## ---- echo = FALSE, message = FALSE--------------------------------------
knitr::opts_chunk$set(collapse = T, comment = "#>")
library(neuroim)

## ------------------------------------------------------------------------
    fileName <- system.file("extdata", "global_mask.nii", package="neuroim")
    vol <- loadVolume(fileName)

## ------------------------------------------------------------------------
    print(vol)

## ------------------------------------------------------------------------
    class(vol)
    
    is.array(vol)
    
    dim(vol)
    
    vol[1,1,1]
    
    vol[64,64,24]
    

## ------------------------------------------------------------------------
    
    vol2 <- vol + vol
    sum(vol2) == 2 * sum(vol)
    
    vol3 <- vol2 - 2*vol
    all(vol3 == 0)

## ------------------------------------------------------------------------
    
    vol2 <- as.logical(vol)
    print(vol2[1,1,1])

## ------------------------------------------------------------------------
    # create an 64X64X64 array of zeros 
    x <- array(0, c(64,64,64))
    
    # create a 'BrainSpace' instance that describes the geometry of the image including, at minimu its dimensions and voxel spacing
    bspace <- BrainSpace(Dim=c(64,64,64), spacing=c(1,1,1))
    vol <- BrainVolume(x, bspace)
    vol

## ------------------------------------------------------------------------
    vol2 <- BrainVolume((vol+1)*25, space(vol))
    max(vol2)
    
    space(vol2)

## ------------------------------------------------------------------------
    writeVolume(vol2, "output.nii")
    
    ## adding a '.gz' extension results ina gzipped file.
    writeVolume(vol2, "output.nii.gz")