This is the command mia-2dsegseriesstats that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
mia-2dsegseriesstats - Evaluate time-intensity curves in masked regions of image series.
SYNOPSIS
mia-2dsegseriesstats -o <original> -g <registered> [options]
DESCRIPTION
mia-2dsegseriesstats This program is used evaluate various time-intensity curves over a
series of images given by a segmentation set. Specifically, the program is taylored to
evaluate average intensities and variations of sections the left ventricle myocardium. The
segmentation set must contain the segmentations for all slices that will be accessed
during evaluation.
OPTIONS
-o --original=(input, required); string
original segmentation set
-g --registered=(input, required); string
registered segmentation set
-k --skip=2
images to skip at the begin of the series, if (k < 0) use RV peak of the
registered set if setimages to skip at the begin of the series, if (k < 0)
use RV peak of the registered set if set
-r --reference=-1
reference frame for automatic curve extraction. Negative values can be used
to indicate specific values (if given in the segmentation set):
-3: Middle of the series
-2: prefererred reference
-1: LV peak if any of the above is not available or the value is < -3,
use the last frame of the series.reference frame for automatic curve
extraction. Negative values can be used to indicate specific values (if
given in the segmentation set):
-3: Middle of the series
-2: prefererred reference
-1: LV peak if any of the above is not available or the value is < -3,
use the last frame of the series.
-c --curves=(output); string
region average value curves, The output files each comprises a table in
plain-text format that contains three columns for each section of the LV
myocardium: The first column contains the values obtained by using the
original segmentation of the reference on all images of the original series,
the second column contains the values obtained by the registered
segmentation of the reference on all images of the registered series, and
the third column contains the values obtained by using the segmentations of
each slice on the original images.
-v --varcurves=(output); string
region variation values, same formt as described above.
-n --nsections=0
number of sections to use, 0=use as segmented, otherwise Otherwise, the LV
myocardium is divided into n sections that enclose equal angles starting at
the right ventricle insertion point moving clock-wise using the LV center as
angular point.number of sections to use, 0=use as segmented, otherwise
Otherwise, the LV myocardium is divided into n sections that enclose equal
angles starting at the right ventricle insertion point moving clock-wise
using the LV center as angular point.
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).
EXAMPLE
Evaluate the two curve typed for 12 sections from segemntation sets orig.set and reg.set
skipping the first 2 frames. The output will be written to curves.txt and varcurves.txt
respectively.
mia-2dsegseriesstats -i org.set -g reg.set -c curves.txt -v varcurves.txt -n 12 -k 2
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'.
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