SYNOPSIS

mia-3ddistance-stats -i <in-labels> -r <ref-labels> -o <out-file> [options]

DESCRIPTION

mia-3ddistance-stats This program is used to evaluate the distance between equally labelled areas in two images. The output file is a csv file containing the distances for each labeled coordinate in the test image in the following form:

  label,n-samples,distance,distance,...

A simple R program to get some per label statistics from this data would look like

    args <- commandArgs(TRUE)
    data <- read.csv(args[1], header=FALSE)
    for ( i in 1:dim(data)[1] )  {
        line <- data[i,]
        label <- as.integer(line[1])
        end_range <- 2 + as.numeric(line[2])
        s <- as.numeric(line[3:end_range])
        result <- sprintf("%d %8.4f %8.4f %8.4f %8.4f
            label, mean(s), sqrt(var(s)),  median(s), max(s))
        cat(result)
    }

OPTIONS

File-IO

-i --in-labels=(input, required); io

input label image For supported file types see PLUGINS:3dimage/io

-r --ref-labels=(input, required); io

reference label image For supported file types see PLUGINS:3dimage/io

-l --label-map=(input); string

optional mapping of label numbers

-o --out-file=(output, required); string

output file name to write the distances to. The output file is a csv file, containing distances listed for each label.

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

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 distances for each label availabe in image.v to the corresponding labels in the image reference.v ans store the result a coma separated list of values, i.e. distances.csv.

mia-3ddistance-stats -i image.v -r reference.v -o distances.csv

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'.