dcm2img: Convert DICOM image to standard image format

SYNOPSIS

dcm2img [options] dcmfile-in [bitmap-out]

DESCRIPTION

The dcm2img utility reads a DICOM image, converts the pixel data according to the selected image processing options and writes back an image in one the following general purpose image formats: BMP, PGM/PPM, PNG, TIFF, JPEG, or JPEG-LS. This utility supports uncompressed as well as JPEG, JPEG-LS and RLE compressed DICOM images.

PARAMETERS

dcmfile-in  DICOM input filename to be converted ("-" for stdin)

bitmap-out  output filename to be written (default: stdout)

OPTIONS

general options

-h --help: print this help text and exit
--version: print version information and exit
--arguments: print expanded command line arguments
-q --quiet: quiet mode, print no warnings and errors
-v --verbose: verbose mode, print processing details
-d --debug: debug mode, print debug information
-ll --log-level [l]evel: string constant: (fatal, error, warn, info, debug, trace) use level l for the logger
-lc --log-config [f]ilename: string: use config file f for the logger

input options

+f --read-file: read file format or data set (default)
+fo --read-file-only: read file format only
-f --read-dataset: read data set without file meta information input transfer syntax:
-t= --read-xfer-auto: use TS recognition (default)
-td --read-xfer-detect: ignore TS specified in the file meta header
-te --read-xfer-little: read with explicit VR little endian TS
-tb --read-xfer-big: read with explicit VR big endian TS
-ti --read-xfer-implicit: read with implicit VR little endian TS

