DICOM stack mean value

[sanata]

Dear all, i am very new to R=)
Actually it is my first day here. I am trying to read the folder with several DICOM files and find a mean value in aech of the slice of the 3 D image
Here is what I wrote so far... But seems that I have only calculated mean value for the fist image in a stack... or not? I expected to get a vector not a value...
thank you in advance

library("oro.dicom")
current_folder <- "C:/NRA/DICOM_test"
DCM <- readDICOM(current_folder, verbose=TRUE)
# remove dicom header, leave just the image part
image<-DCM$img


# remove dicom header, leave just the image part
image<-DCM$img
#rewrite image (mode lyst as a matrix 512 by 512)
#matrix_512 <- matrix(unlist(image), byrow=TRUE, 512) 
matrix_512 <- matrix(unlist(image), 512, 512) 
# creat image
image(t(matrix_512), col=grey(0:64/64), axes=FALSE, xlab="", ylab="")


# 1step: find HU mean
for(i in 1:512)
{
  for(j in 1:512)
  {
    # meam
    M<- mean(matrix_512[,])
  }
  break
}
print(M)

[mattwarkentin]

Hi @sanata,

The DCM$img object returned from oro.dicom::readDICOM is a list of matrices, with one matrix per slice. So you can iterate over the slices and return a mean with the following code:

DCM <- readDICOM(current_folder, verbose=TRUE)
image<-DCM$img
purrr::map_dbl(image, mean)

This will return a vector with a length equal to the number of slices in the series. Hope this is helpful.