OnWorks favicon

cmtk-dcm2image - Online in the Cloud

Run cmtk-dcm2image in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command cmtk-dcm2image that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



dcm2image - DICOM to Image


dcm2image SearchDirList


Combine sets of DICOM slices to 3D image stacks


Global Toolkit Options (these are shared by all CMTK tools)
Write list of basic command line options to standard output.

Write complete list of basic and advanced command line options to standard output.

Write list of command line options to standard output in MediaWiki markup.

Write man page source in 'nroff' markup to standard output.

Write toolkit version to standard output.

Write the current command line to standard output.

--verbose-level <integer>
Set verbosity level.

--verbose, -v
Increment verbosity level by 1 (deprecated; supported for backward compatibility).

--threads <integer>
Set maximum number of parallel threads (for POSIX threads and OpenMP).

Main Options
Disable progress reporting.

Input Options
--recurse, -r
Recurse into directories

Output Options
--out-pattern <string>, -O <string>
Output image path pattern. Use the following substitutions: printf-style %d variante
(image number); %n (image number with automatic number of digits); %N (like %n, but
with a hyphen '-' before number if there is more than one image); %D (DICOM
SeriesDescription); %R (DICOM RepetitionTime - MRI only); %E (DICOM EchoTime - MRI
only); %T (RawDataType - vendor-specific, currently GE MRI only) [Default:
image%n.nii ]

--xml, -x
Write XML sidecar file for each created image.

Include potentially protected identifying information (e.g., UIDs, device serial
numbers, dates) in the created XML sidecar files.

Embed DICOM information into output images as 'description' (if supported by output
file format). Supported values: "StudyID_StudyDate", "PatientName",
"SeriesDescription", "None", where the default is "None", or use one of the

StudyID, tag (0020,0010), then underscore, followed by StudyDate, tag
(0008,0020). Date is appended because StudyID is four digits only and will
repeat sooner or later.

Patient name, tag (0010,0010)

Series description, tag (0008,103e)

Embed no information - leave 'description' field empty. [This is the default]

Filtering Options
--filter <string>
Filter DICOM files and include only those matching the given pattern of the form
'TagName=text', such that the value of the DICOM tag with the given name contains the
given text. If multiple filter patterns are provided via repeated use of this option,
only files that match ALL patterns are included.

--exclude <string>
Exclude all DICOM files matching the given pattern of the form 'TagName=text', such
that the value of the DICOM tag with the given name contains the given text. If
multiple exclusion patterns are provided, all files are excluded that match ANY of
the patterns.

Sorting Options
Do NOT sort files by file name (sorting determines image stack order when resolving
spatial collisions)

Sort files lexicographically by file name. Use this when instance numbers are non-

Sort files by image instance number. Use this when file names are different lengths,
etc. [This is the default]

Stacking Options
Also write output images for single-slice DICOM files that could not be assigned to
any 3D stacks. By default, these are skipped.

Ignore 'AcquisitionNumber' tag for image grouping, i.e., do not separate stacks based
on this tag.

Disable checking of image orientations (to avoid rounding issues)

--tolerance <double>
Tolerance for floating-point comparisons (must be >= 0; 0 = exact matches only;
default: 1e-5). If one or more volumes cannot be stacked because of non-uniform slice
spacing that exceeds this threshold, dcm2image will return an exit code of 3.
[Default: 1e-05]


Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R.
Maurer, Daniel B. Russakoff, and Yaroslav Halchenko

Use cmtk-dcm2image online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Asuswrt-Merlin is a third party
    firmware for select Asus wireless
    routers. Based on the Asuswrt firmware
    developed by Asus, it brings tweaks, new
    features and ...
    Download Asuswrt-Merlin
  • 2
    Atom is a text editor that's
    modern, approachable and full-featured.
    It's also easily customizable- you
    can customize it to do anything and be
    able to ...
    Download Atom
  • 3
    Osu! is a simple rhythm game with a well
    thought out learning curve for players
    of all skill levels. One of the great
    aspects of Osu! is that it is
    Download Osu!
  • 4
    LIBPNG: PNG reference library
    LIBPNG: PNG reference library
    Reference library for supporting the
    Portable Network Graphics (PNG) format.
    Audience: Developers. Programming
    Language: C. This is an application that
    can also...
    Download LIBPNG: PNG reference library
  • 5
    Metal detector based on  RP2040
    Metal detector based on RP2040
    Based on Raspberry Pi Pico board, this
    metal detector is included in pulse
    induction metal detectors category, with
    well known advantages and disadvantages.
    Download Metal detector based on RP2040
  • 6
    PAC Manager
    PAC Manager
    PAC is a Perl/GTK replacement for
    SecureCRT/Putty/etc (linux
    ssh/telnet/... gui)... It provides a GUI
    to configure connections: users,
    passwords, EXPECT regula...
    Download PAC Manager
  • More »

Linux commands