Read an NIfTI file

This is example to read some NIfTI files and execute some basic data manipulation, by using this example code you must be install package oro.nifti,fslr,AnalyzeFMRI first.

Download a NIfTI file from Neurohacking_data repository

library(oro.nifti)

url <- "https://raw.githubusercontent.com/muschellij2/Neurohacking/master/Basic_Data_Manipulations/Kirby21/SUBJ0001-01-MPRAGE.nii.gz"
destfile <- "SUBJ0001-01-MPRAGE.nii.gz"
fname <- file.path(getwd(), destfile)
download.file(url, destfile,mode="wb") # NIfTI is binaryfile format

maskurl <- "https://raw.githubusercontent.com/muschellij2/Neurohacking/master/Basic_Data_Manipulations/Kirby21/SUBJ0001_mask.nii.gz"
maskdestfile <- "SUBJ0001_mask.nii.gz"
maskfname <- file.path(getwd(), maskdestfile)
download.file(maskurl, maskdestfile,mode="wb") # NIfTI is binaryfile format



T1 <- readNIfTI(fname,reorient=FALSE)

mask <- readNIfTI(maskfname, reorient=FALSE)

Show meta data from MPRAGE file

print (T1)
## NIfTI-1 format
##   Type            : nifti
##   Data Type       : 16 (FLOAT32)
##   Bits per Pixel  : 32
##   Slice Code      : 0 (Unknown)
##   Intent Code     : 0 (None)
##   Qform Code      : 1 (Scanner_Anat)
##   Sform Code      : 0 (Unknown)
##   Dimension       : 170 x 256 x 256
##   Pixel Dimension : 1.2 x 1 x 1
##   Voxel Units     : mm
##   Time Units      : sec

As you see the Dimension is : 170 x 256 x 256

Show meta data from MPRAGE file

print (mask)
## NIfTI-1 format
##   Type            : nifti
##   Data Type       : 4 (INT16)
##   Bits per Pixel  : 16
##   Slice Code      : 0 (Unknown)
##   Intent Code     : 0 (None)
##   Qform Code      : 1 (Scanner_Anat)
##   Sform Code      : 1 (Scanner_Anat)
##   Dimension       : 170 x 256 x 256
##   Pixel Dimension : 1.2 x 1 x 1
##   Voxel Units     : mm
##   Time Units      : sec

As you see the of mask is same dimension (170 x 256 x 256).

Visualizing orthographic T1

orthographic(T1)

Visualizing orthographic mask

orthographic(mask)

Visualizing orthographic T1*mask

library(fslr) # you may need install fslr

masked.T1 <- niftiarr(T1, T1*mask)

orthographic(masked.T1)

Visualizing orthographic subtract

library(fslr) # you may need install fslr


followurl <- "https://raw.githubusercontent.com/muschellij2/Neurohacking/master/Basic_Data_Manipulations/Kirby21/SUBJ0001-02-MPRAGE.nii.gz"
followdestfile <- "SUBJ0001-02-MPRAGE.nii.gz"
followfname <- file.path(getwd(), followdestfile)
download.file(followurl, followdestfile,mode="wb")

T1.follow <- readNIfTI(followfname, reorient=FALSE)

subtract.T1 <- niftiarr(T1, T1.follow - T1)
orthographic(subtract.T1)

Visualizing orthographic subtract

library(fslr) # you may need install fslr


baseurl <- "https://raw.githubusercontent.com/muschellij2/Neurohacking/master/Basic_Data_Manipulations/Kirby21/SUBJ0001-01-MPRAGE_N3.nii.gz"
basefile <- "SUBJ0001-01-MPRAGE_N3.nii.gz"
basefname <- file.path(getwd(), basefile)
download.file(baseurl, basefile,mode="wb")



followurl <- "https://raw.githubusercontent.com/muschellij2/Neurohacking/master/Basic_Data_Manipulations/Kirby21/SUBJ0001-02-MPRAGE_N3_REG.nii.gz"
followfile <- "SUBJ0001-02-MPRAGE_N3_REG.nii.gz"
followfname <- file.path(getwd(), followfile)
download.file(followurl, followfile,mode="wb")


T1.base.process <- readNIfTI(basefname, reorient=FALSE)
T1.follow.process <- readNIfTI(followfname, reorient=FALSE)

subtract.T1.process <- niftiarr(T1, T1.follow.process - T1.base.process)
orthographic(subtract.T1.process)