab7b077aa9d05", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dfsp-spirit/actions/runs/25725518811" }, { "r": "4.5.3", "os": "mac", "version": "0.5.6", "date": "2026-05-12T09:34:08.000Z", "commit": "4a8ed444d01f0e7a9124701862539eca7c5e6a53", "fileid": "99ef06feed5d1061d3c1435ffa479ede366af834e49065d22f242ccd719393f8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dfsp-spirit/actions/runs/25725518811" }, { "r": "4.6.0", "os": "mac", "version": "0.5.6", "date": "2026-05-12T09:33:58.000Z", "commit": "4a8ed444d01f0e7a9124701862539eca7c5e6a53", "fileid": "3104233947799711bf4223adfbaa3be32ea60ddf9eb49c9621c09efc3b58470e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dfsp-spirit/actions/runs/25725518811" }, { "r": "4.7.0", "os": "win", "version": "0.5.6", "date": "2026-05-12T09:29:42.000Z", "commit": "4a8ed444d01f0e7a9124701862539eca7c5e6a53", "fileid": "57f8b889a7910231f9b38644848d9f6028fdf18c437156235930f3162497038c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dfsp-spirit/actions/runs/25725518811" }, { "r": "4.5.3", "os": "win", "version": "0.5.6", "date": "2026-05-12T09:29:29.000Z", "commit": "4a8ed444d01f0e7a9124701862539eca7c5e6a53", "fileid": "96ff7548ab09a1ab65b187396c768cd87aec04b028290ba2ab10621f7149f361", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dfsp-spirit/actions/runs/25725518811" }, { "r": "4.6.0", "os": "win", "version": "0.5.6", "date": "2026-05-12T09:29:44.000Z", "commit": "4a8ed444d01f0e7a9124701862539eca7c5e6a53", "fileid": "442015db9a5bb66bf89db7928557b6f86cde0b53b74db9ed9beff31b9a5722b5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dfsp-spirit/actions/runs/25725518811" }, { "r": "4.6.0", "os": "wasm", "version": "0.5.6", "date": "2026-05-22T10:32:42.000Z", "commit": "4a8ed444d01f0e7a9124701862539eca7c5e6a53", "fileid": "7e9beba94ce371ae4140c97d14f19e430a146b51402893a79a9925b6bd229c02", "status": "success", "buildurl": "https://github.com/r-universe/dfsp-spirit/actions/runs/25725518811" } ] }