readDicom | R Documentation |
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()) sortDicom(path = ".", forceStack = FALSE, verbosity = 0L, labelFormat = "T%t_N%n_S%s/%b", depth = 5L, nested = TRUE, keepUnsorted = FALSE) scanDicom(path = ".", forceStack = FALSE, verbosity = 0L, labelFormat = "T%t_N%n_S%s", depth = 5L)
path |
A character vector of paths to scan for DICOM files. Each will
examined in turn. The default is the current working directory.
|
subset |
If |
flipY |
If |
crop |
If |
forceStack |
If |
verbosity |
Integer value between -2 and 3, controlling the amount of
output generated during the conversion. A value of -1 will suppress all
output from |
labelFormat |
A |
depth |
The maximum subdirectory depth in which to search for DICOM
files, relative to each |
interactive |
If |
nested |
For |
keepUnsorted |
For |
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
).
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.
The readDicom
function returns a list of niftiImage
objects, which can be easily converted to standard R arrays or written to
NIfTI-1 format using functions from the RNifti
package. 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.
Jon Clayden <code@clayden.org>
path <- system.file("extdata", "raw", package="divest") scanDicom(path) readDicom(path, interactive=FALSE)
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