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=(required, input); io
-
input label image
For supported file types see PLUGINS:3dimage/io
- -r --ref-labels=(required, input); 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:
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
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 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'.