.TH mia\-2dmyocard\-icaseries 1 "v2.4.7"  "USER COMMANDS"
.SH NAME
mia\-2dmyocard\-icaseries
\- Run an ICA analysis on a series of 2D images
.SH SYNOPSIS
.B  mia\-2dmyocard\-icaseries \-i <in\-file> [options]
.SH DESCRIPTION
.B mia\-2dmyocard\-icaseries
This program is used to run a ICA on a series of myocardial perfusion images given in a segmentation set in order to create sythetic references that can be used for motion correction by image registration. If the aim is to run a full motion compensation then it is better run mia-2dmyoica-nonrigid, since this program is essentially the same without the registration bits.
.SH OPTIONS
.SS File-IO
.RS
.IP "\-i \-\-in-file=(input, required); string"
input perfusion data set

.IP "\-r \-\-references=(output); string"
File name base for the reference images. Image type and numbering scheme are taken from the input images.

.IP "\-c \-\-save-cropped=(output); string"
save cropped set of the original set to this file, the image files will use the stem of the name as file name base

.IP "   \-\-save-feature=(output); string"
save the features images resulting from the ICA and some intermediate images used for the RV\-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.

.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
trace
\(hy Function call trace
.RE
.RS 10
.I
debug
\(hy Debug output
.RE
.RS 10
.I
info
\(hy Low level messages
.RE
.RS 10
.I
message
\(hy Normal messages
.RE
.RS 10
.I
warning
\(hy Warnings
.RE
.RS 10
.I
fail
\(hy Report test failures
.RE
.RS 10
.I
error
\(hy Report errors
.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 "   \-\-fastica=internal"
FastICA implementationto be used
 For supported plugins see PLUGINS:fastica/implementation
.IP "\-C \-\-components=0"
ICA components 0 = automatic estimation

.IP "   \-\-normalize"
normalized ICs

.IP "   \-\-no-meanstrip"
don't strip the mean from the mixing curves

.IP "\-s \-\-segscale=1.4"
segment and scale the crop box around the LV (0=no segmentation)

.IP "\-k \-\-skip=0"
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

.IP "\-E \-\-segmethod=features"
Segmentation method

.RS 10
.I
delta\-feature
\(hy difference of the feature images
.RE
.RS 10
.I
delta\-peak
\(hy difference of the peak enhancement images
.RE
.RS 10
.I
features
\(hy feature images
.RE
.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: fastica/implementation
.TP 10
.B internal
This is the MIA implementation of the FastICA algorithm.
.P
.RS 14
(no parameters)
.RE
.TP 10
.B itpp
This is the IT++ implementation of the FastICA algorithm.
.P
.RS 14
(no parameters)
.RE
.SH EXAMPLE
Evaluate the synthetic references from set segment.set and save them to refXXXX.??? by using five independend components, and skipping 2 images. Per default a bounding box around the LV will be segmented and scaled by 1.4 and the cropped images will be saved to cropXXXX.??? and a segmentation set cropped.set  is created. The image file type ??? is deducted from the input images in segment.set.
.HP
mia\-2dmyocard\-icaseries \-i segment.set \-r ref \-o ref \-k 2 \-C 5
.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'.