mia-3ddistance-stats(1) Evaluate distance statistics for two labeled images.

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'.