MRIaggr-allocContrast: Allocate new contrast parameters
In bozenne/MRIaggr: Management, Display, and Processing of Medical Imaging Data

Description Usage Arguments Details Value See Also Examples

Allocate one or several contrast parameters to a MRIaggr object.

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## S4 replacement method for signature 'MRIaggr'
allocContrast(object, param = NULL, default_value = NULL,
         overwrite = FALSE, verbose = optionsMRIaggr("verbose")) <- value

`object`	an object of class `MRIaggr`. REQUIRED.
`value`	the value of each contrast parameter (in columns) at each voxel (in rows). data.frame. REQUIRED.
`param`	the names of the contrast parameters. character vector or `NULL` leading to use the name of the `value` argument.
`default_value`	the reference values of the contrast parameters (e.g background values). A one row data.frame where the column length must match the length of the `param` argument.
`overwrite`	if a contrast parameters with the same names are already stored in `object@data`, can they be overwritten ? logical.
`verbose`	should the execution of the function be traced ? logical.

FUNCTION:
If the param argument is not specified then the names of the value argument will be used to define the parameter names.

If the default_value argument is NULL then default values "undefined" are attributed to each parameter.

If a parameter named "mask" is intended to be allocated it must be done alone and it must be of type logical.

Parameter names "index", "i", "j" and "k" are reserved and cannot be modified. Nevertheless if value contains parameters "i", "j" and "k", the correspondance between these coordinates and the object coordinates is tested.

None.

calcContralateral, calcRegionalContrast, calcFilter and calcTissueType to compute, modify and allocate cartography.
selectContrast to select contrast parameters in the MRIaggr object.

## load NIFTI files and convert them to MRIaggr
path.Pat1 <- system.file(file.path("nifti"), package = "MRIaggr")
ls.array <- list()
ls.array[[1]] <- readMRI(file.path(path.Pat1, "DWI_t0"),format = "nifti")
ls.array[[2]] <- readMRI(file.path(path.Pat1, "MASK_DWI_t0"),format = "nifti")
MRIaggr.Pat1 <- constMRIaggr(ls.array, identifier = "Pat1", param = c("DWI_t0", "MASK_DWI_t0"))

## allocate a new contrast parameters
allocContrast(MRIaggr.Pat1, param = "noise", overwrite = TRUE) <- rnorm(selectN(MRIaggr.Pat1))

## perform operations on a contrast parameters and store the results
myCarto <- selectContrast(MRIaggr.Pat1 , param = "DWI_t0")
myCarto <- myCarto * 2 + 1
allocContrast(MRIaggr.Pat1, param = "myCarto", overwrite = TRUE) <- myCarto

## import a contrast parameters in an already existing MRIaggr object
nifti.MTT_t0 <- readMRI(file.path(path.Pat1, "MTT_t0"), format = "nifti")
df.MTT_t0 <- array2dt(nifti.MTT_t0, name_newparam = "MTT_t0")$MTT_t0
allocContrast(MRIaggr.Pat1, param = "MTT_t0", overwrite = TRUE) <- df.MTT_t0

## some calc methods automatically save results in the @data slot
calcFilter(MRIaggr.Pat1, param = "MTT_t0", filter = "2D_G3",
           update.object = TRUE, overwrite = TRUE)
res <- selectContrast(MRIaggr.Pat1, param = "MTT_t0_2D_G3")