EnglishFrenchSpanish

OnWorks favicon

cmtk-volume_reconstruction - Online in the Cloud

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

This is the command cmtk-volume_reconstruction 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

PROGRAM:

NAME


volume_reconstruction - Volume reconstruction

SYNOPSIS


volume_reconstruction [options] refImage xform0 inImage0 [xform1 inImage1 ...]

DESCRIPTION


Iterative volume reconstruction from co-registered images using inverse interpolation or
joint deblurring

OPTIONS


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

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

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

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

--version
Write toolkit version to standard output.

--echo
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).

Input Options
--exclude-first-image, -x
Exclude first image from reconstruction as a separate registration target image)

--crop <string>
Crop reference to pixel region x0,y0,z1:x1,y1,z1

--pass-weight <string>, -W <string>
Set contribution weight for a pass in the form 'pass:weight'

Reconstruction Grid
--recon-grid <string>
Define reconstruction grid as Nx,Ny,Nz:dX,dY,dZ[:Ox,Oy,Oz] (dims:pixel:offset)

--recon-grid-path <string>, -R <string>
Give path to grid that defines reconstructed image grid [including offset] [Default:
NONE]

Initial Volume Injection Parameters
--isotropic-injection
Use isotropic volume injection [otherwise: scaled with pass image pixel size per
dimension]

--injection-kernel-sigma <double>, -S <double>
Standard deviation of Gaussian kernel for volume injection in multiples of pixel size
in each direction. [Default: 1]

--injection-kernel-radius <double>, -r <double>
Truncation radius factor of injection kernel. The kernel is truncated at
sigma*radius, where sigma is the kernel standard deviation. [Default: 2]

Volume Reconstruction Options
--inverse-interpolation-kernel
Kernel for the inverse interpolation reconstruction Supported values: "cubic",
"linear", "hamming-sinc", "cosine-sinc", where the default is "cubic", or use one of
the following:

--cubic, -C
Tricubic interpolation [This is the default]

--linear, -L
Trilinear interpolation (faster but less accurate)

--hamming-sinc, -H
Hamming-windowed sinc interpolation

--cosine-sinc, -O
Cosine-windowed sinc interpolation (most accurate but slowest)

--deblurring
Kernel shape to approximate the point spread function for joint deblurring
reconstruction (selecting one of these disables inverse interpolation reconstruction)
Supported values: "box", "gaussian", or use one of the following:

--box
Box-shaped kernel

--gaussian
Gaussian kernel

--psf <string>
Explicitly set point spread function size as x,y,z. Use with 'deblurring' kernel
reconstrunction.

--psf-scale <double>
Scale point spread function size by this value. Use with 'deblurring' kernel
reconstrunction. [Default: 1]

Optimization Parameters
--num-iterations <integer>, -n <integer>
Maximum number of inverse interpolation iterations [Default: 20]

--fourth-order-error, -f
Use fourth-order (rather than second-order) error for optimization.

Regularization Parameters
--l-norm-weight <double>
Set constraint weight for Tikhonov-type L-Norm regularization (0 disables constraint)
[Default: 0]

--no-truncation, -T
Turn off non-linear regional intensity truncation

Output Options
--output <string>, -o <string>
Output path for final reconstructed image [Default: reconstructed.nii ]

--write-injected-image <string>
Write initial volume-injected image to this path [Default: NONE]

--write-lowest-max-error-image <string>
Optional path to write reconstructed image with lowest MAXIMUM error. [Default:
NONE]

--write-images-as-float, -F
Write output images as floating point

AUTHORS


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

Use cmtk-volume_reconstruction online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Clover EFI bootloader
    Clover EFI bootloader
    Project has moved to
    https://github.com/CloverHackyColor/CloverBootloader..
    Features:Boot macOS, Windows, and Linux
    in UEFI or legacy mode on Mac or PC with
    UE...
    Download Clover EFI bootloader
  • 2
    unitedrpms
    unitedrpms
    Join us in Gitter!
    https://gitter.im/unitedrpms-people/Lobby
    Enable the URPMS repository in your
    system -
    https://github.com/UnitedRPMs/unitedrpms.github.io/bl...
    Download unitedrpms
  • 3
    Boost C++ Libraries
    Boost C++ Libraries
    Boost provides free portable
    peer-reviewed C++ libraries. The
    emphasis is on portable libraries which
    work well with the C++ Standard Library.
    See http://www.bo...
    Download Boost C++ Libraries
  • 4
    VirtualGL
    VirtualGL
    VirtualGL redirects 3D commands from a
    Unix/Linux OpenGL application onto a
    server-side GPU and converts the
    rendered 3D images into a video stream
    with which ...
    Download VirtualGL
  • 5
    libusb
    libusb
    Library to enable user space
    application programs to communicate with
    USB devices. Audience: Developers, End
    Users/Desktop. Programming Language: C.
    Categories...
    Download libusb
  • 6
    SWIG
    SWIG
    SWIG is a software development tool
    that connects programs written in C and
    C++ with a variety of high-level
    programming languages. SWIG is used with
    different...
    Download SWIG
  • ce
    manager. Firefly III features a
    double-entry bookkeeping system. You can
    quickly enter and organize your
    transactions i...
    Download Firefly III
  • More »

Linux commands

Ad