NAME

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

input file format:


  +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

frame selection:


  +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
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

general:


  -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