Function reference • RMINC

All functions
`AICc()`	Compute the Corrected AIC for an object
`RMINC`	RMINC: R interface to the MINC universe
`RMINC_MASKED_VALUE`	RMINC Masked Value
`addVolumesToHierarchy()`	Add volumes to an anatomical hierarchy
`add_colour_bar()`	Add a colour bar for a mesh
`add_opacity()`	Add opacity to a mesh
`anatAnova()`	Performs ANOVA on each region specified
`anatApply()`	Apply function over anat structure
`anatCombineStructures()`	Combine left and right volumes
`anatCreateVolume()`	Create a Statistic Volume
`anatFDR()`	Anatomy False Discovery Rates
`anatGetAll()`	Faster AnatGet
`anatGetAll_old()`	Get values given a set of files and an atlas
`anatLm()`	Calculates statistics and coefficients for linear model of specified anat structure
`anatLmer()`	Anatomy Linear Mixed Effects Model
`anatLmerEstimateDF()`	Estimate Degrees of freedom for an anatLmer model
`anatMean()` `anatSum()` `anatVar()` `anatSd()`	anatSummaries
`anatSummarize()`	Summarize anatGetAll results by hierarchy
`as.data.frame(<anatMatrix>)`	Create Anatomy data.frame
`as.minc()`	Coerce to RMINC object
`check_step_sizes()`	Check file step sizes
`civet.CreateBrainViewFile()`	Create a brain view file
`civet.CreateBrainViewROI()`	civet.CreateBrainViewROI
`civet.checkVersion()`	Check for a known Civet Version
`civet.computeNativeToStxRescalingFactor()`	Compute Native to Stereotactic Rescaling Factor
`civet.computeStxTissueVolumes()` `civet.computeNativeTissueVolumes()`	Compute GM, WM, and CSF Tissue Volumes
`civet.flattenForDplyr()`	Flatten CIVET results for dplyr
`civet.getAllFilenames()`	civet.getAllFilenames
`civet.getFilenameClassify()` `civet.getFilenameGrayMatterPve()` `civet.getFilenameWhiteMatterPve()` `civet.getFilenameCsfPve()` `civet.getFilenameStxT1()` `civet.getFilenameCerebrumMask()` `civet.getFilenameSkullMask()` `civet.getFilenameGrayMatterSurfaces()` `civet.getFilenameWhiteMatterSurfaces()` `civet.getFilenameMidSurfaces()` `civet.getFilenamesCorticalThickness()` `civet.getFilenamesCorticalArea()` `civet.getFilenamesCorticalVolume()` `civet.getFilenameMeanSurfaceCurvature()` `civet.getFilenameLinearTransform()` `civet.getFilenameNonlinearTransform()`	Get Selected Civet Filenames
`civet.organizeCivetDatFilesAtlas()`	Organizes CIVET .dat files based on an Atlas
`civet.readAllCivetFiles()`	Read all CIVET files into R
`civet.readCBRAIN()`	Read a CBRAIN project in R
`civet.readCivetDatFiles()`	Read Civet-Generated Dat Files
`civet.readQC()`	Read CIVET QC data
`civet.vertexFilenames()`	Assemble vertex files for a CIVET run
`civet.vertexTable()`	Create a table of vertex measures
`closestVertex()`	Find Closest Vertex
`colour_mesh()`	Colourize a mesh
`compare_models()`	Compare a set of massively-univariate models
`components_to_map()`	Components to map
`connected_components()`	Find connected components of a object graph
`create_mesh()`	Create surface mesh for a bic_obj
`getRMINCTestData()`	Download Example Data
`hanatAnova()`	ANOVA applied to every item in an anatomical tree
`hanatFDR()`	Compute the False Discovery Rate for an anatomical hierarchy
`hanatLm()`	linear model applied to every item in an anatomical tree
`hanatLmer()`	linear mixed effects model applied to every item in an anatomical tree
`hanatLmerEstimateDF()`	Estimates degrees of freedom
`hanatPlot()`	hanatPlot
`hanatToVisGraph()` `hanatView()`	Turns an anatomical tree into a nodes and edges for visNetwork plotting
`hanatToVolume()`	Converts a column from a hierarchical tree into a volume for viewing or saving
`is.minc()`	Check for RMINC objects
`launch_shinyRMINC()`	launch a shiny based inspector
`likeVolume()` `likeVolume<-`()	Get or set a likeVolume
`line_obj_to_voxel()`	Convert Lines to Voxel Coordinates
`lut_to_palette()`	A tool that returns a color function/palette from color lookup files
`makeMICeDefsHierachical()`	Creates a hierarchical anatomical tree
`map_to_colours()`	Generate a vector of colours from a map
`maskFile()` `maskFile<-`()	Get or set a mask file
`mcMincApply()`	Local multicore mincApply
`minc.dimensions.sizes()`	Dimension Sizes
`minc.get.hyperslab()`	Get a hyperslab from a MINC2 file
`minc.ray.trace()`	Call ray_trace to get an image of a rendered slice
