Management, Display, and Processing of Medical Imaging Data

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Documentation for package ‘MRIaggr’ version 1.1.5

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A B C D E F G H I L M O P R S V W

MRIaggr-package Management, display and processing of cerebral imaging data.

-- A --

allocClinic<- Allocate clinical data
allocClinic<--method Allocate clinical data
allocContrast<- Allocate new contrast parameters
allocContrast<--method Allocate new contrast parameters
allocDescStats<- Allocate non standard elements
allocDescStats<--method Allocate non standard elements
allocHemisphere<- Allocate the position of the mid-saggital plan
allocHemisphere<--method Allocate the position of the mid-saggital plan
allocNormalization<- Allocate normalization values
allocNormalization<--method Allocate normalization values
allocOptionsMRIaggr Allocate new default values
allocTable<- Allocate volumic information
allocTable<--method Allocate volumic information
allocW<- Allocate a neighbourhood matrix
allocW<--method Allocate a neighbourhood matrix
array2df Array to data.frame converter

-- B --

boxplotMask Boxplot spatial group characteristics
boxplotMask-method Boxplot spatial group characteristics

-- C --

calcAUPRC Area under the PR curve
calcBlockW Find disjoint spatial blocks of sites
calcBlockW_cpp Find disjoint spatial blocks of sites
calcBrainMask Brain-Background discrimination
calcBrainMask-method Brain-Background discrimination
calcContralateral Compute contraleral normalization values
calcContralateral-method Compute contraleral normalization values
calcContro_cpp Compute contralateral normalization
calcCriteriaGR Assessment of clustering quality
calcDistMask Euclidean distance to a spatial group
calcDistMask-method Euclidean distance to a spatial group
calcDistTissues Compute descriptive statistics
calcDistTissues-method Compute descriptive statistics
calcFilter Image filtration
calcFilter-method Image filtration
calcGR Interface to the Growing Region algorithm
calcGroupsCoords Compute spatial groups
calcGroupsCoords_cpp Find spatial groups
calcGroupsMask Compute spatial groups
calcGroupsMask-method Compute spatial groups
calcGroupsW Compute spatial groups
calcGroupsW_cpp Find spatial groups
calcHemisphere Find the mid-sagittal plan
calcHemisphere-method Find the mid-sagittal plan
calcHemi_cpp Mid-saggital plan search
calcMultiPotential Computation of the spatial potential
calcMultiPotential_cpp Computation of the spatial potential
calcNormalization Compute normalization values
calcNormalization-method Compute normalization values
calcPotts Spatial regularization using ICM
calcPottsParameter Estimation of the local regularization parameters
calcPotts_cpp Iterated conditional means for spatial regularization
calcRadius_cpp Compute geometric caracteristics of a spatial group
calcRegionalContrast Compute regional contrast parameters
calcRegionalContrast-method Compute regional contrast parameters
calcROCthreshold ROC analysis
calcROCthreshold-method ROC analysis
calcSigmaGR Automatic Growing Region algorithm
calcSmoothMask Spatial regularization
calcSmoothMask-method Spatial regularization
calcTableHypoReperf Compute reperfusion and hypoperfusion tables
calcTableHypoReperf-method Compute reperfusion and hypoperfusion tables
calcTableLesion Vertical distribution of the lesion
calcTableLesion-method Vertical distribution of the lesion
calcThreshold Image thresholding
calcThresholdMRIaggr Image thresholding
calcThresholdMRIaggr-method Image thresholding
calcTissueType Probabilistic tissue type segmentation
calcTissueType-method Probabilistic tissue type segmentation
calcW Compute the neighbourhood matrix
calcW-method Compute the neighbourhood matrix
Carto3D class "Carto3D"
Carto3D-class class "Carto3D"
Carto3D2MRIaggr Carto3D to MRIaggr converter
constCarto3D Array constructor for Carto3D objects
constCompressMRIaggr Compress a MRIaggr object
constCompressMRIaggr-method Compress a MRIaggr object
constLatex Constructor for Latex report
constMRIaggr Array constructor for MRIaggr object
constReduceMRIaggr Reduce a MRIaggr
constReduceMRIaggr-method Reduce a MRIaggr

-- D --

df2array data.frame to array converter
dtnorm Truncated Normal distribution

-- E --

EDK Gaussian kernel

-- F --

filtrage2Dmed_cpp 2D median filtering
filtrage2D_cpp 2D filtering
filtrage3Dmed_cpp 3D median filtering
filtrage3D_cpp 3D filtering

