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Interactive image stacks in R

September 19, 2013

I’ve been quiet for the last few months because the work I was doing on pseudolikelihood and critical temperature developed into a paper that I had to write up and submit. Hopefully this will be the second journal article of my PhD thesis by publication, not counting the short paper I’ve submitted to the ICCR 2013 proceedings, nor the 5 manuscript pages of lit review that I’ve contributed to a middle-author paper that’s currently in prep.

A reader of this blog sent me a question about my posts on DICOM (part 1, part 2): specifically how to interact with the DICOM image as a stack of 2D slices. There are two components of this: first, I store the voxel intensity values as a numeric 3D array in R; secondly, I use the excellent misc3d package by Dai Feng and Luke Tierney to scroll interactively through the axial slices. Details (and R code) after the jump:

The first step is to read the image data into R, just like we did before:

dcmImages <- readDICOM("/dev/DICOMRT2", recursive=FALSE, exclude="sql") <- dicomTable(dcmImages$hdr)
for (stack in unique(substring(rownames(,15,20))) {
  if (substring(stack,1,2) == "CT") {
    index <- which(substring(rownames(,15,20) == stack)
    dcm.stack <- list(hdr=dcmImages$hdr[index], img=dcmImages$img[index])
    dcm.nifti <- dicom2nifti(dcm.stack, DIM=3, descrip=c("Manufacturer","ManufacturersModelName"))

## [1] "CT4697"
## NIfTI-1 format
## Type : nifti
## Data Type : 4 (INT16)
## Bits per Pixel : 16
## Slice Code : 0 (Unknown)
## Intent Code : 0 (None)
## Qform Code : 2 (Aligned_Anat)
## Sform Code : 2 (Aligned_Anat)
## Dimension : 512 x 512 x 80
## Pixel Dimension : 0.88 x 0.88 x 2
## Voxel Units : mm
## Time Units : sec

The class nifti extends array, so we can apply any of the R array operations:


## [1] 512 512 80


## [1] 0

sum(dcm.nifti == 0)/prod(dim(dcm.nifti))

## [1] 0.5581

Then the really cool trick is that it only takes a single command to display this (or any) array in an interactive window using Tcl/Tk


## Loading required package: tcltk
## Loading Tcl/Tk interface ...
## done


It is straightforward to apply windowing or other image manipulations to the array prior to calling slices3d. The R package mritc contains routines for image segmentation as well.

From → Imaging, R

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  1. Reading DICOM-RT in R using RadOnc | Matt Moores

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