mia-3dmaskseeded(1)
NAME
mia-3dmaskseeded - Mask an area by seeded region growing
SYNOPSIS
mia-3dmaskseeded -i <in-file> -o <out-file> [options]
DESCRIPTION
mia-3dmaskseeded 3D image segmentation based on region growing from a seed point. Neighboring points are added, either when their intensity is equal or higher than that of the seed point, or of the intensity is lower or equal then that of the neighoring point. After region growing is finished, this mask is used to zero out the region in the original image yielding the resulting image.
OPTIONS
-i --in-file=(input, required); io
input image(s) to be filtered For supported file types
see PLUGINS:3dimage/io
-o --out-file=(output, required); io
output image(s) that have been filtered For supported
file types see PLUGINS:3dimage/io
-s --seed=[0,0,0]
seed pointseed point
-n --neighborhood=6n
neighborhood shapeneighborhood shape For supported
plugins see PLUGINS:3dimage/shape
Help & Info
-V --verbose=warning
verbosity of output, print messages of given level and
higher priorities. Supported priorities starting at
lowest level are:
info Low level messages
trace Function call trace
fail Report test failures
warning Warnings
error Report errors
debug Debug output
message Normal messages
fatal Report only fatal errors
--copyright
print copyright information
-h --help
print this help
-? --usage
print a short help
--version
print the version number and exit
Processing
--threads=-1
Maxiumum number of threads to use for processing,This
number should be lower or equal to the number of logical
processor cores in the machine. (-1: automatic
estimation).Maxiumum number of threads to use for
processing,This number should be lower or equal to the
number of logical processor cores in the machine. (-1:
automatic estimation).
PLUGINS: 3dimage/io
analyze Analyze 7.5 image
Recognized file extensions: .HDR, .hdr
Supported element types:
unsigned 8 bit, signed 16 bit, signed 32 bit, floating
point 32 bit, floating point 64 bit
datapool Virtual IO to and from the internal data pool
Recognized file extensions: .@
dicom Dicom image series as 3D
Recognized file extensions: .DCM, .dcm
Supported element types:
signed 16 bit, unsigned 16 bit
hdf5 HDF5 3D image IO
Recognized file extensions: .H5, .h5
Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16
bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit,
signed 64 bit, unsigned 64 bit, floating point 32 bit,
floating point 64 bit
inria INRIA image
Recognized file extensions: .INR, .inr
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned
16 bit, signed 32 bit, unsigned 32 bit, floating point
32 bit, floating point 64 bit
mhd MetaIO 3D image IO using the VTK implementation
(experimental).
Recognized file extensions: .MHA, .MHD, .mha, .mhd
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned
16 bit, signed 32 bit, unsigned 32 bit, floating point
32 bit, floating point 64 bit
nifti NIFTI-1 3D image IO. The orientation is transformed in the
same way like it is done with 'dicomtonifti --no-reorder'
from the vtk-dicom package.
Recognized file extensions: .NII, .nii
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned
16 bit, signed 32 bit, unsigned 32 bit, signed 64 bit,
unsigned 64 bit, floating point 32 bit, floating point
64 bit
vff VFF Sun raster format
Recognized file extensions: .VFF, .vff
Supported element types:
unsigned 8 bit, signed 16 bit
vista Vista 3D
Recognized file extensions: .-, .V, .VISTA, .v, .vista
Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16
bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit,
floating point 32 bit, floating point 64 bit
vti 3D image VTK-XML in- and output (experimental).
Recognized file extensions: .VTI, .vti
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned
16 bit, signed 32 bit, unsigned 32 bit, floating point
32 bit, floating point 64 bit
vtk 3D VTK image legacy in- and output (experimental).
Recognized file extensions: .VTK, .VTKIMAGE, .vtk,
.vtkimage
Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16
bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit,
floating point 32 bit, floating point 64 bit
PLUGINS: 3dimage/shape
18n 18n neighborhood 3D shape creator
(no parameters)
26n 26n neighborhood 3D shape creator
(no parameters)
6n 6n neighborhood 3D shape creator
(no parameters)
sphere Closed spherical shape neighborhood including the pixels
within a given radius r., supported parameters are:
r = 2; float in (0, inf)
sphere radius.
EXAMPLE
Run a region growing on input.v starting at point <10,23,21> and use the 18n neighbourhood. mia-3dmaskseeded -i image.v -o masked.v -s '<10,23,21>' -n 18n
AUTHOR(s)
Gert Wollny
COPYRIGHT
This software is Copyright (c) 19992015 Leipzig, Germany and Madrid, Spain. It comes with ABSOLUTELY NO WARRANTY and you may redistribute it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 (or later). For more information run the program with the option '--copyright'.
Opportunity
Personal Opportunity - Free software gives you access to billions of dollars of software at no cost. Use this software for your business, personal use or to develop a profitable skill. Access to source code provides access to a level of capabilities/information that companies protect though copyrights. Open source is a core component of the Internet and it is available to you. Leverage the billions of dollars in resources and capabilities to build a career, establish a business or change the world. The potential is endless for those who understand the opportunity.
Business Opportunity - Goldman Sachs, IBM and countless large corporations are leveraging open source to reduce costs, develop products and increase their bottom lines. Learn what these companies know about open source and how open source can give you the advantage.
Free Software
Free Software provides computer programs and capabilities at no cost but more importantly, it provides the freedom to run, edit, contribute to, and share the software. The importance of free software is a matter of access, not price. Software at no cost is a benefit but ownership rights to the software and source code is far more significant.
Free Office Software - The Libre Office suite provides top desktop productivity tools for free. This includes, a word processor, spreadsheet, presentation engine, drawing and flowcharting, database and math applications. Libre Office is available for Linux or Windows.
Free Books
The Free Books Library is a collection of thousands of the most popular public domain books in an online readable format. The collection includes great classical literature and more recent works where the U.S. copyright has expired. These books are yours to read and use without restrictions.
Source Code - Want to change a program or know how it works? Open Source provides the source code for its programs so that anyone can use, modify or learn how to write those programs themselves. Visit the GNU source code repositories to download the source.
Education
Study at Harvard, Stanford or MIT - Open edX provides free online courses from Harvard, MIT, Columbia, UC Berkeley and other top Universities. Hundreds of courses for almost all major subjects and course levels. Open edx also offers some paid courses and selected certifications.
Linux Manual Pages - A man or manual page is a form of software documentation found on Linux/Unix operating systems. Topics covered include computer programs (including library and system calls), formal standards and conventions, and even abstract concepts.
