Combine images of a series to sets.
mia-2dseries2sets -o <out> [options] <PLUGINS:2dimage/io>
mia-2dseries2sets This program takes all image files that are given as free parameters on the command line and creates segmentation sets based on information found in the images. Used information is the z-location of the slice and the acquisition number. The code is taylored to used the according descriptors defined in the DICOM standard. All images with the same slice location will be grouped together in one segmentation set and ordered according to their aquisition number. Slice locations are rounded to three digits accuracy to make proper comparison of floating point values feasable.
output directory (needs to exist and be writable)
don't copy image files to output directory
verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:
info \(hy Low level messages
trace \(hy Function call trace
fail \(hy Report test failures
warning \(hy Warnings
error \(hy Report errors
debug \(hy Debug output
message \(hy Normal messages
fatal \(hy Report only fatal errors
print copyright information
print this help
print a short help
print the version number and exit
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).
bmp
BMP 2D-image input/output support
Recognized file extensions: .BMP, .bmp
Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit
datapool
Virtual IO to and from the internal data pool
Recognized file extensions: .@
dicom
2D image io for DICOM
Recognized file extensions: .DCM, .dcm
Supported element types:
signed 16 bit, unsigned 16 bit
exr
a 2dimage io plugin for OpenEXR images
Recognized file extensions: .EXR, .exr
Supported element types:
unsigned 32 bit, floating point 32 bit
jpg
a 2dimage io plugin for jpeg gray scale images
Recognized file extensions: .JPEG, .JPG, .jpeg, .jpg
Supported element types:
unsigned 8 bit
png
a 2dimage io plugin for png images
Recognized file extensions: .PNG, .png
Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit
raw
RAW 2D-image output support
Recognized file extensions: .RAW, .raw
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
tif
TIFF 2D-image input/output support
Recognized file extensions: .TIF, .TIFF, .tif, .tiff
Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit
vista
a 2dimage io plugin for vista images
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
Create the segmentation sets from a series of DICOM images and copy the files to the output directory (copying is the default). mia-2dseries2sets -o /home/user/series /net/dicoms/patient1/series1/*.dcm
Gert Wollny
This software is Copyright (c) 1999\(hy2013 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'.