-- G --

GRalgo Growing Region algorithm

-- H --

heatmapMRIaggr Correlation between contrast parameters
heatmapMRIaggr-method Correlation between contrast parameters

-- I --

initCol Color initialization
initDirPat_constLatex Initializateurs for the constLatex function
initDisplayWindow Device management
initFilter Initialization of a filter
initGR Growing Region initialization
initIndex Index initialization
initMask Initialization of the slice numbers
initMask-method Initialization of the slice numbers
initNeighborhood Initialization of a neighbourhood filter
initNum Initialization of the slice numbers
initNum-method Initialization of the slice numbers
initParameter parameter initialization
initParameter-method parameter initialization
initPlot_constLatex Initializateurs for the constLatex function
initSection_constLatex Initializateurs for the constLatex function
initWindow Display initialization
inv.logit Logistic transform

-- L --

legendMRI Diplay a legend of a contrast map
legendMRI2 Diplay a legend of a contrast map
logit Logistic transform

-- M --

MRIaggr Class "MRIaggr"
MRIaggr-class Class "MRIaggr"
MRIaggr.Pat1_red Example of processed MRIaggr object
multiplot Slice by slice display
multiplot-method Slice by slice display

-- O --

optionsMRIaggr Set or Query Default Values for MRIaggr
outline Outline a region on a slice
outlineMRIaggr Outline a region on a slice
outlineMRIaggr-method Outline a region on a slice

-- P --

plotDistClass Plot the distribution of the contrast parameter
plotDistClass-method Plot the distribution of the contrast parameter
plotLesion3D 3D plot of the lesion
plotLesion3D-method 3D plot of the lesion
plotMRI Diplay a contrast parameter by coordinates
plotSigmaGR Display quality criteria for the GR algorithm
plotTableLesion Lesion volume displayed by slices
plotTableLesion-method Lesion volume displayed by slices
pointsHemisphere Add the position of the mid-sagittal plan
pointsHemisphere-method Add the position of the mid-sagittal plan
pointsOutline Compute the outline of a spatial group

-- R --

readMRI Read an image file
rhoLvfree Estimation of the local regularization parameters
rhoMF Estimation of the local and regional spatial correlation
rtnorm Truncated Normal distribution

-- S --

selectClinic Extract clinical data
selectClinic-method Extract clinical data
selectContrast Extract contrast parameters
selectContrast-method Extract contrast parameters
selectCoords Extract spatial coordinates
selectCoords-method Extract spatial coordinates
selectDefault_value Extract reference values
selectDefault_value-method Extract reference values
selectDescStats Extract non-stardard elements
selectDescStats-method Extract non-stardard elements
selectFieldDim Extract the data dimension
selectFieldDim-method Extract the data dimension
selectHemispheres Extract the position of the lesion in each hemisphere
selectHemispheres-method Extract the position of the lesion in each hemisphere
selectHistory Extract the call of the methods applied on the object
selectHistory-method Extract the call of the methods applied on the object
selectIdentifier Extract the identifier
selectIdentifier-method Extract the identifier
selectMidplane Extract the position of the mid-sagittal plan
selectMidplane-method Extract the position of the mid-sagittal plan
selectN Extract the number of observations
selectN-method Extract the number of observations
selectNormalization Extract the normalization values
selectNormalization-method Extract the normalization values
selectOptionsMRIaggr Extract default values
selectParameter Extract parameters
selectParameter-method Extract parameters
selectTable Extract volumic information
selectTable-method Extract volumic information
selectVoxelDim Extract the dimensions of a voxel
selectVoxelDim-method Extract the dimensions of a voxel
selectW Extract a neighbourhood matrix
selectW-method Extract a neighbourhood matrix
show-method Summary Method for Class "MRIaggr"
simulPotts Draw a sample from a Potts model
simulPottsFast_cpp Potts model simulation
simulPotts_cpp Potts model simulation
summary-method Summary Method for Class "MRIaggr"
supprContrast<- Remove a contrast parameter
supprContrast<--method Remove a contrast parameter
supprDescStats<- Remove an element of ls_descStats
supprDescStats<--method Remove an element of ls_descStats

-- V --

validCharacter Checking argument validity
validClass Checking argument validity
validDim_matrix Checking argument validity
validDim_vector Checking argument validity
validInteger Checking argument validity
validLogical Checking argument validity
validNames Checking argument validity
validNumeric Checking argument validity
validPath Checking argument validity

-- W --

writeMRI Write an image file
writeMRIaggr Write an image file
writeMRIaggr-method Write an image file