image processing options

+F --frame [n]umber: integer: select specified frame (default: 1)
+Fr --frame-range [n]umber [c]ount: integer: select c frames beginning with frame n
+Fa --all-frames: select all frames rotation:
+Rl --rotate-left: rotate image left (-90 degrees)
+Rr --rotate-right: rotate image right (+90 degrees)
+Rtd --rotate-top-down: rotate image top-down (180 degrees) flipping:
+Lh --flip-horizontally: flip image horizontally
+Lv --flip-vertically: flip image vertically
+Lhv --flip-both-axes: flip image horizontally and vertically scaling:
+a --recognize-aspect: recognize pixel aspect ratio when scaling (default)
-a --ignore-aspect: ignore pixel aspect ratio when scaling
+i --interpolate [n]umber of algorithm: integer: use interpolation when scaling (1..4, default: 1)
-i --no-interpolation: no interpolation when scaling
-S --no-scaling: no scaling, ignore pixel aspect ratio (default)
+Sxf --scale-x-factor [f]actor: float: scale x axis by factor, auto-compute y axis
+Syf --scale-y-factor [f]actor: float: scale y axis by factor, auto-compute x axis
+Sxv --scale-x-size [n]umber: integer: scale x axis to n pixels, auto-compute y axis
+Syv --scale-y-size [n]umber: integer: scale y axis to n pixels, auto-compute x axis color space conversion (JPEG compressed images only):
+cp --conv-photometric: convert if YCbCr photometric interpretation (default)
+cl --conv-lossy: convert YCbCr to RGB if lossy JPEG
+cg --conv-guess: convert to RGB if YCbCr is guessed by library
+cgl --conv-guess-lossy: convert to RGB if lossy JPEG and YCbCr is guessed by the underlying JPEG library
+ca --conv-always: always convert YCbCr to RGB
+cn --conv-never: never convert color space bits stored:
+bs --bits-stored-fix: correct inconsistent bits stored value (default) # If the value of BitsStored in the compressed bitstream is smaller # than the value in the DICOM dataset, update the value in the dataset # (JPEG compressed images only)
-bs --bits-stored-keep: preserve inconsistent bits stored value # Keep the value of BitsStored even if inconsistent with the # compressed bitstream. This may help in correctly decoding some # defective images JPEG compressed images only) workaround options for incorrect encodings (JPEG compressed images only):
+w6 --workaround-pred6: enable workaround for JPEG lossless images with overflow in predictor 6 # DICOM images with 16 bits/pixel have been observed "in the wild" # that are compressed with lossless JPEG and need special handling # because the encoder produced an 16-bit integer overflow in predictor # 6, which needs to be compensated (reproduced) during decompression. # This flag enables a correct decompression of such faulty images, but # at the same time will cause an incorrect decompression of correctly # compressed images. Use with care.
+wi --workaround-incpl: enable workaround for incomplete JPEG data # This option causes dcm2img to ignore incomplete JPEG data # at the end of a compressed fragment and to start decompressing # the next frame from the next fragment (if any). This permits # images with incomplete JPEG data to be decoded.
+wc --workaround-cornell: enable workaround for 16-bit JPEG lossless Cornell images with Huffman table overflow # One of the first open-source implementations of lossless JPEG # compression, the "Cornell" library, has a well-known bug that leads # to invalid values in the Huffmann table when images with 16 bit/sample # are compressed. This flag enables a workaround that permits such # images to be decoded correctly. modality LUT transformation:
-M --no-modality: ignore stored modality LUT transformation
+M --use-modality: use modality LUT transformation (default) VOI LUT transformation:
-W --no-windowing: no VOI windowing (default)
+Wi --use-window [n]umber: integer: use the n-th VOI window from image file
+Wl --use-voi-lut [n]umber: integer: use the n-th VOI look up table from image file
+Wm --min-max-window: compute VOI window using min-max algorithm
+Wn --min-max-window-n: compute VOI window using min-max algorithm, ignoring extreme values
+Wr --roi-min-max-window [l]eft [t]op [w]idth [h]eight: integer: compute ROI window using min-max algorithm, region of interest is specified by l,t,w,h
+Wh --histogram-window [n]umber: integer: compute VOI window using Histogram algorithm, ignoring n percent
+Ww --set-window [c]enter [w]idth: float: compute VOI window using center c and width w
+Wfl --linear-function: set VOI LUT function to LINEAR
+Wfs --sigmoid-function: set VOI LUT function to SIGMOID presentation LUT transformation:
+Pid --identity-shape: set presentation LUT shape to IDENTITY
+Piv --inverse-shape: set presentation LUT shape to INVERSE
+Pod --lin-od-shape: set presentation LUT shape to LIN OD overlay:
-O --no-overlays: do not display overlays
+O --display-overlay [n]umber: integer: display overlay n (0..16, 0=all, default: +O 0)
+Omr --ovl-replace: use overlay mode "Replace" (default for Graphic overlays)
+Omt --ovl-threshold: use overlay mode "Threshold Replace"
+Omc --ovl-complement: use overlay mode "Complement"
+Omv --ovl-invert: use overlay mode "Invert Bitmap"
+Omi --ovl-roi: use overlay mode "Region of Interest" (default for ROI overlays)
+Osf --set-foreground [d]ensity: float: set overlay foreground density (0..1, default: 1)
+Ost --set-threshold [d]ensity: float: set overlay threshold density (0..1, default: 0.5) display LUT transformation:
+Dm --monitor-file [f]ilename: string: calibrate output according to monitor characteristics defined in f
+Dp --printer-file [f]ilename: string: calibrate output according to printer characteristics defined in f
+Da --ambient-light [a]mbient light: float: ambient light value (cd/m^2, default: file f)
+Di --illumination [i]llumination: float: illumination value (cd/m^2, default: file f)
+Dn --min-density [m]inimum optical density: float: Dmin value (default: off, only with +Dp)
+Dx --max-density [m]aximum optical density: float: Dmax value (default: off, only with +Dp)
+Dg --gsd-function: use GSDF for calibration (default for +Dm/+Dp)
+Dc --cielab-function: use CIELAB function for calibration compatibility:
+Ma --accept-acr-nema: accept ACR-NEMA images without photometric interpretation
+Mp --accept-palettes: accept incorrect palette attribute tags (0028,111x) and (0028,121x)
+Mc --check-lut-depth: check 3rd value of the LUT descriptor, compare with expected bit depth based on LUT data
+Mm --ignore-mlut-depth: ignore 3rd value of the modality LUT descriptor, determine bits per table entry automatically
+Mv --ignore-vlut-depth: ignore 3rd value of the VOI LUT descriptor, determine bits per table entry automatically TIFF format:
+Tl --compr-lzw: LZW compression (default)
+Tr --compr-rle: RLE compression
+Tn --compr-none: uncompressed
+Pd --predictor-default: no LZW predictor (default)
+Pn --predictor-none: LZW predictor 1 (no prediction)
+Ph --predictor-horz: LZW predictor 2 (horizontal differencing)
+Rs --rows-per-strip [r]ows: integer (default: 0): rows per strip, default 8K per strip PNG format:
+il --interlace: create interlaced file (default)
-il --nointerlace: create non-interlaced file
+mf --meta-file: create PNG file meta information (default)
-mf --meta-none: no PNG file meta information JPEG format:
+Jq --compr-quality [q]uality: integer (0..100, default: 90): quality value for compression (in percent)
+Js4 --sample-444: 4:4:4 sampling (no subsampling)
+Js2 --sample-422: 4:2:2 subsampling (horizontal subsampling of chroma components, default)
+Js1 --sample-411: 4:1:1 subsampling (horizontal and vertical subsampling of chroma components) JPEG-LS format:
+Trl --rendered-lossless: lossless compression of rendered image (default)
+Tll --true-lossless: lossless compression of raw image
+f8 --force-8-bit: force output bit depth to 8 bits (not with --true-lossless) other transformations:
+G --grayscale: convert color image to grayscale (monochrome)
+P --change-polarity: change polarity (invert pixel output)
+C --clip-region [l]eft [t]op [w]idth [h]eight: integer: clip image region (l, t, w, h)

