.TH mia\-2dmyocard\-segment 1 "17 October 2014" "2.0.10"  "USER COMMANDS"
.SH NAME
mia\-2dmyocard\-segment \- Work in progress
.SH SYNOPSIS
.B  mia\-2dmyocard\-segment \-i <in\-file> \-o <out\-file> [options]
.SH DESCRIPTION
.B mia\-2dmyocard\-segment
This program is work in progress
.SH OPTIONS
.SS File-IO
.RS
.IP "\-i \-\-in-file=(input,required)"
input perfusion data set 
.IP "\-o \-\-out-file=(output,required)"
output myocardial mask  For supported file types see PLUGINS:2dimage/io
.IP "\-f \-\-save-features=(output)"
save ICA features to files with this name base 
.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 ICA
.RS
.IP "\-C \-\-components=0"
ICA components 0 = automatic estimation testing 4 and 5 
.IP "   \-\-normalize"
normalized ICs 
.IP "   \-\-no-meanstrip"
don't strip the mean from the mixing curves 
.IP "\-k \-\-skip=2"
skip images at the beginning of the series as they are of other modalities 
.IP "\-m \-\-max-ica-iter=400"
maximum number of iterations in ICA 
.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). 
.RE
.SH PLUGINS: 2dimage/io
.TP 10
.B bmp
BMP 2D-image input/output support
.P
.RS 14
Recognized file extensions:  .BMP, .bmp
.RE
 
.RS 14
Supported element types: 
.RS 2
binary data, unsigned 8 bit, unsigned 16 bit
.RE
 
.RE
.TP 10
.B datapool
Virtual IO to and from the internal data pool
.P
.RS 14
Recognized file extensions:  .@
.RE
 
.TP 10
.B dicom
2D image io for DICOM
.P
.RS 14
Recognized file extensions:  .DCM, .dcm
.RE
 
.RS 14
Supported element types: 
.RS 2
signed 16 bit, unsigned 16 bit
.RE
 
.RE
.TP 10
.B exr
a 2dimage io plugin for OpenEXR images
.P
.RS 14
Recognized file extensions:  .EXR, .exr
.RE
 
.RS 14
Supported element types: 
.RS 2
unsigned 32 bit, floating point 32 bit
.RE
 
.RE
.TP 10
.B jpg
a 2dimage io plugin for jpeg gray scale images
.P
.RS 14
Recognized file extensions:  .JPEG, .JPG, .jpeg, .jpg
.RE
 
.RS 14
Supported element types: 
.RS 2
unsigned 8 bit
.RE
 
.RE
.TP 10
.B png
a 2dimage io plugin for png images
.P
.RS 14
Recognized file extensions:  .PNG, .png
.RE
 
.RS 14
Supported element types: 
.RS 2
binary data, unsigned 8 bit, unsigned 16 bit
.RE
 
.RE
.TP 10
.B raw
RAW 2D-image output support
.P
.RS 14
Recognized file extensions:  .RAW, .raw
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.TP 10
.B tif
TIFF 2D-image input/output support
.P
.RS 14
Recognized file extensions:  .TIF, .TIFF, .tif, .tiff
.RE
 
.RS 14
Supported element types: 
.RS 2
binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit
.RE
 
.RE
.TP 10
.B vista
a 2dimage io plugin for vista images
.P
.RS 14
Recognized file extensions:  .V, .VISTA, .v, .vista
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.SH EXAMPLE
Example
.HP
mia\-2dmyocard\-segment Example
.SH AUTHOR(s)
Gert Wollny
.SH COPYRIGHT
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'.