Provided by: mia-tools_2.4.6-1_amd64 
NAME
('mia\-3ddistance\-stats',) - 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 %8.4f0
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).
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:
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 available 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'.
USER COMMANDS v2.4.6 mia-3ddistance-stats(1)