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'.