output options

-im --image-info: print image details (requires verbose mode)
-o --no-output: do not create any output (useful with -im) filename generation (only with --frame-range or --all-frames):
+Fc --use-frame-counter: use 0-based counter for filenames (default)
+Fn --use-frame-number: use absolute frame number for filenames image format:
+oa --write-auto: determine file format from filename extension (default for files) # If the output filename contains no extension or an # unknown/unsupported one, a warning is printed and a BMP file # is written (see --write-bmp).
+op --write-raw-pnm: write 8-bit binary PGM/PPM
+opb --write-8-bit-pnm: write 8-bit ASCII PGM/PPM (default for stdout)
+opw --write-16-bit-pnm: write 16-bit ASCII PGM/PPM
+opn --write-n-bit-pnm [n]umber: integer: write n-bit ASCII PGM/PPM (1..32)
+ob --write-bmp: write 8-bit (monochrome) or 24-bit (color) BMP
+obp --write-8-bit-bmp: write 8-bit palette BMP (monochrome only)
+obt --write-24-bit-bmp: write 24-bit truecolor BMP
+obr --write-32-bit-bmp: write 32-bit truecolor BMP
+ot --write-tiff: write 8-bit (monochrome) or 24-bit (color) TIFF
+on --write-png: write 8-bit (monochrome) or 24-bit (color) PNG
+on2 --write-16-bit-png: write 16-bit (monochrome) or 48-bit (color) PNG
+oj --write-jpeg: write 8-bit lossy JPEG (baseline)
+ol --write-jpls: write JPEG-LS

NOTES

The following preferred interpolation algorithms can be selected using the –interpolate option:

1 = free scaling algorithm with interpolation from pbmplus toolkit
2 = free scaling algorithm with interpolation from c't magazine
3 = magnification algorithm with bilinear interpolation from Eduard Stanescu
4 = magnification algorithm with bicubic interpolation from Eduard Stanescu

The –write-tiff option is only available when DCMTK has been configured and compiled with support for the external libtiff TIFF library. The availability of the TIFF compression options depends on the libtiff configuration.

The –write-png option is only available when DCMTK has been configured and compiled with support for the external libpng PNG library. Option –interlace enables progressive image view while loading the PNG file. Only a few applications take care of the meta info (TEXT) in a PNG file.

