npointmerge

#!/usr/bin/env Rscript

#### Make sure packages are installed and load them 

#rniftilib is not in this location
#if (!suppressPackageStartupMessages(require(Rniftilib))) install.packages("Rniftilib", repos="http://R-Forge.R-project.org")
suppressPackageStartupMessages(library(RNifti))

# collect arguments
args <- commandArgs(TRUE)

if (length(args) < 2) {
    stop("Usage: npointmerge outputfile.nii.gz merge1.nii.gz merge2.nii.gz ...")
}

# get name of outputfile
outputfile <- args[1]

# get name of first merge file
firstmerge <- args[2]

# get the number of files to merge
ntomerge <- length(args)-2

###############################################################################
#### Read in the first file to merge. It must exist.
tryCatch({
    firstmerge.nii <- readNifti(firstmerge);
}, error=function(e) {
    cat("Could not read nifti file: ", firstmerge, "\n")
    stop(e)
})

###############################################################################
#### Check to make sure output file does not exist, renaming if it does,
#### and set up the output file
if (file.exists(outputfile)) {
        stop(paste("The output file", outputfile, "exists. Please delete any old results before proceeding."))
    }
nimdat <- firstmerge.nii


###############################################################################
#### Read in all the files to merge and add them to the output image

while(ntomerge > 0) {
    idx <- ntomerge+2
    mim <- readNifti(args[idx])
    nimdat <- nimdat + mim
    ntomerge <- ntomerge -1
}
                
###############################################################################
#### Write out the merged output image
writeNifti(nimdat, outputfile, template=firstmerge.nii, datatype="float")