Lecture 2 NIfTI

NifTI (Neuroimaging Informatics Tehcnology Image) -Standardized representation of images -Most commonly used tpy eof analytic file -Developed to facilitate cross-platform, cross-software interpretability -3-dimensional array: stacking individual slices on top of each other -DICOM: one sheet of paper; NIfTI: stack of papers

2.1 From DICOM to NIfTI

-DICOM to NIFTI using the dicom2nifti function in the oro.dicom package -The nifti object becomes an R object -After saving a file to a nifti file it can be used without R

Let’s read all DICOM images:

library(oro.dicom)

## oro.dicom 0.5.3

all_slices_T1 = readDICOM("Neurohacking_data/BRAINIX/DICOM/T1")
dim(all_slices_T1$img[[11]])

## [1] 512 512

hdr = all_slices_T1$hdr[[11]]
hdr[hdr$name == "PixelSpacing", "value"]

## [1] "0.46875 0.46875"

Now lets’s convert them to NIFTI:

nii_T1 = dicom2nifti(all_slices_T1)

## Warning in create3D(dcm, ...): ImagePositionPatient is moving in more than one
## dimension.

## Warning in swapDimension(img, dcm): Oblique acquisition in
## ImageOrientationPatient (hope for the best).

## Warning in is.axial(imageOrientationPatient): Oblique acquisition in
## ImageOrientationPatient.

## Warning in is.coronal(imageOrientationPatient): Oblique acquisition in
## ImageOrientationPatient.

## Warning in is.sagittal(imageOrientationPatient): Oblique acquisition in
## ImageOrientationPatient.

d = dim(nii_T1); d; class(nii_T1)

## [1] 512 512  22

## [1] "nifti"
## attr(,"package")
## [1] "oro.nifti"

And plot one slice:

# Plot the 11th slice
image(1:d[1], 1:d[2], nii_T1[,,11], col=gray(0:64/64), xlab="", ylab="")

2.2 Write and Read NIfTI files

• Use the writeNIfTI, readNIfTI functions in the oro.nifti package
• Default for writeNIfTI is to save the compressed NIfTI files

library(oro.nifti)

## oro.nifti 0.10.1

dir_name = "Neurohacking_data/BRAINIX/NIfTI/"
fname = "Output_3D_File"
writeNIfTI(nim=nii_T1, file = paste0(dir_name, fname))

And check that the file si there after saving

list.files(dir_name, pattern = fname)

## [1] "Output_3D_File.nii.gz"

Now lets read a different file:

list.files(dir_name, pattern="T") #Check that file is in directory

## [1] "T1.nii.gz" "T2.nii.gz"

nii_T2=readNIfTI(paste0(dir_name,"T2.nii.gz"), reorient=FALSE)
dim(nii_T2)

## [1] 512 512  22

2.3 Compressed Image Files

-A non-compressed file can be obtained using the argument gzipped=FALSE in the function writeNIfTI