`minc.separation.sizes()`	Slice Separations
`mincAnova()`	Voxel-wise ANOVA Compute a sequential ANOVA at each voxel
`mincApply()`	Apply arbitrary R function at every voxel
`mincApplyRCPP()`	Perform Arbitrary calculations on a collection of mincVolumes
`mincArray()`	A utility function to give a MINC object spatial dimensions
`mincAttributes()` `setMincAttributes()`	Get and Set Minc Specific Attributes
`mincContour()`	Draw contour lines from a MINC volume
`mincConvertTagToMincArrayCoordinates()`	convert tags from world coordinates to mincArray coordinates
`mincConvertVoxelMatrix()`	Convert Voxel to World Coordinates
`mincConvertVoxelToWorld()`	Voxel to World
`mincConvertWorldMatrix()`	Convert World to Voxel Coordinates
`mincConvertWorldToVoxel()`	World to Voxel
`mincFDR()`	False Discovery Rates
`mincFDRMask()`	mincFDRMask
`mincFDRThresholdVector()`	a utility function to compute thresholds
`mincFileCheck()`	Minc File Check
`mincFindPeaks()`	Finds peak values in a MINC file or volume
`mincGetMask()`	Minc Masks
`mincGetTagFile()`	read a tag file
`mincGetVector()`	Voxel Vector
`mincGetVolume()`	Read a MINC file
`mincGetVoxel()`	Retrieve Voxel Values
`mincGetWorldVoxel()`	World Vector
`mincImage()`	Plot a slice from a MINC volume
`mincLabelPeaks()`	label peaks with the name of the atlas structure they are in
`mincLm()`	Linear model at Every Voxel
`mincLmer()`	mincified version of lmer from lme4
`mincLmerEstimateDF()`	Estimate the degrees of freedom for parameters in a mincLmer model
`mincLogLikRatio()`	run log likelihood ratio tests for different mincLmer objects
`mincLogLikRatioParametricBootstrap()`	computes parametric bootstrap on mincLogLikRatio output
`mincPairedTtest()`	Minc Paired T Test
`mincPlotAnatAndStatsSlice()`	Anatomy and Statistics Slice
`mincPlotPeak()`	Plotting of peaks
`mincPlotSliceSeries()`	MINC Slice Series
`mincRandomize()`	Run a permutation test on a `mincLm` result
`mincRayTraceStats()`	Create an image of a statistical peak.
`mincSelectRandomVoxels()`	selects a few random indices from a volume
`mincSummary()` `mincMean()` `mincVar()` `mincSum()` `mincSd()` `mincCorrelation()`	Minc Voxel Summary Functions
`mincTFCE()`	Threshold Free Cluster Enhancement
`mincTriplanarSlicePlot()`	Plot Slice Along Each Axis
`mincTtest()`	Minc T-test
`mincVectorToVoxelCoordinates()`	converts a vector index to the voxel indices in MINC
`mincWilcoxon()`	Minc Wilcoxon
`mincWriteVolume()`	Write a MINC volume to file
`minc.get.history()` `minc.append.history()`	Minc History
`obj_montage()`	Brain Montage
`obj_to_graph()`	Object to Graph
`pMincApply()`	Parallel MincApply
`plot(<bic_lines>)`	Plot A bic_lines object
`plot(<bic_obj>)`	Plot a BIC obj
`plot(<obj_mesh>)`	Plot an BIC obj mesh
`pt2()`	Two tailed version of pt
`qMincApply()` `qMincRegistry()` `qMincMap()` `qMincReduce()`	True cluster mincApply
`read_line_obj()`	Read a BIC-obj line file
`read_obj()`	Read BIC .obj files
`runRMINCTestbed()`	Run Testbed
`setRMINCMaskedValue()`	Set Masked Value
`simplify2minc()`	Collate Minc
`simplify_masked()`	Simplify Masked Results
`thresholds()`	Get Probability Thresholds
`verboseRun()`	Run function with/without output silenced
`vertexAnova()`	Performs ANOVA on each vertex point specified
`vertexApply()`	Apply function over vertex Files
`vertexFDR()`	Vertex False Discovery Rates
`vertexFindPeaks()`	Vertex find peaks
`vertexLm()`	Calculates statistics and coefficients for linear model of specified vertex files
`vertexLmer()`	Vertex Mixed Effects Models
`vertexLmerEstimateDF()`	Estimate the degrees of freedom for parameters in a vertexLmer model
`vertexLookup()`	Vertex Lookup
`vertexSelect()`	Select Vertices From a Surface
`vertexMean()` `vertexSum()` `vertexVar()` `vertexSd()`	Create descriptive statistics across a series of vertex files
`vertexTFCE()`	Threshold Free Cluster Enhancement
`vertexTable()`	Create a table of vertex values
`volume.combineMaskVolumes()`	Combine Multiple Mask Volumes into a Single Mask Volume
`volume.explodeLabelVolume()`	Explode a Label Volume into its Components
`voxel_atlas_defs`	Voxel Atlas Definitions
`writeVertex()`	Writes vertex data to a file with an optional header

Reference

All functions

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