CODEWITHSUNDEEP
rdicom
Jin
Jin

Reputation: 555

Extracting dicom headers in R

I'm trying to use this dataset here

https://mri.radiology.uiowa.edu/VHDicom/VHMCT1mm/VHMCT1mm_Head.tar.gz

to test out the oro.dicom package in R.

I try out the code 

dcmImages <- readDICOM("C:\\Users\\Host\\Documents\\SCANS\\Head", verbose = TRUE,
                       recursive = TRUE)

then I try out the extractHeader function like this 

extractHeader(dcmImages$hdr, string="InstitutionName")

and I get a bunch of NA's. However, I can clearly see when I run this 

dcmImages$hdr

I can see in the console that institution name is listed as the National Library of Medicine. What is causing the discrepancy?

Update: Eventually the answer below started working but previously it wasn't and I'm not sure why. I'm on Windows 10 OS and I updated R from 3.5.3 to 3.6 and then it started working but this error that says signed = FALSE' is only valid for integers of sizes 1 and 2' persists when running the readDICOM function. However, I now have output from the headers instead of NAs

Upvotes: 1

Views: 452

Answers (1)

Ben
Ben

Reputation: 30474

Try:

library(oro.dicom)
dcmImages <- readDICOM("/<my path>/Head", verbose = TRUE, recursive = TRUE)
extractHeader(dcmImages$hdr, string="InstitutionName", numeric=FALSE)

(The default for numeric is TRUE, and values are converted to numbers when TRUE.)

R> extractHeader(dcmImages$hdr, string="InstitutionName", numeric=FALSE)
  [1] "National Library of Medicine" "National Library of Medicine" "National Library of Medicine"
  [4] "National Library of Medicine" "National Library of Medicine" "National Library of Medicine"
  [7] "National Library of Medicine" "National Library of Medicine" "National Library of Medicine"
 [10] "National Library of Medicine" "National Library of Medicine" "National Library of Medicine"

Upvotes: 1

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