Man pages for Mouse-Imaging-Centre/RMINC
Statistical Tools for Medical Imaging NetCDF (MINC) Files

add_colour_barAdd a colour bar for a mesh
add_opacityAdd opacity to a mesh
addVolumesToHierarchyAdd volumes to an anatomical hierarchy
AICcCompute the Corrected AIC for an object
anatAnovaPerforms ANOVA on each region specified
anatApplyApply function over anat structure
anatCombineStructuresCombine left and right volumes
anatCreateVolumeCreate a Statistic Volume
anatFDRAnatomy False Discovery Rates
anatGetAllFaster AnatGet
anatGetAll_oldGet values given a set of files and an atlas
anatLmCalculates statistics and coefficients for linear model of...
anatLmerAnatomy Linear Mixed Effects Model
anatLmerEstimateDFEstimate Degrees of freedom for an anatLmer model
anatSummarizeSummarize anatGetAll results by hierarchy Anatomy data.frame
as.mincCoerce to RMINC object
check_step_sizesCheck file step sizes
civet.checkVersionCheck for a known Civet Version
civet.computeNativeToStxRescalingFactorCompute Native to Stereotactic Rescaling Factor
civet.computeTissueVolumesCompute GM, WM, and CSF Tissue Volumes
civet.CreateBrainViewFileCreate a brain view file
civet.flattenForDplyrFlatten CIVET results for dplyr
civet.getFilenameGet Selected Civet Filenames
civet.organizeCivetDatFilesAtlasOrganizes CIVET .dat files based on an Atlas
civet.readAllCivetFilesRead all CIVET files into R
civet.readCBRAINRead a CBRAIN project in R
civet.readCivetDatFilesRead Civet-Generated Dat Files
civet.readQCRead CIVET QC data
civet.vertexFilenamesAssemble vertex files for a CIVET run
civet.vertexTableCreate a table of vertex measures
closestVertexFind Closest Vertex
colour_meshColourize a mesh
compare_modelsCompare a set of massively-univariate models
components_to_mapComponents to map
connected_componentsFind connected components of a object graph
create_meshCreate surface mesh for a bic_obj
extract_columnInternal function to read in a table or csv file potentially...
getRMINCTestDataDownload Example Data
hanatAnovaANOVA applied to every item in an anatomical tree
hanatFDRCompute the False Discovery Rate for an anatomical hierarchy
hanatLmlinear model applied to every item in an anatomical tree
hanatLmerlinear mixed effects model applied to every item in an...
hanatLmerEstimateDFEstimates degrees of freedom
hanatToVisGraphTurns an anatomical tree into a nodes and edges for...
hanatToVolumeConverts a column from a hierarchical tree into a volume for...
is.mincCheck for RMINC objects
launch_shinyRMINClaunch a shiny based inspector
likeVolumeGet or set a likeVolume
line_obj_to_voxelConvert Lines to Voxel Coordinates
lut_to_paletteA tool that returns a color function/palette from color...
makeMICeDefsHierachicalCreates a hierarchical anatomical tree
map_to_coloursGenerate a vector of colours from a map
maskFileGet or set a mask file
mcMincApplyLocal multicore mincApply
mincAnovaVoxel-wise ANOVA Compute a sequential ANOVA at each voxel
mincApplyApply arbitrary R function at every voxel
mincApplyRCPPPerform Arbitrary calculations on a collection of mincVolumes
mincArrayA utility function to give a MINC object spatial dimensions
mincAttributesGet and Set Minc Specific Attributes
mincContourDraw contour lines from a MINC volume
mincConvertTagToMincArrayCoordinatesconvert tags from world coordinates to mincArray coordinates
mincConvertVoxelMatrixConvert Voxel to World Coordinates
mincConvertVoxelToWorldVoxel to World
mincConvertWorldMatrixConvert World to Voxel Coordinates
mincConvertWorldToVoxelWorld to Voxel
minc.dimensions.sizesDimension Sizes
mincFDRFalse Discovery Rates
mincFDRThresholdVectora utility function to compute thresholds
mincFileCheckMinc File Check
mincFindPeaksFinds peak values in a MINC file or volume
minc.get.hyperslabGet a hyperslab from a MINC2 file
mincGetMaskMinc Masks
mincGetTagFileread a tag file
mincGetVectorVoxel Vector
mincGetVolumeRead a MINC file
mincGetVoxelRetrieve Voxel Values
mincGetWorldVoxelWorld Vector
minc_historyMinc History
mincImagePlot a slice from a MINC volume
mincLabelPeakslabel peaks with the name of the atlas structure they are in
mincLmLinear model at Every Voxel
mincLmermincified version of lmer from lme4
mincLmerEstimateDFEstimate the degrees of freedom for parameters in a mincLmer...
mincLogLikRatiorun log likelihood ratio tests for different mincLmer objects
mincLogLikRatioParametricBootstrapcomputes parametric bootstrap on mincLogLikRatio output
mincPairedTtestMinc Paired T Test
mincPlotAnatAndStatsSliceAnatomy and Statistics Slice
mincPlotPeakPlotting of peaks
mincPlotSliceSeriesMINC Slice Series
mincRandomizeRun a permutation test on a 'mincLm' result
minc.ray.traceCall ray_trace to get an image of a rendered slice
mincRayTraceStatsCreate an image of a statistical peak.
mincSelectRandomVoxelsselects a few random indices from a volume
minc.separation.sizesSlice Separations
mincSummaryMinc Voxel Summary Functions
mincTFCEThreshold Free Cluster Enhancement
mincTriplanarSlicePlotPlot Slice Along Each Axis
mincTtestMinc T-test
mincVectorToVoxelCoordinatesconverts a vector index to the voxel indices in MINC
mincWilcoxonMinc Wilcoxon
mincWriteVolumeWrite a MINC volume to file
obj_montageBrain Montage
obj_to_graphObject to Graph
plot.bic_linesPlot A bic_lines object
plot.bic_objPlot a BIC obj
plot.obj_meshPlot an BIC obj mesh
pMincApplyParallel MincApply
pt2Two tailed version of pt
qMincApplyTrue cluster mincApply
read_line_objRead a BIC-obj line file
read_objRead BIC .obj files
RMINCRMINC: R interface to the MINC universe
runRMINCTestbedRun Testbed
setRMINCMaskedValueSet Masked Value
simplify2mincCollate Minc
simplify_maskedSimplify Masked Results
thresholdsGet Probability Thresholds
verboseRunRun function with/without output silenced
vertexAnovaPerforms ANOVA on each vertex point specified
vertexApplyApply function over vertex Files
vertexAtlasApplyApply a structure summary function across vertices
vertexEffectSizeEffect Sizes
vertexFDRVertex False Discovery Rates
vertexFindPeaksVertex find peaks
vertexLmCalculates statistics and coefficients for linear model of...
vertexLmerVertex Mixed Effects Models
vertexLmerEstimateDFEstimate the degrees of freedom for parameters in a...
vertexLookupVertex Lookup
vertexSelectSelect Vertices From a Surface
vertexSummariesCreate descriptive statistics across a series of vertex files
vertexTableCreate a table of vertex values
vertexTFCEThreshold Free Cluster Enhancement
volume.combineMaskVolumesCombine Multiple Mask Volumes into a Single Mask Volume
volume.explodeLabelVolumeExplode a Label Volume into its Components
voxel_atlas_defsVoxel Atlas Definitions
writeVertexWrites vertex data to a file with an optional header
Mouse-Imaging-Centre/RMINC documentation built on May 7, 2019, 5:01 p.m.