.TH mia\-2dsegshiftperslice 1 "v2.4.3"  "USER COMMANDS"
.SH NAME
mia\-2dsegshiftperslice \- Translate a segmentation by the given amount.
.SH SYNOPSIS
.B  mia\-2dsegshiftperslice \-i <in\-file> \-o <out\-file> \-S <shift> [options]
.SH DESCRIPTION
.B mia\-2dsegshiftperslice
This program move the segmentation(s) of an image series by using a shift that is given on a per-slice base. The program can be used to correct the segmentation of the images if a linear registration was executed that only applies a translation and does not correct the segmentation automatically. 
.SH OPTIONS
.RS
.IP "\-i \-\-in-file=(input, required); string"
input segmentation set 
.IP "\-o \-\-out-file=(output, required); string"
output segmentation set 
.IP "\-g \-\-image-file=crop"
output image filename base 
.IP "\-S \-\-shift=(required); string"
shift of segmentation \- base name  
.RE
.SS Help & Info
.RS
.IP "\-V \-\-verbose=warning"
verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: 
.RS 10
.I
info
\(hy Low level messages
.RE
.RS 10
.I
trace
\(hy Function call trace
.RE
.RS 10
.I
fail
\(hy Report test failures
.RE
.RS 10
.I
warning
\(hy Warnings
.RE
.RS 10
.I
error
\(hy Report errors
.RE
.RS 10
.I
debug
\(hy Debug output
.RE
.RS 10
.I
message
\(hy Normal messages
.RE
.RS 10
.I
fatal
\(hy Report only fatal errors
.RE
.IP "   \-\-copyright"
print copyright information 
.IP "\-h \-\-help"
print this help 
.IP "\-? \-\-usage"
print a short help 
.IP "   \-\-version"
print the version number and exit 
.RE
.SS Processing
.RS
.IP "   \-\-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). 
.RE
.SH EXAMPLE
Shirt the segmentation given in set segment.set by files shiftXXXX.txt and store the result in shifted.set. Note, the numbering of the shiftXXXX.txx files must coincide.
.HP
mia\-2dsegshiftperslice \-i segment.set \-o shifted.set \-g shifted \-S shift
.SH AUTHOR(s)
Gert Wollny
.SH COPYRIGHT
This software is Copyright (c) 1999\(hy2015 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'.