Package index • RMINC

Package overview

RMINC RMINC-package: RMINC: R interface to the MINC universe

Voxel-wise statistics

Massively-univariate models fit independently at every voxel.

mincLm(): Linear model at Every Voxel
mincAnova(): Voxel-wise ANOVA
mincTtest(): Minc T-test
mincPairedTtest(): Minc Paired T Test
mincWilcoxon(): Minc Wilcoxon
mincSummary() mincMean() mincVar() mincSum() mincSd() mincCorrelation(): Minc Voxel Summary Functions
mincLogLikRatio(): run log likelihood ratio tests for different mincLmer objects
mincLogLikRatioParametricBootstrap(): computes parametric bootstrap on mincLogLikRatio output

Voxel summaries & effect sizes

mincSummary() mincMean() mincVar() mincSum() mincSd() mincCorrelation(): Minc Voxel Summary Functions
mincTable(): Read a collection of minc volumes
vertexEffectSize() mincEffectSize() anatEffectSize(): Effect Sizes

Voxel mixed-effects models

mincLmer(): mincified version of lmer from lme4
mincLmerEstimateDF(): Estimate the degrees of freedom for parameters in a mincLmer model

Multiple comparisons (voxel)

mincFDR(): False Discovery Rates
mincFDRMask(): mincFDRMask
mincFDRThresholdVector(): a utility function to compute thresholds
mincTFCE(): Threshold Free Cluster Enhancement
mincRandomize(): Run a permutation test on a mincLm result
thresholds(): Get Probability Thresholds

Surface / vertex statistics

Vertex-wise models for cortical surface data.

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
vertexAnova(): Performs ANOVA on each vertex point specified
vertexApply(): Apply function over vertex Files
vertexAtlasApply(): Apply a structure summary function across vertices
vertexEffectSize() mincEffectSize() anatEffectSize(): Effect Sizes
vertexFDR(): Vertex False Discovery Rates
vertexFindPeaks(): Vertex find peaks
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
writeVertex(): Writes vertex data to a file with an optional header

ROI / anatomy analysis (flat)

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
anatAnova(): Performs ANOVA on each region specified
anatApply(): Apply function over anat structure
anatCombineStructures(): Combine left and right volumes
anatCreateVolume(): Create a Statistic Volume
vertexEffectSize() mincEffectSize() anatEffectSize(): Effect Sizes
anatFDR(): Anatomy False Discovery Rates
anatGetAll(): Faster AnatGet
anatGetAll_old(): Get values given a set of files and an atlas
as.data.frame(<anatMatrix>): Create Anatomy data.frame
voxel_atlas_defs: Voxel Atlas Definitions
anatMean() anatSum() anatVar() anatSd(): anatSummaries
anatSummarize(): Summarize anatGetAll results by hierarchy
anatToVolume(): Converts a column from an anatLm model into a volume for viewing or saving

Hierarchical anatomy atlases

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
addVolumesToHierarchy(): Add volumes to an anatomical hierarchy
makeMICeDefsHierachical(): Creates a hierarchical anatomical tree

Model selection

compare_models(): Compare a set of massively-univariate models
AICc(): Compute the Corrected AIC for an object
flexLm(): Flexible Linear Model with Voxel-Varying Covariates

Parallel & HPC execution

batchtools-based local and cluster parallelism.

mincApply(): Apply arbitrary R function at every voxel
mincApplyRCPP(): Perform Arbitrary calculations on a collection of mincVolumes
pMincApply(): Parallel MincApply
mcMincApply(): Local multicore mincApply
qMincApply() qMincRegistry() qMincMap() qMincReduce(): True cluster mincApply
runRMINCTestbed(): Run Testbed
verboseRun(): Run function with/without output silenced

I/O & low-level access

mincGetVolume(): Read a MINC file
mincWriteVolume(): Write a MINC volume to file
mincArray(): A utility function to give a MINC object spatial dimensions
mincGetVoxel(): Retrieve Voxel Values
mincGetWorldVoxel(): World Vector
mincVectorToVoxelCoordinates(): converts a vector index to the voxel indices in MINC
mincConvertTagToMincArrayCoordinates(): convert tags from world coordinates to mincArray coordinates
mincConvertVoxelToWorld(): Voxel to World
mincConvertWorldToVoxel(): World to Voxel
mincConvertVoxelMatrix(): Convert Voxel to World Coordinates
mincConvertWorldMatrix(): Convert World to Voxel Coordinates
minc.dimensions.sizes(): Dimension Sizes
minc.separation.sizes(): Slice Separations
minc.get.hyperslab(): Get a hyperslab from a MINC2 file
minc.get.history() minc.append.history(): Minc History
mincAttributes() setMincAttributes(): Get and Set Minc Specific Attributes
mincGetTagFile(): read a tag file
mincSelectRandomVoxels(): selects a few random indices from a volume
mincFindPeaks(): Finds peak values in a MINC file or volume
mincLabelPeaks(): label peaks with the name of the atlas structure they are in
mincFileCheck(): Minc File Check
mincGetMask(): Minc Masks
mincGetVector(): Voxel Vector
extract_column(): Internal function to read in a table or csv file potentially with many columns and extract just the one we need
volume.combineMaskVolumes(): Combine Multiple Mask Volumes into a Single Mask Volume
volume.explodeLabelVolume(): Explode a Label Volume into its Components

MINC object helpers

as.minc(): Coerce to RMINC object
is.minc(): Check for RMINC objects
likeVolume() `likeVolume<-`(): Get or set a likeVolume
maskFile() `maskFile<-`(): Get or set a mask file
simplify2minc(): Collate Minc
simplify_masked(): Simplify Masked Results
setRMINCMaskedValue(): Set Masked Value
RMINC_MASKED_VALUE: RMINC Masked Value

Visualization

mincPlotSliceSeries(): MINC Slice Series
mincTriplanarSlicePlot(): Plot Slice Along Each Axis
mincPlotAnatAndStatsSlice(): Anatomy and Statistics Slice
mincPlotPeak(): Plotting of peaks
mincImage(): Plot a slice from a MINC volume
mincContour(): Draw contour lines from a MINC volume
mincRayTraceStats(): Create an image of a statistical peak.
minc.ray.trace(): Call ray_trace to get an image of a rendered slice
add_colour_bar(): Add a colour bar for a mesh
add_opacity(): Add opacity to a mesh
colour_mesh(): Colourize a mesh
map_to_colours(): Generate a vector of colours from a map
lut_to_palette(): A tool that returns a color function/palette from color lookup files
obj_montage(): Brain Montage
obj_to_graph(): Object to Graph
plot(<bic_lines>): Plot A bic_lines object
plot(<bic_obj>): Plot a BIC obj
plot(<obj_mesh>): Plot an BIC obj mesh
launch_shinyRMINC(): launch a shiny based inspector

Meshes & manifold smoothing

create_mesh(): Create surface mesh for a bic_obj
read_obj(): Read BIC .obj files
read_line_obj(): Read a BIC-obj line file
closestVertex(): Find Closest Vertex
connected_components(): Find connected components of a object graph
components_to_map(): Components to map
clean_up_manifold_triangles(): Clean up manifold mesh
line_obj_to_voxel(): Convert Lines to Voxel Coordinates
laplace_beltrami_operator(): Compute Laplace-Beltrami operator
laplace_beltrami_smoothing(): Smoothing on manifold
check_step_sizes(): Check file step sizes

CIVET

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

Test data & helpers

getRMINCTestData(): Download Example Data
pt2(): Two tailed version of pt