Read an NIfTI files
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)
