mia-3dimagestatistics-in-mask(1) | General Commands Manual | mia-3dimagestatistics-in-mask(1) |
NAME
mia-3dimagestatistics-in-mask - Evaluate statistics within a masked region of the input data.
SYNOPSIS
mia-3dimagestatistics-in-mask -i <image> -m <mask> [options]
DESCRIPTION
mia-3dimagestatistics-in-mask This program evaluates the statistics of an image within a masked region of the image. Possible outputs are a summary statistics and a histogram of the values.
OPTIONS
File-IO
- -i --image=(input, required); io
- input image to be analyzed
For supported file types see PLUGINS:3dimage/io - -m --mask=(input, required); io
- mask image to use to restrict the analysis
For supported file types see PLUGINS:3dimage/io - -s --summary=(output); string
- File to write the summary statistics to as plain text.
- -H --histogram=(output); string
- File to write the histogram to
Help & Info
- -V --verbose=warning
- verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:
- --copyright
- print copyright information
- -h --help
- print this help
- -? --usage
- print a short help
- --version
- print the version number and exit
Parameters
- --struct-name=undefined
- Name of the structure the statistics are evaluated for
- -l --limit=20; uint in [20, inf)
- Number of pixels the mask should at least contain.
- -b --bins=8; ulong in [4, inf)
- number of histogram bins to be used
- --hmin=0
- lower bound for the histogram mapping. All values below this value will be mapped into the lowest bin. If this parameter is equal or larger than hmax, the histogram range is evaluated automatically.
- --hmax=0
- hpper bound for the histogram mapping. All values above this valuewill be mapped into the highest bin. If this parameter is equal or smaller than hmin, the histogram range is evaluated automatically.
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).
PLUGINS: 3dimage/io
- analyze
- Analyze 7.5 image
- datapool
- Virtual IO to and from the internal data pool
- dicom
- Dicom image series as 3D
- hdf5
- HDF5 3D image IO
- inria
- INRIA image
- mhd
- MetaIO 3D image IO using the VTK implementation (experimental).
- 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.
- vff
- VFF Sun raster format
- vista
- Vista 3D
- vti
- 3D image VTK-XML in- and output (experimental).
- vtk
- 3D VTK image legacy in- and output (experimental).
EXAMPLE
evaluate the summary statistics on the input and a histogram with 10 bins and automtically evaluated boundaries. Save summary in summary.txt and the histogram in hist.txt
mia-3dimagestatistics-in-mask --image image.v.gz --mask mask.v.gz --summary summary.txt --histogram hist.txt
AUTHOR(s)
Gert Wollny
COPYRIGHT
This software is Copyright (c) 1999‐2015 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'.
v2.4.7 | USER COMMANDS |