Management, Display, and Processing of Medical Imaging Data

Documentation for package ‘MRIaggr’ version 1.0

DESCRIPTION file.
Code demos. Use demo() to run them.

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

MRIaggr-package

Management, display and processing of cerebral imaging data.

-- A --

affectClinic<-	Affect clinical data
affectClinic<--method	Affect clinical data
affectContrast<-	Affect new contrast parameters
affectContrast<--method	Affect new contrast parameters
affectDescStats<-	Affect non standard elements
affectDescStats<--method	Affect non standard elements
affectHemisphere<-	Affect the position of the mid-saggital plan
affectHemisphere<--method	Affect the position of the mid-saggital plan
affectNormalization<-	Affect normalization values
affectNormalization<--method	Affect normalization values
affectTable<-	Affect volumic information
affectTable<--method	Affect volumic information
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
calcBrainMask	Brain-Background discrimination
calcBrainMask-method	Brain-Background discrimination
calcControlateral	Compute contraleral normalization values
calcControlateral-method	Compute contraleral normalization values
calcContro_cpp	Compute controlateral 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-saggital plan
calcHemisphere-method	Find the mid-saggital plan
calcHemi_cpp	Mid-saggital plan search
calcNormalization	Compute normalization values
calcNormalization-method	Compute normalization values
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 neighborhood matrix
calcW-method	Compute the neighborhood 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
constMRIaggr	Array constructor for MRIaggr object
constReduceMRIaggr	Reduce a MRIaggr
constReduceMRIaggr-method	Reduce a MRIaggr
constSweave	Constructor for Sweave report

-- D --

df2array

data.frame to array converter

-- 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
initDisplayWindow	Device management
initFilter	Initialization of a filter
initGR	Growing Region initialization
initIndex	Index initialization
initNeighborhood	Initialization of a neighborhood filter
initNum	Initialization of the slice numbers
initNum-method	Initialization of the slice numbers
initParameter	parameter initialization
initParameter-method	parameter initialization
initWindow	Display initialization

-- L --

legendMRI

Diplay a legend of a contrast map

-- M --

MRIaggr	Class "MRIaggr"
MRIaggr-class	Class "MRIaggr"
MRIaggr.Pat1_red	Example of processed MRIaggr object
multiplot	Spatial display using coordinates
multiplot-method	Spatial display using coordinates

-- O --

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
plotTableLesion	Lesion volume displayed by slices
plotTableLesion-method	Lesion volume displayed by slices
pointsHemisphere	Add the position of the mid-saggital plan
pointsHemisphere-method	Add the position of the mid-saggital plan
pointsOutline	Compute the outline of a spatial group

-- R --

readMRI

Read imaging file

-- 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
selectHemispheres	Extract the position of the lesion in the hemispheres
selectHemispheres-method	Extract the position of the lesion in the hemispheres
selectHistory	Extract the history of the object
selectHistory-method	Extract the history of the object
selectIdentifier	Extract the identifier
selectIdentifier-method	Extract the identifier
selectMidplane	Extract the position of the mid-saggital plan
selectMidplane-method	Extract the position of the mid-saggital 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
selectParameter	Extract parameters
selectParameter-method	Extract parameters
selectTable	Extract volumic information
selectTable-method	Extract volumic information
selectVoxelDim	Extract the data dimension
selectVoxelDim-method	Extract the data dimension
selectVoxelSize	Extract the dimensions of a voxel
selectVoxelSize-method	Extract the dimensions of a voxel
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