Uses Chris Rorden's dcm2nii from
http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html to convert
DICOM files to NIfTI format. Should Need run install_dcm2nii before running.
dcm2nii(basedir = ".", files = NULL, copy_files = TRUE,
progdir = system.file(package = "dcm2niir"), verbose = TRUE,
dcm2niicmd = c("dcm2niix", "dcm2nii_2009", "dcm2nii"),
merge_files = FALSE, ignore_derived = FALSE, unzip_files = TRUE,
opts = paste0("-9 ", ifelse(ignore_derived, "-i y ", ""),
ifelse(merge_files, " -m y ", ""), paste0(" -v ", as.numeric(verbose)),
" -z y -f %p_%t_%s"), ...)
dcm2nii_par_rec(file = list.files(pattern = "[.](par|PAR)"),
copy_files = TRUE, verbose = TRUE, ...)
dcm2nii_bids_sidecar(basedir, progdir = system.file(package =
"dcm2niir"), dcm2niicmd = c("dcm2niix", "dcm2nii_2009", "dcm2nii"),
...)
fix_sidecar(file)| basedir | (character) directory to get files |
|---|---|
| files | (character) vector of files to segment. Will override
|
| copy_files | (logical) Should files be copied to a temporary directory? |
| progdir | (character) directory of bash scripts, no user input needed unless
binaries were installed elsewhere. Passed to |
| verbose | (logical) print diagnostic printouts |
| dcm2niicmd | (character) either "dcm2niix", "dcm2nii", or "dcm2nii_2009", which
are different versions of dcm2nii. Passed to |
| merge_files | Should files be merged,
passed do |
| ignore_derived | Should derived images be ignored,
passed do |
| unzip_files | if |
| opts | list of arguments to pass to |
| ... | arguments to be passed to |
| file | A Par/REC file |
List of result of system command, names of files before and after
conversion
library(utils)
install_dir = tempdir()
sysname = tolower(Sys.info()["sysname"])
cmake = Sys.which("cmake")
if (file.exists(cmake) && sysname == "windows" &&
nzchar(Sys.getenv("APPVEYOR")) && FALSE) {
source_clone_dir = fs::path(Sys.getenv("APPVEYOR_BUILD_FOLDER"),
"inst", "dcm2niix_clone")
install_dcm2nii(
progdir = install_dir,
overwrite = TRUE,
from_source = TRUE,
verbose = 2,
source_clone_dir = source_clone_dir)
} else {
install_dcm2nii(progdir = install_dir)
}
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#> [1] TRUE
## dcm_file = paste0("ftp://medical.nema.org/medical/Dicom/",
## "DataSets/WG30/MGH/MR/MouseBrainSiemens15T_20150410/",
## "Converted/DICOM/mghmousetoenhancedmr_T1w_pre.dcm")
dcm_file = paste0("http://johnmuschelli.com/dcm2niir/",
"mghmousetoenhancedmr_T1w_pre.dcm")
tdir = tempfile()
dir.create(tdir)
destfile = tempfile(fileext = ".dcm", tmpdir = tdir)
ci = Sys.getenv("CI")
method = ifelse(ci == "", "auto", "curl")
dl = download.file(url = dcm_file, method = method,
destfile = destfile, mode = "wb")
dl == 0
#> [1] TRUE
stopifnot(file.exists(destfile))
fs = file.size(destfile)
fs
#> [1] 0
if (fs <= 2e5) {
dl = download.file(url = dcm_file, destfile = destfile, mode = "wb")
}
fs = file.size(destfile)
fs
#> [1] 2002638
stopifnot(fs > 2e5)
list.files(tdir)
#> [1] "file8cd1564a9332.dcm"
dcm2niir::install_dcm2nii(progdir = install_dir)
#> [1] TRUE
res = dcm2niir::dcm2nii(basedir = tdir, verbose = 1)
#>
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#> #Copying Files
#> # Converting to nii
#> '/home/runner/work/_temp/Library/dcm2niir/dcm2niix_linux' -9 -v 1 -z y -f %p_%t_%s '/tmp/RtmpCLDM83/file8cd1e8e21bc'
stopifnot(res$result == 0)
res = dcm2niir::dcm2nii(files = destfile, verbose = 1)
#> #Copying Files
#> # Converting to nii
#> '/home/runner/work/_temp/Library/dcm2niir/dcm2niix_linux' -9 -v 1 -z y -f %p_%t_%s '/tmp/RtmpCLDM83/file8cd14b192c79'
destfile = R.utils::gzip(destfile)
res = dcm2niir::dcm2nii(files = destfile, verbose = 1, unzip_files = FALSE)
#> #Copying Files
#> # Converting to nii
#> '/home/runner/work/_temp/Library/dcm2niir/dcm2niix_linux' -9 -v 1 -z y -f %p_%t_%s '/tmp/RtmpCLDM83/file8cd134df71af'
#> Warning: Result indicated an error! Please check results.
stopifnot(res$result != 0)
res = dcm2niir::dcm2nii(files = destfile, verbose = 1, unzip_files = TRUE)
#> #Copying Files
#> # Converting to nii
#> '/home/runner/work/_temp/Library/dcm2niir/dcm2niix_linux' -9 -v 1 -z y -f %p_%t_%s '/tmp/RtmpCLDM83/file8cd174390b88'
stopifnot(res$result == 0)