writeNIfTI-methods | R Documentation |
This function saves a NIfTI-class object to a single binary file in NIfTI format.
## S4 method for signature 'nifti' writeNIfTI( nim, filename, onefile = TRUE, gzipped = TRUE, verbose = FALSE, warn = -1, compression = 9 ) ## S4 method for signature 'niftiExtension' writeNIfTI( nim, filename, onefile = TRUE, gzipped = TRUE, verbose = FALSE, warn = -1, compression = 9 ) ## S4 method for signature 'anlz' writeNIfTI( nim, filename, onefile = TRUE, gzipped = TRUE, verbose = FALSE, warn = -1, compression = 9 ) ## S4 method for signature 'array' writeNIfTI( nim, filename, onefile = TRUE, gzipped = TRUE, verbose = FALSE, warn = -1, compression = 9 )
nim |
is an object of class |
filename |
is the path and file name to save the NIfTI file (.nii) without the suffix. |
onefile |
is a logical value that allows the scanning of single-file
(.nii) or dual-file format (.hdr and .img) NIfTI files (default =
|
gzipped |
is a character string that enables exportation of compressed
(.gz) files (default = |
verbose |
is a logical variable (default = |
warn |
is a number to regulate the display of warnings (default = -1).
See |
compression |
The amount of compression to be applied when writing a
file when |
The writeNIfTI
function utilizes the internal writeBin
and
writeChar
command to write information to a binary file.
Current acceptable data types include
DT BINARY (1 bit per voxel)
DT SIGNED SHORT (16 bits per voxel)
DT SINGED INT (32 bits per voxel)
DT FLOAT (32 bits per voxel)
DT DOUBLE (64 bits per voxel)
DT UNSIGNED SHORT (16 bits per voxel)
Nothing.
Convert ANALYZE object
to class nifti
and write the NIfTI volume to disk.
Convert array to class nifti
and write the NIfTI volume to
disk.
Write NIfTI volume to disk.
Brandon Whitcher bwhitcher@gmail.com,
Volker Schmid
volkerschmid@users.sourceforge.net
NIfTI-1
http://nifti.nimh.nih.gov/
writeAFNI
, writeANALYZE
norm <- dnorm(seq(-5, 5, length=32), sd=2) norm <- (norm-min(norm)) / max(norm-min(norm)) img <- outer(outer(norm, norm), norm) img <- round(255 * img) img[17:32,,] <- 255 - img[17:32,,] img.nifti <- nifti(img) # create NIfTI object fname = file.path(tempdir(), "test-nifti-image-uint8") writeNIfTI(img.nifti, fname, verbose=TRUE) ## These files should be viewable in, for example, FSLview ## Make sure you adjust the min/max values for proper visualization data <- readNIfTI(fname, verbose=TRUE) image(img.nifti, oma=rep(2,4), bg="white") image(data, oma=rep(2,4), bg="white") abs.err <- abs(data - img.nifti) image(as(abs.err, "nifti"), zlim=range(img.nifti), oma=rep(2,4), bg="white") ## Not run: ## Loop through all possible data types datatypes <- list(code=c(2, 4, 8, 16, 64), name=c("uint8", "int16", "int32", "float", "double")) equal <- vector("list") for (i in 1:length(datatypes$code)) { fname <- paste("test-nifti-image-", datatypes$name[i], sep="") fname = file.path(tempdir(), fname) rm(img.nifti) img.nifti <- nifti(img, datatype=datatypes$code[i]) writeNIfTI(img.nifti, fname, verbose=TRUE) equal[[i]] <- all(readNIfTI(fname) == img) } names(equal) <- datatypes$name unlist(equal) ## End(Not run)
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