These functions are R wrappers around the DICOM-to-NIfTI conversion routines
provided by dcm2niix. They scan directories containing DICOM files,
potentially pertaining to more than one image series, read them and/or merge
them into a list of niftiImage objects.
readDicom(path = ".", subset = NULL, flipY = TRUE, crop = FALSE,
forceStack = FALSE, verbosity = 0L, labelFormat = "T%t_N%n_S%s",
depth = 5L, interactive = base::interactive(), output = NULL)convertDicom(path = ".", subset = NULL, flipY = TRUE, crop = FALSE,
forceStack = FALSE, verbosity = 0L, labelFormat = "T%t_N%n_S%s",
depth = 5L, interactive = base::interactive(), output = path)
sortDicom(path = ".", forceStack = FALSE, verbosity = 0L,
labelFormat = "T%t_N%n_S%s/%b", depth = 5L, nested = NA,
keepUnsorted = FALSE, output = path)
scanDicom(path = ".", forceStack = FALSE, verbosity = 0L,
labelFormat = "T%t_N%n_S%s", depth = 5L)
readDicom and convertDicom return a list of
niftiImage objects if output is NULL; otherwise
(invisibly) a vector of paths to NIfTI-1 files created in the target
directory. The scanDicom function returns a data frame containing
information about each DICOM series found. sortDicom is mostly
called for its side-effect, but also (invisibly) returns a list detailing
source and target paths.
A character vector of paths to scan for DICOM files. Each will
examined in turn. The default is the current working directory.
readDicom (only) will accept paths to individual DICOM files,
rather than directories. Alternatively, for readDicom and
sortDicom, a data frame like the one returned by scanDicom,
from which file paths will be read.
If path is a data frame, an expression which will be
evaluated in the context of the data frame to determine which series to
convert. Should evaluate to a logical vector. If path is a
character vector, scanDicom is called on the path(s) first to
produce the data frame. If this is specified, and does not evaluate to
NULL, the read will be noninteractive, irrespective of the value of
the interactive argument.
If TRUE, the default, then images will be flipped in the
Y-axis. This is usually desirable, given the difference between
orientation conventions in the DICOM and NIfTI-1 formats.
If TRUE, then dcm2niix will attempt to crop excess
neck slices from brain images.
If TRUE, images with the same series number will
always be stacked together as long as their dimensions are compatible. If
FALSE, the default, images will be separated if they differ in
echo, coil or exposure number, echo time, protocol name or orientation.
Integer value between -2 and 3, controlling the amount of
output generated during the conversion. A value of -1 will suppress all
output from dcm2niix except warnings and errors; -2 also suppresses
warnings.
A sprintf-style string specifying the
format to use for the final image labels or paths. See Details.
The maximum subdirectory depth in which to search for DICOM
files, relative to each path.
If TRUE, the default in interactive sessions, the
requested paths will first be scanned and a list of DICOM series will be
presented. You may then choose which series to convert.
The directory to write converted or copied NIfTI files to, or
NULL. In the latter case, which isn't valid for sortDicom,
images are converted in memory and returned as R objects.
For sortDicom, should the sorted files be created
within the source directory (TRUE), or in the current working
directory (FALSE)? Now soft-deprecated in favour of output,
which is more flexible.
For sortDicom, should the unsorted files be left
in place, or removed after they are copied into their new locations? The
default, FALSE, corresponds to a move rather than a copy. If
creating new files fails then the old ones will not be deleted.
Jon Clayden code@clayden.org
The scanDicom function parses directories full of DICOM files and
returns information about the acquisition series they contain.
readDicom reads these files and converts them to (internal) NIfTI
images (whose pixel data can be extracted using as.array).
convertDicom performs the same conversion but writes to NIfTI files
by default, instead of retaining the images in memory. sortDicom
renames the files, but does not convert them.
The labelFormat argument describes the string format used for image
labels and sorted files. Valid codes, each escaped with a percentage sign,
include a for coil number, b for the source file base name,
c for image comments, d for series description, e for
echo number, f for the source directory, i for patient ID,
j for the series instance UID, k for the study instance UID,
l for the procedure step description, m for manufacturer,
n for patient name, p for protocol name, q for
scanning sequence, r for instance number, s for series number,
t for the date and time, u for acquisition number, v
for vendor, x for study ID and z for sequence name. For
sortDicom the label forms the new file path, and may include one or
more slashes to create subdirectories. A ".dcm" suffix will be added to file
names if no extension is specified.
path <- system.file("extdata", "raw", package="divest")
scanDicom(path)
readDicom(path, interactive=FALSE)
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