OnWorks favicon

dicomtonifti - Online in the Cloud

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

This is the command dicomtonifti 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



dicomtonifti - vtk-dicom CLI


dicomtonifti -o file.nii file1.dcm [file2.dcm ...]

dicomtonifti -o directory --batch file1.dcm [file2.dcm ...]

-o <output.nii[.gz]>
The output file (or directory, if --batch).

-z --compress
Compress output files.

-r --recurse
Recurse into subdirectories.

-b --batch
Do multiple series at once.

-s --silent
Do not echo output filenames.

-v --verbose
Verbose error reporting.

-L --follow-symlinks
Follow symbolic links when recursing.

--fsl Format axial image for use in FSL.

Reformat the image into axial orientation.

Never reorder the slices.

Never reorder the rows.

Never reorder the columns.

Never reorder slices, rows, or columns.

Don't include a qform in the NIFTI file.

Don't include an sform in the NIFTI file.

--volume N
Set the volume to output (starts at 0).

Print the version and exit.

Print source and build version.

--help Documentation for dicomtonifti.

This program will convert a DICOM series into a NIfTI file.

It reads the DICOM Position and Orientation metadata, and uses this information to
generate qform and sform entries for the NIfTI header, after doing a conversion from the
DICOM coordinate system to the NIfTI coordinate system.

By default, it will also reorder the columns of the image so that columns with higher
indices are further to the patient's right (or in the case of sagittal images, further
anterior). Likewise, rows will be rearranged so that rows with higher indices are
superior (or anterior for axial images). Finally, it will reorder the slices so that the
column direction, row direction, and slice direction follow the right-hand rule.

It is also possible to reformat the images into the axial orientation via the
--reformat-to-axial option This option is mutually exclusive with the no-reordering
options. The resulting orientation matrix will be the identity matrix.

If the output NIFTI files are to be used with the FMRIB FSL package, then use the --fsl
option to reformat the images to match the standard FSL orientation: axial images with the
slices arranged from inferior to superior, column number increasing from right to left,
and row number increasing from posterior to anterior. This will also convert the data
type from unsigned 16-bit to signed 16-bit if necessary.

If batch mode is selected, the output file given with "-o" can be constructed from DICOM
attributes, by providing the attribute names within curly braces. For example, consider
the following: "{PatientID}-{StudyDate}/{SeriesDescription}-{SeriesNumber}.nii" or
something similar to produce a hierarchichal directory structure. The attributes used in
the path should be from the following list:

PatientID, PatientName, PatientBirthDate, PatientSex, StudyID, StudyDescription,
StudyDate, StudyTime, StudyInstanceUID, SeriesNumber, SeriesDescription,
SeriesInstanceUID, Modality, AccessionNumber.

Here is an example of batch mode that recurses into subdirectories and compresses the
output files, putting the results in the current directory:

./obj-x86_64-linux-gnu/bin/dicomtonifti -brz -o {SeriesDescription}-{SeriesNumber}.nii

Use dicomtonifti online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Fork of TeamWinRecoveryProject(TWRP)
    with many additional functions, redesign
    and more Features:Supports Treble and
    non-Treble ROMsUp-to-date Oreo kernel,
    Download OrangeFox
  • 2
    itop - ITSM  CMDB OpenSource
    itop - ITSM CMDB OpenSource
    IT Operations Portal: a complete open
    source, ITIL, web based service
    management tool including a fully
    customizable CMDB, a helpdesk system and
    a document man...
    Download itop - ITSM CMDB OpenSource
  • 3
    Clementine is a multi-platform music
    player and library organizer inspired by
    Amarok 1.4. It has a fast and
    easy-to-use interface, and allows you to
    search and ...
    Download Clementine
  • 4
    ATTENTION: Cumulative update 2.4.3 has
    been released!! The update works for any
    previous 2.x.x version. If upgrading
    from version v1.x.x, please download and
    Download XISMuS
  • 5
    Modular headtracking program that
    supports multiple face-trackers, filters
    and game-protocols. Among the trackers
    are the SM FaceAPI, AIC Inertial Head
    Tracker ...
    Download facetracknoir
  • 6
    PHP QR Code
    PHP QR Code
    PHP QR Code is open source (LGPL)
    library for generating QR Code,
    2-dimensional barcode. Based on
    libqrencode C library, provides API for
    creating QR Code barc...
    Download PHP QR Code
  • 7
    Cuckoo Sandbox
    Cuckoo Sandbox
    Cuckoo Sandbox uses components to
    monitor the behavior of malware in a
    Sandbox environment; isolated from the
    rest of the system. It offers automated
    analysis o...
    Download Cuckoo Sandbox
  • More »

Linux commands

  • 1
    rsbac-admin - Rule Set Based Access
    Control DESCRIPTION: rsbac-admin is a
    set of tool used to manage systems using
    a Rule Set Based Access Control (RSBAC)
    Run acl_gran
  • 2
    rsbac-admin - Rule Set Based Access
    Control DESCRIPTION: rsbac-admin is a
    set of tool used to manage systems using
    a Rule Set Based Access Control (RSBAC)
    Run acl_grant
  • 3
    cpupower idle-set - Utility to set cpu
    idle state specific kernel options
    SYNTAX: cpupower [ -c cpulist ]
    idle-info [options] DESCRIPTION: The
    cpupower idle-se...
    Run cpupower-idle-set
  • 4
    cpupower-info - Shows processor power
    related kernel or hardware
    configurations ...
    Run cpupower-info
  • 5
    g15daemon - provides access to extra
    keys and the LCD available on the
    logitech G15 keyboard. DESCRIPTION:
    G15Daemon allows users access to all
    extra keys by d...
    Run g15daemon
  • 6
    laditools - tools to control and
    monitor LADI (JACK and ladish) systems ...
    Run g15ladi
  • More »