TRANSFER SYNTAXES

dcm2img supports the following transfer syntaxes for input (dcmfile-in):

LittleEndianImplicitTransferSyntax             1.2.840.10008.1.2
LittleEndianExplicitTransferSyntax             1.2.840.10008.1.2.1
DeflatedExplicitVRLittleEndianTransferSyntax   1.2.840.10008.1.2.1.99 (*)
BigEndianExplicitTransferSyntax                1.2.840.10008.1.2.2
JPEGLSLosslessTransferSyntax                   1.2.840.10008.1.2.4.80
JPEGLSLossyTransferSyntax                      1.2.840.10008.1.2.4.81
JPEGProcess10_12TransferSyntax                 1.2.840.10008.1.2.4.55
JPEGProcess14SV1TransferSyntax                 1.2.840.10008.1.2.4.70
JPEGProcess14TransferSyntax                    1.2.840.10008.1.2.4.57
JPEGProcess1TransferSyntax                     1.2.840.10008.1.2.4.50
JPEGProcess2_4TransferSyntax                   1.2.840.10008.1.2.4.51
JPEGProcess6_8TransferSyntax                   1.2.840.10008.1.2.4.53
RLELosslessTransferSyntax                      1.2.840.10008.1.2.5

(*) if compiled with zlib support enabled

LOGGING

The level of logging output of the various command line tools and underlying libraries can be specified by the user. By default, only errors and warnings are written to the standard error stream. Using option –verbose also informational messages like processing details are reported. Option –debug can be used to get more details on the internal activity, e.g. for debugging purposes. Other logging levels can be selected using option –log-level. In –quiet mode only fatal errors are reported. In such very severe error events, the application will usually terminate. For more details on the different logging levels, see documentation of module "oflog".

In case the logging output should be written to file (optionally with logfile rotation), to syslog (Unix) or the event log (Windows) option –log-config can be used. This configuration file also allows for directing only certain messages to a particular output stream and for filtering certain messages based on the module or application where they are generated. An example configuration file is provided in < etcdir>/logger.cfg.

COMMAND LINE

All command line tools use the following notation for parameters: square brackets enclose optional values (0-1), three trailing dots indicate that multiple values are allowed (1-n), a combination of both means 0 to n values.

Command line options are distinguished from parameters by a leading '+' or '-' sign, respectively. Usually, order and position of command line options are arbitrary (i.e. they can appear anywhere). However, if options are mutually exclusive the rightmost appearance is used. This behavior conforms to the standard evaluation rules of common Unix shells.

In addition, one or more command files can be specified using an '@' sign as a prefix to the filename (e.g. @command.txt). Such a command argument is replaced by the content of the corresponding text file (multiple whitespaces are treated as a single separator unless they appear between two quotation marks) prior to any further evaluation. Please note that a command file cannot contain another command file. This simple but effective approach allows one to summarize common combinations of options/parameters and avoids longish and confusing command lines (an example is provided in file < datadir>/dumppat.txt).

ENVIRONMENT

The dcm2img utility will attempt to load DICOM data dictionaries specified in the DCMDICTPATH environment variable. By default, i.e. if the DCMDICTPATH environment variable is not set, the file < datadir>/dicom.dic will be loaded unless the dictionary is built into the application (default for Windows).

The default behavior should be preferred and the DCMDICTPATH environment variable only used when alternative data dictionaries are required. The DCMDICTPATH environment variable has the same format as the Unix shell PATH variable in that a colon (":") separates entries. On Windows systems, a semicolon (";") is used as a separator. The data dictionary code will attempt to load each file specified in the DCMDICTPATH environment variable. It is an error if no data dictionary can be loaded.

FILES

< datadir>/camera.lut - sample characteristics file of a camera
< datadir>/monitor.lut - sample characteristics file of a monitor
< datadir>/printer.lut - sample characteristics file of a printer
< datadir>/scanner.lut - sample characteristics file of a scanner