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PROGRAM:

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:
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

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.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.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).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

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

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'.

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