Provided by: mia-tools_2.4.7-13build4_amd64 
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:
trace ‐ Function call trace
debug ‐ Debug output
info ‐ Low level messages
message ‐ Normal messages
warning ‐ Warnings
fail ‐ Report test failures
error ‐ Report errors
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
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
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:
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
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'.
USER COMMANDS v2.4.7 mia-3dimagestatistics-in-mask(1)